Avian Influenza Resources

Below please find a collection of resources pertaining to HPAI, with a focus on Australia:

Oceania is the only continent free from clade HPAI H5N1 (April 2024). Wild migratory birds will be returning to Australia between August – November, and therefore this constitutes the highest risk period for a viral incursion.

Current avian influenza reports in Australia

Updated 7 June

HPAI H7N3 reported in 4 poultry farms near Meredith. The IPs are located in the Restricted and Control Areas in the Golden Plains Shire where movement restrictions were already in place.A property near Terang is also positive for HPAI H7N9, and is linked to the first IP in Meredith. Both a housing order and movement restrictions are in place. These outbreaks are the result of a low pathogenic domestic strain from Australian wild birds entering poultry production, where high pathogenicity evolved. All previous HPAI outbreaks in Australia have been due to domestic HPAI H7 viruses, including the HPAI H7N7 outbreak in Victoria in 2020. In response, the USA and Japan have imposed trade restrictions; in general trade restrictions are imposed in countries/regions with HPAI in poultry, or which use HPAI vaccines. Updates from Agriculture Victoria. To support the outbreak response, our teams are out catching ducks in Victoria, and will contribute samples and testing results previously collected to understand the viral burden and diversity of LPAI H7 in Victorian wild birds.

LPAI H9N2 reported in Western Australia. This outbreak is the result of a domestic strain from Australian wild birds entering poultry production. To date, only H5 and H7 viruses have evolved to HPAI. LPAI H9N2 is found in Australia wild birds, and is endemic in Asian poultry.

A returned traveller tested positive for HPAI H5N1 clade Information is available in the Department of Health press release and a Promed post. Two previous human infections have been caused by this clade (previously in Nepal and India). Importantly, this is not the same clade of virus as is causing the global panzootic (clade Australia remains free from HPAI H5N1 clade

What to do if you see sick or dead birds in Australia?

Video from the Northern Australia Biosecurity Strategy (NABS) [link]

What does a sick bird look like?

– Neurological signs such as loss of coordination and balance, trembling head and body, or twisting of the neck

– Lethargy and depression, unresponsiveness, lying down, drooping wings, dragging legs

– Closed and excessively watery eyes, possibly with opaque cornea or darkened iris (new sign associated with Gannets in current outbreak)

– Respiratory distress such as gaping (mouth breathing), nasal snicking (coughing sound), sneezing, gurgling, or rattling

Video of a dying Sandwich Tern, from Rijks et al. 2022. EID

Video of seabirds birds with HPAI at rehabilitation centres, from SANCOB

Official guidelines (Australia):

High Pathogenicity Avian Influenza clade incursion risk assessment for Australia

Wildlife Health Australia: Highly Pathogenic Avian Influenza (HPAI) and Wild Animals in Australia: A RISK MITIGATION TOOLBOX FOR WILDLIFE MANAGERS (2024 update)

Wildlife Health Australia: Technical Issue Update – Global High Pathogenicity Avian Influenza Events (updated Sept 2023)

Wildlife Health Australia: Risk management advice for bird banders, wildlife rangers and researchers (updated May 2024)

Wildlife Health Australia: Advice for veterinarians and animal health professionals (updated May 2024)

Wildlife Health Australia: Advice for people who encounter sick or dead wild birds (updated May 2024)

Wildlife Health Australia: Communicates guide for managers of wildlife populations (version Dec 2023)

World Organisation for Animal Health: Risk management for people working with wild birds

World Organisation for Animal Health: Practical guide for authorised field responders to HPAI outbreaks in marine mammals, with a focus on biosecurity, sample collection for virus detection and carcass disposal.

World Health Organisation: Public health resource pack for countries experiencing outbreaks of influenza in animals: revised guidance

World Health Organisation: Public health resource pack for countries experiencing outbreaks of influenza in animals

The Risk of Avian Influenza in the Southern Ocean: a practical guide

Agreement on the Conservation of Albatrosses and Petrels – Guidelines for working with albatrosses and petrels during the high pathogenicity avian influenza (HPAI) H5N1 panzootic

AUSVETPLAN response strategy avian influenza

AUSVETPLAN Guidance document: Risk based assessment of disease control options for rare and valuable animals

AUSVETPLAN Operational Procedures Manual Wild Animal Response Strategy

Australian Government, Department of Agriculture, Fisheries and Forestry: Information on Avian Influenza (bird flu)

Australian Government, Department of Agriculture, Fisheries and Forestry: Information for bird owners

Wildlife Health Australia: National Wildlife Biosecurity Guidelines

Farm Biosecurity: National Farm Biosecurity Manual for Poultry Production

Zoo and Aquarium Association Australia: Zoo and Aquarium Biosecurity

Australian Veterinary Association: Guidelines for veterinary personal biosecurity

Australian Department of Health and Aged Care information on Avian influenza in humans

If avian influenza emerges in Australia, outbreak details will be hosted on the Australian Government outbreaks portal (no information here currently)

More about what we are doing in Australia:

We have performed a comprehensive risk assessment of HPAI incursion and evaluation of the current surveillance system, commissioned by the Department of Agriculture, Fisheries and Forestry. An abridged version has been provided by Wildlife Health Australia.

The National Avian Influenza in Wild Birds Program continues to do surveillance across Australia for avian influenza. Enhanced surveillance by Michelle Wille and Marcel Klaassen in 2022 and 2023 demonstrated no evidence for HPAI H5N1 incursion into Australia. We will again enter a high risk period in spring 2024.

Popular science article outlining the global situation and our response in Australia in Pursuit: Bird flu, human cases, and the risk to Australia

See more about our work on low pathogenic avian influenza, revealing the ecology of low pathogenic avian influenza (Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds), and evolutionary genetics (Australia as a global sink for the genetic diversity of avian influenza A virus), and demonstrating how viruses enter and spread (Contrasting dynamics of two incursions of low pathogenicity avian influenza virus into Australia) in Australia

More about what we are doing in Antarctica:

Comprehensive risk mapping was prepared, attempting to identify regions with the highest incursion risk and species that may be involved in viral introduction. The first detection of HPAI in the region occurred on South Georgia (British Antarctic) in October 2023. HPAI has also been detected in the Falkland Islands, and genetic analysis shows that the two seperate incursions occurred into the region (Kudos to APHA and BAS for the rapid analysis and sequence release!).

We have brought together all testing and observation data generated in the austral summer of 2022/23, prior to the first cases, now available as a preprint on bioRxiv

We will have members of the SCAR Antarctic Wildlife Health Network visiting various locations across the Antarctic during the austral summer 2023/24, facilitated by Intrepid. A second expedition, supported by IAATO, was led by Meagan Dewar, to collect samples and learn more about the impact of HPAI on Antarctic wild birds.

Data we generate, and that from other scientists in Antarctica, will be collated in the SCAR AWHN mortality database.

Global situation:

FAO situation report (global)

WOAH Situation reports (global)

EFSA Avian influenza overview Dec 2024 – March 2024 (European)

European Union Reference Laboratories dashboard (European)

RSPB: Avian influenza: a major thread to our struggling seabirds (UK)

APHIS 2022-2023 Detections of Highly Pathogenic Avian Influenza (USA)

Wildlife Health Information Sharing Partnership (USA)

Canadian Wildlife Health Cooperative dashboard (Canada)

Chilean Scernapesca dashboard (Chile)

Chilean SAG dashboard (Chile)

Brazilian Dashboard (Brazil)

Peruvian dashboard (Peru)

H5Nx Nexstrain portal with all relevant sequence data

Response plans and recommendations:

DEFRA: Mitigation strategy for avian influenza in wild birds in England and Wales.

Recommendations from the Invasive Species Council: High pathogenicity avian influenza in wildlife: Is Australia prepared?

Scientific Task Force on Avian Influenza and Wild Birds statement on: H5N1 High pathogenicity avian influenza in wild birds – Unprecedented conservation impacts and urgent needs

Mitigation strategy for avian influenza in wild birds in England and Wales

Scottish wild bird highly pathogenic avian influenza response plan

WOAH: Avian influenza: why strong public policies are vital

OFFLU: Southward expansion of high pathogenicity avian influenza H5 in wildlife in South America: estimated impact on wildlife populations, and risk of incursion into Antarctica

OFFLU: Continued expansion of high pathogenicity avian influenza H5 in wildlife in South America
and incursion into the Antarctic region

Summary of the FAO Global Consultations on Highly Pathogenic Avian Influenza

RSPB. Avian Influenza: a major threat to our struggling seabirds

EFSA: Guidance for reporting 2023 laboratory data on avian influenza

WOAH: Considerations for emergency vaccination of wild birds against high pathogenicity avian influenza in specific situations

EFSA: Vaccination of poultry against highly pathogenic avian influenza – part 1. Available vaccines and vaccination strategies

EFSA: Vaccination of poultry against highly pathogenic avian influenza – Part 2. Surveillance and mitigation measures

CDC: Highly Pathogenic Avian Influenza A(H5N1) Virus : Identification of Human Infection and Recommendations for Investigations and Response

HAIRS risk statement: Avian influenza A(H5N1) in livestock

Human health risk:

A quadripartite risk assessment determined that the risk of infection with HPAI for the general population was low, and for occupationally exposed people (e.g. poultry or dairy workers) the risk was low to medium (but with high uncertainty). Prior to 2023, all human infections with HPAI have been in people interacting with birds, particularly poultry (chickens, turkeys and ducks), however in 2024, one human case was associated with dairy production. Human infections have occurred in Asia, Europe, Africa, North and South America. Reassuringly, no onward transmission between humans has been detected. Details on human cases are listed below (last updated ~ July 2023). Please verify information below with the latest information from WHO.

CDC: Highly Pathogenic Avian Influenza A(H5N1) Virus : Identification of Human Infection and Recommendations for Investigations and Response

CDC: Updated Interim Recommendations for Worker Protection and Use of Personal Protective Equipment (PPE) to Reduce Exposure to Novel Influenza A Viruses Associated with Disease in Humans

CDC: Global reported A(H5N1) human cases, January 2022 through April 25, 2024

Cases of gs/gd H5Nx in humans since 2020
– 85 human cases of H5N6 in China 2014-2023. Most cases have confirmed link to poultry [aggregation]
– 7 poultry workers containing an outbreak of H5N8 in poultry in Russia, 2020 [WHO notification, scientific article]
– 1 human case of H5N6 in Laos in 2021 [scientific article]
– 3 poultry workers infected with H5Nx in Nigeria in 2021. Likely to comprise environmental carriage rather than bona fide infection [news story]
– 1 human case of H5N1 in India in 2022 [scientific article]
– 1 human case of H5N1 in Viet Nam in 2022 [Vietnamese ministry of health, english language news story]
– 1 human case of H5N1 in UK in 2022. Kept flock of ducks in the home. Likely to comprise environmental carriage rather than bona fide infection [scientific article]
– 2 poultry workers infected  of H5N1 in Spain in 2022. Likely to comprise environmental carriage rather than bona fide infection [scientific article]
– 1 poultry worker infected with H5N1 in USA in 2022. Likely to comprise environmental carriage rather than bona fide infection [WHO notification]
– 2 human cases of H5N1 in China in 2022-23 [news story]
– 2 human cases of H5N1 in Cambodia in 2023 [WHO notification]
– 2 poultry workers infected  of H5N1 in UK in 2023. One case likely comprises environmental carriage rather than bona fide infection [news story]
– 1 human case of H5N1 in Ecuador in 2023 [WHO notification]
– 1 human case of H5N1 in Chile in 2023 [WHO notification]
– 2 human cases of H5N1 in the UK in 2023 [WHO information]
– 5 human cases of H5N1 in Cambodia in 2024 [CDC information]
– 1 human case of (unconfirmed) H5N1 in Vietnam in 2024 [CIDRAP information]
– 3 human cases of H5N1 in the USA in dairy workers in 2024 [1. CDC information][2. CIDRAP information][3. CDC notification]
– 1 human case of H5N1 in Australia in a return traveller from India in 2024 [Dept Health notification]
– 1 human case of H5N2 (pathotype undisclosed) in Mexico in 2024 [WHO notification]

Intersting paper outlining the challenges of interpreting qPCR detections in humans – infection or environmental contamination? https://www.sciencedirect.com/science/article/pii/S1201971223007063

In addition to human cases with H5Nx, there have been human cases with H3, H7, H9, H10.

HPAI in Dairy Cattle:

Information updated here 7 June 2024

84 farms, 11 states. 3 human cases. Alpacas. Mice
> This dashboard contains not only information on detections, but is loaded with lots of resources and recommendations. 

Genomic Data are available in the North America H5Nx public NextStrain build: https://nextstrain.org/groups/moncla-lab/h5nx/north-america/ha?c=species_group
Sequence data from HPAI H5N1 outbreak in cattle more easily available on GenBank.

CDC Wastewater dashboard
For interpretation, it is important to note that this dashboard shows results from influenza A testing. Influenza A virus is found in humans, horses, pigs, birds, cattle. This dashboard does not show results of only avian influenza, so interpretation should be done with care. i.e. just because there are high levels in some state, doesn’t mean there are high levels of HPAI in cattle in that state.

Is milk safe to drink?

Lots more work done on assessing pasteurization efficiency in the US. Looks like that, while a huge proportion of the milk supply tested was positive by qPCR, there is no evidence for replicative virus in the milk. Egg isolation of qPCR positive milk samples was unsuccessful.

Raw milk is not safe to drink.

Guidance from FDA on milk safety during HPAI outbreaks
> https://www.fda.gov/food/milk-guidance-documents-regulatory-information/questions-and-answers-regarding-milk-safety-during-highly-pathogenic-avian-influenza-hpai-outbreaks#:~:text=Because%20of%20the%20limited%20information,those%20infected%20with%20avian%20influenza.
> https://www.fda.gov/food/alerts-advisories-safety-information/updates-highly-pathogenic-avian-influenza-hpai
> https://flutrackers.com/forum/forum/national-international-government-ngo-preparation-response/us-fda/989686-fda-updates-on-highly-pathogenic-avian-influenza-hpai-april-26-2024

Canadian Food Inspection Agency has first results from commercial #H5N1 milk testing. CFIA tested 142 milk samples from across Canada. As of today, none tested positive for fragments of virus behind avian flu, “with no evidence of disease in dairy cattle detected in milk.”

Is beef safe to eat?

On May 1, NVSL reported that all samples (30 samples of retail ground beef) tested negative for #H5N1.”
> https://flutrackers.com/forum/forum/national-international-government-ngo-preparation-response/usda-aa/989896-usda-on-may-1-nvsl-reported-that-all-samples-30-samples-of-retail-ground-beef-tested-negative-for-h5n1

Despite this, Colombia has put in trade restrictions for US beef : https://www.reuters.com/markets/commodities/colombia-becomes-first-country-restrict-us-beef-due-bird-flu-dairy-cows-2024-04-25/

SDA researchers have done a “ground beef cooking study” to test at what temperature #H5N1 in meat is killed. “There was no virus present in the burgers cooked to 145 degrees internal temperature, or roughly medium, or 160 degrees, which equates with a well done burger, which is the recommended cooking temperature” At lower temperatures, some virus survived. “Cooking to I believe it was 120 degrees did show that there was virus still in the cooked hamburger patty, although at much, much reduced levels.”

Updates on H5N1 Beef Safety Studies

> beef tissue from 96 cull dairy cows condemned at select FSIS-inspected facilities. Meat from condemned cows is prohibited from entering the food supply. On May 22, 2024, viral particles were detected in tissue samples, including muscle, from one cow
> no virus detected in beef from grocery stores. 

How is it spreading?

AFIA statement on litter feeding and HPAI: The USDA and FDA have not found a link to HPAI virus transmission in dairy cattle through chicken litter. FDA stated that chicken litter does not pose an animal or public health threat warranting usage restriction 
> A study from 2021 assessing the practice and how common the practice actually is: https://www.sciencedirect.com/science/article/pii/S095965262102343X?via=ihub 

Genomic analysis has indicated that there was a single virus introduction into cattle, mostly likely in Texas. This occured months ago, so the virus has likely been spreading in cattle for much longer than appreciated.

Infection seems to primarily be occurring in the mammary glands of cattle. Interestingly, cattle have avian-type receptors in the mammary glad, which may explain why infection is occurring there. Infection in the mammary glads is leading to lots of virus in the milk of cows, and they spread is believed to be facilitated through milking of cattle. Recent studies have showed virus in milk can survive on surfaces for at least an hour lending evidence to this.

Cats in infected barns are ingesting infected milk.

Bird flu may be spreading in cows via milking and herd transport

Genomic analysis has indicated that there was a single virus introduction into cattle, mostly likely in Texas. This occured months ago, so the virus has likely been spreading in cattle for much longer than appreciated.

Only in USA cattle or elsewhere?

Fredrich Loeffler Institute has done a survey of HPAI in cattle in Germany, and all cattle negative thus far.
“ FLI scientists also investigated the susceptibility of cattle to the then circulating H5N1 virus in the context of the 2006-2008 H5N1 avian influenza outbreak in Germany, but found only a very low risk of infection for the animals. However, no lactating cows were tested at that time. However, the cattle developed antibodies and the FLI recommended that the situation be monitored further. “

Canadian Food Inspection Agency: “no evidence of disease in dairy cattle detected in milk.”

Surveillance has found no evidence in cattle or farm workers in Pakistan.

Effects on humans?

CDC confirmed a third H5 bird flu human infection in the U.S. tied to dairy cow outbreaks. While the risk to the general public remains low, people with certain animal exposures should take precautions: https://t.co/Z2PnuiObHe 
– second case in Michigan but not linked to the other case (different farm)
– reported cough and eye discomfort with watery discharge
– given oseltamivir, isolating

WHO webinar on public health risk of avian influenza in dairy cattle with lots of good stuff in there (06/05/2024)

Avian Influenza A(H5N1) U.S. Situation Update and CDC Activities
> Testing confirmed that the A(H5N1) virus from the human case in Texas is susceptible to baloxavir marboxil, in addition to the neuraminidase inhibitors, which was announced last week
> Looking at antiviral resistance properties of more than 200 H5N1 publicly posted virus sequences from cattle. CDC found one virus from a cow with a marker known to be associated with reduced susceptibility to the neuraminidase inhibitors (a change at NA-T438I).
> Data to date – including genetic analysis and testing of ferret antisera from multiple clade candidate vaccine viruses – suggest vaccination will offer good cross-protection against cattle outbreak viruses. (The human case in Texas was a virus.)

Joint FAO/WHO/WOAH preliminary assessment of recent influenza A(H5N1) viruses
Joint WHO/FAO/WOAH risk assessment. Risk to humans still considered low,

Inactivated influenza A/H5N8-like vaccine elicits cross-reactive antibodies to a H5N1 strain from cattle. https://t.co/g03sLPCa6H 

NIAID Monovalent Inactivated Influenza A/H5N8 Clinical Trials

WHO page up now RE infected dairy worker:

Highly Pathogenic Avian Influenza A(H5N1) Virus: Identification of Human Infection and Recommendations for Investigations and Response

Genetic analysis of the human case by the CDC


Technical Report: Highly Pathogenic Avian Influenza A(H5N1) Viruses

Antiviral Susceptibility Testing of Highly Pathogenic Avian Influenza A(H5N1) Viruses Isolated From Dairy Cattle in the United States, 2024

USDA’s control strategy:

WOAH GF-TAD Americas teleconference
GF-TADs Meeting: Detection of HPAI in Ruminants and Humans in the USA – Americas (woah.org)

DEFRA (UK) have done an outbreak assessment for HPAI of avian origin in domestic livestock
A good review of the stuation in the US, and implications for Great Britiain.
“The most likely routes of entry of this American H5N1 virus into Great Britain are via trade in bovine products from affected farms in the USA, or by migratory wild birds. There is no trade in live cattle.”
“Therefore, there could be a route of entry to Great Britain of virus through unpasteurised dairy products imported from affected farms in the USA, although the vast majority of dairy products from the USA are pasteurised, such as cheese and whey, along with smaller amounts of yogurt, condensed milk and dairy spreads”

USDA Actions to Protect Livestock Health From Highly Pathogenic H5N1 Avian Influenza

FDA Updates on Highly Pathogenic Avian Influenza (HPAI)

APHIS has put in further guidelines around cattle movement to increase traceability

Avian Influenza A(H5N1) U.S. Situation Update and CDC Activities
Current Situation Highlights Importance of Preventive Measures for People with Exposures
– Recommendations for Worker Protection and Use of Personal Protective Equipment (PPE) to Reduce Exposure to Novel Influenza A Viruses Associated with Severe Disease in Humans
– Results of antiviral susceptibility tests showing that H5N1 is susceptible to neuraminidase inhibitors.

USDA Confirms Cow-to-Cow Transmission a Factor in Avian Flu Spread

Avian influenza A(H5N1) in dairy farms: An update on public health and food safety concerns

Updates on Highly Pathogenic Avian Influenza (HPAI)

APHIS Recommendations for Highly Pathogenic Avian Influenza (HPAI) H5N1 Virus in Livestock For State Animal Health Officials, Accredited Veterinarians and Producers: https://www.aphis.usda.gov/sites/default/files/recommendations-hpai-livestock.pdf
Producers should practice enhanced biosecurity, minimize animal movements, test animals before movement, and isolate animals moved on or off premises

Detection of Highly Pathogenic Avian Influenza (H5N1) in Dairy Herds: Frequently Asked Questions

WOAH Statement

USDA’s Testing recommendations for cattle

Scientific studies addressing influenza in (dairy cattle)

Canadians have updated (4 June) their milking pre-print. I expect there will be rolling updates. 
Longitudinal Influenza A Virus Screening of Retail Milk from Canadian Provinces (Rolling Updates)

Does pasteurization inactivate bird flu virus in milk?
Evaluation of thermal stability of HPAI H5N1, human H3N2 virus, H1, H3, H7, H9, H10. avian H3 virus = highest , HPAI = moderate thermal stability. standard pasteurization methods = effective.

Pasteurisation temperatures effectively inactivate influenza A viruses in milk
Pasteurisation effective for inactivation of human + avian influenza, influenza D, and recombinant IAVs carrying contemporary avian or bovine H5N1 glycoproteins. infectivity rapidly lost + undetectable before recommended pasteurisation time.

Cross-Species Transmission of Highly Pathogenic Avian Influenza (HPAI) H5N1 Virus in the U.S. Dairy Cattle: A Comprehensive Review
Yet another review of current epidemiological landscape of HPAI H5N1 in U.S. dairy cows and the recent interspecies transmission events of HPAI H5N1 in other mammals reported in other countries.

Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in U.S. Dairy Cattle and Detection of Two Human Cases — United States, 2024

Cow’s Milk Containing Avian Influenza A(H5N1) Virus — Heat Inactivation and Infectivity in Mice
Milk samples from HPAI H5 affected herd in New Mexico, viruses isolated. Heat treatment at 63°C reduced virus titers below the detection limit. HPAI remain infectious for several weeks in raw milk kept at 4°C. Infected mice had disease at 1dpi.

The mammary glands of cows abundantly display receptors for circulating avian H5 viruses
2344b HPAI H5 from cattle bind significantly in the mammary gland, whereas classical H5 proteins failed to do so.  9-O-acetyl modification prominent in all tissues , 5-N-glycolyl modification is not. receptors are available in the lungs, and lower respiratory tract infections are often not efficiently transmitted and cause severe disease.

Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm
Isolation of HPAI H5N1 from environmental swab samples from a dairy farm in Kansas. Two distinctive mutations in the PB2 (E249G) and NS1 (R21Q) genes, 1.7% of reads w PB2 E627K. PB2 and NS most closely related to human case.

Longitudinal Influenza A Virus Screening of Retail Milk from Canadian Provinces (Rolling Updates)
Pan-Canadian Milk (PCM) Network: 8 retail milk samples from Canada (NL, NB, QC, MB, and AB) and all have tested negative for influenza A virus RNA. Routine surveillance of retail milk = cost-effective, standardized, scalable and easily accessible manner.

From birds to mammals: spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle led to efficient intra- and interspecies transmission
Brilliant paper addressing key questions in cattle HPAI. 3-20% cattle affected, disease 5-14 days. More shedding in clinical cattle. Staining of tissues = tropism  for the epithelial cells lining the alveoli of the mammary gland. Genomic analysis reveals multidirectional interspecies transmissions. And they have mapped how virus spread between farms. This paper is worth the time. 

Avian Influenza Virus (H5N1) Was Not Detected Among Dairy Cattle and Farm Workers in Pakistan
HPAI not detected in dairy cattle and farm workers in Pakistan. Samples originally collected for influenza D work. Some previous testing also in Canada and Germany, negative. Seems that infection in dairy cows localised to US (for now)

Detection of Hemagglutinin H5 Influenza A Virus Sequence in Municipal Wastewater Solids at Wastewater Treatment Plants with Increases in Influenza A in Spring, 2024
Monitoring of 190 wastewater treatment plants across US  ???? IAV RNA concentrations at 59 in spring 2024. Specific H5 testing showed increase due to H5 in 4 tested, all which catch discarded animal waste.

Characterization of highly pathogenic avian influenza virus in retail dairy products in the US
297 samples of Grade A pasteurised retail milk products (23 types) collected from 17 US states over 132 processors in 38 states. 20.2% positive by qPCR, all neg by egg innocs.

Influenza H5N1 and H1N1 viruses remain infectious in unpasteurized milk on milking machinery surfaces
HPAI H5N1 and H1N1 spiked into milk and put onto surfaces. HPAI remained infectious on surfaces for more than an hour = unpasteurized milk containing the H5N1 virus will remain infectious on milking equipment.

Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities.
19 of 23 monitored sites had at least one detection event, and the H5N1 serotype became dominant over seasonal influenza over time. 

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle 
(Part 1 of 2)
(Part 2 of 2)
This comprises the summary of genetic analysis of the sequences generated by USDA undertaken by evolutionary biologists. Highlights features such as reassortment prior to entering cattle, a single point of introduction into cattle, estimated date of virus introduction into the cattle population, mostly likely to have originated in Texas, and the presence of potentially adaptive mutations in cattle. 

The avian and human influenza A virus receptors sialic acid (SA)-α2,3 and SA-α2,6 are widely expressed in the bovine mammary gland
Turns out that cattle have avian type receptors in their mammary glands, which may explain why this is the “preferred” site of replication in cattle, and why there havent been to many occurences of the PB2 mutation in the cattle sequences. 

Highly Pathogenic Avian Influenza A(H5N1) Virus Infection in a Dairy Farm Worker
Description of human case

Highly Pathogenic Avian Influenza A(H5N1) Clade Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024
Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows.

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle
Great to see the analysis by the USDA and folks involved in the cattle outbreaks. Genomic analysis and epidemiological investigation showed a reassortment event in wild bird populations preceded a single wild bird-to-cattle transmission episode.. 

Potential Pathways of Spread of Highly Pathogenic Avian Influenza A/H5N1 Clade Across Dairy Farms in the United States
Led by folks at the Kirby using spatial models to understand how spread may have occurred. Assumes that spread is occurring in real time.. Rather than identification of cases as more testing has been done.

Experimental Infection of Cattle with Highly Pathogenic Avian Influenza Virus (H5N1)
4 calves experimentally infected with HPAI H5 (2006 strain). All remained healthy with no clinical signs. Limited shedding in nasal swabs, but shed low amounts of virus at 1dpi, 2dpi. All seroconverted.

Further Experiments Relating to the Propagation of Virus in the Bovine Mammary Gland
From 1953: Human influenza type persisted
in the mammary gland for ~ 2 weeks, titres rose in milk and persisted for several days, neutralizing antibodies
detected soon after the virus had disappeared.

Studies relating to the formation of neutralizing antibody following the propagation of influenza and Newcastle disease virus in the bovine mammary gland
A follow up, in 1955, w PR8 (these days a laboratory strain) (in goats as a sub for cattle). Infection in the mammary glad. Removal of mammary glad = decrease in antibody content in blood = neutralising antibodies being produced in mammary glad.

Significant rising antibody titres to influenza A are associated with an acute reduction in milk yield in cattle
Sporadic cases of “milk drop” investigated in a Holstein Friesian dairy herd in Devon, with increased antibody titres against human H3N2 and H1N1 associated with an acute fall in milk production

Influenza A in Bovine Species: A Narrative Literature Review
There is a long history of influenza A in cattle. First case is 1949 with 160,000 cattle affected in Japan. Generally mammalian H1 and H3 subtypes implicated.

Influenza D virus
Cattle are, of course, the central reservoir for influenza D viruses (a different virus species). Lots of scope for interesting work still to be done on influenza viruses in cattle.

Research articles, since ~ Nov 2022 (ongoing):

Follow me on Twitter/X for real-time publication sharing @DuckSwabber

Avian influenza viruses in New Zealand wild birds, with an emphasis on subtypes H5 and H7: Their distinctive epidemiology and genomic properties
Great to see this study from NZ colleagues on LPAI H5/H7. Of interest is that for neither H5 nor H7 do sequences from AUS/NZ fall into the same lineage. Likely 2 separate introductions, and little connectivity between. 

Massive outbreak of Influenza A H5N1 in elephant seals at Península Valdés, Argentina: increased evidence for mammal-to-mammal transmission 
Illuminating results from marine mammal HPAI in S. Am. (1) Marine mammal clade = mammal<->mammal transmission (2) different evolutionary rate in mammal clade compared to birds (3) specific mutations for virulence, mammal adaptation? Concerning situation
In discussions with the authors, all samples were collected into inactivating media, so no chance of an isolate for ferret experiments. But the human case in Chile, which was part of the same clade, has been put in ferrets, and does transmit between ferrets via direct contact, but not respiratory/droplet transmission.
Highly pathogenic avian influenza A(H5N1) virus of clade isolated from a human case in Chile causes fatal disease and transmits between co-housed ferrets

Assessment of Survival Kinetics for Emergent Highly Pathogenic Clade H5Nx Avian Influenza Viruses
How long can HPAI last? Incubated virus at temps rep N.  European winter (4C), summer (20C), S. European summer (30C). Lower temperature prolonged virus survival

IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data
Bioinformatic pipeline implementing flexible analysis of the segmented IAV genome, obtaining a representative consensus from raw reads, and a straightforward method for detecting possible reassortment through phylogenetic tree construction. Most have their own pipelines and/or use IRMA, so not sure how this will compete with established approaches. 

Specificity of the interaction between Neuraminidase N1 of the avian influenza A virus H1N1 1918 and a2-3 or a2-6 glycan receptors of avian and human cell targets
## No access

Outbreaks of H5N1 High Pathogenicity Avian Influenza in South Africa in 2023 Were Caused by Two Distinct Sub-Genotypes of Clade Viruses
In S. Africa: H5Nx, H7Nx, H9Nx, H11Nx, H6N2, and H12N2 in wild birds and ostriches in 2023, but H5Nx predominant. SA13 in coastal seabirds,SA15 caused chicken outbreaks. Great overview of the situation from the S. Africans

The H5 subtype of avian influenza virus jumped across species to humans – a view from China
Thoughts on the American dairy cow situation from chinese authors. Not that useful. 

Highly pathogenic Avian Influenza H5N8 and H5N1 outbreaks in Algerian avian livestock production.
2 HPAI H5 outbreaks in Algerian poultry: 2020-2021 and 2022-2023 – 70% mortality due to H5N8, 40% due to H5N1. Systemic congestive-hemorrhagic syndrome in poultry.

The H4 subtype of avian influenza virus: a review of its historical evolution, global distribution, adaptive mutations and receptor binding properties
Review of the historical evolution, global distribution, adaptive mutations, receptor-binding preferences, and host range of H4 AIV.

Avian Influenza outbreaks: Human infection risks for beach users – One health concern and environmental surveillance implications

Highly Pathogenic Avian Influenza A(H5N1) in Animals: A Systematic Review and Meta-Analysis

RNF216 Inhibits the Replication of H5N1 Avian Influenza Virus and Regulates the RIG-I Signaling Pathway in Ducks 
#cant seem to access 

Biological Characteristics of H6N1 Subtype Avian Influenza Virus from 2019 to 2022 in China
English abstract. Think the text is in Chinese – cant get pdf to load. They found some H6 viruses. 

COBRA HA and NA vaccination elicits long-live protective immune responses against pre-pandemic H2, H5, and H7 influenza virus subtypes
Mice vaccinated with COBRA H2, H5, H7, N1, N2, fully protected against lethal challenge with H5N6 influenza virus. Cross-reactive IgG antibodies against wild-type H2, H5, H7, N1 N2 proteins. Protective antibodies up to 4 months. 

A geospatial perspective towards the role of migratory birds and poultry in the spread of Avian Influenza
Review integrating bird migration, poultry trade, and HPAI movement 2020-2023. Typically uninformed – no recent literature included. I mena, there have been a number of phylogenetic studies working this out very carefully – none cited. Just trying to jump on the bandwagon. 

Pandemic preparedness through vaccine development for avian influenza viruses
Review on pandemic preparedness for avian influenza viruses – vaccines in animal models and clinical trials on H5N1, H7N9, and H9N2 vaccines in humans

Proximal Origin of Epidemic Highly Pathogenic Avian Influenza H5N1 Clade and Spread by Migratory Waterfowl
Absolutely total deranged bs.
“The proximal origins of HPAI H5N1 Clade may be the USDA Southeast Poultry Research Laboratory (SEPRL) in Athens, Georgia and the Erasmus Medical Center in Rotterdam, the Netherlands.”

Reducing the risk of highly pathogenic avian influenza A virus H5N1 transmission during the Hajj
The Hajj provides a unique opportunity to fully implement a ‘One Health’ approach to mass-gathering preparedness that can improve H5N1 surveillance and assist with other zoonosis. Risks and recommendations provided. 

Diversity of Genotypes and Pathogenicity of H9N2 Avian Influenza Virus Derived from Wild Bird and Domestic Poultry
# no access yet.
11 H9N2 viruses from overwintering wild birds and their proximate domestic poultry in Yunnan Provence, China

First Detection of Highly Pathogenic Avian Influenza Virus in a Crested Caracara
# no access.

Re-evaluating efficacy of vaccines against highly pathogenic avian influenza virus in poultry: A systematic review and meta-analysis 
Meta-analysis of experimental trials to assess efficacy of HPAI vaccines. Vaccines prevent mortality (78% to 97%) – vaccine platforms and match (or mismatch) at play. What about transmission?

Evaluation of the immune effect of a triple vaccine composed of fowl adenovirus serotype 4 fiber-2 recombinant subunit, inactivated avian influenza (H9N2) vaccine, and Newcastle disease vaccine against respective pathogenic virus challenge in chickens
Triple vaccine (Adeno, NDV, H9N2) could provide up to 100% immune protection against 3 viruses in chickens without interference. No viral shedding detected in larynx and cloaca on the fifth day after challenge. 

A two-strain avian–human influenza model with environmental transmission: Stability analysis and optimal control strategies
Developed mathematical model to determine optimal control strategies if AIV mutates to sustain human-human transmission and found quarantining infected humans is the most cost-effective strategy.

Parallel evolution in the emergence of highly pathogenic avian influenza A viruses
Old paper, from before the updates. Parallel emergence of HP AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. mutational panel = reveal new links bw virulence evolution and other traits = prediction of future HP events?

Risk assessment of influenza transmission between workers and pigs on US indoor hog growing units
Not avian influenza, but perhaps useful regardless. Influenza transmission between workers and pigs on US indoor hog farms: Very low and Extremely low for H1N1, H1N2, H3N2. Control methods needed to ????risks of inter-species influenza transmission. Important given 2009 pandemic was pigs to humans. 

Severe Avian Influenza A H5N1 Clade Virus Infection in a Human with Continuation of SARS-CoV-2 Viral RNAs
Co-infections certainly happen – here HPAI H5N1 and COVID in a farmer in China with exposure to sick poultry. Patient recovered, and discharged after 44 days, after sportive and symptomatic treatment and use of antiviral drugs.

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
Really exciting stuff. In the past, ferret experiments to try to reveal mutations important for human transmission. Lead to mortatorim on gain of function research. Here, they make all possible mutations in HA and then assess the phenotypes of all the mutations. So now we know what SNPs potentially mean. Data useful for tracking mutations in 2344b!

Development of a Fully Protective Pandemic Avian Influenza Subunit Vaccine in Insect Pupae
Here, alternative technology for manufacturing subunit influenza HA-based vaccines by using insect pupae w baculovirus vectors. Vaccinated birds had no clinical disease, but shedding still present.

Pathological and phylogenetic characteristics of fowl AOAV-1 and H5 isolated from naturally infected Meleagris Gallopavo
Detection of avian paramyxovirus 1 and HPAI H5N1 2344b in turkeys in Egypt with respiratory signs and mortality. congestion and hemorrhage in the lungs, liver, and intestines with leukocytic infiltration. Endemic viruses in egyptian poultry is a real issue. 

Characterizing the domestic-wild bird interface through camera traps in an area at risk for avian influenza introduction in Northern Italy
Published version of a preprint already reviewed. Important to understand the wild bird: poultry interface. Here, identification of wild bird species in poultry house surroundings and characterize the spatiotemporal patterns of visits: 27 different species – magpies, pheasants, doves most common.

Red knots in Europe – a dead end host species or a new niche for highly pathogenic avian influenza?
Red Knot is a species we target in our spring enhanced surveillance, and from our work on LPAI has “higher” prevalence within the waders. Here, great overview of discrete genotype of HPAI in Knots in German Wadden Sea in 2020 – HPAI H5N3 reassortant in the knots, which was not detected elsewhere.

Pathogenicity and Transmission of Novel Highly Pathogenic H7N2 Variants Originating from H7N9 Avian Influenza Viruses in Chickens
Four HPAI H7N2 isolated in China during 2019 = reassortants with H7N9-derived HA genes and H9N2-derived NA genes. HA genes may be a critical virulence contributor to novel H7 avian influenza viruses.

Human neutralizing antibodies target a conserved lateral patch on H7N9 hemagglutinin head
H7N9 caused thousands of human cases, with 30% CFR. Here, isolation of 4 HA-reactive mAbs: 3 directed to globular head + 1 to stalk. Description of mAbs and experiments to reveal effects. Overall, antibodies to a conserved lateral HA1 supersite combined with a HA2-directed non-neutralizing mAb augment protection.

Global Dynamics Analysis of Non-Local Delayed Reaction-Diffusion Avian Influenza Model with Vaccination and Multiple Transmission Routes in the Spatial Heterogeneous Environment
Modelling study shows prolonging the incubation period, controlling the movement of infected poultry, and regular disinfecting the environment are all effective ways to prevent avian influenza outbreaks. Its maths heavy and it wasn’t immediately obvious what the input data was. 

Highly pathogenic avian influenza A (H5N1) virus outbreak in Peru in 2022–2023
More HPAI H5N1 genomes from Peru. In sequence from sea lion: I352K and 1368C>T mutations in the HA gene and in the PB2 D701N and Q591K

Panzootic HPAIV H5 and risks to novel mammalian hosts
In order to mitigate the zoonotic risk of HPAI H5, essential to understand + monitor at avian-mammal interface.

Detection of a reassortant swine- and human-origin H3N2 influenza A virus in farmed mink in British Columbia, Canada
Not avian influenza, but I have included it as I think its an important study to be aware of. Reassortant H3N2 from reassortment of swine H3N2 (clade 1990.4h), human seasonal H1N1 (pdm09), and swine H1N2 (clade 1A.1.1.3) found in a mink farm in Canada. been subsequently observed in swine and poultry in N. Am. closer surveillance in mink needed!

Deciphering bat influenza H18N11 infection dynamics in male Jamaican fruit bats on a single-cell level
Not avian influenza, but a really exciting study of bat H18N11 in Jamaican Fruit Bats. We know that bats seem to tolerate infections with viruses really well. H18N11  infection = moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. human leukocytes, particularly macrophages, were also susceptible to H18N11.

Effect of Enteromorpha polysaccharides on gut-lung axis in mice infected with H5N1 influenza virus
Demonstrated enteromorpha polysaccharides (sugar) potential in protecting host from HPAI H5N1. Found body weight of mice recovered and pathological damage to the lung and intestine was reduced after EPP inclusion. 

Infection dynamics of subtype H9N2 low pathogenic avian influenza A virus in turkeys
Turkeys infected w H9N2 in a target-cell limited model. Turkeys had a different set of infection characteristics, compared with humans and ponies. Clearance rate similar bw turkeys and ponies, cell death and tramission similar bw turkeys and humans. Paper is weird. Where does ponies even come from?

Assessing avian influenza surveillance intensity in wild birds using a One Health lens
AIV surveillance in Ontario, Canada. 2562 samples. Identify spatial variations in surveillance intensity relative to human population density, poultry facility density, and wild mallard abundance. Data to improve Onehealth response.

Prevalence and risk factor for H9N2 avian influenza virus in poultry retail shops of Madhya Pradesh
H9N2 endemic in poultry in Asia. 500 poultry tissue and 700 environmental samples in India. 9% prevalence (by egg isolation), 50% districts positive. Risk factors for H9N2 identified – e.g. procuring birds from wholesaler.

Proactive surveillance for avian influenza H5N1 and other priority pathogens at mass gathering events
Public health preparedness and careful planning and surveillance before and during mass gathering events remain important for preventing major outbreaks. Call for proactive surveillance for H5N1 in humans.

To vaccinate or not against highly pathogenic avian influenza?
To vaccinate or not vaccinate against HPAI H5N1. Lots of factors, and of course contexts to consider. Can be a useful tool to control HPAI if done properly, but important to avoid further evolution and silent spread.

Avian ‘Bird’ Flu – undue media panic or genuine concern for pandemic potential requiring global preparedness action?
“Striking the right balance between the existing pandemic in birds with the pandemic potential for humans is the essence.” OneHeath framework critical. 

A highly sensitive and accurate dual-channel fluorescent immunochromatographic assay for simultaneous quantitative detection of influenza A virus and adenovirus antigens
Rapid diagnostics is the future for animal disease emergencies. Here, a dual dual-channel immunochromatographic assay for both influenza and adenovirus in poultry from pharyngeal swab samples.

Revealing novel and conservative T-cell epitopes with MHC B2 restriction on H9N2 Avian Influenza Virus (AIV)
H9N2 is the main epidemic subtype in Chinese poultry despite vaccination programs. Here, identify CD8+ T cell epitopes targeting H9N2 to lay the foundation for the potential development of T-cell epitope vaccines.

Guanylate-binding protein 1 inhibits inflammatory factors produced by H5N1 virus through Its GTPase activity
Guinea pig guanosine monophosphate binding protein 1 (gGBP1) downregulates cytokine production induced by influenza. Here shown to be important for H5N1 in guinea pig cell lines.

Sequence-based epitope mapping of high pathogenicity avian influenza H5 clade in Latin America
Lots of suggestion that HPAI in S.America is different (due to widespread marine mammal outbreaks). 3 major subtypes and eight sub-genotypes identified, with 3 potential antigenic variants, indicating the HA-C group as the dominant variant.

The complete coding sequence of Influenza A/Unknown/Chelyabinsk/206/H7N4
Characterisation of an H7N4 virus found in Russia. Potentially first H7 genome from Russia.

Nucleic acid detection and genomic sequence analysis of one H5N1 avian influenza virus from wide birds around Qinghai Lake.
Link seems problematic?

US Public Health Preparedness and Response to Highly Pathogenic Avian Influenza A(H5N1) Viruses
Survey of  US state epidemiologists in 55 jurisdictions for H5N1 virus ID, monitoring, antiviral and vccines.  In 50, human exposure to animals from backyard flocks (88%), wild birds (54%), and sick/dead mammals (18%)

Spatial and Temporal Characteristic Analysis and Risk Assessment of Global Highly Pathogenic Avian Influenza H5N8 Subtype
Found midlatitude areas (30-60 degrees) at higher risk of HPAI H5N8 occurrence. Key variables influencing occurrence are chicken density, duck density, population density, annual mean temperature and land cover. Note wild bird migration data not used in modelling. 

Simultaneous construction strategy using two types of fluorescent markers for HVT vector vaccine against infectious bursal disease and H9N2 avian influenza virus by NHEJ-CRISPR/Cas9
Demonstrated recombinant virus rHVT-VP2-HA provided 100% simultaneous protection against G2d lineage of Infectious Bursal Disease Virus and Y280 lineage of HPAI H9N2 (stops replication) in chickens.

Detection of clade highly pathogenic H5N1 influenza virus in New York City
Publication of a previously reviewed preprint. Multiple HPAI H5N1 genotypes detected in four different avian species in New York City highlighting risk of zoonotic infections extends into urban centres.

Development of a nucleoside-modified mRNA vaccine against clade H5 highly pathogenic avian influenza virus
mRNA lipid nanoparticle vaccine encoding HA of H5N1 = strong T cell + antibody responses in mice, w neutralizing antibodies + broadly-reactive anti-HA stalk antibodies. Prevents morbidity and mortality of ferrets in challenge.

Avian influenza virus neuraminidase stalk length and haemagglutinin glycosylation patterns reveal molecularly directed reassortment promoting the emergence of highly pathogenic clade A (H5N1) viruses
What makes the a panzootic virus? Here,  revealed that the seven glycosylation sites in HA was critical in driving its pairing with long stalk N1 = increased fitness and pathogenicity. HA-NA pairing not stoichastic.

Risk assessment of a highly pathogenic H5N1 influenza virus from mink
Important study investigating mammalian infection + transmission of HPAI isolated from the 2022 mink outbreak in spain. Direction transmission 75% contacts, airborne transmission 37.5% contacts. PB2 T271A important for mortality + airborne transmission. But sequence analysis found no known mutations associated with mammalian transmission
Pop Sci Summary: https://afludiary.blogspot.com/2024/05/nature-dispatch-risk-assessment-on-hpai.html

On-Site and Visual Detection of the H5 Subtype Avian Influenza Virus Based on RT-RPA and CRISPR/Cas12a
New RT-RPA/CRISPR-based detection method allows for rapid detection of HPAI, and easy to use test strips. 80.70% positive detection rate across 81 clinical samples tested. 

Efficacy of live and inactivated recombinant Newcastle disease virus vaccines expressing clade H5 hemagglutinin against H5N1 highly pathogenic avian influenza in SPF chickens, Broilers, and domestic ducks
NDV-vectored vaccine w H5 HA developed and assessed. Vaxx achieved complete survival against HPAI and NDV challenges and significantly reduced viral shedding in chickens, decreased shedding in ducks. Doesn’t stop infection/transmission. Aligns with the strategy of Differentiating Infected from Vaccinated Animals (DIVA)

Building global preparedness for avian influenza
Commentary on how to prepare for human infection with HPAI, suggestions for improved surveillance and detection. 

H6N2 reassortant avian influenza virus isolate in wild birds in Jiangxi Province, China
Uncommon for Asian LPAI viruses to have gene segments from Americas in my experience. Here the N2 of an H6N2 virus in China closely related to California bufflehead virus. More wild bird sampling +sequencing in Asia could resolve this. 

Dual N-linked glycosylation at residues 133 and 158 in the hemagglutinin are essential for the efficacy of H7N9 avian influenza virus like particle vaccine in chickens and mice
N-linked glycosylation-engineered H7N9 virus like particle vaccines conferred complete protection against H7N9 viruses and and significantly suppressed virus replication and lung pathology in chickens and mice

Duration of Highly Pathogenic Avian Influenza Virus and Newcastle Disease Virus Infectivity in Dried Ornithologic Study Skins
Can HPAI survive on ornithological study skins? At 4 weeks viable virus could not be detected on the prepared study skins (of poultry, which were infected)

Inactivated H9N2 vaccines developed with early strains do not protect against recent H9N2 viruses: Call for a change in H9N2 control policy
H9N2 is endemic in poultry in Asia, and causes human cases each year. Inactivated H9N2 vaccines developed with early strains do not protect against recent H9N2 viruses – time for an update? Vaccine pressure on virus evolution?

Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Virus in Seals, St. Lawrence Estuary, Quebec, Canada
Previously summarised preprint, now published. In 2022, 209 dead/sick seals reported in Quebec (Harbor, Gray, Harp, Hooded seals). Many sick birds, so expected bird-> seal transmission. meningoencephalitis (100%), fibrinosuppurative alveolitis, multiorgan acute necrotizing inflammation.

A systematic review of laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America
First comprehensive database following compliation of available literature reporting pathobiology of AIV’s in all wild birds in over a decade. = tool for researchers, providing generalized estimates of pathobiology for wild avian families, knowledge gap?

Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift
Epic review of the epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift

Evidence of reassortment of avian influenza A (H2) viruses in Brazilian shorebirds
Great to see more data on LPAI in shorebirds from South America. Looong branch lengths in the trees demonstrate clear lack of sampling/sequencing. Similar to both N. and S. American segments – long distance movement?

DNA Vaccine Encoding a Modified Hemagglutinin Trimer of Avian Influenza A Virus H5N8 Protects Mice from Viral Challenge
pVAX-H5 DNA vaccine encoding a modified trimer of AIV H5N8 hemagglutinin. In BALB/c mice. high level of neutralizing antibodies and T-cell response. Both liquid and lyophilized forms provided 100% protection of immunized mice.

Infectivity of Wild-Bird Origin Influenza A Viruses in Minnesota Wetlands across Seasons
How long to avian influenza viruses survive in the environment? limited evidence for the extended persistence of IAVs held in mesocosms in the field (in contrast to temperature controlled water in the lab). Context important for environmental studies

Structural and functional characterization of avian influenza H9N2 virus neuraminidase with a combination of five novel mutations
Combo of 5 novel amino acid substitutions in the NA, near the sialic acid binding site  = ????substrate binding and altered surface characteristics to LPAI H9N2.

Nucleotide sequence as key determinant driving insertions at influenza A virus hemagglutinin cleavage sites
Another banger from the Erasmus crew and Im fairly sure this is the final published version of a preprint I shared in the past. How are aa’s acquired when LPAI->HPAI. Nucleotide sequence is a key determinant of insertions in the HA CS. Indels readily detected in a consensus H5 LPAI CS at low frequency (but not for other LPAI). Great mechanism paper.

Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation

Antibodies to Influenza A(H5N1) Virus in Hunting Dogs Retrieving Wild Fowl, Washington, USA
Antibodies to H5N1 in 4/194 (2%) dogs from Washington, USA, that hunted wild birds. Historical data provided by dog owners showed seropositive dogs had high levels of exposure to waterfowl.

Iceland: an underestimated hub for the spread of high-pathogenicity avian influenza viruses in the North Atlantic
Given 2 jumps of HPAI over Atlantic Ocean, role of Iceland important to be clarified. Diversity of HPAI in 2022 & 2023, incld novel introduction in 2023. Bridge for intercontinental introduction. 

Pigs are highly susceptible to but do not transmit mink-derived highly pathogenic avian influenza virus H5N1 clade
Nice follow-up to better understand transmission potential of HPAI H5N1 detected in mink farm, speculated to have been transmitting mammal-to-mammal. PIgs highly susceptible. Mammalian adaptive mutations PB2-E627K + HA-Q222L emerged at low frequencies. No transmission between pigs.

A multi-species, multi-pathogen avian viral disease outbreak event: Investigating potential for virus transmission at the wild bird – poultry interface
Nice case study demonstrating how HPAI can go from infected poultry property into wild birds (here predators and scavenging birds). Also compound an HPAI outbreak with detection of paramyxovirus wild birds. 

Update of the target list of wild bird species for passive surveillance of H5 HPAI viruses in the EU
Report from Sovon outlining target list of bird species for passive surveillance in EU. It would be good for us to develop something like this actually – ensure that jurisdictions are focussing on waterbirds/waterfowl/seabirds/shorebirds and raptors.

Novel Genotype of HA Clade H5N8 Subtype High Pathogenicity Avian Influenza Virus Emerged at a Wintering Site of Migratory Birds in Japan, 2021/22 Winter
Detection of HPAI H5N8 in Japan 2021/22 winter. 6/8 genes closely related to H5N8 in G2a group = was responsible for outbreaks in poultry farms in November 2021 in Japan. 2 segments from LPAI. Infectivity of this virus different from G2a H5N8.

Spatio-temporal dynamics and drivers of highly pathogenic avian influenza H5N1 in Chile
Using data from only 1 database in Chile, 7 significant clusters. H5N1 correlated w bird richness, human pop, distance to SAG’s office, and mean diurnal range. Negative correlation to a few metrics (isothermality, temperature annual range, precipitation of the warmest quarter, and coldest quarter). Take with grain of salt due to use of only 1 database, and not sure this is super appropriate in an active outbreak setting. 

Avian Influenza Virus Infections in Felines: A Systematic Review of Two Decades of Literature
Rather timely review of HPAI in cats. cat-to-cat transmission has been demonstrated experimentally, and real-world outbreaks have been reported. Detections in cats have occurred for as long as HPAI H5 has been circulating.

Novel Avian Influenza A(H5N6) in Wild Birds, South Korea, 2023
Novel H5N6 viruses emeged in Korea. all 8 genes shared highest nucleotide identity (99.77%–100%) w H5N6 in peregrine falcon in Japan. N6 similar to H5N6 found in humans and poultry in China. 

Concurrent Infection with Clade Highly Pathogenic Avian Influenza H5N6 and H5N1 Viruses, South Korea, 2023
https://wwwnc.cdc.gov/eid/article/30/6/24-0194_article H5N6 and H5N1 simultaneously introduced into S. Korea at end of 2023, w broiler farm co-infected. Emerged H5N6 viruses spread coincidently throughout  winter in East Asia

Mapping Genetic Markers Associated with Antigenicity and Host Range in H9N2 Influenza A Viruses Infecting Poultry in Pakistan
Can’t access full article.

Blowflies are potential vector for avian influenza virus at enzootic area in Japan
Blowflies are attracted to decaying animals and feces, and migrate to lowland areas of Japan from northern regions in early winter, coinciding with HPAI season. 2.2% prevalence, w highest occurrence near a crane colony (14.9%). Indicator, or transmitter?

Viral Pathogen Detection in U.S. Game-Farm Mallard (Anas platyrhynchos) Flags Spillover Risk to Wild Birds
Accepted, but no pdf available yet. 

Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses
In Canada, mortalities due to HPAI in 2023 were 93% lower vs 2022 (v positive news!) but encompassed a more taxonomically diverse array of species. Winter = waterfowl, summer = seabirds. 3 notable mortality events in 2023 (eg 1,646 Greater Snow Geese)

Joint FAO/WHO/WOAH preliminary assessment of recent influenza A(H5N1) viruses
“Individuals with activities that involve exposure to infected animals and/or contaminated environments are at higher risk and should take necessary precautions to prevent infection.18 At the present time, based on available information, WHO assesses the overall public health risk posed by A(H5N1) to be low, and for those with exposure to infected birds or animals or contaminated environments, the risk of infection is considered low-to-moderate”

Highly Pathogenic Avian Influenza A(H5N1) Clade Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024
Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows.

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle
Great to see the analysis by the USDA and folks involved in the cattle outbreaks. Genomic analysis and epidemiological investigation showed a reassortment event in wild bird populations preceded a single wild bird-to-cattle transmission episode.. 

What is the pandemic potential of avian influenza A(H5N1)?
“Although sequencing of viruses from the patient and cattle in Texas did not ring alarm bells regarding the potential of HPAI A(H5N1) clade for sustained human transmission, the next flu pandemic—whether caused by an avian influenza A(H5N1) virus or otherwise—seems inevitable. The threat of a pandemic remains high, and we urge international leaders to reach an agreement on a pandemic accord before it is too late”

Evolutionary dynamics and comparative pathogenicity of clade H5 subtype avian influenza viruses, China, 2021–2022
Mostly in China, include N1, N6, N8, but all likely evolved from H5N8. H5N1 have higher evolutionary rate 2021-22, more positive selected sites 2015-22. H5N1 antigenically distinct from H5N8/N6. Heterogeneous virulence in mammals.

Pathogen Surveillance in Swallows (family Hirundinidae): Investigation into Role as Avian Influenza Vector in Eastern Canada Agricultural Landscapes
Swallows, abundant in agricultural ecosystems, have been proposed as possible (bridge) species for HPAI transmission between wild and domestic birds. All tested swallows negative for both HPAI and LPAI.

Phylogeography and gene pool analysis of highly pathogenic avian influenza H5N1 viruses reported in India from 2006 to 2021
Co-circulation of many clades of HPAI H5N1 in India. 5 separate introductions of HPAI:  via Indonesia or Korea (2002), Bangladesh (2009), Bhutan (2010), and China (2013, 2018), with 8 reassortant genotypes.

Cross-species spill-over potential of the H9N2 bat influenza A virus
Some issue on the page, so no summary

Surveillance for highly pathogenic avian influenza A (H5N1) in a raptor rehabilitation center—2022
At a raptor centre in 2022, 996 birds acros 20 different species were tested for HPAI, and 213 birds were confirmed HPAI positive. contributed 75% of the HPAI positive raptor detections within the state of Minnesota. 

Detection of hemagglutinin H5 influenza A virus sequence in municipal wastewater solids at wastewater treatment plants with increases in influenza A in spring, 2024
Wastewater monitoring may be useful for HPAI monitoring. In USA, substantial increase in H5 detections. At 2 wastewater plants industrial discharges containing animal waste, including milk byproducts, were permitted to discharge into sewers.

Factors affecting highly pathogenic avian influenza vaccination practices at poultry farms in Tra Vinh, Vietnam
166 poultry farms with 14894 poultry in VietNam to determine socioeconomic and production characteristics to understand effect on HPAI vaccination practices. <50% of farms vaccinate.

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: implications for bird-mammal transmission in South America
Good to see this published. HPAI viruses from Uruaguay suggest pinnipeds ancestral to birds. Viruses in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route. Big implications!

Development and evaluation of a multiplex real-time RT-PCR assay for simultaneous detection of H5, H7, and H9 subtype avian influenza viruses
Multiplex H5/7/9 rRT-PCR assay optimized to simultaneously detect H5, H7, and H9.

Epidemiological characteristics of human infections with avian influenza A(H5N6) virus, China and Laos: A multiple case descriptive analysis, February 2014–June 2023
From 2014-2023, 85 human cases with HPAI H5N6. Case fatality rate: 39%. increased frequency from 2021 to present day. 84% reported contact with birds prior to illness onset.

Modeling the transmission dynamics of H9N2 avian influenza viruses in a live bird market
Great to see this modelling study of H9N2 in LBM. Many supplied birds arrive already exposed to H9N2, indigenous backyard chickens entering with pre-existing immunity. Susceptible chickens infected within one day at the market.

Repeatability and reproducibility of hunter-harvest sampling for avian influenza virus surveillance in Great Britain
Application of rapid diagnostics for samples collected from hunter-harvested waterfowl offers potential as an early warning system for HPAI.

Mapping the interaction sites of human and avian influenza A viruses and complement factor H
human FH can bind directly to IAVs of both human and avian origin, and the interaction is mediated via the HA. Interaction overlapped with the receptor binding site. Important for understanding mechanisms of infection and protection.

Sequence-based epitope mapping of High Pathogenicity Avian Influenza H5 clade in Latin America Unraveling Molecular and Antigenic Profile of Highly Pathogenic Avian Influenza H5 in Latin America
No access yet.

Highly Pathogenic Avian Influenza A(H5N1) Virus : Identification of Human Infection and Recommendations for Investigations and Response

First human case of avian influenza A (H10N3) in Southwest China
Case report of first human case of H10N3. H10 seems to infect a broad host range. Patient w severe pneumonia, type I respiratory failure, complications w fungi & bacteria. four mutations potentially hazardous to human health.

Human infection caused by avian influenza A (H10N5) virus
Case report of human infection with H10N5. Patient co-infected with human H3N2. female farmer aged over 60, with underlying comorbidities, who experienced symptoms of cough, sore throat. The patient had a history of exposure to live poultry

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections
Important not to forget pigs are important hosts for influenza (implicated in H1N1 pandemic). Similarities in patterns of genetic diversity and evolution b/w humans and pigs, including the role of stochastic processes in shaping within-host IAV dynamics.

Timor Leste has reported HPAI. It seems the diagnostics was done by ACDP 01/09/2022. 4 domestic birds. No lineage information.

Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation
Replication of avian influenza in mammalian cells is hindered by variation in ANP32. Cryo-electron microscopy of avian H5N1 FluPolA with human ANP32B =enhance understanding of molecular processes underpinning mammalian adaptations to avian influenza

Reply to León et al. (2024): Interpretation and Use of In-Field Diagnostics for High Pathogenicity Avian Influenza (HPAI) in Antarctica– A Cautionary Tale
We wrote a response to a recent preprint which claimed HPAI in apparently healthy penguins in Antarctica. Turns out they used an H5 assay which detects both LPAI and HPAI, so unclear what they found exactly. 

Molecular characterization of the whole genome of H9N2 avian influenza virus isolated from Egyptian poultry farms
H9N2 endemic in poultry, cause sporradic human cases. Common in Egypt. Virus from 2021: G1 sublineage of the Eurasian lineage, internals similar to Egyptian viruses. Subs in HA (191H and 234L) = predilection for attaching to human-like receptors

Evolution and Antigenic Differentiation of Avian Influenza A(H7N9) Virus, China
Vaccination of birds against HPAI can help us tremendously, but if done improperly, may drive virus evolution. Here a detailed look at H7N9, and the conclusion that vaccination may be preventing reassortment. Understanding vaccine effects critical.

Highly pathogenic avian influenza A(H5N1) virus in a common bottlenose dolphin (Tursiops truncatus) in Florida
In 2022, a stranded bottle-nosed dolphin in Florida tested positive for HPAI. Largest amount of virus in the brain (qPCR), neuronal necrosis and inflammation of the brain and meninges. S246N NA sub = ???? inhibition by oseltamivir.

Isolation and genetic characterization of multiple genotypes of both H5 and H7 avian influenza viruses from environmental water in the Izumi plain, Kagoshima prefecture, Japan during the 2021/22 winter season
While samples from birds are critical for HPAI, environmental samples can provide additional data. Both H5Nx and H7 detected in environment water in Japan during the 2021/22 winter season when HPAI prev high.

Molecular Characterization of Non-H5 and Non-H7 Avian Influenza Viruses from Non-Mallard Migratory Waterbirds of the North American Flyways, 2006–2011
Most avian influenza surveillnce systems focussed on Mallard. What is going on in other species? 1158 samples, 2006 & 2011 in USA, 87 LPAI. blue-winged teal, American wigeon, and American black duck species key players. 

Contrasting dynamics of two incursions of low pathogenicity avian influenza virus into Australia
Our study looking at recent virus incursions into Australia – H4 viruses found in shorebirds, seemed to stay in shorebirds and H10 viruses which appeared across australia pretty rapidly, and infected a large diversity of different hosts. Hopefully shed a bit more light on the process of virus entry, relevant for HPAI planning…

Bat-borne H9N2 influenza virus evades MxA restriction and exhibits efficient replication and transmission in ferrets
​A highly divergent bat H9 influenza (similar to avian H9) was described in 2017. Bat H9N2: high replication + transmission potential in ferrets, infects human lung explant cultures, is able to evade antiviral inhibition by MxA in transgenic B6 mice

Vaccination of poultry against highly pathogenic avian influenza – Part 2. Surveillance and mitigation measures
And related is Vaccination of poultry against highly pathogenic avian influenza – part 1. Available vaccines and vaccination strategies

Immunogenicity and protective efficacy of a multivalent herpesvirus vectored vaccine against H9N2 low pathogenic avian influenza in chicken
Building better vaccines for avian influenza: herpes vectored H9 & NDV vaccine. Vaccine elicited systemic NDV F- and AIV H9-specific antibodies but also local antibodies in eye wash fluid and oropharyngeal swabs. ???? viral load, doesn’t block infection

Highly Pathogenic Avian Influenza (HPAI) H5 Clade Virus Infection in Birds and Mammals
Review of HPAI. Includes details on outcomes of many experimental studies which is useful. If comprehensive, demonstrates how few experimental studies on panzootic strain are available (although probably in the works). 

Rapid mortality in captive bush dogs (Speothos venaticus) caused by influenza A of avian origin (H5N1) at a wildlife collection in the United Kingdom
In 2022, an unusual mortality event of captive bush dogs with HPAI. Enclosure of 15 bush dogs, 10 died in 9 days w some dogs exhibiting neurological disease. Ingestion of infected meat.

Evaluating the epizootic and zoonotic threat of an H7N9 low pathogenicity avian influenza virus (LPAIV) variant associated with enhanced pathogenicity in turkeys
Despite poultry vaccination, H7N9 has not been eradicated. HA Q217 is now dominant in China following vaccination, has affected antigenicitiy = can generate novel variants with increased risk via altered pathogenicity and potential HA antigenic escape.

Highly pathogenic avian influenza H5N1 virus infections of dairy cattle and livestock handlers in the United States of America
Editorial summary of events. 

The infectious disease trap of animal agriculture
Its really critical for us to reflect upon the role of animal agriculture in emerging infection diseases and zoonotic diseases. Current HPAI panzootic result of endemicity of disease in poultry systems for decades.

Confirmation of Highly Pathogenic Avian Influenza (HPAI) H5N1 Associated with an Unexpected Mortality Event in South Polar Skuas (Stercorarius maccormicki) during 2023-2024 Surveillance Activities in Antarctica
First mortality event in Antarctica (south of 60°S) by HPAI H5N1 was South polar skuas, 28 Feb 2024, James Ross Island. Would be great to see future sequencing results from this. 

Sero-epidemiology of Highly Pathogenic Avian Influenza viruses among wild birds in subarctic intercontinental transition zones
Seroprevalence study for HPAI in Alaska, Iceland – important stepping stones to North America. Samples from 2010–2019, wild migratory seabirds & waterfowl. seroprev of HPAI = 7.3%, variability per year, more in Alaska vs Iceland.

Proteomics analysis of duck lung tissues in response to highly pathogenic avian influenza virus
In duck lungs, infection by HPAI (old 2011 strain), 2028 proteins differentially expressed. Activation of RIG-I-like receptor and Jak-STAT signaling pathways = induction of interferon stimulated gene  expression = protective antiviral immune response

High-pathogenicity avian influenza in wildlife: a changing disease dynamic that is expanding in wild birds and having an increasing impact on a growing number of mammals
Review of HPAI with a nice overview of what is happening mammals, including diversity affected, and disease signs outlined.

The virus is out of the barn: the emergence of HPAI as a pathogen of avian and mammalian wildlife around the globe
Review on emergence of HPAI affecting avian and mammalian wildlife around the globe. 

Genetic and virological characteristics of a reassortant avian influenza A H6N1 virus isolated from wild birds at a live-bird market in Egypt
H6N1 caused human infection in Taiwan in 2013. Surveillance in Egyptian live bird markets, detected H6N1= replicated efficiently in mice w/o prior adaptation, + grew faster w higher titers tvs the ancestral strain. 

Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses
Lovely to see more H13 data, here from Republic of Buryatia. Viruses have no host data (but likely to be gulls), and have extensive reassortment, which aligns with work I did in 2011.

Influenza at the human-animal interface

Avian Influenza Virus and Avian Paramyxoviruses in Wild Waterfowl of the Western Coast of the Caspian Sea (2017–2020)
Outcome of influenza and paramyxo surveillance from western coast of Caspian Sea, 2017 to 2020. 1438 individuals of 26 species collected. 21 AIV strains, but no HPAI. 12 avian paramyxoviruses incl AMPV-1, AMPV-4, APMV-6.

Isolation and genetic characteristics of Novel H4N1 Avian Influenza viruses in ChongQing, China
Hgh AIV prevalence in poultry market in China, with isolation of H4N1. Genome signs of reassortment between wild and domesticated waterfowl, multiple mutations and demonstrates potential for host transfer.

Stranding and Mass Mortality in Humboldt Penguins (Spheniscus humboldti), Associated to HPAIV H5N1 Outbreak in Chile.
January and August 2023, 2,788 Humbolt Penguins stranded/died = increase in mortality coinciding w introduction of HPAIV H5N1 in Chile. 2 sequences generated, do not belong to the same subcluster = evidencing independent introductions

Emerging Threats: Is Highly Pathogenic Avian Influenza A(H5N1) in Dairy Herds a Prelude to a New Pandemic?
This paper was written entirely independently from the people doing the work. Its always disappointing to see things like this in the literature. 

Detection of clade highly pathogenic H5N1 influenza virus in New York City
HPAI is truly affecting animals everywhere. Surveillance in the urban environs of NY city, over 1700 samples collected and virus detected in 4 different bird species. Viruses w different genotypes. Important for risk, response, biosecurity

In Ovo Models to Predict Virulence of Highly Pathogenic Avian Influenza H5-Viruses for Chickens and Ducks
The development of in ovo models to understand virulence of HPAI decreases time requried and cost (compared to IVPI). Remarkable differences in virulence  observed bw poultry species, differences in replication rate, systemic virus dissemination

Drivers for a pandemic due to avian influenza and options for One Health mitigation measures
New from EFSA: guidance for public health authorities in EU/EEA countries on how to interpret the current situation of HPAI outbreaks in animals, includes mitigation measures. Useful guidance document.

Hemagglutinin and neuraminidase of an H7N7 non-pathogenic avian influenza virus coevolved during the acquisition of intranasal pathogenicity in chickens
To better be able to predict the emergence of HPAI, we need to clarify the steps in the process of LPAI to HPAI. Here, a low path virus with a polybasic cleavage site passaged to reveal required adaptations

Long-term co-circulation of multiple influenza A viruses in pigs, Guangxi, China
Surveillance of pigs in 12 cities in China = 192 positive samples, 19 genomes. Eurasian avian-like H1N1 swIAVs (G4) still remained predominant in pig populations, and multiple novel H3N2 genotypes from N. A. triple reassotant present w matrix of H9N2. Somewhat concerning. 

High pathogenic avian influenza A(H5) viruses of clade in Europe – why trends of virus evolution are more difficult to predict
Incredible overview of HPAI in Europe. 1956 genomes, spatial temporal patterns of diffusion, reassortment galore, emergence of gull genotype, adaptive mutations. Tour de force!

Avian Influenza A (H5N1) Outbreak 2024 in Cambodia: Worries Over the Possible Spread of the Virus to Other Asian Nations and the Strategic Outlook for its Control
Another paper wherein no one from Cambodia who is doing the work has been cited. 

Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events
H6 one of the most common LPAI subtypes in birds. From 2014-2019 168 viruses, 98 genotypes H6N6 in China, and isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events.

Avian influenza outbreaks in domestic cats: another reason to consider slaughter-free cell-cultured poultry?
This article debates that technology allowing the production of slaughter-free meat, including poultry, from cell and tissue cultures could be considered as a part of a mitigation strategy to decrease the overall burden and threat of adaptation of avian influenza viruses to human hosts

Naturally occurring highly pathogenic avian influenza virus H5N1 clade infection in three domestic cats in North America during 2023
Cats, like most predators/scavengers, have been repeatedly affected by HPAI. Here, three cats with neurological abnormalities. Pulmonary congestion + oedema, and cerebrocortical malacia w haemorrhage. 1 cat survived 10 days after onset of encephalitis. 

Mammalian Adaptation Risk in HPAI H5N8: A Comprehensive Model Bridging Experimental Data with Mathematical Insights
Here, mathematical models used to evaluate the growth, selection, and RNA load of eight recombinant viruses with mammalian adaptive markers + interplay. Revealed risk from adaptive markers of HPAI H5N8 in mammals. 

Field and laboratory investigation of highly pathogenic avian influenza H5N6 and H5N8 in Quang Ninh province, Vietnam, 2020 to 2021
In Viet Nam, 38 cases H5N6 clade viruses and 3H5N8 clade viruses. Raising poultry in uncovered ponds, poultry traders visiting the farm, farms with 50 – >2000 birds associated with HPAI outbreaks.

Surveillance and Genetic Analysis of Low-Pathogenicity Avian Influenza Viruses Isolated from Feces of Wild Birds in Mongolia, 2021 to 2023
Intro of HPAI in Korea linked to reassortment in bird breeding areas. Here, 10,149 samples from wild birds in Mongolia, = 1.01% prevalence, 77 isolated strains. No HPAI, but link bw Mongolia and Korea. Great collab and big picture thinking!

Generation and characterization of a nanobody against the avian influenza virus H7 subtype
A neutralising antibody with high HAI activity was enhanced via antiviral activity through oligomerization, = potential for developing effective agents for the prevention, diagnosis, and treatment of H7.

Evolutional dynamics of highly pathogenic avian influenza H5N8 genotypes in wintering bird habitats: Insights from South Korea’s 2020–2021 season
>7000 samples collected from S. Korea 2020-21, of which 5% positive for H5N8, predominantly from bird carcasses. Reassortment at play, with emergence of “G2” genotype. S. Korea a high density wintering area, a hot spot for potentially virus evolution.

Following outbreak of HPAI in Gannet colonies in Newfoundland: reproductive success 17% = adults abandoning nests, many dying. Birds also had extremely long foraging trips, and inter-colony movement. In addition to HPAI, marine heatwave also occuring.

Wildlife under threat as avian influenza reaches Antarctica

Evolutionary Events Promoted Polymerase Activity of H13N8 Avian Influenza Virus
H13’s are pretty weird, and almost exclusively found in gulls. Experimental reassortment of H13N8 with H9N2 viruses results in viruses with enhanced capacity for mammalian adaptations. Paper is a bit sensationalist, and I wonder about the ethics of the experiments performed.

Association of biosecurity and hygiene practices with avian influenza A/H5 and A/H9 virus infections in turkey farms
24.68% of turkey samples in Bangladesh positive for AIV (5.95% H5, 6.81% H9). Presence of footbaths, absence of nearby poultry farms, concrete flooring, and avoidance of mixing newly purchased turkeys with existing stock reduce the risk.

TRIM21 Promotes Oxidative Stress and Ferroptosis through the SQSTM1-NRF2-KEAP1 Axis to Increase the Titers of H5N1 Highly Pathogenic Avian Influenza Virus
TRIM21 is involved in signal transduction and antiviral responses, and is upregulated during H5N1 infection in A549 cells, which alleviates oxidative stress and ferroptosis.

Avian influenza virus cross-infections as test case for pandemic preparedness: From epidemiological hazard models to sequence-based early viral warning systems
What can we learn from human infections with avian influenza for pandemic preparedness? CDC IRAT and WHO TIPRA risk models for risk prediction, and genomic sequence data useful. Mink farms and animal markets concerning. I actually struggled to find the point of this paper

Host proteins interact with viral elements and affect the life cycle of highly pathogenic avian influenza A virus H7N9
Twelve host proteins have intricate interactions with viral proteins to modulate HPAI H7N9, including 6 which appear unique to H7N9 (relative to other influenzas). Important in understand infections and outcomes.

Seroprevalence of Avian Influenza A(H5N6) Virus Infection, Guangdong Province, China, 2022
While HPAI H5N1 is problematic globally, China struggled with H5N6: 86 human cases. Serology study in humans Jan-March 2022: 1 of >6000 humans positive, BUT poultry workers excluded. Low risk of human infection in general population, in alignment w WHO.

Upper Respiratory Tract Disease in a Dog Infected by a Highly Pathogenic Avian A/H5N1 Virus
Remember the HPAI outbreak in cats in Poland in 2023? Well, a dog was also infected. Respiratory disease signs consistent with “kennel cough” –  dog did not respond to initial treatment with antibiotics, later fluA test result positive.

Genetic Diversity of Avian Influenza Viruses Detected in Waterbirds in Northeast Italy Using Two Different Sampling Strategies
In Italy, across 2 sites, Aug 2021-April 2022: LPAI H5N3, H1N1, H9N2 detected, related to viruses in Black Sea/Mediterranean migratory flyway. No HPAI detected

A Phase 2 Clinical Trial to Evaluate the Safety, Reactogenicity, and Immunogenicity of Different Prime-Boost Vaccination Schedules of 2013 and 2017 A(H7N9) Inactivated Influenza Virus Vaccines Administered with and without AS03 Adjuvant in Healthy US Adults

Lack of Highly Pathogenic Avian Influenza H5N1 in the South Shetland Islands in Antarctica, Early 2023
Great to see the publication of more HPAI surveillance in the Antarctic. Surveillance efforts in the South Shetland Islands in January 2023 all negative, consistent with observations that HPAI likely didnt reach the peninsula until later in the season.

Index case of H5N1 clade highly pathogenic avian influenza virus in wild birds, South Korea, November 2023
No pdf yet.

Comparison of the Clinical Manifestation of HPAI H5Nx in Different Poultry Types in the Netherlands, 2014–2022
Important to remember that HPAI has different impacts on different poultry types, and that different clades have also had different impacts. Here, a careful comparison of H5N1, H5N8, H5N6, b/w 2014, 2018,  2020, 2022 for different poultry types and ages

Experimental Evaluation for the Dual Infection of Low Pathogenic Avian Influenza virus H9N2 and Escherichia Coli in H9N2 Immunized and Non-immunized Broiler Chickens
Significant mortality in chickens co-infected w H9N2 and E.coli (50-90% deaths) and severe clinical illness compared to influenza alone. Use of H9N2 vaccines can protect broilers from mortality + minimize shedding post-challenge.

Long-Distance Avian Migrants Fail to Bring HPAI H5N1 Into Australia for a Second Year in a Row
Summary of our “enhanced surveillance” activities in 2023. 

Avian influenza overview December 2023 – March 2024
Updated EFSA

Highly pathogenic avian influenza A(H5N1) virus of clade isolated from a human case in Chile causes fatal disease and transmits between co-housed ferrets
Human case of HPAI in Chile tested in ferrets to understand infection in mammals, and possibility of transmission. Virus transmitted to naïve contacts via direct contact but NOT via respiratory droplets or fomite transmission models. So, virus can transmit in “unnatural” setting, but cant transmit via airbourne transmission which is needed for effective mammal-to-mammal transmission.

Divergent Pathogenesis and Transmission of Highly Pathogenic Avian Influenza A(H5N1) in Swine
Assessment of susceptibility of pigs to avian and mammalian HPAI H5N1 All strains replicated in the lung of pigs w lesions consistent with influenza. But, viral replication in the nose + transmission only observed when using mammalian viruses.

Amino acids in the polymerase complex of shorebird-isolated H1N1 influenza virus impact replication and host-virus interactions in mammalian models
Diversity of LPAI in wild birds, zoonotic risk mostly uknown. H1N1 viruses in birds in US assessed. Viruses with key subs in the PB2 ????replication kinetics, ???? infectivity, ????polymerase complexes, ????replication kinetics. Pathogenicity in the mouse????.

Host proteins interact with viral elements and affect the life cycle of highly pathogenic avian influenza A virus H7N9

Avian Influenza in Low and Middle-Income Countries (LMICs): Outbreaks, Vaccination Challenges and Economic Impact

Role of the World Organisation for Animal Health in global wildlife disease surveillance
Overview of the role of WOAH, and surveillance data being shared. E.g. b/w 2019–2023, 154 countries reported 68862973 cases for 84 diseases. 150 countries reported 68672115 cases in domestic animals and 95 countries reported 190858 cases in wild animals.

Genetic and biological properties of H9N2 avian influenza viruses isolated in central China from 2020 to 2022
H9N2 is most common subtype in poultry in China; is zoonotic. In Shanxi Province, across 14 viruses, 7 genotypes, 2 antigenic clusters? High transmission efficiency & diverse replication ability in chickens. Viruses replicate efficiently in mice lungs.

Natural Infection with H5N1 Highly Pathogenic Influenza (HPAI) Virus in 5- and 10-Day-Old Commercial Pekin Ducklings (Anas platyrhynchos domesticus)
No access

Assessment of Knowledge and Biosecurity Practices Related to Avian Influenza Among Poultry Workers in a District of South India
No access

Complex N-glycans are important for interspecies transmission of H7 influenza A viruses
HAs bind to glycan receptors with terminal sialic acids, which are either NeuAc or NeuGc (mainly found in horses and pigs but not in birds and humans). NeuGc-adapting mutations in avian H7 IAVs in vitro and in vivo. Affect viral replication in chicken cells, not duck cells, positively affect replication in horse cells. Mutations reduce virus virulence and mortality in chickens.

Control of highly pathogenic avian influenza through vaccination
China been using vaccines to control HPAI H5 since 2004, with more than 300 billion doses used by 2022. Paper outlines suggestions regarding requirements for vaccine selection and effectiveness. Should be taken with consideration, and some studies have conflicting conclusions with regards to effect of vaccines on virus evolution.

Recent H9N2 avian influenza virus lost hemagglutination activity due to a K141N substitution in hemagglutinin
Increasingly, H9N2 strains have a loss of hemagglutination activity at 37°C, = challenges for detection & monitoring = K141N in HA. N141K mutation impedes H9N2 ability to bind to receptors, enhances viral thermostability, reduces plaque size on MDCK

MDCK-Adaptive Mutation of A169S Changes Glycosylation Pattern of Hemagglutinin and Enhances MDCK-Based H7N9 Vaccine Virus Production without Loss of Antigenicity and Immunogenicity
Adaptation of egg-derived H7N9 CVV in mammalian cell line is an approach to make high-growth virus for mass production of vaccine manufacturing. Investigation of mutations that arise in the process and impact on replication and vaccine responses.

Surveillance for highly pathogenic avian influenza A (H5N1) in a raptor rehabilitation center — 2022
No full text access

H5N1 high pathogenicity avian influenza virus in migratory birds exhibiting low pathogenicity in mallards increases its risk of transmission and spread in poultry
HPAI virus from crane in china: highly pathogenic to chickens, moderately pathogenic to BALB/c mice, highly infectious but not lethal to mallards. Minor antigenic drift compared with the H5-Re14 vaccine strain (used in China).

Pacific and Atlantic sea lion mortality caused by highly pathogenic Avian Influenza A(H5N1) in South America
Good to see this pre-print now published. Excellent description of HPAI spread in sea lions of south america – down the pacific coast, and back up the Atlantic coast. Huge impact on these animals.

Genomic epidemiology of highly pathogenic avian influenza A (H5N1) virus in wild birds in South Korea during 2021–2022: Changes in viral epidemic patterns

H5N1 high pathogenicity avian influenza virus in migratory birds exhibiting low pathogenicity in mallards increases its risk of transmission and spread in poultry
2021–2022, 1 H5N8 + 43 H5N1 HPAI viruses in wild birds in South Korea. 5 genotypes. Wild birds play a vital role in viral transmission and long-term maintenance

Rapid adaptive substitution of L226Q in HA protein increases the pathogenicity of H9N2 viruses in mice
More than 100 human cases due to H9N2 – all cases from China assayed in mice: low or no pathogenicity in mice, L226Q in HA rapidly emerged which was responsible for severe infections/fatalities. 226Q = a competitive advantage in mice.

Highly Pathogenic Avian Influenza A (H5N1) Suspected in penguins and shags on the Antarctic Peninsula and West Antarctic Coast
Suspected HPAI in Adélie penguins and Antarctic shags. Detections at 2/13 sites; limited to Antarctic Peninsula.

Analysis of H5N8 influenza virus infection in chicken with mApple reporter genes in vivo and in vitro
Labelled H5N8 viruses used to infect monocytes/macrophages in PBMCs – detected the mApple in 55.1%-80.4%, = chicken primary monocytic/macrophages are important target cells for avian influenza. Found in chicken lung CD45+ cells, CD4 + CD8 T cells.

Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia
No access beyond pubmed?

Long distance avian migrants fail to bring HPAI H5N1 into Australia for a second year in a row
The summary of our enhanced surveillance program, targeted to incoming migratory birds to Australia is now out. We sampled ~ 1000 birds, with no indication of HPAI. Oceania last continent free from HPAI

Molecular characterization of avian influenza viruses (H5N2, H5N8, H5Nx and H9N2) isolated from chickens and ducks in the South of Egypt 2020 –  2021
143 samples from chicken and duck farms in Egypt, 2020 w H5N2, H5N8, H5Nx, H9N2. clade with close relation to H5N8 isolates from Egypt in 2021 and Kazakhstan in 2020.

Molecular detection of highly pathogenic avian influenza A (H5N8) virus isolated from domestic ducks and chickens in Egypt across 2018-2021
Vaccinated duck and chicken flocks in 2018-2021 from different provinces, Egypt. Flocks with respiratory, nervous signs, with 90% mortality. Egyptian H5N8 viruses clustered in group B Russian like reassortant H5N8 viruses of clade

H5N1 high pathogenicity avian influenza virus in migratory birds exhibiting low pathogenicity in mallards increases its risk of transmission and spread in poultry
https://www.sciencedirect.com/science/article/abs/pii/S0378113524000609 in Grey Crane in China, w some segments similar to human cases. Substitutions for enhanced replication & mammalian pathogenicity. Highly pathogenic to chickens, moderately pathogenic to BALB/c mice, and infectious but not lethal to mallards. Some drift from current vaccine

Wild Bird-Origin H6N2 Influenza Virus Acquires Enhanced Pathogenicity after Single Passage in Mice
H6 is very common in wild birds. Here a virus from a wild bird in China passaged in mice. Initially replication poor, but upon second passage 2 mutations. Retained the α-2, 3-linked sialic acid binding property and failed to transmit in guinea pigs. PB2 E627K enhanced polymerase activity and HA A110V decreased the pH of HA activation

Genetics of H5N1 and H5N8 High-Pathogenicity Avian Influenza Viruses Isolated in Japan in Winter 2021–2022
In 2021–2022, H5N1 + H5N8 HPAI caused serious outbreaks in Japan: 25 at poultry farms + 107 in wild birds/environment. Three genetic groups, but at different locations/time. Strong links bw viruses in Japan and Siberia. 

Monitoring avian influenza in mammals with real-time data
Open access database https://github.com/fbranda/avian-mammals and a corresponding visualization https://tinyurl.com/avianflu-mammals-map designed to more easily monitor reported cases in mammals across various countries. Essentially just WAHIS data, but they are trying to make it easier to access. 

The H9N2 avian influenza virus increases APEC adhesion to oviduct epithelia by viral NS1 protein-mediated activation of the TGF-β pathway
H9N2 viruses enhance secondary APEC [E.coli] infection in chickens via enhancing fibronectin, which promotes bacterial adhesion. Viral NS1 transforms growth factor beta (TGF-β) signalling pathway.

Avian H6 Influenza Viruses in Vietnamese Live Bird Markets during 2018–2021
Plenty of H6 viruses found in Vietnamese live bird markets. Most viruses highly similar, but reassortment present. Amino acid motif in HA confers binding to both avian- and human-type receptors on host cells

Genetic evolution analysis of hemagglutinin and neuraminidase genes of H9N2 avian influenza virus in external environment of some areas of Yunnan Province, China from 2020 to 2023
HA and NA of H9N2 in Yunnan Province evolved continuously, but still Y280 clade. Ability to bind to the mammalian sialic acid α-2,6 sialic acid receptor. Small and descriptive study.

Highly Pathogenic Avian Influenza A(H5N1) Viruses from Multispecies Outbreak, Argentina, August 2023.
HPAI from birds and marine mammals in Argentina: not related to first cases in Argentina, seperate introduction? 9 mutations in marine mammals viruses w Q591K and D701N in PB2 = mammalian adaptation mutations. pinniped-to-pinniped transmission?

Descriptive Epidemiology and Phylodynamics of the “First Wave” of an Outbreak of Highly Pathogenic Avian Influenza (H5N1 Clade in British Columbia and the Yukon, Canada, April to September 2022
Since November 2021, Canada experienced its longest and largest outbreak of HPAI in history. 21 wild bird species, 2 mammalian species, 4 commercial + 12 domestic small flocks. 5 genetic clusters, Eurasian+NAmerican segments

PB2 residue 473 contributes to the mammalian virulence of H7N9 avian influenza virus by modulating viral polymerase activity via ANP32A
H7N9 caused >1000 human infections since 2013. Mutation at 473 and 627 in PB2 critical, but species-specific usage of ANP32A host factor affected mammalian adaption of AIV polymerase. PB2 473 novel viral host range determinant.

H7N6 highly pathogenic avian influenza in Mozambique, 2023
H7N6 avian influenza outbreak in commercial layers in Mozambique. HPAI cleavage site PEPPKGPRFRR/GLF. Similar to viruses from South Africa in May 2023. Spread of HPAI viruses from South Africa, or an independant event in Mozambique?

Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus
New tool to describe genotypes of influenza A viruses (all influenza A’s). Interpretation of results show lack of domain expertise, so wouldnt read into it too much. 

Avian influenza virus circulation and immunity in a wild urban duck population prior to and during a highly pathogenic H5N1 outbreak
Sero-study of ducks in Newfoundland, demonstrating infection events across population in 2021 & 2022. Demonstrates clear power of serology in studying outbreaks, and that HPAI clearly spread through 100% of the ducks, twice = limited long term immunity?

Species-specific emergence of H7 highly pathogenic avian influenza virus is driven by intrahost selection differences between chickens and ducks
Co-innoculating HPAI and LPAI H7 in chickens and ducks leads to differential outcomes. HPAI selected for in chickens, LPAI selected in ducks. =HPAI selected intrahost, w species specific differences in tropism. Why HPAI H5 still selected in wildbirds?

N-Glycan Profiles of Neuraminidase from Avian Influenza Viruses
Characterisation of N-glycans. 

An algorithm for the characterization of influenza A viruses from various host species and environments
You have an influenza outbreak. Now what? Herein, a framework for influenza testing across environment, wildlife, livestock, humans.

Comparative examination of a rapid immunocytochemical test for the detection of highly pathogenic avian influenza virus in domestic birds, in field outbreaks.
Diagnosing avian influenza using smears analysed with immunohistochemistry can be a useful, rapid approach when PCR diagnostics not available, but basic veterinary labs are. 

Enhanced Downstream Processing for a Cell-Based Avian Influenza (H5N1) Vaccine
There are still few approved HPAI vaccines on the market. Here, a two step downstream process as an efficient and cost-effective platform technology for cell-based H5N1 vaccines

Development of Virus-like Particle Plant-Based Vaccines against Avian H5 and H9 Influenza A Viruses
Virus like particle vaccine for H5 and H9 developed. In mice, H5 VLP elicit robust antibody and Tcell response. Single dose of H5 VLP in chickens stimulated antibody response to neutralise virus infectivity. 

Association of biosecurity and hygiene practices with Avian Influenza A/H5 and A/H9 virus infections in turkey farms
No full text available yet.

Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa
H9N2 in Mali – G1 lineage similar to viruses in W & N Africa. Multiple molecular markers associated with an increased potential for zoonotic transmission and virulence, RSNR cleavage site. Likely arrived in Africa in 2015 via single introduction. 

Pathological investigation of high pathogenicity avian influenza H5N8 in captive houbara bustards (Chlamydotis undulata), the United Arab Emirates 2020
Outbreak of H5N8 in captive Houbara Bustards in UAE in 2020. Detailed pathology reveals hyperacute/acute forms exhibiting marked pantropism, endotheliotropism and neurotropism

Cross-Species Transmission Potential of H4 Avian Influenza Viruses in China: Epidemiological and Evolutionary Study
H4s are one of the most common subtypes in wild birds. Over ~13 years, 31 isolates in Chinese poultry markets. Lots of genetic diversity , and some mutation of interest. Important not to lose sight of subtypes other than H5/H7/H9

Rapid loss of maternal immunity and increase in environmentally mediated antibody generation in urban gulls
Antibodies across life stages: avian influenza antibodies present widely across all live stages of gulls, but maternal antibodies declined exponentially after hatching, but differences in nestling antibody levels due to parental effects.

Evaluation of different transport media for survival of H5N1 highly pathogenic avian influenza virus.
Sample collection methods have big impacts on laboratory analysis. Herein, various media tested for HPAI collection. They find that VTM not that great, but dont specify which VTM they used and how it was stored in the field. Also, stored at 37C before testing, which probably explains why VTM didnt do so well. 

Highly Pathogenic Avian Influenza A(H5N1) Virus Clade in Domestic Ducks, Indonesia, 2022
preprint now published – first report of in Indonesian domestic ducks. 4430/5770 (76.8%) ducks died. From 2022-23, molecular surveillance didnt detect it further. As our nearest neighbour, high relevance to Australia.

Characterization of a human H3N8 influenza virus
Characterisating of 2022 strain of H3N8 found in humans. Minor weight loss in ferrets, replicated efficiently in upper resp tract. Transmission via droplets occurred. SNPs in HA affecting receptor specificity. Antibodies found in some human sera

Caught Right on the Spot: Isolation and Characterization of Clade H5N8 High Pathogenicity Avian Influenza Virus from a Common Pochard (Aythya ferina) Being Attacked by a Peregrine Falcon (Falco peregrinus) 
No access

Spatio-temporal Dynamics and Risk Cluster Analysis of Highly Pathogenic Avian Influenza HPAI (H5N1) in Poultry: Advancing Outbreak Management through Customized Regional Strategies in Egypt
H5N1 is endemic in Egypt, detailed studies show shifting epidemiology. Menofia, important in early poultry impacts, but initial outbreaks didn’t originate there. Predominant hot spot region in rural villages, w fewer outbreaks in urbanized areas

An overlooked poultry trade network of the smallholder farms in the border provinces of Thailand, 2021: implications for avian influenza surveillance
To understand virus transmission, we need to understand poultry movements. Here >300 poultry farmers and traders interviewed in Thailand. 99 subdistricts and 181 trade links with different in-degree and out-degree centralities

A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families
We still have a long way to go to understand the duck immune response. Here, a chromosome scale duck genome assembly, with a complete genomic map of MHC. Gene arrangement primordial, but some expansions. Useful resource!

First confirmed cases of HPAI on the Antarctic Peninsula

A pan-influenza monoclonal antibody neutralizes H5 strains and prophylactically protects through intranasal administration
Human therapuetics in case widespread HPAI in humans. An epitope on stem domain of H5 HA is highly conserved and  the human monoclonal antibody CR9114 potently neutralizes all H5 viruses, even in the rare case of substitutions in its epitope.

Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic
The dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. Temporal–spatial coincidence bw the outbreak of H5N8 G1 virus and autumn migration may have expanded the H5 viral spread

Applied Research Note: Development and Validation of a Highly Specific Polyclonal Antibody Targeting Neuraminidase of Novel H3N8 Avian Influenza Virus

Are all avian influenza outbreaks in poultry the same? The predicted impact of poultry species and virus subtype
Are all influenza outbreaks on poultry farms the same?Simulations predicted large differences in the duration and severity of outbreaks, depending on the virus subtypes (only H7 and H7), outbreaks of HPAI shorter duration than LPAI

High pathogenicity avian influenza (HPAI) in the UK and Europe

Highly pathogenic avian influenza virus H5N1 clade from Peru forms a monophyletic group with Chilean isolates in South America
More work to understand HPAI introduction and spread in South America. Critically, more evidence that events in Chile and Peru were due to same virus, falling to a monophyletic clade.

Protection conferred by an H5 DNA vaccine against highly pathogenic avian influenza in chickens: The effect of vaccination schedules
DNA vaccine with A/gyrfalcon( showed good protection in chickens infected with with or without adjuvant, but with 2 doses. Also, good humoral immunity in birds 18 – 25 weeks old. 

Genetic insertion of mouse Myxovirus-resistance gene 1 increases innate resistance against both high and low pathogenic avian influenza virus by significantly decreasing replication in chicken DF1 cell line
Introduction of mouse Mx (which has strong antiviral acivity) to chicken cells efficiently reduced avian influenza infection load and less CPE. Foundation for gene editing of chickens to help resist HPAI?

Recent Changes in Patterns of Mammal Infection with Highly Pathogenic Avian Influenza A(H5N1) Virus Worldwide
Excellent overview of impacts of HPAI on mammals. Big skew towards carnivores & scavengers (not surprising if we imagine lots of bird carcasses in the environment). SeaLions and Elephant Seals really raise questions of mammal-to-mammal transmission.

Genetic Characterization and Phylogeographic Analysis of the First H13N6 Avian Influenza Virus Isolated from Vega Gull in South Korea
Another H13 genome, this time from a gull in South Korea. Sequences largely fall into gull-associated lineages, and phylogeographic origin is largely Eurasian, but with some exceptions. Certainly more work to do in gulls. 

Genome sequences of hemagglutinin cleavage site predict the pathogenicity phenotype of avian influenza virus: statistically validated data for facilitating rapid declarations and reducing reliance on in vivo testing
Whether an avian influenza virus is HPAI or LPAI is usually confirmed using IVPI ($$, ethics, time). New study shows statistically robust association with cleavage site sequence and pathogenicity. Great resource!

Avian Influenza: a major threat to our struggling seabirds
The data is horrific. 25% decline in Gannets (at least half of all NOrthern Gannets are found in the UK). 76% decline of breeding numbers of Great Skua in Scotland (60% of all great skuas are found in scotland)

Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders
Great to see this published. How has spread amongst different region and species (in Eurasia): synchrony b/w bird migration and virus lineage movement, and differing bird orders at origins and destinations, including accipitriformes.

Novel H10N3 avian influenza viruses: a potential threat to public health
H10 viruses, particularly in Asia, remain concerning. H10N3 found in 41 year old man in China. These H10 viruses also found in poultry markets (2020-22). Human & poultry viruses bind sialic acid-α-2,6-galactose receptors, poultry viruses lethal to mice

HPAIV outbreak triggers short-term colony connectivity in a seabird metapopulation
Now published. During HPAI outbreaks in gannet colonies, GPS tracked individuals nstigated long-distance movements beyond well-documented previous ranges and prospected other colonies. Facilitated spread?

A systematic review of influenza virus in water environments across human, poultry, and wild bird habitats
Meta-analysis assess influenza in the environment including waste water. Features influenza A and B, and LPAI and HPAI. Really lacking any details that would make it useful.

Detection of clade highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji-Nguru wetland, Nigeria 2022
Diversity of influenza viruses in wild birds in Nigeria in 2022, including in clinically healthy wild birds (from Jacanas to nighjars to ducks). E627K is present in some., but different from HPAI in Nigerian poultry in 2021.

Recombinant parainfluenza virus 5 expressing clade H5 hemagglutinin protein confers broad protection against H5Ny influenza viruses
Interrogation of potential HPAI vaccine – parainfluenza virus 5 -based vaccine candidate expressing H5 HA. Intranasal immunization in ferrets stimulated antibody responses in mice, provide sterile immunity in mice and ferrets

High pathogenicity avian influenza A (H5N1) clade virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022
November 2022, HPAI caused an outbreak in a zoological park in the south of France, with the death of a Tibetan black bear and several bird species. PB2 E627K mutation in minute quantities in the gull, whereas it predominated in the bear

Incursion of Highly Pathogenic Avian Influenza A(H5N1) Clade Virus, Brazil, 2023
HPAI in Royal terns and Cabot’s terns in Brazil, June 2023. Phylodynamics suggests incursion from Chile, although noting long branch lengths (missings sequences)

Comparative analysis and prediction of avian influenza in Shangrao city, China from 2016 to 2022
Relationship between vaccination, COVID-19 pandemic, and bird migration on avian influenza in Shangrao City. Of concern is highly prevant H9, and increase of H5. Migratory birds and the COVID-19 pandemic have led to an increase in H9 subtype positivity. Take with a grain of salt.

Immunogenic and Protective Properties of Recombinant Hemagglutinin of Influenza A (H5N8) Virus
Recombinant HA (H5N8) protein may be a useful antigen candidate for developing subunit vaccines against HPAI with suitable immunogenicity and protective efficacy.

A highly pathogenic avian influenza virus H5N1 clade detected in Samara Oblast, Russian Federation
Good to see some data from Russia, an important breeding area for migratory birds across Eurasia and Africa. A virus found in a teal in Samara Oblast was related to field isolates from Russia, Nigeria, Bangladesh, and Benin

Bivalent Hemagglutinin Cleavage-Site Peptide Vaccines Protect Chickens from Lethal Infections with Highly Pathogenic H5N1 and H5N6 Avian Influenza Viruses
Bivalent peptide vaccines containing H5 cleavage sites of viruses from both H5N6 and clade 1 H5N1 designed to protect chickens from both H5N1 and H5N6 avian influenza viruses. immunised chickens were protected with no shedding in OP or C.

Guidance for reporting 2023 laboratory data on avian influenza

Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic
Massive gull mortality and poultry outbreaks in Czech Republic 2022/23. Almost 1 million birds culled. Four HPAI genotypes, with BB mainly in gulls, and in turkey outbreak.

Avian ANP32A incorporated in avian influenza A virions promotes interspecies transmission by priming early viral replication in mammals
Species-specific differences in the host factor ANP32A determine the restriction of avian-signature polymerase in mammalian cells. ANP32 proteins incorporated into viral particles through combo w polymerase>transferred to cells> support replication. vian ANP32A (avANP32A) delivered by avian influenza A virions primes early viral replication in mammalian cells, thereby favoring the downstream interspecies transmission event by increasing the total amount of virus carrying adaptive mutations.

Genetic and Biological Characteristics of Duck-Origin H4N6 Avian Influenza Virus Isolated in China in 2022
In 2022, samples from duck farms at Poyang Lake, China, with 3 H4N6 viruses isolated. Dual receptor binding properties and replicate efficiently not only in avian cells but also in mammalian cells. Viruses could infect mice without prior adaptation.

Emergence of a Novel Reassortant H5N6 Highly Pathogenic Avian Influenza Virus of Clade from domestic poultry in China
Detection of clade H5N6 virus in China, against expectation of Result of complex pattern of reassortment among clade and clade H5 and H6N6.

In turkeys, unlike chickens, the non-structural NS1 protein does not play a significant role in the replication and tissue tropism of the H7N1 avian influenza virus
NS1 does not play a role in the virulence or replication of HPAIV H7N1 in turkeys, illustrating genetic determinants of HPAIV between turkeys and chickens.

Host determination role of some amino acid sequences in the receptor-binding site and phylogenetic analysis of a high pathogenic Avian Influenza (H5N1) viruses isolated from Northern Turkey
Retrospective study of HPAI in Turkey in 2006. Clade 2.2 and clade 2.2.1 and were closely related to European and Asian isolates

Detection of highly pathogenic avian influenza virus H5N1 clade in great skuas in Great Britain
Great summary of pathology of Great Skuas which died due to HPAI in Scotland.

Considerations for emergency vaccination of wild birds against high pathogenicity avian influenza in specific situations

Transient RNA structures underlie highly pathogenic avian influenza virus genesis

The contribution of individual characteristics of Anas and Aythya individuals to their susceptibility to low‐pathogenic avian influenza viruses in the south of Western Siberia

“Smart markets”: harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets

Veterinarians’ knowledge and experience of avian influenza and perspectives on control measures in the UK

Genetic properties and pathogenicity of a novel reassortant H10N5 influenza virus from wild birds

Transmission dynamics and pathogenesis differ between pheasants and partridges infected with clade H5N8 and H5N1 high-pathogenicity avian influenza viruses

Complete Genome Sequence of an H10N5 Avian Influenza Virus Isolated from Pigs in Central China

New Patterns for Highly Pathogenic Avian Influenza and Adjustment of Prevention, Control and Surveillance Strategies: The Example of France

Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats

Markets as drivers of selection for highly virulent poultry pathogens

Molecular evolution of avian influenza A (H9N2) virus in external environment in Anhui, 2019-2021

Public Health Implications of Antimicrobial Resistance in Wildlife at the One Health Interface

Differing Expression and Potential Immunological Role of C-Type Lectin Receptors of Two Different Chicken Breeds against Low Pathogenic H9N2 Avian Influenza Virus

Detection of Influenza A viruses and Avian H5 Subtype using a triplex qRT-PCR assay on the ABI Quantstudio 7 PCR system

Multifaceted analysis of temporal and spatial distribution and risk factors of global poultry HPAI-H5N1, 2005-2023

Farm biosecurity practices affecting avian influenza virus circulation in commercial chicken farms in Bangladesh

Genetic Analysis of H5N1 High-Pathogenicity Avian Influenza Virus following a Mass Mortality Event in Wild Geese on the Solway Firth

Avian influenza virus cross-infections as test case for pandemic preparedness: From epidemiological hazard models to sequence-based early viral warning systems

Emergence of a triple reassortment avian influenza virus (A/H5N6) from wild birds

Differential Protection of Chickens against Highly Pathogenic H5 Avian Influenza Virus Using Polybasic Amino Acids with H5 Cleavage Peptide

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

Transboundary Determinants of Avian Zoonotic Infectious Diseases: Challenges for Strengthening Research Capacity and Connecting Surveillance Networks

The risks and consequences of a high pathogenicity avian influenza outbreak in Aotearoa New Zealand

A Comprehensive Analysis of H5N1 Evolution: Phylogenetic Insights and Emerging Mutations in Turkey’s Avian Influenza Landscape

Running the gauntlet; flyway-wide patterns of pollutant exposure in blood of migratory shorebirds

Lesions and viral antigen distribution in bald eagles, red-tailed hawks, and great horned owls naturally infected with H5N1 clade highly pathogenic avian influenza virus

A case-control study of the infection risk of H5N8 highly pathogenic avian influenza in Japan during the winter of 2020–2021

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

Efficacy of an inactivated influenza vaccine adjuvanted with Toll-like receptor ligands against transmission of H9N2 avian influenza virus in chickens

Simultaneous Differential Detection of H5, H7, H9 and Nine NA Subtypes of Avian Influenza Viruses via a GeXP Assay

Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade Virus in Wild Birds, South Korea, 2022-2023.

HA N193D substitution in the HPAI H5N1 virus alters receptor binding affinity and enhances virulence in mammalian hosts

Catastrophic mortality of southern elephant seals caused by H5N1 avian influenza

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

Evolution and biological characteristics of the circulated H8N4 avian influenza viruses

Meta-analysis of RNA Seq Datasets in Duck Lungs Infected with Highly Pathogenic Avian Influenza Viruses

Comprehensive genome‑wide analysis of the chicken heat shock protein family: identification, genomic organization, and expression profiles in indigenous chicken with highly pathogenic avian influenza infection

Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck 

Mortality in Sea Lions is associated with the introduction of the H5N1 clade virus in Brazil, October 2023: Whole genome sequencing and phylogenetic analysis

Avian Influenza A(H5N1) Neuraminidase Inhibition Antibodies in Healthy Adults after Exposure to Influenza A(H1N1)pdm09

Neu5Gc binding loss of subtype H7 influenza A virus facilitates adaptation to gallinaceous poultry following transmission from waterbirds but restricts spillback

H5N1 avian influenza virus PB2 antagonizes duck IFN-β signaling pathway by targeting mitochondrial antiviral signaling protein

The role of PB1-F2 in adaptation of high pathogenicity avian influenza virus H7N7 in chickens

Identification of specific neutralising antibodies for highly pathogenic avian influenza H5 clades to facilitate vaccine design and therapeutics

Human behaviors driving disease emergence

A recent sovon report indicates that high path. avian #influenza has killed a high percentage of some bird populations in the #Netherlands. Sandwich tern, summer 2022: up to 56% estimated mortality. Peregrine falcon, winter 2021/2022: up to 56% estimated mortality.https://x.com/thijskuiken/status/1742922644864000491?s=20

Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck

Highly pathogenic H5n1 avian influenza in free-living griffon vultures

Trends and Spatiotemporal Patterns of Avian Influenza Outbreaks in Italy: A Data-Driven Approach

Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus

Avian influenza overview September–December 2023

Antigenic Architecture of the H7N2 Influenza Virus Hemagglutinin Belonging to the North American Lineage

Highly pathogenic avian influenza virus H5N1 infection in skua and gulls in the United Kingdom, 2022

The risk of highly pathogenic avian influenza in the Southern Ocean: a practical guide for operators and scientists interacting with wildlife

Continued expansion of high pathogenicity avian influenza H5 in wildlife in South America and incursion into the Antarctic region

Active surveillance for influenza virus and coronavirus infection in Antarctic birds and mammals in environmental fecal samples, South Shetland Islands

Detection and Phylogenetic Analysis of Contemporary H14N2 Avian Influenza A Virus in Domestic Ducks in Southeast Asia (Cambodia) 

Environmental Surveillance and Detection of Infectious Highly Pathogenic Avian Influenza Virus in Iowa Wetlands 

A naturally occurring HA-stabilizing amino acid (HA1-Y17) in an A(H9N2) low-pathogenic influenza virus contributes to airborne transmission 

Development and application of a triplex real-time PCR assay for the detection of H3, H4, and H5 subtypes of avian influenza virus 

Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice 

Efficacy of recombinant H5 vaccines delivered in ovo or day of age in commercial broilers against the 2015 U.S. H5N2 clade highly pathogenic avian Influenza virus 

Highly pathogenic avian influenza H5N1 virus infection of companion animals

Virulence and transmission characteristics of clade H5N6 subtype avian influenza viruses possessing different internal gene constellations

Characterization of Highly Pathogenic Avian Influenza A (H5N1) Viruses isolated from Cats in South Korea, 2023

Low Pathogenic Avian Influenza H9N2 Viruses in Morocco: Antigenic and Molecular Evolution from 2021 to 2023

Genetically Related Avian Influenza H7N9 Viruses Exhibit Different Pathogenicity in Mice

First Report of Low Pathogenic Avian Influenza Subtype H9N2 in African Houbara Bustards (Chlamydotis undulata undulata) and Gamebirds in Morocco: Clinico-Pathological Findings, Molecular Characterization, and Associated Coinfections

Highly pathogenic avian influenza: Unprecedented outbreaks in Canadian wildlife and domestic poultry

Highly Pathogenic Avian Influenza and its Complex Patterns of Reassortment

Responding to avian influenza A H5N1 detection on a hospital property in Maine—An interdisciplinary approach

Author response: Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade viruses with spatial cross-validation

Molecular modeling and phylogenetic analyses highlight the role of amino acid 347 of the N1 subtype neuraminidase in influenza virus host range and interspecies adaptation

Mapping genetic markers associated with antigenicity and host range in H9N2 Influenza A viruses infecting poultry in Pakistan 

Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021/2022

Detection of Clade Highly Pathogenic Avian Influenza H5 Viruses in Healthy Wild Birds in the Hadeji-Nguru Wetland, Nigeria, 2022

Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species

Baloxavir marboxil use for critical human infection of avian influenza A H5N6 virus

H7 influenza A viruses bind sialyl-LewisX, a potential intermediate receptor between species

Connectivity of marine predators over the Patagonian Shelf during the highly pathogenic avian influenza (HPAI) outbreak

A broad antibody class engages the influenza virus hemagglutinin head at its stem interface

Rapid detection of H5 subtype avian influenza virus using CRISPR Cas13a based-lateral flow dipstick

Recombinant A(H6N1)-H274Y avian influenza virus with dual drug resistance does not require permissive mutations to retain the replicative fitness in vitro and in ovo

Low Pathogenic Avian Influenza H9N2 Viruses in Morocco: Antigenic and Molecular Evolution from 2021 to 2023

Effect of 2020–21 and 2021–22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands

Native and invasive bird interactions increase the spread of Newcastle disease in urban environments

Epidemiological Disclosing and Molecular Subtyping for the Highly Pathogenic Avian Influenza Viruses H5N8 in Commercial Broilers and Layer Chickens in some Egyptian Governorates

Utility of Feathers for Avian Influenza Virus Detection in Commercial Poultry

Effect of avian influenza scare on transmission of zoonotic avian influenza: A case study of influenza A (H7N9)

Highly pathogenic avian influenza H5N1 virus infection of companion animals

Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies

Different routes of infection of H5N1 lead to changes in infecting time

A multiplex qRT-PCR assay for detection of Influenza A and H5 subtype targeting new SNPs present in high pathogenicity avian influenza Canadian 2022 outbreak strains

Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice

Pigs are highly susceptible to but do not transmit mink-derived highly pathogenic avian influenza virus H5N1 clade

Efficacy of recombinant H5 vaccines delivered in ovo or day of age in commercial broilers against the 2015 U.S. H5N2 clade highly pathogenic avian Influenza virus

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

Annual report on surveillance for avian influenza in poultry and wild birds in Member States of the European Union in 2022

Has avian influenza virus H9 originated from a bat source?

Unraveling molecular basis for reduced neuraminidase inhibitors susceptibility in highly pathogenic avian influenza A (H5N1) viruses isolated from chickens in India

Survey of exposure to stranded dolphins in Japan to investigate an outbreak of suspected infection with highly pathogenic avian influenza (H5N1) clade in humans

Identification of Pre-Emptive Biosecurity Zone Areas for Highly Pathogenic Avian Influenza Based on Machine Learning-Driven Risk Analysis
How do we reduce unnecessary culling of poultry after HPAI incursion into farms? Here a data-driven method to generate rule tables and risk scores for individual farms, with an accuracy of 84%.

Genetically Related Avian Influenza H7N9 Viruses Exhibit Different Pathogenicity in Mice
Revisiting the surge of human cases of H7N9. Viruses found in poultry had ability to bind mammalian receptors, had PB2-627K marker, and were pathogenic in mice. Monitoring of viruses in poultry is critical. Not particularly novel, I think this was pretty well established. 

Influenza virus immune imprinting dictates the clinical outcomes in ferrets challenged with highly pathogenic avian influenza virus H5N1
Full version not yet available. “Ferrets were imprinted following H1N1 and H2N3 virus infections were completely protected against lethal H5N1 influenza virus challenge (100% survival) with little to no clinical symptoms” suggesting human influenza infection with H1N1 could be protective for humans (but not H3N2)

Effect of 2020–21 and 2021–22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands
HPAI detected in 51 bird species in the Netherlands, alone. In 2020/21 mostly in Anatidae, and in 2021/22 mostly seabirds. Challenge in predicting future trends, so monitoring critical.

Analysis of miRNA expression in the trachea of Ri chicken infected with the highly pathogenic avian influenza H5N1 virus
miRNA expression patterns of tracheal tissues from H5N1-infected Ri chickens showed differential expression in transforming growth factor-beta, mitogen-activated protein kinase, and Toll-like receptor signaling pathways.

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region
Analysis of genomes from South Georgia and the Falklands. They are unlinked, so 2 independent incursions into the region.

Pathogenicity in Chickens and Turkeys of a 2021 United States H5N1 Highly Pathogenic Avian Influenza Clade Wild Bird Virus Compared to Two Previous H5N8 Clade Viruses
In comparing H5N1 to previous HPAI viruses, there are key differences in clinical signs, mean death times, and virus transmissibility bw chickens and turkeys

The role of vaccination and environmental factors on outbreaks of high pathogenicity avian influenza H5N1 in Bangladesh
Vaccination against HPAI in Bangladesh resulted in a ten-fold ⬇️ in outbreak risk. Increase in outbreak rate were low ambient temperatures, literacy rate, chicken density, crop density, and presence of highways.

Outbreak of Highly Pathogenic Avian Influenza Virus H5N1 in Seals in the St. Lawrence Estuary, Quebec, Canada
Outbreak of HPAI in in Harbour and Grey Seals in the St. Lawrence estuary. Infection likely due to presence of large numbers of bird carcasses infected with H5N1 at haul-out sites.

Avian influenza viruses in wild birds in Canada following incursions of highly  pathogenic H5N1 virus from Eurasia in 2021/2022
In Canada, 6,246 sick/dead wild birds across 12 taxonomic orders and 80 species tested for HPAI = 27.4% HPAI positive. A further 11,295 asymptomatic harvested/live captured wild birds tested = 5.2% HPAI +ve. Huge and comprehensive effort!

Challenges for Precise Subtyping and Sequencing of a H5N1 Clade Highly Pathogenic Avian Influenza Virus Isolated in Japan in the 2022–2023 Season Using Classical Serological and Molecular Methods
The continuous evolution of HPAI means that diagnostics need to be constantly evaluated for sensitivity against new strains. Comprehensive overview using case study in Japan.

Risk for waterborne transmission and environmental persistence of avian influenza virus in a wildlife/domestic interface in Mexico
Many questions still unanswered around survival/transmissibility of AIV in the environment. Water a key factor. e.g all poultry farms evidence a moderate or high risk of waterborne transmission especially farms close to water bodies

Genotype Diversity, Wild Bird-to-Poultry Transmissions, and Farm-to-Farm Carryover during the Spread of the Highly Pathogenic Avian Influenza H5N1 in the Czech Republic in 2021/2022
Close relationships between H5N1 genomes from poultry and wild birds and secondary transmission in commercial geese in Czech Republic, and six different HPAI genotypes and reassortment with LPAI viruses. 

Optimizing environmental viral surveillance: bovine serum albumin increases RT-qPCR sensitivity for high pathogenicity avian influenza H5Nx virus detection from dust samples
Environmental sampling for HPAI, especially dust a useful sample type: cheap, non-invasive for animals, simpler, and quicker to carry out. BUT, high amounts of organic substances that can inhibit RT-qPCR reactions. Bovine serum albumin may be useful.

Factors influencing highly pathogenic avian influenza preventive behavior among live poultry market vendors
Preventive behaviour of live bird market vendors is essential in blocking the transmission of HPAI and reducing occupational exposure. Perceived severity and perceived benefits positively influenced the vendors’ ability to adopt preventive behavior

Identification of key residues of B cell epitopes in hemagglutinin of H6 influenza A virus
Antigenic sites of some HA subtypes (H1, H3, H5, H9), characterized, but H6, one of the most common in birds, is poorly understood. Here, key residues of antigenic epitopes in H6 mapped through escape mutants using a panel of MAbs.

Weathering the Storm of High Pathogenicity Avian Influenza in Waterbirds
Review of HPAI

A single immunization with H5N1 virus-like particle vaccine protects chickens against divergent H5N1 influenza viruses and vaccine efficacy is determined by adjuvant and dosage
H5N1 virus-like particle vaccine based using insect cell-baculovirus expression system induced high levels of HI antibody titers and provided effective protection against homologous virus hallenge comparable to the commercial inactivated vaccine

Emergence of novel reassortant H3N3 avian influenza viruses with increased pathogenicity in chickens in 2023
H3 is a pretty common subtype of influenza in wild birds, generally causing no disease in waterfowl. Morbidity issues in several large-scale egg farms in Jiangsu province, due to H3 infections. HA sequences similar to human H3N8 cases.

Highly Pathogenic Avian Influenza A(H5N1) Virus Clade Infections in Wild Terrestrial Mammals, United States, 2022
HPAI in 67 wild terrestrial mammals in the USA. Infected mammals showed primarily neurologic signs – Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions. Viruses genetically similar to birds.

Neurotropic Highly Pathogenic Avian Influenza A(H5N1) Virus in Red Foxes, Northern Germany
A 1-year survey in northern Germany, found 5/110 foxes were infected with HPAI, w a cluster from Jan‒March 2023. Encephalitis and strong cerebral virus replication. Pb2 E627K mutations sporadic.

Highly Pathogenic Avian Influenza A(H5N1) from Wild Birds, Poultry, and Mammals, Peru
HPAI in wild birds, poultry, and a lion in Peru from November 2022–February 2023. Markers associated with transmission adaptation and antiviral drug resistance detected.

Recombinant duck enteritis virus bearing the hemagglutinin genes of H5 and H7 influenza viruses is an ideal multivalent live vaccine in ducks
Farmed ducks play a key role in HPAI transmission. Here a recombinant duck enteritis virus H5/H7 vaccine designed for ducks, specifically. Induced long-lasting HI antibodies against H5 & H7 viruses and provided complete protection against challenge

Environmental Surveillance and Detection of Infectious Highly Pathogenic Avian Influenza Virus in Iowa Wetlands
How long does HPAI last in the environment? Virus isolated from wetlands near HPAI outbreaks. One month later, no detection: increased water temperatures, precipitation, biotic and abiotic factors may have played a role.

Spillover of an endemic avian Influenza H6N2 chicken lineage to ostriches and reassortment with clade H5N1 high pathogenicity viruses in chickens
First detection of reassortant viruses: H6N2 chicken-adapted viruses and HPAI H5N1. These reassortant viruses caused an outbreak in ostriches in South Africa

Evolution and biological characterization of H5N1 influenza viruses bearing the clade hemagglutinin gene
HPAI viruses in China, 2017-2020. Subclades to detected, with 58 reassortant genotypes. Viruses were antigenically well-matched with the H5-Re12 vaccine strain used in China

Amplification of avian influenza viruses along poultry marketing chains in Bangladesh: a controlled field experiment
Live bird markets are a hotspot for HPAI. New study investigates AIV infections during marketing chains, and with testing during transport/trade, intervention group had lower shedding once arrived at LBM.

Pathogen-prey-predator relations of avian raptors during epizootics of highly pathogenic avian influenza virus HPAIV H5N1 (clade in Germany
Raptors are important indicators of HPAIV and its genetic diversity, but sadly are victims in this panzootic. Serosurvey found of 5.0-7.9% HPAI antibodies among White tailed sea eagle nestlings. However, breeding success seems stable. Long term effects?

Mutations in HA and PA affect the transmissibility of H7N9 avian influenza virus in chickens
Detailed interrogation of H7N9 viruses show that mutations in the HA and PA protein reduced the viral transmissibility in chickens, decreasing the threat for poultry.

Molecular characterization and phylogenetic analysis of highly pathogenic H5N1 clade virus in Bosnia and Herzegovina
Detailed interrogation of HPAI in Mute Swan in Bosnia and Herzegovina. Similar to other European sequences. Mutations in HA (N110S and T139P) and NA genes (H155Y) facilitate host specificity shift and resistance to some antiviral drugs.

Mutational antigenic landscape of prevailing H9N2 influenza virus hemagglutinin spectrum
Sharp increase in human cases of H9N2 in 2021/22. R164Q, I220T mutations increase viral replication in avian and mammalian cells. T150A, I220T mutations enhance viral replication in mice

Key Amino Acid Residues That Determine the Antigenic Properties of Highly Pathogenic H5 Influenza Viruses Bearing the Clade Hemagglutinin Gene
Amino acid changes at position 120, 126, 141, 156, 185, or 189 (H5 numbering) may be important in antigenic changes within Amino acids at 126, 156, and 189 acted as immunodominant epitopes of H5 viruses.

Hooded Vultures Necrosyrtes monachus scavenge on a mass wreckage of large terns in a major HPAI outbreak in The Gambia: a photo report of scraper-feeder type damage to carcasses
Hooded Vultures scavenging on tern carcasses following HPAI outbreak in The Gambia. 10,000 dead terns along entire coastline, with vultures focussing on the cervical vertebrae and tempero-mandibular areas of dead terns.

Global Prevalence and Hemagglutinin Evolution of H7N9 Avian Influenza Viruses from 2013 to 2022
Summary of H7N9 sequences since 2013, which includes pre and post vaccination periods in China.

Hemagglutinin affects replication, stability and airborne transmission of the H9N2 subtype avian influenza virus
The “internal genes” of H9N2 played a key role in zoonotic spillover events of other avian influenzas. This study shows the key role of PA, and importantly HA, for replication, stability, and airborne transmission of H9N2 viruses between poultry.

Genetic and Biological Properties of H10Nx influenza viruses in China
H10 avian influenzas have a broad host range, infecting not only all kinds of birds, but also mammals and humans. Detailed analysis of H10N3 isolate from poultry in China replicated efficiently in mice lungs and nasal turbinates without prior adaptation

Clade H5 chimeric cold-adapted attenuated influenza vaccines induced cross-reactive protection in mice and ferrets
Human cases of H5N6 continue to tick along in China. Here, a cold-adapted attenuated influenza vaccine induces humoral antibody response, mucosal immune response, and cellular immune response in mice models. Also good protective immunity in ferrets.

Highly Pathogenic Avian Influenza (H5N1) in humans after the emergence of clade in 2020.
Summary of human cases.

Molecular detection and characterization of highly pathogenic H5N1 clade avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska
Two independant incursions over the Atlantic, now a new study shows 3 independant incursions via Alaska. Lots of HPAI moving around the globe. More evidence that if it arrives here, its unlikely to arrive just once…

Antibodies elicited by Newcastle disease virus-vectored H7N9 avian influenza vaccine are functional in activating the complement system
NDV vectored avian influenza vaccines result in undetectable H7N9-specific HI, but high IgG antibodies in chickens. Study clarifies role of complement in protection.

Prevalence of Avian Influenza Virus in Synanthropic Birds Associated with an Outbreak of Highly Pathogenic Strain EA/AM H5N1
Prevalence of HPAI in synanthropic birds (Columbiformes, Galliformes, and Passeriformes), but higher in raptors. Consumption of infected carcasses is a key pathway. Small study of cases in North America. 

Molecular diagnosis and identification of avian influenza H5N8 in Pekin ducks
A six-weeks-old flock of Pekin ducks showed sudden mortality without any signs, and birds that survived had depression, repository and/or nervous signs. HPAI detected, and similar to sequences from Egypt and Asia.

Pacific and Atlantic Sea Lion Mortality Caused by Highly Pathogenic Avian Influenza A(H5n1) in South America
Incredible overview of sealion outbreaks due to HPAI in South America. More than 24,000 died in Peru, Chile, Argentina, and Uruguay bw Jan- Sept 2023. Route of infection likely eating infected birds.

Mass Mortality of Sea Lions Caused by Highly Pathogenic Avian Influenza A(H5N1) Virus
Detailed summary of sea lion outbreaks in Peru. 5224 animals died, coinciding with breeding aggregation. Clinical signs of agonal individuals were mainly neurologic (tremors, convulsions, paralysis) and respiratory. Article includes some videos showing disease signs.

Factors influencing highly pathogenic avian influenza preventive behavior among live poultry market vendors
Perceived severity and perceived benefits positively influenced the bird market vendors ability to adopt preventive behavior while perceived barriers negatively affected self-efficacy. Timely HPAI information really important!

Highly Pathogenic Avian Influenza A(H5N1) Virus-Induced Mass Death of Wild Birds, Caspian Sea, Russia, 2022
In May 2022, 25,157 Great black-headed gulls, 3,507 Caspian gulls, 5,641 Caspian terns, and 14 Dalmatian pelicans died due to HPAI in the Caspian Sea ?. Nearly all chicks died.

Rapid Detection of H5 Subtype Avian Influenza Virus Using CRISPR Cas13a Based-Lateral Flow Dipstick
full article isn’t available yet.

Serological exposure to influenza A in cats from an area with wild birds positive for avian influenza
Seroprevalence of HPAI in stray cats in Spain is ~2.19%. Not all mammals munching infected birds are dying. Sadly, they left out the Polish cat outbreaks in their overview.

Isolation and Identification of Novel Highly Pathogenic Avian Influenza Virus (H5N8) Subclade from Geese in Northeastern China
An old paper I think I missed. In January 2021, a novel HPAI strain A/goose/China/1/2021(H5N8) was detected. This is prior to the start of the panzootic, and it was a virus.

High pathogenicity avian influenza (H5N1) in Northern Gannets (Morus bassanus): Global spread, clinical signs and demographic consequences
A previously featured preprint now published in Ibis – amazing summary of HPAI in Northern Gannets in 2022. Affected almost all colonies in the north Atlantic, devastating effects on Bass Rocks, and that some birds survive (with changed eye colour)

Identification of Pre-emptive Biosecurity Zone Areas for Highly Pathogenic Avian Influenza Based on Machine Learning-Driven Risk Analysis
Mass culling for HPAI has welfare and food security implications. Here a data driven model to enhance preventative measures and should help to select farms for monitoring and management of HPAI.

Lessons for cross-species viral transmission surveillance from highly pathogenic avian influenza Korean cat shelter outbreaks

High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020–2022
Seroprevalence of HPAI is strikingly high in carnivores – serological evidence for infection was 20% ? in the Netherlands from 2020-2022. Virology high too, with 9.9% infection in 2022.

Highly pathogenic avian influenza A(H5N1) virus infection in foxes with PB2-M535I identified as a novel mammalian adaptation, Northern Ireland, July 202
Two foxes and two gulls found in Ireland positive for HPAI. Viruses closely related (=common infection source), but mutations at three locations were unique to the fox sequences including PB2 mutations.

Characterization of high pathogenicity avian influenza H5Nx viruses from a wild harbor seal and red foxes in Denmark, 2021 and 2022
Five mammals tested positive for clade H5Nx HPAIVs in Denmark in 2021-22. Virus from the cubs and the adult fox belonged to two different genotypes, and virus from seal similar to virus from German seal sequence. PB2-E627K in seal & 1 fox cub

The episodic resurgence of highly pathogenic avian influenza H5 virus
The story of HPAI H5 since the beginning, leading us to how we got here. Multiple waves, genetic changes, and importantly, a big shift in the epicentre of activity. 

Avian influenza A viruses exhibit plasticity in sialylglycoconjugate receptor usage in human lung cells
Avian influenza virus strains utilize a broader repertoire and can use less prevalent glycoconjugates, for host cell infection vs human influenza A strains. Both infect human lung via N-glycans, O-glycans, and glycolipids.

Analysis of avian influenza A (H3N8) viruses in poultry and their zoonotic potential, China, September 2021 to May 2022
H3N8 viruses in Chinese duck farms, poultry markets, 2021-22. Internal genes shared with H9N2 viruses. Viruses have residues that may favour binding to human-type receptors + replication in mammals. Viruses replicate in mice, but are not lethal.

Dissection of key factors correlating with H5N1 avian influenza virus driven inflammatory lung injury of chicken identified by single-cell analysis
Transcriptome of 16 cell types in lung tissue of chickens infected with HPAIV and H9N2 LPAI. Infiltrating inflammatory macrophages w massive viral replication, pro-inflammatory cytokines and interaction of various cell populations = poor outcomes

Creating resistance to avian influenza infection through genome editing of the ANP32 gene family
Gene edited chickens may lead to influenza resistant chickens via host protein ANP32A. After influenza infection challenge, 9/10 edited chickens remain uninfected. But, virus was quick to evolve to instead use ANP32 proteins, chicken ANP32B and ANP32E.

Establishment of two assays based on reverse transcription recombinase-aided amplification technology for rapid detection of H5 subtype avian influenza virus
New tools for rapid detection of HPAI: real-time fluorescence and reverse transcription recombinase-aided amplification (RF-RT-RAA) and reverse transcription recombinase-aided amplification combined lateral flow dipstick (RT-RAA-LFD). Results in 30min.

Avian influenza overview June–September 2023
Another update from EFSA: June-Sept 2023. High activity continues, particularly in colony breeding seabirds. Fewer detections in poultry. Be sure to read thoroughly for a comprehensive update!

Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail (Coturnix c. japonica)
Antigenic mapping is a really useful tool to ensure vaccines appropriately match circulating strains. Here, extensive work done on H9 viruses, useing quail sera. Substitutions at 149, 150, and 180 were impactful, with E180A, R131K/E180A critical.

Genetic characteristics of the first human infection with the G4 genotype eurasian avian-like H1N1 swine influenza virus in Shaanxi Province,China
Not avian influenza, but perhaps of interest. Couldn’t seem to manage to access the paper itself.

Predominance of low pathogenic avian influenza virus H9N2 in the respiratory co-infections in broilers in Tunisia: a longitudinal field study, 2018–2020
Predominance of low pathogenic avian influenza virus H9N2, Northern and Western African GI lineage strains in particular, in respiratory co-infections in broilers in Tunisia.

High pathogenicity avian influenza A (H5N1) clade virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022
In November 2022, HPAI caused an outbreak in a zoological park in S France = dead Tibetan black bear, captive and wild birds. Virus recovered from formalin fixed tissues. Bear and gull sequences shared 99.998% and PB2 E627K mutation.

A systematic review of mechanistic models used to study avian influenza virus transmission and control
What can mechanistic models tell us about avian influenza transmission and control? Optimal control strategies varied between subtypes and local conditions, and depended on the overall objective

Influenza from a One Health Perspective: Infection by a Highly Versatile Virus
hefty book chapter. 

Prevention of zoonotic spillover: From relying on response to reducing the risk at source

No evidence for highly pathogenic avian influenza virus H5N1 (clade in the Antarctic region during the austral summer 2022/23
We pulled together all testing and observational survey data for HPAI in Antarctica during the austral summer 2022/23. No evidence of any HPAI last year – the virus has, however, arrived this year.

Discovery of Influenza A (H7N2) in a Cat After Admission to an Animal Shelter : A Case Report
Discovery of Influenza A (H7N2) in a Cat After Admission to an Animal Shelter. Cat was found 1 block from a live bird market (in the USA), however H7 has not been detected in the market since 2006. 

Investigation of H9N2 avian influenza immune escape mutant that lacks haemagglutination activity

An immune H9N2 escape mutate, with a G149E mutation in the HA, lost hte ability to agglutinate chicken erythrocytes, while still maintaining replication comparable to the wild-type virus in chicken embryos and cells.

Vaccination of poultry against highly pathogenic avian influenza – part 1. Available vaccines and vaccination strategies
Comprehensive review of avian influenza vaccines available, efficacy and strategies in this EFSA report. An incredible resource worth a detailed read.

Determinants for the presence of avian influenza virus in live bird markets in Bangladesh: Towards an easy fix of a looming one health issue
Avian influenza is extremely common in live bird markets in Bangladesh, with 49% of stalls selling infected poultry. Biosecurity practices, however, heavily influence the circulation of these viruses in markets.

Genetic characterization of a novel H5N6 subtype highly pathogenic avian influenza virus from goose in China
HPAI H5N6 virus from a goose similar to that reported from a farmed dog in China. Many mutations that could enhance virus replication or increase virulence in mammals were also identified in the goose virus.

Evolutionary history of human infections with highly pathogenic H5 avian influenza a virus: a new front-line global health threat established in South America
More information pertaining to the human case of HPAI in Ecuador. Genetically, virus similar to what was circulating in poultry.

Characterization of highly pathogenic clade H5N1 mink influenza viruses
HPAI from spanish mink outbreak tested for pathogenicity & transmission potential. Viruses highly virulent in mice. High titres in resp organs, brain, elsewhere. In mink, exposed animals infected but did not transmit (contact animals did not seroconvert)

Low Level of Concern Among European Society About Zoonotic Diseases
Recent survey of public opinion in six European countries (n = 2415 participants) suggests a low concern among Europeans about the risk associated with zoonotic emerging diseases.

Exploring the alternative virulence determinants PB2 S155N and PA S49Y/D347G that promote mammalian adaptation of the H9N2 avian influenza virus in mice
Are mutations other than PB2 627K, 701N important in mammalian adaptation? PB2 + PA mutations ⬆️ pol activity, viral transcription and replication in mammalian cells, severe interstitial pneumonia, excessive inflammatory cellular infiltration in mice

Study of the Interface between Wild Bird Populations and Poultry and Their Potential Role in the Spread of Avian Influenza
A census of wild birds around poultry farms (2019, Italy) show that waterfowl arent often near/on poultry farms, but species like magpies, blackbirds, egrets, doves are. More data on bridge hosts required!

Sequence Analysis of the Malaysian Low Pathogenic Avian Influenza Virus Strain H5N2 from Duck
Distinct characteristics of the Malaysian LPAI H5N2, compared to HPAI H5N2 or H5N1 from ducks or chickens

Many potential pathways to future pandemic influenza
Concern about an H5N1 avian influenza pandemic has caused alarm since 1997, but there are many other possible routes to pandemic influenza

Vaccination and Antiviral Treatment against Avian Influenza H5Nx Viruses: A Harbinger of Virus Control or Evolution
Review of avian influenza in Egypt, including discussion on implementation of prophylactic and therapeutic control strategies, leading to continuous flock outbreaks with remarkable virus evolution scenarios

Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry
Nanopore R9 had limitations in resolving low-complexity regions e.g. hemagglutinin cleavage site. R10.4.1 = increased data output, higher average quality ,lower minor pop insertion & deletion freq. For the cleavage site, R10.4.1 90% resolved.

Antiviral Susceptibility of Highly Pathogenic Avian Influenza A(H5N1) Viruses Circulating Globally in 2022–2023
Phenotypic testing of and HPAI viruses revealed broad susceptibility to NAIs and baloxavir = viruses remain susceptible to key human antivirals. Novel NA mutations caused reduced zanamivir and peramivir inhibition.

Avian Sarcoma/Leukosis Virus (RCAS)-mediated Over-expression of IFITM3 Protects Chicks from Highly Pathogenic Avian Influenza Virus Subtype H5N1
Over-expression of the interferon-stimulated gene IFITM3 protects chicks from HPAI clade Is the future virus-resistant chickens?

Modeling long-distance airborne transmission of highly pathogenic avian influenza carried by dust particles

What is the role of long distance airbourne transmission of HPAI? Overall, via modelling, concentrations of airborne AI, deposited AI, and combined AI transmitted to other farms were lower than the minimal infective dose for poultry. Validation?

Limited Outbreak of Highly Pathogenic Influenza A(H5N1) in Herring Gull Colony, Canada, 2022
Limited outbreak of HPAI in Herring Gulls in Canada, summer 2022 – less than 10% of the colony affected.

FLIGHT RISKS – Migratory birds efficiently ferry pathogens around the world. As a warming climate reshapes their journeys, infectious disease experts are on guard for new threats to humans

HPAI reports in waders from IWSG2023

Genetic and antigenic analyses of H5N8 and H5N1 subtypes high pathogenicity avian influenza viruses isolated from wild birds and poultry farms in Japan in the winter of 2021–2022
Three HPAI genome constellations circulating in Japan 2021/22 (H5N8 and H5N1). Multiple H5 HPAI and LPAIVs disseminate to Japan via transboundary winter migration of wild birds

Environmental transmission of influenza A virus in mallards
Detailed studies of LPAI transmission indicate that viral load in water was the strongest predictor of transmission. Also, highly dependant on point of infection course in individual (before or after peak levels) whether it is able to transmit.

Mass Mortality Event in South American Sea Lions (Otaria flavescens) Correlated to Highly Pathogenic Avian Influenza (HPAI) H5N1 Outbreak in Chile.
Overview of sea lion strandings in Chile since 2009, featuring the current HPAI mass mortalities. Strong correlations between widespread mortality of South Americans sea lions and the occurrences of HPAI in wild birds.

Ecological characterization of 175 low-pathogenicity avian influenza viruses isolated from wild birds in Mongolia, 2009–2013 and 2016–2018
Surveillance in Mongolia [2009–2013, 2016–2018] demonstrates substantial diversity of avian influenzas. Mongolia is situated as a crossroad of multiple migratory flyways

Deadly avian flu reaches Galápagos Islands Concerns rise for boobies, finches, and other endemic species

Influenza A(H5N1) Virus Infections in 2 Free-Ranging Black Bears (Ursus americanus), Quebec, Canada
HPAI in black bear mother and cub in Canada. Virus detected by immunohistochemistry in brain and liver. Both had PB2 D701N mutation. Viruses similar to Newfoundland H5N1 (2021).

Transmission dynamics and pathogenesis differ between pheasants and partridges infected with clade H5N8 and H5N1 high-pathogenicity avian influenza viruses
Outbreak of HPAI in pheasant farms, but partridges unaffected. High does of H5N1 required for transmission, and partridges infected with H5N8 failed to shed or transmit. Fewer mortalities when experimentally infected

Emergence of Highly Pathogenic Avian Influenza A (H5N8) Clade Viruses in Grebes in Inner Mongolia and Ningxia, China, 2021
Outbreak of HPAI in black-necked grebes in 2021, Inner Mongolia, China. Fecal environmental samples from Eurasian spoonbills. HPAI H5N8 detected, and share a common ancestor with sequences in China in 2020

Evolution and Current Status of Influenza A Virus in Chile: A Review
Substantial overview of avian influenza virus in Chile, since ~2002 and featuring HPAI. Would note that the authors currently publishing on HPAI in Chile seem to be absent from this review.

Highly Pathogenic Avian Influenza (HPAI) strongly impacts wild birds in Peru
In only a few months H5N1 killed >100,000 birds of 24 different species in protected areas of Peru, with huge impacts on boobies, cormorants and pelicans. Virus has severely affected bird populations and the ecosystem services they provide. Peer-reviewed paper of pre-print already shared

Highly Pathogenic Avian Influenza A(H5N1) Clade Virus in Wild Birds, Chile
Detection and genome sequencing of HPAI from Chile show that sequences from Chile and Peru were closely related to a recent ancestor from North America that was detected during October–November 2022. Suggest multiple incursions. Peer-reviewed paper of pre-print already shared

Can Citizen Science Contribute to Avian Influenza Surveillance?
Mortality databases allowing for the public to report sick and dead birds is extremely useful to the HPAI response. Here, results show that HPAI outbreaks officially reported by WOAH overlapped with sudden increases in records of sick/dead birds. I would want highlight the mortality reporting database they are using: Observation.org

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences
Great summary of HPAI outbreaks in Northern Gannets in 2022: Unusually high mortality was recorded at 75% of global total colonies. Adult survival substantially lower than the preceding 10-year average. Description of black irises in survivors. Peer-reviewed paper of pre-print already shared

Looking beyond the H5 avian influenza viruses
Great overview of avian influenza H3, which is being overshadowed by the H5N1 panzootic. Importantly, avian H3’s have caused 3 human cases, and transmits between ferrets (measurement of mammal-to-mammal transmission ability).

Comparative analysis of PB2 residue 627E/K/V in H5 subtypes of avian influenza viruses isolated from birds and mammals
Few PB2 mutations found in LPAI H5, but an increased prevalence of E627K in avian HPAI H5 sequences, and also more mammalian cases. ~40% conversion of E -> K in human sequences of H5

Using surveillance data for early warning modelling of highly pathogenic avian influenza in Europe reveals a seasonal shift in transmission, 2016–2022
Analysis of publicly available surveillance data for HPAI integrated into time-series models may help to predict HPAI in different countries . Also shows substantial shift in seasonality in 2021-22

Distribution and risks of the infections of humans and other mammals with H5 subtype highly pathogenic avian influenza viruses in 2020–2023
A small anaysis of mammalian cases of HPAI reported to WOAH. 285 outbreaks, most of which occurred in Europe/Americas (sampling bias?). Sadly shows limitations of WOAH data as 20,000 dead S. american sealions not highlighted here.

Detection of H5N1 High Pathogenicity Avian Influenza Viruses in Four Raptors and Two Geese in Japan in the Fall of 2022
In 2022, HPAI arrived early in Japan, with outbreaks in geese and raptors. Genetically, viruses were similar to those found in Japan in 2021, but likely reintroduction from Asia/Siberia via early waterfowl migration

Investigation of risk factors for introduction of highly pathogenic avian influenza H5N1 virus onto table egg farms in the United States, 2022: a case–control study
Factors relevant to HPAI outbreaks in egg farms: wild waterfowl presence, wild bird access to feed, existing control zones, moving vegetation less than 4 times per month, off side method of daily mortality disposal. Lots of protective effects as well.

A Fatal A/H5N1 Avian Influenza Virus Infection in a Cat in Poland
A fatal HPAI infection in a cat in Poland: outdoor cat, fed a diet of raw chicken meat. Respiratory distress and neurological signs. Perivascular infiltration of lymphocytes and histiocytes into brain, with neuronal necrosis

Different Outcomes of Chicken Infection with UK-Origin H5N1-2020 and H5N8-2020 High-Pathogenicity Avian Influenza Viruses (Clade
Direct inoculation of layer chickens with HPAI showed that H5N8-2020 was more infectious than H5N1-2020, death time was longer for H5N8. Tranmission to contact chickens inefficient. More abundant histological lesions and viral antigens for H5N1.

Strong breeding colony fidelity in northern gannets following high pathogenicity avian influenza virus (HPAIV) outbreak
HPAIV killed at least 50 % of northern gannets, with presence antibodies in juveniles. GPS-tracked adults remained faithful to their breeding sites despite outbreak – no prospecting other colonies

Spreading of the High-Pathogenicity Avian Influenza (H5N1) Virus of Clade into Uruguay
Great to see more data from South America -this time from Uruguay! The viruses shared a common ancestor with viruses detected in Chile/Peru and likely introduced from Argentina

HVT-vectored H7 vaccine protects chickens from lethal infection with the highly pathogenic H7N9 Avian influenza virus
Novel H7 vaccine, using recombinant turkey herpesvirus vector, rHVT-H7HA, that expresses the HA glycoprotein of HPAIV H7N9. Immunization of chickens with the rHVT-H7HA significantly reduces viral load.

Highly pathogenic avian influenza A virus (HPAIV) H5N1 infection in two European grey seals (Halichoerus grypus) with encephalitis
HPAI in grey seals from coastal waters of Netherlands and Germany in Dec 2022 / Feb 2023. Brain and lung tested positive = encephalitis in the absence of a systemic infection. PB2-E627K mutation

Spatio-temporal distribution & seasonality of highly pathogenic avian influenza H5N1 & H5N8 outbreaks in India, 2006-2021
Analysis of HPAI data from FAO (EMPRES?), shows 284 outbreaks since 2006, with large surge in 2021. Outbreaks occuring post monsoon until pre summer (Oct – March), with peak in January. 

Highly pathogenic avian influenza (H5N1) infection in crows through ingestion of infected crow carcasses
Experimental infection of House Crows with HPAI shows neurological signs. Infected carcasses were eaten by other crows = transmission confirmed

Detection of H5N1 High Pathogenicity Avian Influenza Viruses in Four Raptors and Two Geese in Japan in the Fall of 2022
In 2022, HPAI arrived early in Japan, with outbreaks in geese and raptors. Genetically, viruses were similar to those found in Japan in 2021, but likely reintroduction from Asia/Siberia via early waterfowl migration

Distribution and risks of the infections of humans and other mammals with H5 subtype highly pathogenic avian influenza viruses in 2020–2023
A small anaysis of mammalian cases of HPAI reported to WOAH. 285 outbreaks, most of which occured in Europe/Americas (sampling bias?). Sadly shows limitations of WOAH data as 20,000 dead S. american sealions not highlighted here

Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru
Comprehensive overview of HPAI in Peru, including overview of clinical signs. Genetic analysis confirms viruses are Eurasian-N.American reassortants, & Peru-Chile clade descend from single viral introduction ~ October 2022. PB2 D701N in sea lions.

The neuropathogenesis of highly pathogenic avian influenza H5Nx viruses in mammalian species including humans
Comprehensive review outlining neuropathogenic features in humans and mammals, due to neuroinvasive and neurotropic potential of HPAI, with viruses able to replicate in various CNS cell types.

Refined semi-lethal aerosol H5N1 influenza model in cynomolgus macaques for evaluation of medical countermeasures
Model for humans. 

Baloxavir marboxil use for critical human infection of avian influenza A H5N6 virus
When delayed oseltamivir showed poor effects on high respiratory viral load, baloxavir was prescribed and viral load had a rapid reduction

Asymptomatic infection with clade highly pathogenic avian influenza A(H5N1) in carnivore pets, Italy, April 2023
HPAI in 1 domestic dog and 5 cats living on a rural backyard poultry farm. Poultry infected with BB genotype that was characterised by the presence of a PB2 mutation related to mammalian adaptation

Virulence and transmission characteristics of clade H5N6 subtype avian influenza viruses possessing different internal gene constellations
Genome constellations have differential outcomes of HPAI. H5N6 in China, with two genome constellations: constellation w H9 PB2 & PB1 genes on H5 backbone better infect mice, mammalian cells but worse in avian cells, bird transmission.

Highly pathogenic avian influenza affects vultures’ movements and breeding output
Satellite tracked Griffon Vultures in Europe display inferred sickness behaviour via immobility during HPAI infection. Most chicks died but most adults recovered. Great to see integration of movement data to HPAI studies.

Recurring Trans-Atlantic Incursion of Clade H5N1 Viruses by Long Distance Migratory Birds from Northern Europe to Canada in 2022/2023
Evidence for yet another viral incursion into North America, likely via the Atlantic between Dec2022-Jan2023. Brings us to 3 incursion events into North America

Epidemiological and clinical characteristics of human infections with avian influenza A (H7N9) and A (H5N6) viruses in Guangdong province, 2013-2018
Summary of epidemiological and clinical characteristics of human infections with avian influenza H7N9 (n=259, CFR 38%)) and H5N6 (n=8, CFR 62%) viruses in Guangdong province, 2013-2018. (In Chinese, unsure how to access)

Surveillance of environmental avian influenza virus in Fujian province, 2017-2021
4214 samples collected from Fujian province (2017-2021). 2.5% H5, 1.16% H7, 23.16 H9. AIV prevalence highest n urban and rural live poultry markets – cage srufaces, cleaning poultry sewage and chopping boards (In Chinese, unsure how to access)

Epidemiological investigation of the first confirmed human case of avian influenza A(H5N6) virus infection in Beijing
Human infection of H5N6 – patient cooked frozen chicken from a market. Sample from patient bronchoalveolar lavage fluid and frozen poultry samples were highly similar. (In Chinese, unsure how to access)

Interpretation of molecular detection of avian influenza A virus in respiratory specimens collected from live bird market workers in Dhaka, Bangladesh: Infection or contamination?
In 1,273 influenza-like illness cases in Banglaesh, 34 (2.6%) had H5, 56 (4%) had H9 by qPCR. Of 192 asymptomatic workers, H5 was detected in 8 (4%). Of 28 ILI cases with H5 or H9 detected, no seroconversion. Infection or environmental contamination?

Advocating a watch-and-prepare approach with avian influenza
short note, with a strong focus on human infections and barriers to human infections. Key messages: (1) “H5 HPAIV remains unlikely to acquire the ability to infect and stably circulate among the human population” (2) “The impact of the current outbreak on livestock industries and wild animal populations is immense and demands intervention”

Will climate change amplify epidemics and give rise to pandemics?

Key amino acid position 272 in neuraminidase determines the replication and virulence of H5N6 avian influenza virus in mammals
Most human HPAI cases are due to H5N6. Since 2015, an increase in the NA-D272N mutation in wild birds, which is associated with increased replication and virulence in mice and induced higher levels of inflammatory cytokines in human cells.

Severe pigeon paramyxovirus 1 infection in a human case with probable post-COVID-19 condition
Not influenza, but probably of importance. Recent case of pigeon paramyxovirus (a genotype of avian paramyxovirus 1) in humans in China. The infected person had long COVID – so likely immunocompromised.

Chicken miR-26a-5p modulates MDA5 during highly pathogenic avian influenza virus infection
Downregulation in gga-miR-26a [chicken microRNA] in lung of chickens during HPAI infection. Findings suggest that this microRNA serves as an important regulator in the MDA5 signaling pathway and therefore in antiviral response

Immunogenicity and Cross-Protective Efficacy Induced by an Inactivated Recombinant Avian Influenza A/H5N1 (Clade Vaccine against Co-Circulating Influenza A/H5Nx Viruses
Multiple strains of HPAI circulating in Egypt and vaccine mismatch reported. Here, 3 reverse-genetics H5Nx vaccines generated. Superior immunogenicity and cross-protective efficacy of the rgH5N1_2.3.4.4 in comparison to rgH5N8_2.3.4.4 and rgH5N1_2.2.1.2

Emergence and Persistent Circulation of Highly Pathogenic Avian Influenza Virus A(H5N8) in Kosovo, May 2021–May 2022
Three outbreaks of HPAI in Kosovo: May–June 2021, September–November 2021, and January–May 2022 with 32 backyard+10 commercial poutry houses affected = 179,198 poultry. H5N8 clade viruses implicated.

Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? 
“future viral epidemics are unavoidable, but that their societal impacts can be minimized by strategic investment into basic virology research, epidemiological studies of neglected viral diseases, and antiviral drug discovery”. Would add surveillance!

Emergence of a new genotype of clade H5N1 highly pathogenic avian influenza A viruses in Bangladesh
Novel clade H5N1 virus from ducks in free-range farms in Bangladesh. Similar to viruses first detected in October 2020 in The Netherlands but with a different PB2

Pilot of asymptomatic swabbing of humans following exposures to confirmed avian influenza A(H5) in avian species in England, 2021/2022
1617 human exposures to HPAI in England. Asymptomatic swabbing of humans revealed 1 detection. Human surveillance (at human: poultry interface) critical for ongoing HPAI monitoring!

Innate immune control of influenza virus interspecies adaptation
IFITM3 [host antiviral factor] deficiency in humans due to SNPs, with 20% of some human pops homozyg for deficient gene. IFITM3 facilitates zoonotic influenza infects & adaptation. IFITM3 deficiencies = vulnerability for emergence of new pandemic viruses

Exploring the responses of smallscale poultry keepers to avian influenza regulations and guidance in the United Kingdom, with recommendations for improved biosecurity messaging
Regulations only work if understood and accepted. Survey of small scale poultry keepers in UK in 2021/22. Need for guidance tailored to smallscale poultry keepers including clear action points w simple, practical, affordable and sustainable suggestions

Functional traits explain waterbirds’ host status, subtype richness, and community-level infection risk for avian influenza
The host range of HPAI has expanded dramatically, although many species likely just dead-end spill over hosts. New study shows the key role of functional traits in explaining HPAI infection risk: functional diversity can reduce infection risk

no access ☹

Infection and tissue distribution of Highly Pathogenic Avian Influenza A type H5N1 (clade in Red Fox kits (Vulpes vulpes)
Fox kits infected with HPAI have severe neurological signs and brain (and lung) tissue lesions. Labelled showed infection was clustered and overlapped the brain lesions, neurons, and grey matter. V292I mutation in PB2.

Human infection with avian-origin H5N6 influenza a virus after exposure to slaughtered poultry
Human case of HPAI H5N6 virus in China after exposure to freshly slaughtered chicken (not live birds). Q226 & G228 mutation in HA – affect binding affinity of α-2,6-linked sialic acid receptor. No PB2 mutation. Viruses related to those in poultry market.

Clinical features of the first critical case of acute encephalitis caused by the avian influenza A (H5N6) virus
Acute encephalitis with mild pneumonia in a child in China caused by the H5N6 virus. HPAI found in patient’s serum, CSF, and tracheal aspirate specimens. Virus similar virus in human infection and in ducks in China.

Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China
Major switches to antigenic properties in novel H9N2 lineage, potentially having ramifications for H9 vaccination in China. There is a history of vaccine effectiveness against H9 being persistently challenged with the evolution of new lineages.

Identification of catalytically active domain epitopes in neuraminidase protein of H9N2 subtype of avian influenza virus
Rather than focus on only the HA, the authors argue that the NA should also be considered in vaccine design for H9N2. Slower antigenic drift in NA compared to HA, and identified epitopes are highly conserved.

Evolution of prevalent H9N2 subtype of avian influenza virus during 2019 to 2022 for the development of a control strategy in China
Current circling H9N2 viruses in China have diversified into h9.4.2.5 subclade, which is genetically distant from commonly used commercial vaccine strains. Development of novel recombinant vaccine with new strain outperformed existing vaccine in trials.

Avian influenza A(H5N1) and the continuing outbreak
From the National Collaborating Centre for Environmental Health (Canada)

Assessment of contaminants, health and survival of migratory shorebirds in natural versus artificial wetlands – The potential of wastewater treatment plants as alternative habitats
New paper by Marcel’s PhD student Toby, investigating pollutants and links to waste water treatment sites and disease burden in wild birds.

Scottish wild bird highly pathogenic avian influenza response plan
Compliments sections in the UK response plan and also provides sections on “HPAI in wild birds – research and monitoring” and Advice for Rehab organisations”

The plight and role of wild birds in the current bird flu panzootic
We outline the plight of wild birds in the HPAI panzootic, and our concerns around the severe discrepancy in reporting of mortality data.

‘One Health’ Genomic Surveillance of Avian and Human Influenza A Viruses Through Environmental Wastewater Monitoring
Wastewater has been useful for virus detection from humans. Water treatment plants are extremely important environments for birds, and so an intersting environmental sample type for detection of HPAI

Research Note: A Recombinant Duck-derived H6N2 Subtype Avian Influenza Virus can Replicate and Shed in Young Chickens and Cause Disease
H6 avian influenza causing high morbidity in poultry in China. In challenge, caused morbidity in chickens but not ducks. PB1 most similar to that of an H5N6 virus.

The first known human death after infection with the avian influenza (A/H3N8) virus: Guangdong Province, China, March 2023
Case report of human cause of H3N8 in an immunocompromised patient causing mortality in China. No mammalian adaptations. Testing of local market environment had evidence of H3 in cutting tools, feeding trough and sinks

Alteration of the chicken upper respiratory microbiota, following H9N2 avian influenza virus infection
AIV infection has ramifications for the microbiomes of birds. H9 lowers alpha diversity in the upper resp tract in chickens, with enrichment of Lactobacillis. Also, microbial community didn’t return to normal after infection.

Comparative analysis of PB2 residue 627E/K/V in H5 subtypes of avian influenza viruses isolated in birds and mammals
ahead of print, no details yet.

Diagnostic Detection of H7N3 Low Pathogenicity Avian Influenza in a Commercial Game Bird Flock
no access ?

The emergence of new antigen branches of H9N2 avian influenza virus in China due to antigenic drift on hemagglutinin through antibody escape at immunodominant sites
Detailed mapping of resides important for antigenic drift (away from vaccine strains) in china. Nice to see structural mapping in addition to sequence analysis.

Enhanced Thermostability and Provides Effective Immune Protection against Lethal H7N9 Virus Challenge in Chickens
Adding a T169A mutation to the HA of H7 increased therostability, and vaccinating chickens with this strain also increases cross reactivity and cytokine secretion. In challenge trials, 90% of chickens had no viral shedding.

Pathogenicity of H5N8 avian influenza virus in chickens and in duck breeds and the role of MX1 and IFN-α in infection outcome and transmission to contact birds
A duck is not a duck is not a duck. Differential disease outcomes when comparing Muscovy, Pekin and Mallard ducks infected with HPAI H5N8. No Mallards died, and had highest Mx and INF expression and highest shedding.

Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus
Old paper that I had missed. Nice to see infection experience of species other than mallards for once. And they used RNASeq as well. Outcomes are prtty much as expected. Lots happening in the illum. Lots of the innate immne genes upregulated. 

Novel Reassortant Avian Influenza A(H5N6) Virus, China, 2021
Description of clade HPAI H5N6 in China. These viruses havestrong immune-escape capacity and complex genetic reassortment, suggesting further transmission risk

H5N1 highly pathogenic avian influenza clade in wild and domestic birds: Introductions into the United States and reassortments, December 2021–April 2022
Huge study of HPAI genetics in the USA. THREE!! distinct HPAI viruses (3 introductions?), local reassortment with LP viruses, and complex patterns of spatial diffusion

Prediction of highly pathogenic avian influenza vaccine efficacy in chickens by comparison of in vitro and in vivo data: A meta-analysis and systematic review
Huge evaluation of vaccines for HPAI. HI titers when using the challenge virus as antigen = good predictor of vaccine efficacy. HA1 relatedness has limitations when predicting efficacy for rHVT-vector and RP vaccines. Lots of good stuff

Influenza A Virus in Pigs in Senegal and Risk Assessment of Avian Influenza Virus (AIV) Emergence and Transmission to Human
In a survey of pigs in Senegal, avian influenza H5, H7, H9 antibodies found in pigs (although more typical H1 and H3 swine and human lineages found via virology).

Outbreak of highly pathogenic avian influenza A(H5N1) clade virus in cats, Poland, June to July 2023
Detailed report on 25 of the Polish cats, interrogation of 19 full HPAI genomes. No clustering based on geography. To date, are the only sequences with dual PB2 526R/627K mutations for mammalian infection

Emergence and potential transmission route of avian influenza A (H5N1) virus in domestic cats in Poland, June 2023
A nice summary of the cluster of HPAI cases in Polish cats (at least 89!), including indoor cats. Genomes from all cats identical, including 2 PB2 mutations (PB2-E627K and PB2-K526R). HPAI detected in frozen chicken meat – infected via food.

Highly pathogenic avian influenza A(H5N1) virus infection on multiple fur farms in the South and Central Ostrobothnia regions of Finland, July 2023
From 14-27 July, 20 fur farms affected by HPAI, Finland. (There are 500 in Finland). Animal in cages, with a roof, but no walls. Genome sequence similar to gulls and birds have access to the houses. PB2 mutations detected. Animals will be culled.

Characterization of the haemagglutinin properties of the H5N1 avian influenza virus that caused human infections in Cambodia
Detailed work on the HPAI viruses [] that infected people in Cambodia shows similar profiles to old strains with no evidence of improved binding to humans but improved acid and thermal stability. Virus poses limited zoonotic risk.

Waterfowl show spatiotemporal trends in influenza A H5 and H7 infections but limited taxonomic variation
Detailed interrogation of the drivers affecting prevalence of (low path) H5 and H7 in the US. H5 viruses in late autumn and H7 viruses in spring. Large differences in trends over all influenzas, but few differences for these subtypes.

Evolution and Reassortment of H6 Subtype Avian Influenza Viruses
Report of H6 viruses from poultry and wild birds in China, collected since 2001. Viruses common in ducks – reflecting results from elsewhere.

Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018–2021
Between 2018-2021 (prior to the start of the panzootic), and H5N6 dominated in live bird markets of Vietnam. In 2016-17, also present.

Evolution of Prevalent H9N2 Subtype of Avian Influenza Virus during 2019-2022 for the Development of a Control Strategy in China
H9N2 viruses in China diversified into h9.4.2.5, which was genetically distant from commonly used commercial vaccine strains. A new vaccine generated showed improved outcomes (due to a better match).

The Feather Epithelium Contributes to the Dissemination and Ecology of clade H5 High Pathogenicity Avian Influenza Virus in Ducks
We know that you can detect AI on bird feathers, and this may play a role in transmission. In HPAI outbreaks, viruses exhibited persistent and marked feather epitheliotropism in infected commercial ducks = source of environmental infectious material.

Emergence of a novel reassortant H5N6 subtype highly pathogenic avian influenza virus in farmed dogs in China
https://www.sciencedirect.com/science/article/pii/S0163445323003869 HPAI H5N6 found in the spleen of a farmed dog in China.

Characterization of avian influenza A (H4N2) viruses isolated from wild birds in Shanghai during 2019-2021
H4 LPAI viruses are some of the most common in duck surveillance systems. Additional sequences from China, although H4N2 rather than H4N6. Most internal genes were LPAI, but the PB1 of one virus most similar to a HPAI H5N8 virus

Susceptibility of common dabbling and diving duck species to clade H5N1 high pathogenicity avian influenza virus: an experimental infection study
Observations from previous outbreaks have suggested that diving ducks are hard hit when infected with HPAI. Experimental infections (with confirm this, with higher titres and mortality in Tufted ducks compared to wigeons mallards and pintails.

Highly Pathogenic Avian Influenza A(H5N1) Clade Virus in Wild Birds, Chile
Ahead of print, so can’t get to the pdf to read it yet.

Mortality in Wild Turkey (Meleagris gallopavo) Associated with Natural Infection with H5N1 Highly Pathogenic Avian Influenza Virus (HPAIV) Subclade
No access ☹

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh
More data from Bangladesh, wherein there is co-circulating lineages of HPAI H5, as well as H9 and others. ducks from nomadic farms, juvenile, and sick ducks had a higher risk of AIV

Genetic and Biological Characterization of H3N2 Avian Influenza Viruses Isolated from Poultry Farms in China between 2019 and 2021
Large diversity of AIVs, but also isolated H3N2 in poultry in China. Since some of the H3N2 viruses replicated without preadaptation and caused body weight loss in mice (due to a PB2 E627K) Note. They also detected H14!!

Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks
Using antibiotic to promote poultry growth makes chicks more susceptible to H9N2! More studies linking the gut microbiome with influenza virus susceptibility!

Antiviral susceptibility of clade highly pathogenic avian influenza A(H5N1) viruses isolated from birds and mammals in the United States, 2022
Sporadic drug resistance in HPAI viruses in the USA: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T)

 The SUMO-interacting motif in NS2 promotes adaptation of avian influenza virus to mammals
HPAI is still an avian virus, and often requires adaptive mutations to allow for infection in mammals. In H9N2, they found that the NS2 protein can also help overcome mammalian restriction to the avian polymerase. Good explanation twitter thread here: https://twitter.com/ejustin46/status/1684198237547245569?s=20

Phylogenetic and Pathogenicity Comparison of Three H5N6 Avian Influenza Viruses in Chickens, Ducks and Mice
HPAI H5N6 causes numerous human cases in China. Comparison of 3 strains from birds shows Mutations with cross-species transmission and enhanced pathogenicity found. Differences in infection outcomes in chickens, ducks and mice

Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany
Old one, but shows how poultry clusters are connected. Wild bird-mediated entries into backyard holdings, several clusters of poultry holdings, local virus circulation, farm-to-farm transmission and spill-over into the wild bird populations

Loss of amino acids 67-76 in the neuraminidase protein under antibody selection pressure alters the tropism, transmissibility and innate immune response of H9N2 avian influenza virus in chickens
Minor changes to the neuraminidase alters the tropism and host immune response against H9N2 in poultry. These changes have been identified in nature, and antibody selection plays role in evolution of H9N2

Highly pathogenic avian influenza A(H5N1) virus in a common bottlenose dolphin (Tursiops truncatus) in Florida
Case report of HPAI in a bottle nosed dolphin in Florida. Neuronal necrosis, inflammation of the brain, highest viral load in brain. S246N neuraminidase substitution = reduced inhibition by the neuraminidase inhibitor oseltamivir

Quail Rearing Practices and Potential for Avian Influenza Virus Transmission, Bangladesh
Survey of people who have Quail, all respondents (67) reported keeping quail with other birds in cages, feeding quail, cleaning feeding pots, removing quail faeces, slaughtering sick quail, and discarding dead quail. Children played with quail and assisted in slaughtering of quail. Most respondents (94%) reported rinsing hands with water only after slaughtering and disposing of wastes and dead quail. No personal protective equipment was used during any activities.

Impact of palmiped farm density on the resilience of the poultry sector to highly pathogenic avian influenza H5N8 in France
Palmiped = web footed
Decreasing density of ducks/geese in the areas of highest density substantially decreases Ro in HPAI outbreaks. Much higher benefit compared to reducing chicken densities. Great study from France.

Investigation of risk factors for introduction of highly pathogenic avian influenza H5N1 virus onto table egg farms in the United States, 2022: a case-control study
Final version not yet available.

Safety and Immunogenicity of a Delayed Heterologous Avian Influenza A(H7N9) Vaccine Boost Following Different Priming Regimens: A Randomized Clinical Trial
In a randomised controlled study, humans that received an H7N9 vaccine with an adjuvant, and a prime and boost regime had the best serological response.

Art of the Kill: Designing and Testing Viral Inactivation Procedures for Highly Pathogenic Negative Sense RNA Viruses
Chemical inactivation works well. Heat does so, when done properly. Some SOPs provided also.

Avian Influenza: A Potential Threat to Human Health
book chapter

Mink farming poses risks for future viral pandemics
Great summary from @PeacockFlu and Wendy Barclay on risk of minks (and other fur farmed species) play in viral pandemics, including HPAI. And see this great Twitter thread by Tom Peacock: https://twitter.com/PeacockFlu/status/1682696057744916480?s=20

Evaluation of the Effect of Pb Pollution on Avian Influenza Virus-Specific Antibody Production in Black-Headed Gulls (Chroicocephalus ridibundus)
Increased blood lead (Pb) levels in Black-headed gulls associated with a significant decrease in avian influenza antibody titre. Wonder if its a factor in the current black-headed gull HPAI outbreaks?

Annual trading patterns and risk factors of avian influenza A/H5 and A/H9 virus circulation in turkey birds (Meleagris gallopavo) at live bird markets in Dhaka city, Bangladesh
H5 and H9 found in turkeys in Bangladesh. Turkeys traded ~180km. AIV increases in retail vendor business and the bird’s health status is sick or dead. Seasonality also at play.

Subtype specific virus enrichement with immunomagnetic separation method followed by NGS unravels the mixture of H5 and H9 avian influenza virus
Sequencing samples co-infected with avian influenza is challenging (which segment belongs to which virus?). Here, an immunomagnetic separation method is proposed, prior to NGS sequencing.

Cross-species infection potential of avian influenza H13 viruses isolated from wild aquatic birds to poultry and mammals
H13 is host restricted to gulls with few detections in other avian taxa. Infection experiments show they can replicate in chicken (but not quail or turkey) and mammalian cells lines. Serology screening showed 4.6-10% antibody positive in farm animals!


A Dutch highly pathogenic H5N6 avian influenza virus showed remarkable tropism for extra-respiratory organs and caused severe disease but was not transmissible via air in the ferret model
Also, the mammalian mutation D701N was positively selected for.

Highly pathogenic avian influenza A(H5N1) virus clade in domestic ducks, Indonesia, 2022
HPAI was detected in Indonesia in April 2022 for the first time (other lineages do circulate in Indonesia). In a clade of viruses in Asia, including China and Japan in 2021/2022. Results important for understanding risk to Australia

Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks
co SNPS on AIV-related differentially expressed genes and effects that occur in both the duck and chicken genomes help reveal shared immune pathways in these species

Relationship between some H5 commercial vaccines and the highly pathogenic H5N8 avian influenza virus that is recently circulating in Egypt
I cant figure out how to access the article yet as its ahead of print, so I will just flag this as something that is likely to be interesting to read once its out.

Development and Validation of Competitive ELISA for Detection of H5 Hemagglutinin Antibodies
Development of cELISA that detects H5 antibodies (including HPAI and LPAI H5) in wild bird and poultry.

Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile
23 avian and 3 mammal orders were tested for HPAI in Chile, with sequences now from 77 birds and 8 mammals. Sequences cluster monophyletically with viruses from Peru = single introduction from NAmerica. 3 scenarios for spread of mammalian mutation D701N

The synergistic effect of residues 32T and 550L in the PA protein of H5 subtype avian influenza virus contributes to viral pathogenicity in mice
H5 subtype AIV PA protein strongly suppresses host antiviral defense in mammals, specifically 2 mutations inhibit the IFN-mediated immune response.

Animal Markets and Zoonotic Disease in the United States
A report commissioned to understand the zoonotic risk from mass produced animals.

Summary of Influenza Risk Assessment Tool (IRAT) Results (4 July 2023)
CDC has updated the risk assessment of HPAI, taking into consideration the viruses from the mink farm outbreak. The newer virus from the minks scored higher than the earlier duck virus on 6 of the 10 risk elements, which included antiviral treatment options, disease severity and pathogenesis, genomic analysis, human infections, infections in animals, and transmission in animal models.

Genetic characteristics of waterfowl-origin H5N6 highly pathogenic avian influenza viruses and their pathogenesis in ducks and chickens
Since 2013 HPAI found in ducks in China. Experimental infections show ducks survive, and some have mild clinical infections but chickens have severe disease

Biological features of human influenza A(H3N8) viruses in China
More work on those human H3N8 viruses. Human H3N8 exhibited dual receptor binding profiles (avian H3N8 viruses bound to only avian type). All H3N8 viruses were sensitive to the antiviral drug oseltamivir

Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020–2022
Virus genomic data from the UK eloquently demonstrate the shift to H5N1 at the end of 2021 from H5Nx the previous year. Large diveresity of reassortants.

Continuous surveillance of potentially zoonotic avian pathogens detects contemporaneous occurrence of highly pathogenic avian influenza viruses (HPAIV H5) and flaviviruses (USUV, WNV) in several wild and captive birds
Literature review to reveal overlap in host range for orthomyxos (HPAI) and flavis (West Nile, Usutu) in Europe to better understand role of wild birds in maintenance of zoonotic viruses.

Estimated mortality of the highly pathogenic avian influenza pandemic on northern gannets (Morus bassanus) in southwest Ireland
Given limits in collection of wild bird mortality data during HPAI, authors attempted to estimate mortality of Northern Gannets in SW Ireland: the estimated minimum local population mortality was 3126 birds.

Vogelgriep panzoötie leidt tot massastrandingen van Jan-van-genten Morus bassanus in Nederland, april-oktober 2022 [In Dutch]
Summary of HPAI leading to mass strandings of wild birds in the Netherlands (April – Oct 2022) [In Dutch].

A Comparison of Host Responses to Infection with Wild-Type Avian Influenza Viruses in Chickens and Tufted Ducks
Differences in immune responses of tufted ducks and chicken to LPAI from Mallards – reveals immune responses in the event of cross species transmission events.

Detection of intercontinental reassortant H6 avian influenza viruses from wild birds in South Korea, 2015 and 2017
Studies of LPAI have been key to helping us how viruses cross geographic boundaries (Antlantic/Pacific Ocean). Recent study finds H6 viruses with combination of genes from America (NP, NS) and Eurasia. Phenomenon usually limited to gulls and HPAI

The Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021–2022
467 outbreaks of HPAI in Nigeria from 2021-22, in backyard, semi intensive and intensive operations with mix of chickens and ducks. Two HA clades -Nigerian/European H5N1/N2 & Nigerian/Europe/Asian H5N8. Novel genome constellation in H5N2 fro H5N1+H9N2

Highly Pathogenic Avian Influenza A(H5N1) Clade Virus in Domestic Cat, France, 2022
Case report of HPAI in a domestic cat in France. Cat lived with family next to duck farm, on which HPAI was confirmed and 8375 ducks culled. Neurologic and respiratory (dyspnea) symptoms in cat. Genetically same virus as ducks.

BTN3A3 evasion promotes the zoonotic potential of influenza A viruses
Despite plenty of exposure, why are there so few human cases of HPAI? New study shows importance of a human gene BTN3A3 as an inhibitor of avian influenza, but not human influenza. Lots of great threads on this article, including this one: https://twitter.com/SpyrosLytras/status/1674339262894948353?s=20

Flu hits breeding rate of UK’s largest bird of prey

Healthy adults possess cross-reactive neuraminidase inhibition antibodies to an A(H5N1) clade avian influenza virus A/Black Faced Spoonbill/Hong Kong/AFCD-HKU-22-21429-01012/2022
Cross reactive NA antibodies against HPAI found in 63 humans in Hong Kong, but no cross reactive HA antibodies. These NA antibodies likely from exposure to human H1N1. Partial protection from season influenza against avian influenza?

Highly Pathogenic Avian Influenza (H5N1) in Humans after the emergence of clade in 2020
List of H5N1 cases. Doesn’t delineate bona fide infection from those “Environmental carriers”.

Influenza A in Shorebirds in the Tropical Landscape of Guatemala
Only 1 seropositive shorebirds, not qPCR positive shorebirds – LPAI

The UK joint Human Animal Infections and Risk Surveillance (HAIRS) group have published a risk assessment
Assessment of the risk of infection in the UK
General UK population: Very Low
The probability of infection would be considered Low for those exposed to infected live or dead non-avian wildlife.
The impact on the general UK population would be considered Very Low, while it would be considered Low for high risk groups (for example individuals with occupational exposure to infected wildlife and/or immunocompromised or paediatric cases).
Level of confidence in assessment of risk

Newly emerged genotypes of highly pathogenic H5N8 avian influenza viruses in Kagoshima prefecture, Japan during winter 2020/21
Study from Japan addresses HPAI H5N8 in 2020/21, prior to the dominance of H5N1. Detection of G1 in the winter, and G2 only in late winter, suggestion more than one introduction. Lots of evidence for reassortment with locally circulating LPAI.

Highly Pathogenic Avian Influenza Virus (H5N1) Clade Introduced by Wild Birds, China, 2021
HPAI viruses isolated in China 2021, belonged to G07 (originated E. Asia), and G10(originated Russia) lineage. Viruses were moderately pathogenic in mice but were highly lethal in ducks. Fall in the same antigenic cluster as H5 vaccine used in China.

Genetic Characterization and Pathogenesis of H5N1 High Pathogenicity Avian Influenza Virus Isolated in South Korea during 2021–2022
HPAI caused 47 outbreaks in poultry farms, S. Korea 2021-22, phylogenetically similar to viruses in Europe. When inoculated chickens showed virulent pathogenicity & high mortality. In ducks no mortality, high transmission rates & long viral shedding

Low Susceptibility of Pigs against Experimental Infection with HPAI Virus H5N1 Clade
Despite the assertion that pigs are “mixing vessels”, and that historically avian lineages circulate in pigs, they arent very susceptible to HPAI. After experimental innoc, only 1 pig seroconverted.

The importance of rapid and robust availability of epidemiological data for real-time mapping of the risk of avian influenza a (H5N1) spread
Data accessibility and sharing critical in our response to HPAI. Here a collation of HPAI data from various sources, and easily machine readable. Less comprehensive than WAHIS, but data easier to access (and likely, analyze).

Validation of an RNAscope assay for the detection of avian influenza A virus
New approach to detecting avian influenza from formalin-fixed, paraffin-embedded tissues: RNAScope. Substantially higher sensitivity of detection within positive tissues, but challenging to differential nucleus vs cytoplasmic positives.

Mammalian infections with highly pathogenic avian influenza viruses renew concerns of pandemic potential
Mammalian infections with HPAI renews concerns of pandemic potential. Infection of mammals increases the opportunity for the virus to acquire mutations that enhance efficient infection, replication, and spread in mammals

Diverse infectivity, transmissibility, and pathobiology of clade H5Nx highly pathogenic avian influenza viruses in chickens
Comparative pathology of seven HPAI lineages in chickens. Clade viruses showed 100% mortality, but no transmission to co-housed chickens. All the infected chickens died showing systemic infection, irrespective of subgroup.

 The first case of human infection with H5N1 avian influenza a virus in Chile
More information about the human HPAI case in Chile. > patient’s residence is located one block from the seashore where seabirds infected with H5N1 viruses had previously been detected. Sequence similar to wild bird viruses in Chile.

Evaluating Effects of AIV Infection Status on Ducks Using a Flow Cytometry-Based Differential Blood Count
Despite work on immune systems of chickens, our understanding of the immune response of ducks is poor. A new flow cytometry-based duck WBC differential for quantification of mallard immune cells including B cells, CD4+ T cells, CD8+ cytotoxic T cells

Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses
A new HA sutbype found in birds, related to H9, but only ~60% similar.

Multiple infections with H5N8 subtype high pathogenicity avian influenza viruses in a feral mallard
Case report of a duck in Asia co-infected with two different genome constellations of HPAI. Of course not surprising, this is a key requirement for reassortment to occur.

Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 Clade Virus
Majority of pigs tested, which were in contact with infected birds, were serologically positive for the hemagglutination inhibition test and microneutralization assay.

Efficient and Informative Laboratory Testing for Rapid Confirmation of H5N1 (Clade High-Pathogenicity Avian Influenza Outbreaks in the United Kingdom
APHA have published a new qPCR based assay for confirmation of HPAI.

The Molecular Epidemiology of Clade H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022
Great summary of HPAI in Southern Africa since 2021. clade H5N1 first found in ZA poultry in April 2021. 7 constellations in initial outbreaks, but by 2022 only 2 remained. 83% poultry outbreaks linked to wild birds

Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016–Early 2022
Once introduced North America, HPAI spread more rapidly (compared to within Europe). Geographic proximity is a key predictor of virus spread = long distance transport rare. An increase in temperature was predictive of reduced spread.

Rapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America
Shows the different phenotypic properties of the many HPAI reassortants in North America. Lots of work in ferrets here.

The first meeting of the Standing Group of Experts on HPAI for Europe
> Conclusions and recommendations (draft)
5. Members’ Veterinary Authorities and WOAH Reference Laboratories for avian influenza exchange information related to the development, testing and use of vaccines against HPAI and modelling activities that inform collective assessment of possible vaccination strategies and policy contributing to ensure that proper vaccination is implemented avoiding use of unreliable vaccines or wrong vaccination strategies ensuring also that surveillance in vaccinated populations is robust and capable of detecting infection with wild-type viruses.
6. Members encourage research institutions and vaccine manufacturers to invest and collaborate on research and development of effective and safe HPAI vaccines adapted to different species of poultry in accordance with the standards in the Terrestrial Manual;

US will vaccinate birds against avian flu for first time — what researchers think
Vaccination has been approved for California Condors, comprising the first approval for HPAI vaccines in the US. It took 20 years to help the species recover, the 21 dead birds found has been highly concerning. First trials occurring in Black Vultures.

Avian influenza overview March – April 2023
update from EFSA: 106 domestic and 613 wild bird outbreaks across 24 countries. On going outbreaks in Black-headed Gulls

High number of HPAI H5 Virus Infections and Antibodies in Wild Carnivores in the Netherlands, 2020-2022
Testing of 500 dead mammals in the Netherlands: virological evidence for HPAI infection in 0.8% (2020), 1.4%(2021), 9.9% (2022). highest prevalence in foxes, polecats and stone martens. 20% seropositive. PB2 mutations found in viral genomes.

Highly pathogenic avian influenza causes mass mortality in Sandwich tern (Thalasseus sandvicensis) breeding colonies across northwestern Europe
Sandwich Terns in Europe absolutely devastated by HPAI last year, with most colonies affected. “20,531 adult Sandwich terns were found dead, which is >17% of the total northwestern European breeding population. Inside the colonies almost all chicks died”

Multiple introductions of highly pathogenic avian influenza H5N1 clade into South America
More evidence of at least 4 incursions into South America.

Novel Highly Pathogenic Avian Influenza A(H5N1) Clade Virus in Wild Birds, South Korea
Additional diversity in genome constellations found in wild birds in South Korea in 2022, with some evidence of similarity to the “G10” constellation [reassortant of HPAI and PB2 LPAI) found in China in 2022/23

Extensive Diversity and Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021-2022
Between 2021-22, 467 outbreaks of HPAI detected in Nigeria. Widespread distribution of the H5Nx clade and similarity with the HPAI H5Nx viruses detected in Europe since late 2020. Detection of reassortant with H9N2.

Novel Avian Influenza Virus (H5N1) Clade Reassortants in Migratory Birds, China
HPAI viruses from swans in China in 2021 fall into clade, and have unique genome constellations. Spread analysis suggests internal segments originally from Africa, via Europe to China.

Spatio-temporal analysis of Highly Pathogenic Avian Influenza HPAI (H5N1) in poultry in Menofia governorate, Egypt
Tracking of HPAI in Egypt from 2006-2017 demonstrates 6 waves through poultry. Includes clade, Rural districts and villages key hotspots. Challenging to get data due to lack of notification, effects of vaccination, compensation issues.

Highly Pathogenic Avian Influenza H5N8 Outbreak in Backyard Chickens in Serbia
Outbreak report of HPAI H5N8 in 2016, and recently H5N1 in Serbia in 2021/22. Following outbreaks, strict control measures were implemented on farms and backyard holdings to prevent the occurrence and spread of the disease.

Surveillance of avian influenzas viruses from 2014 to 2018 in South Korea
Study on LPAI in Korea between 2014-2018. Apparently not HPAI detected at all.

An amplicon-based nanopore sequencing workflow for rapid tracking of avian 2 influenza outbreaks, France, 2020-2022
Real time, field based protocol for rapid HPAI sequencing in the field. Probably very useful for us to have in the back pocket.

Culture-Independent Workflow for Nanopore MinION-Based Sequencing of Influenza A Virus
Real time, field based protocol for rapid HPAI sequencing in the field. Looks like it can work for more than just H5N1 though.

A real-time colorimetric reverse transcription loop-mediated isothermal 2 amplification (RT-LAMP) assay for the rapid detection of highly pathogenic H5 3 clade avian influenza viruses
Rapid detection of HPAI with LAMP. “specific detection of HPAIV H5Nx clade within 30 minutes with a sensitivity of 86.11%” .

Avian influenza, new aspects of an old threat
“To tackle the threat of avian influenza, a One Health approach is needed through rapid sharing of information about outbreaks, provision of sequence data and reference viruses, and close collaboration between the different sectors locally and globally.”

Epidemiology and molecular characterization of avian influenza A viruses H5N1 and H3N8 subtypes in poultry farms and live bird markets in Bangladesh
Avian influenza prevalence in LBMs in Bangladesh comprising 40.20% – 52.38% in chicken, 46.96% in waterfowl, 31.1% in turkey. H5 comprised the highest prevalence: clade (circulating since 2015). H3N8 viruses similar to those in China.

Epidemiological Distribution of respiratory viral pathogens in marketable vaccinated broiler chickens in six governorates in the Nile Delta, Egypt, January to October 2022
In 2022, 293/359 poultry flocks tested positive for respiratory viruses in Egypt. NDV found to be the most common, followed by IBV, H9 and H5. Lots of co-infections.

High proportion of H3 avian influenza virus circulating in chickens-an increasing threat to public health
Reanalysis of H3N8 show human and poultry cases in China form a monophyletic clade. Surveillance data for the past three years: H3 widely distributed in many provinces of China, with prevalence of ~60% in chickens, 31% in ducks, 7% in pigeons.

Synchrony of Bird Migration with Avian Influenza Global Spread; 2 Implications for Vulnerable Bird Orders
Seasonal bird migration can explain salient features of the global dispersal of – differing vulnerable bird orders at geographical origins and destinations of HPAIV H5 lineage movements – role of Suliformes and Ciconiformes

Mixed selling of different poultry species facilitates emergence of public-health-threating avian influenza viruses
“mixed poultry selling at retail live poultry markets has increased the genetic diversity of AIVs, which might facilitate the emergence of novel viruses that threaten public health”

Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera 2 from Japanese quail (Coturnix c. japonica).
Vaccination against H9 is widely employed in the MiddleEast/Asia. New antigenic maps have now been produced, with important implications for understanding antigenic drift and improving vaccine development and use.

The bat-borne influenza A virus H9N2 exhibits a set of unexpected pre-pandemic features
H9N2 influenza A virus in Egyptian bat exhibits high replication and transmission potential in ferrets, efficient infection of human lung cultures and escape from the antiviral activity of MxA. = criteria for pre-pandemic virus.

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences
In 2022, unusually high mortality was detected in 75% of Northern Gannet colonies, globally, with HPAI confirmed in 58% of cases. Decreased adult survival and breeding success. Some birds survived – with black irises.

Remote Sensing and Ecological Variables Related to Influenza a Prevalence and Subtype Diversity in Wild Birds in the Lluta Wetland of Northern Chile
AIV prevalence is dictacted by numerous factors. New study from Chile show diversity of LPAI in the Lluta River wetland, and that prevalence correspond to Normalized Difference Vegetation Index, abundance of migratory birds

Circulation of highly pathogenic avian influenza virus H5N1 clade in highly diverse wild bird species from Peru
More HPAI data from Peru. Viral isolates and sequences from pelicans, gulls, cormorants, penguins, and an array of raptors. Viruses similar to those from Chile.

Development of a nucleoside-modified mRNA vaccine against clade H5 highly pathogenic avian influenza virus
Development of an mRNA vaccine against HPAI, although targetted towards mammals, with the vaccine immunogenic in mice and ferrets and prevents morbidity and mortality of ferrets following challenge.

Wild birds’ plight and role in the current bird flu panzootic

Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States
Nice study on H13, including AIV work and tracking and migration stuff.

HPAIV outbreak triggers long-distance movements in breeding Northern gannets — implications for disease spread

Environmental Samples Test Negative for Avian Influenza Virus H5N1 Four Months after Mass Mortality at A Seabird Colony
At Foula, Shetland, 1500 breeding adult great skuas Stercorarius skua, totalling about two tonnes of decomposing virus-laden material, died at the colony in May−July 2022… No viral genetic material was detected four months after the mortality, suggesting a low risk of seabird infection from the local environment when the seabirds would return the next breeding season
This is in contrast to studies of LPAI that found infectious virus for almost a year!
For example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7542776/

Viruses: How avian influenza viruses spill over to mammals
Lovely summary of the recent canine influenza paper, relevant in demonstrating that avian viruses may emerge and adapt to mammals.

Detection and Genomic Characterization of an Avian Influenza Virus Subtype H5N1 (Clade Strain Isolated from a Pelican in Peru
Short note about the sequencing of a single viral isolate using nanopore.

Comprehensive analysis of the key amino acid substitutions in the polymerase and NP of avian influenza virus that enhance polymerase activity and affect adaptation to mammalian hosts
More efforts to map mutations required for avian influenza viruses to infect mammals, focussing on genetic screens of internal segments and experiments with H7. Mutations other than PB2 E627K at play.

Highly Pathogenic H5 Influenza Viruses Isolated between 2016 and 2017 in Vietnamese Live Bird Markets
# 2344f. 2344g and 2321c

Potential Effects of Habitat Change on Migratory Bird Movements and Avian Influenza Transmission in the East Asian-Australasian Flyway
Modelling and telemetry shows that minor changes in land-use in China may have large ramifications for stopover sites, and thus HPAI risk.

Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 Clade Virus
Pigs reared on same property as infected birds showed extensive seroconversion to 61% positive using HI and of 9 tested using MN, all positive?. Raises questions about whether all pigs exposed to infected birds/dust/particles or transmission?

Transmission of lethal H5N1 clade avian influenza in ferrets
Here we show that multiple naturally circulating H5N1 viruses can replicate in primary human airway epithelial cells and cause lethal disease in multiple mammalian species. One isolate, A/Red Tailed Hawk/ON/FAV-0473-4/2022, efficiently transmitted by direct contact between ferrets, resulting in lethal outcomes…. uncharacterized, genetic signatures may be important determinants of mammalian adaptation and pathogenicity of these viruses

Replication of Novel Zoonotic-Like Influenza A(H3N8) Virus in Ex Vivo Human Bronchus and Lung
Virus has affinity for both α-2,3 and α-2,6, but inefficient replication in human bronchial tissues and has limited efficiency for human-to-human transmission

Risk for Infection in Humans after Exposure to Birds Infected with Highly Pathogenic Avian Influenza A(H5N1) Virus, United States, 2022
Of 4,000 persons exposed to HPAI H5N1–infected birds, only 1 has ever had qPCR confirmed case. This person was unlikely actually infected, but rather was a case of putative environmental contamination.

Identification of a duck H9N2 influenza virus possessing tri-basic hemagglutinin cleavage sites genetically close to the human H9N2 isolates in China, 2022
Detection of an H9N2 virus in ducks in China, linked to ongoing human cases, and with a tribasic PSRSRR/GLF motif and shows a preference for binding to α-2,6 human-like receptors

Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile
Since 7 Dec 2022, Chile has reported 197 HPAI outbreaks, with 478 individual cases in birds, and 14 statistically significant clusters including a poultry production centre, and Tocopilla (human case here). Wave-like spread from north to south.

Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated to the highly pathogenic clade
In Nov 2022, HPAI was first detected in Ecuador. By Feb 2023 1.1 million poultry were culled. Virus similar to those from Peru and Chile and closely related to sequences from Venezuelan pelicans.

Interventions to Reduce Risk for Pathogen Spillover and Early Disease Spread to Prevent Outbreaks, Epidemics, and Pandemics

PAHO seeks to strengthen regional avian influenza surveillance and response [16 Mar 2023] PAHO = The Pan American Health Organization

HPAI in Great Britain: evaluation and future actions | Gov.uk 30 March 2023
“The HPAIG [Scientific Advisory Group in highly pathogenic avian influenza] was tasked with addressing four key issues with regards to the current epidemic of HPAI in Great Britain (England, Scotland and Wales)
– the host range of the current virus and their potential roles
– the possibility of interventions to reduce impact on wild birds
– the potential to supplement current approaches to control with vaccination
– the potential to model the expected future trajectory of the outbreak

Evolution of Avian Influenza Virus (H3) with Spillover into Humans, China

Human Infection with highly pathogenic avian influenza A(H5N1) virus in Chile
## this is an addendum to a technical report: https://www.cdc.gov/flu/avianflu/spotlights/2022-2023/h5n1-technical-report.htm

NatureScot Scientific Advisory Committee Sub-Group on Avian Influenza Report on the H5N1 outbreak in wild birds 2020-2023

Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human–live bird market interface in China

Efficacy of multivalent recombinant herpesvirus of turkey vaccines against high pathogenicity avian influenza, infectious bursal disease, and Newcastle disease viruses

Emergence and rapid dissemination of highly pathogenic avian influenza virus H5N1 clade in wild birds, Chile

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade

Targeted genomic sequencing of avian influenza viruses in wetlands sediment from wild bird habitats

The pathogenesis of a 2022 North American highly pathogenic clade H5N1 avian influenza virus in mallards (Anas platyrhynchos)

Using integrated wildlife monitoring to prevent future pandemics through one health approach

41% of Pelicans in Peru now dead due to HPAI

Prevalence, evolution, replication and transmission of H3N8 avian influenza viruses isolated from migratory birds in eastern China from 2017 to 2021
## highly relevant given the recent human case of avian H3

H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks

Human influenza A virus H1N1 in marine mammals in California, 2019

Gradual adaptation of animal influenza A viruses to human-type sialic acid receptors

The role of airborne particles in the epidemiology of clade H5N1 high pathogenicity avian influenza virus in commercial poultry production units

Avian influenza H5N1 in a great white pelican (Pelecanus onocrotalus), Mauritania 2022

Welcome on EURL Avian Flu Data Portal

The changing dynamics of highly pathogenic avian influenza H5N1: Next steps for management & science in North America

Active wild bird surveillance of avian influenza viruses, a report
It outlines active surveillance designs, movement informed site selections, integration and analyses of ornithological data, practicalities of field sampling, virus informed epidemiology, climate and bird migration data etc. Obviously from a European lens, but Im sure there are still lots of good lessons tucked in here.

H7N9 influenza A virus transmission in a multispecies barnyard model

Protective efficacy of a bivalent H5 influenza vaccine candidate against both clades and high pathogenic avian influenza viruses in SPF chickens

How human ecology landscapes shape the circulation of H5N1 avian influenza: A case study in Indonesia

Highly pathogenic avian influenza (HPAI A H5N1) outbreak in Spain: its mitigation through the One Health approach – a short communication

A protective measles virus-derived vaccine inducing long-lasting immune responses against influenza A virus H7N9

Statistical Analysis of the Performance of Local Veterinary Laboratories in Molecular Detection (rRT-PCR) of Avian Influenza Virus via National Proficiency Testing Performed during 2020–2022

Letter to the editor: Highly pathogenic influenza A(H5N1) viruses in farmed mink outbreak contain a disrupted second sialic acid binding site in neuraminidase, similar to human influenza A viruses
This is a response to the original mink paper.. there appears to be some discussion happening about what all the mutations they found mean.

Characterization of an H7N9 Influenza Virus Isolated from Camels in Inner Mongolia, China

Whole-genome sequence and genesis of an avian influenza virus H5N1 isolated from a healthy chicken in a live bird market in Indonesia: accumulation of mammalian adaptation markers in avian hosts

Influenza A(H5N1) detection in two asymptomatic poultry farm workers in Spain, September to October 2022: suspected environmental contamination

Letter to the Editor: Knowledge gap in assessing the risk of a human pandemic via mammals’ infection with highly pathogenic avian influenza A(H5N1)

Characterization of neurotropic HPAI H5N1 viruses with novel genome constellations and mammalian adaptive mutations in free-living mesocarnivores in Canada

Infection of wild rats with H5N6 subtype highly pathogenic avian influenza virus in China

First case of human infection with highly pathogenic H5 avian influenza a virus in South America: a new zoonotic pandemic threat for 2023?

Being ready for the next influenza pandemic?

Virological and Genetic Characterization of the Unusual Avian Influenza H14Nx Viruses in the Northern Asia
The H14 story continues, with detections in Russian waterfowl.
Reasons for low prevalence? Perhaps waterfowl detections are only spillovers from other bird groups, not included in AIV surveillance?

Evolution of highly pathogenic H5N1 influenza A virus in the central nervous system of ferrets
Given most mammals infected with HPAI are showing neurological signs, this study is timely in showing that HPAI can enter the CNS of mammals and undergo positive selection while there

Infection of wild rats with H5N6 subtype highly pathogenic avian influenza virus in China
via metagenomics HPAI H5N6 found in rats in China. Rats may have been exposed from local poultry market. SNPs for mammalian infection detected.
Bona fide infection, or detection of HPAI in diet following eating infected poultry scraps?

First case of human infection with highly pathogenic H5 avian Influenza A virus in South America: A new zoonotic pandemic threat for 2023?
More details now available pertaining to human case of HPAI in Ecuador in Dec 2022. Girl was in contact with sick and dead backyard poultry. Unfortunately no genome sequences generated and there was limited surveillance in humans or birds at the time

Characterization of neurotropic HPAI H5N1 viruses with novel genome constellations and mammalian adaptive mutations in free-living mesocarnivores in Canada
Summary of mammalian cases of HPAI in Canada.
-Mammals were infected with wholly Eurasian viruses, but also EU-NA reassorted viruses.
-17% had PB2 mutation, other mammalian adapted mutations also found.
-Some Red Foxes survived infection.

Whole-genome sequence and genesis of an avian influenza virus H5N1 isolated from a healthy chicken in a live bird market in Indonesia: accumulation of mammalian adaptation markers in avian hosts
Great to see some HPAI genomes from Indonesia, albeit lineage, and not the same as Reassortment between, and H3 virus, and an H5N1 Indonesian endemic virus

Characterization of an H7N9 Influenza Virus Isolated from Camels in Inner Mongolia, China
New report of H7N9 avian influenza in camels. Other than humans (2013-2017), H7N9 has never caused mammalian infections (that we know of). The virus had mammalian adaptations (e.g. PB2 mutation), higher SA-α2 binding and mammalian cell replication.

Comparative Analysis of Different Inbred Chicken Lines Highlights How a Hereditary Inflammatory State Affects Susceptibility to Avian Influenza Virus
Chickens in industrial poultry farming are highly inbred.
Different chicken lines, respond differently to avian influenza infection. Useful to understand immunity. Also, we should better consider infection resistance in selecting/breeding chicken lines.

Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade in wild terrestrial mammals in the United States in 2022
Great summary outlining pathological findings of 62 dead mammals infected with HPAI.
“Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions”

Highly pathogenic avian influenza A (H5N1) virus infections in wild carnivores connected to mass mortalities of pheasants in Finland
Great study linking mammalian cases of HPAI in Finland to an outbreak in farmed and released pheasants.
“avian influenza cases in mammals were spatially and temporally connected with avian mass mortalities”

Highly pathogenic avian influenza in wild birds in the United Kingdom in 2022: impacts, planning for future outbreaks, and conservation and research priorities.
Report on virtual workshops held in November 2022
Great resource from the BTO on impacts, planning for future outbreaks, and conservation and research priorities in regards to HPAI

Bird flu can jump to mammals – should we worry?

Avian influenza spread and seabird movements between colonies
How does avian influenza spread within and between seabird colonies? Seabird movements such as dispersal, prospecting, foraging and migration in addition to direct contact certainly at play

Descriptive Epidemiology of and Response to the High Pathogenicity Avian Influenza (H5N8) Epidemic in South African Coastal Seabirds, 2018
Unlike the Northern Hem which experienced large scale outbreaks of HPAI in seabirds in 2022 for the first time, S. African seabirds have experienced re-occuring outbreaks for many years now. Many lessons we can learn from their experiences.

Influenza A(H5N1) detection in two asymptomatic poultry farm workers in Spain, September to October 2022: suspected environmental contamination
The scale of HPAI outbreaks is huge.
This figure demonstrates the number of outbreaks in Spain alone, including wild birds, poultry, mink, and most recently 2 putative human cases (although the latter may be environmental contamination…)

Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses
The cool story of H14 (a relatively rare influenza subtype) in teals of Guatemala continues.
The high level of H14 in Guatemala may be due to epizootic events from a single introduction, followed by local clonal expansion followed by maintenance

Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET
RIG-I is part of the first line of defense against avian influenza infection, and while present in ducks is missing in chickens. A screen of the avian tree of life indicates absence in other avian families too (penguins, shearwaters)

Pathology of naturally acquired high pathogenicity avian influenza virus H5N1 infection in seabirds
Pathology studies of HPAI in seabirds. “Across the birds, epitheliotropism was evident… This was, in contrast, not observed in the 2021 summer mortality event in great skuas and may be significant for the disease epidemiology observed in 2022”

Waterfowl recently infected with low pathogenic avian influenza exhibit reduced local movement and delayed migration
Revisiting the cost of infection of low path influenza – affect of infection on migration.
Telemetry of 165 individuals of 4 species of duck. Antibody pos NOPI = 12 days stopovers. PCR pos Canvasback delayed migration 28 days.

Wild Bird Densities and Landscape Variables Predict Spatial Patterns in HPAI Outbreak Risk across The Netherlands
What predicts when and where HPAI outbreaks will occur?
Wild bird densities and landscape variables (which generally correlate with higher bird densities such as rivers) are key.

Experimental and natural infections of white-tailed sea eagles (Haliaeetus albicilla) with high pathogenicity avian influenza virus of H5 subtype
In addition to reservoirs (like ducks), raptors are also suffering wide-spread mortality due to HPAI (likely from eating infected ducks). This study further shows the capacity for transmission between raptors of

Zoonotic Mutation of Highly Pathogenic Avian Influenza H5N1 Virus Identified in the Brain of Multiple Wild Carnivore Species
Zoonotic mutation PB2-E627K of HPAI H5N1 identified in the brain of multiple wild carnivore species: fox, polecat, otter, and badger

Highly Pathogenic Avian Influenza H5N1 Virus Infections in Wild Red Foxes (Vulpes vulpes) Show Neurotropism and Adaptive Virus Mutations
Continued concern about mammalian adaption in HPAI (given ? mammalian cases and Spanish mink). An interrogation of viruses found in foxes in the NL – presence of E627K PB2 mutation. Genomic surveillance of HPAI in mammals continues to be very important

First Mass Mortality of Marine Mammals Caused by Highly Pathogenic Influenza Virus (H5N1) in South America
Lots of HPAI activity in S America, with >50,000 wild birds dead, a human case, and now a mass mortality event in sea lions (634 animals)
Extremely concerning, demonstrates the potential scale of outbreaks that may occur if this virus enters Australia

Clade H5N1 high pathogenicity avian influenza virus (HPAIV) from the 2021/22 epizootic is highly duck adapted and poorly adapted to chickens
Lots of questions abt why we have seen explode in birds since 2021.
This study argues that virus is highly duck adapted (?transmission & environ contamin) and poorly chicken adapted. Evidence to the idea that wild birds are now a reservoir.

Statement on avian influenza and mammals
The World Organisation for Animal Health have released a statement on avian influenza.
In short: surveillance, prevention, control, protection, monitoring, reporting and SHARING genetic sequence (hopefully in a timely manner).

No evidence for HPAI H5N1 incursion into Australia in 2022
The highest risk period for HPAI incursion into Australia is when the migratory birds arrive in the spring. Here
we report the results of our surveillance of migratory birds from Sept-Dec 2022. No HPAI detected.

An Evaluation of Avian Influenza Virus Whole Genome Sequencing Approaches Using Nanopore Technology
Great to see further development of Nanopore sequencing for HPAI.
Unlike SARS-CoV-2, influenza is segmented, so a slightly different approach is warranted.

Consequences and global risks of highly pathogenic avian influenza outbreaks in poultry in the United Kingdom
Consequences of HPAI infection in the UK
– higher risk of human infections
– 4.6 million birds culled 1 Oct – 13 Jan 2023
– egg shortage + ? egg $
– end of free range?

Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade Virus in Chile, 2022
Increased viral prevalence of avian influenza in Chile corresponded with the arrival of migratory birds at the end of 2022, and HPAI was detected in seabirds: Pelicans, gulls, terns and skimmers. Genomes similar to poultry & wild bird viruses in S. Am.

Homo- and Heterosubtypic Immunity to Low Pathogenic Avian Influenza Virus Mitigates the Clinical Outcome of Infection with Highly Pathogenic Avian Influenza H5N8 Clade in Captive Mallards (Anas platyrhynchos)
Why do some ducks have asymptomatic infections with HPAI H5? Pre-exposure to LPAI H5!
“The mallards pre-exposed to LPAIV H5N1 .. were asymptomatic and showed a significant reduction of viral RNA shedding, .. no disease.. antigen not detected in organs”

Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020
Lovely analysis demonstrating bidirectional movement of HPAI H5N8 avian influenza viruses between Europe and Asia. Specifically that temporal estimates from virology data match bird migration timing

Avian influenza leads to mass mortality of adult Great Skuas in Foula in summer 2022
Summary of mass mortality event of Great Skuas on Foula in summer 2022 due to avian influenza.
“a decline in the order of magnitude of 60–70% in occupied territories is more likely”

Migratory patterns of two major influenza virus host species on tropical islands
Interrogating how avian influenza is maintained and transmitted between Indian ocean islands. Also reinforces the role of Noddies as hosts for AIV.
Combines bird tracking data and influenza data.

Avian flu threatens Neotropical birds
– HPAIv killed more than 22,000 wild birds in just 4 weeks in 2022 in Peru
– December 2022, the virus had been found in birds in Ecuador, Colombia, Venezuela, and Chile

In Vitro and In Vivo Characterization of H5N8 High-Pathogenicity Avian Influenza Virus Neurotropism in Ducks and Chickens
Why are there differences in disease between chickens and ducks infected with HPAI?
Ducks better control replication in their lungs, so limited respiratory signs & eventual neurological signs. Chickens succumbed to initial resp infections.

Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds
Our latest study showing the role of host phylogeny (and ecological effects as previously shown) on host competency for avian influenza is finally out
Culmination of MANY years of sampling to reveal avian influenza dynamics in Australia

Highly pathogenic avian influenza H5N1 virus outbreak among Cape cormorants (Phalacrocorax capensis) in Namibia, 2022
In January 2022, more than 6500 Cape cormorants died due to HPAI on Bird Island, Walvis Bay. Phylogenetics indicate clade, and highly similar to H5N1 in chickens in Lesotho in May 2021 and poultry and wild birds in Botswana in June 2021

Detection of Clade Avian Influenza A(H5N8) Virus in Cambodia, 2021
Avian influenza H5 viruses have been routinely detected in Cambodia for a number of years, particularly since 2014. Here was first detected in late 2021.

Emergence of Highly Pathogenic Avian Influenza A Virus (H5N1) of Clade in Egypt, 2021–2022
Overview of avian influenza H5N1 in Egypt. Overall, the Egyptian strains shared genetic traits, markers associated with mammalian adaption, and virulence traits similar to those found in HPAI H5N1 strains detected in Europe and Africa

Bald eagle mortality and nest failure due to clade highly pathogenic H5N1 influenza a virus
Avian influenza having considerable effects on wild birds beyond waterfowl.
“infection manifested beyond the scale of individual eagles, and directly affected population recruitment dynamics through elevated rates of reproductive failures.”

Pathogenicity of highly pathogenic avian influenza H5N8 subtype for herring gulls (Larus argentatus): impact of homo- and heterosubtypic immunity on the outcome of infection
Gulls are highly susceptible to HPAI, although birds with previous exposure to LPAI H5 fared considerably better than naive birds. Birds previously exposed to H13 (gull specific influenza) faired almost as well as those pre-exposed to LPAI H5

Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America
Another paper interrogating the introduction of HPAI from Europe into N.America – this one with data from Iceland.

Rapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America
Different genotypes of H5N1 isolated in North America are phenotypically diverse, with many causing severe disease with dramatic neurologic involvement, in mammals. Reassortment following introduction to N. Am a key driver of genetic change.

Great Skuas and Northern Gannets on Foula, summer 2022 – an unprecedented, H5N1 related massacre
1501 Great Skuas found dead on Foula (Scotland). This outbreak likely has pop & species level effects with <10% of the population of Scotland affected. This is following substantial outbreaks in 2021 in this species.

Mass Mortality Caused by Highly Pathogenic Influenza A(H5N1) Virus in Sandwich Terns, the Netherlands, 2022
A summary of the tern outbreaks in the Netherlands out today.
“…out of a total of 18,151 breeding pairs, 8,001 adult Sandwich terns were found dead, and only a few chicks fledged”
Phylogenetic analysis demonstrates two different sublineages of

The impact of avian influenza 2022 on Dalmatian pelicans was the worst ever wildlife disaster in Greece
Probably one of the most poignant paper titles. 2286 pelicans died in Greece due to HPAI, comprising 40% of the SE European pop, and 10% of the global pop.

Calls grow for global avian flu jabs
with some good quotes from Les Simms and David Swayne at the @WOAH_Global in Paris, out in Vet Record

H6N8 avian influenza virus in Antarctic seabirds demonstrates connectivity between South America and Antarctica
Very cool study interrogating an H6N8 avian influenza virus found in penguins and skuas in Antarctica, and through phylogeny, demonstrating viral introduction most likely from South America

Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones
Detailed study of influenza movement with wild birds, particularly revisiting the recent introduction into North America via the Atlantic shows the importance of bird migration via the arctic and subarctic.

Shift in HPAI infection dynamics causes significant losses in seabird populations across Great Britain
Shift in HPAI infection dynamics causes significant losses in seabird populations, here with data from Great Britain. 1454 positive wild birds across 61 species (Although numbers of infected birds expected to be much higher in reality)

Most avian influenza news is coming out of Europe and North America, but it’s a global problem. Emergence of a Reassortant Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021
New paper from Burkina Faso, with H5N1 viruses detected in clade, closely related to HPAI H5N1 viruses identified in Nigeria and Niger, and H9N2

Long-Term Protective Effect of Serial Infections with H5N8 Highly Pathogenic Avian Influenza Virus in Wild Ducks
What is the impact of repeated waves of HPAI H5 on wild bird populations? Experimental infections show protective immunity of 2014 H5N8 virus in ducks when later exposed to 2016 H5N6. May explain how virus is maintained in wild bird populations

Has Epizootic Become Enzootic? Evidence for a Fundamental Change in the Infection Dynamics of Highly Pathogenic Avian Influenza in Europe, 2021
Huge question: Has Epizootic HPAI H5 Become Enzootic? Importantly, it is likely that we now have continuous circulation in wild birds (genetic drift of circulating viruses) and novel introductions in N Europe. Implications for both prevent and control.

Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian influenza A subtypes among North American wild reservoir species
A more host specific analysis was recently done in another recent paper, showing lots of transitions within avian orders, but fewer transitions between them. And that transition influenced by breeding habitat range overlap, and not host genetic distance

Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America
How are avian influenza viruses maintained in multi-species wild bird populations? Complex patterns of virus dissemination between different host groups across many flyways are implicated. Important for surveillance to go beyond Anas ducks.

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe
Key question in HPAI is the role of wild birds vs poultry. In 2016, HPAI was likely introduced to farms from wild birds, but in many countries epidemic was dominated by farm-to-farm transmission. Key data for prevention, mitigation and control in future

Avian Influenza NS1 Proteins Inhibit Human, but Not Duck, RIG-I Ubiquitination and Interferon Signaling
How does influenza by-pass the host immune response? Here, NS1 from both LPAI and HPAI was shown to inhibit human RIG-I but not duck RIG-I. Differences by NS1 may contribute to the unique disease resistance by avian influenza characteristic of mallards

Avian influenza antibody prevalence increases with mercury contamination in wild waterfowl
What modulates the susceptibility of birds to avian influenza infection? Heavy metals, like mercury, play play a key role and explain why we see prevalence differences in closely related species

Influenza A(H11N2) Virus Detection in Fecal Samples from Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarcticus) Penguins, Penguin Island, Antarctica
H11N2 avian influenza viruses have been found again in the Antarctic Peninsula area. Repeat detections over a few years tell us these viruses are endemic. Of interest is that there has been no reassortment with other influenza viruses between years.

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl
We wanted to understand what features of influenza allow it to reinfect a population of Mallards year after year.
Lineage replacement and reassortment are key features

A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways
In more #HPAI news, it looks like H5N1 entered North America more than once in 2022. The Atlantic Route being described in Caliendo et al, but recent analysis shows that a secondary incursion also occurred, perhaps over the pacific.

Want to understand how #HPAI is being transmitted? Key paper shows the role of wild bird vs farm-farm transmission in Europe 2016-17
Disentangling the Role of Poultry Farms and Wild Birds in the Spread of Highly Pathogenic Avian Influenza Virus in Europe

Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America
For wild birds, lineage H5Nx has been devastating, with thousands dying in mortality events. For example, in early 2021, approximately 10% of Barnacle Geese that breed in Svalbard died due to this disease