Avian Influenza Resources


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

Australia (and Antarctica) are the only continents free from clade 2.3.4.4.b HPAI H5N1 (June 2023). Wild migratory birds will be returning to Australia between August – November, and therefore this constitutes the highest risk period for a viral incursion.

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:

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

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 Aug 2023)

Wildlife Health Australia: Advice for veterinarians and animal health professionals (updated Aug 2023)

Wildlife Health Australia: Advice for people who encounter sick or dead wild birds (updated Aug 2023)

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

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

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

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 demonstrated no evidence for HPAI H5N1 2.3.4.4b incursion into Australia in 2022We are currently repeating this effort in 2023, and thus far all samples are negative.

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) 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. More details to follow.

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 Sept – Dec 2023 (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:

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

ACAP Intersessional Group on High Pathogenicity Avian Influenza H5N1. Guidelines for working with albatrosses and petrels during the high pathogenicity avian influenza (HPAI) H5N1 panzootic.

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

Human health risk:

A European assessment determined that the risk of infection with HPAI for the general population was low, and for occupationally exposed people (e.g. poultry workers) the risk was low to medium (but with high uncertainty). To date, all human infections with HPAI have been in people interacting with birds, particularly poultry (chickens, turkeys and ducks). 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):

– 85 human cases of 2.3.4.4. H5N6 in China since 2014. Most cases have confirmed link to poultry [aggregation]
– 7 poultry workers containing an outbreak of 2.3.4.4. H5N8 in poultry in Russia, 2020 [WHO notification, scientific article]
– 1 human case of 2.3.4.4.h 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 2.3.4.4b H5N1 in Viet Nam in 2022 [Vietnamese ministry of health, english language news story]
– 1 human case of 2.3.4.4b 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 2.3.4.4b H5N1 in Spain in 2022. Likely to comprise environmental carriage rather than bona fide infection [scientific article]
– 1 poultry worker infected with 2.3.4.4b 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 2.3.2.1c H5N1 in Cambodia in 2023 [WHO notification]
– 2 poultry workers infected  of 2.3.4.4b H5N1 in UK in 2023. One case likely comprises environmental carriage rather than bona fide infection [news story]
– 1 human case of 2.3.4.4b H5N1 in Ecuador in 2023 [WHO notification]
– 1 human case of 2.3.4.4b H5N1 in Chile in 2023 [WHO notification]
– 2 human cases of 2.3.4.4b H5N1 in the UK in 2023 [WHO information]
– 4 human cases of 2.3.2.1c H5N1 in Cambodia in 2024 [CDC information]

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

Research articles, since ~ Nov 2022 (ongoing):

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

Avian influenza virus circulation and immunity in a wild urban duck population prior to and during a highly pathogenic H5N1 outbreak
https://www.biorxiv.org/content/10.1101/2024.02.22.581693v1?rss=1
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011942
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
https://www.mdpi.com/1999-4915/16/2/190
Characterisation of N-glycans. 

An algorithm for the characterization of influenza A viruses from various host species and environments
https://onlinelibrary.wiley.com/doi/10.1111/irv.13258
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.
https://www.tandfonline.com/doi/full/10.1080/03079457.2024.2320699
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
https://www.mdpi.com/2076-393X/12/2/138
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
https://www.mdpi.com/2306-7381/11/2/93
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
https://www.frontiersin.org/articles/10.3389/fvets.2024.1319618/abstract
No full text available yet.

Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa
https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veae011/7610485
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
https://www.nature.com/articles/s41598-024-54884-2
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
https://www.mdpi.com/1999-4915/16/3/353
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
https://www.nature.com/articles/s41598-024-54796-1
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.
https://www.researchsquare.com/article/rs-3908312/v1
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 2.3.4.4b in Domestic Ducks, Indonesia, 2022
https://wwwnc.cdc.gov/eid/article/30/3/23-0973_article
preprint now published – first report of 2.3.4.4b 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
https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(24)00069-0/fulltext
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 2.3.4.4b H5N8 High Pathogenicity Avian Influenza Virus from a Common Pochard (Aythya ferina) Being Attacked by a Peregrine Falcon (Falco peregrinus) 
https://meridian.allenpress.com/avian-diseases/article-abstract/doi/10.1637/aviandiseases-D-23-00062/499167/Caught-Right-on-the-Spot-Isolation-and?redirectedFrom=fulltext
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
https://www.researchsquare.com/article/rs-3361650/v1
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
https://www.frontiersin.org/articles/10.3389/fvets.2024.1301513/full
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
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-024-01817-0
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
https://ciencia.gob.es/Noticias/2024/febrero/gripe-aviar-antartida.html

A pan-influenza monoclonal antibody neutralizes H5 strains and prophylactically protects through intranasal administration
https://www.nature.com/articles/s41598-024-53049-5
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
https://journals.asm.org/doi/abs/10.1128/jvi.01401-23
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
https://www.sciencedirect.com/science/article/pii/S1056617124000187

Are all avian influenza outbreaks in poultry the same? The predicted impact of poultry species and virus subtype
https://onlinelibrary.wiley.com/doi/full/10.1111/zph.13116 
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
https://assets.publishing.service.gov.uk/media/65d5fade2197b2001d7fa79e/highly-pathogenic-avian-influenza-europe-240216.pdf

Highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b from Peru forms a monophyletic group with Chilean isolates in South America
https://www.nature.com/articles/s41598-024-54072-2
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
https://www.sciencedirect.com/science/article/pii/S0264410X23014226
DNA vaccine with A/gyrfalcon(2.3.4.4c) showed good protection in chickens infected with 2.3.4.4b 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
https://www.biorxiv.org/content/10.1101/2024.02.12.579928v1.abstract
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
https://wwwnc.cdc.gov/eid/article/30/3/23-1098_article
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
https://www.mdpi.com/1999-4915/16/2/285
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
https://www.tandfonline.com/doi/full/10.1080/03079457.2024.2317430
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
https://www.rspb.org.uk/birds-and-wildlife/seabird-surveys-project-report
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
https://www.nature.com/articles/s41467-024-45462-1
Great to see this published. How 2.3.4.4b 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
https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00409-3/fulltext
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
https://www.nature.com/articles/s41598-024-53550-x
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
https://www.sciencedirect.com/science/article/pii/S2589914723000464
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 2.3.4.4 highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji-Nguru wetland, Nigeria 2022
https://onlinelibrary.wiley.com/doi/10.1111/irv.13254
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. 2.3.4.4b, but different from HPAI in Nigerian poultry in 2021.

Recombinant parainfluenza virus 5 expressing clade 2.3.4.4b H5 hemagglutinin protein confers broad protection against H5Ny influenza viruses
https://journals.asm.org/doi/10.1128/jvi.01129-23
Interrogation of potential HPAI vaccine – parainfluenza virus 5 -based vaccine candidate expressing 2.3.4.4b 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 2.3.4.4b virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022
https://journals.asm.org/doi/10.1128/spectrum.03736-23
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 2.3.4.4b Virus, Brazil, 2023
https://wwwnc.cdc.gov/eid/article/30/3/23-1157_article
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
https://www.sciencedirect.com/science/article/abs/pii/S0042682224000163
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
https://www.mdpi.com/2076-393X/12/2/143
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 2.3.4.4 detected in Samara Oblast, Russian Federation
https://www.frontiersin.org/articles/10.3389/fvets.2024.1244430/full
Good to see some data from Russia, an important breeding area for migratory birds across Eurasia and Africa. A 2.3.4.4b 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
https://www.imrpress.com/journal/FBL/29/2/10.31083/j.fbl2902061/htm
Bivalent peptide vaccines containing H5 cleavage sites of viruses from both 2.3.4.4 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
https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/sp.efsa.2024.EN-8629

Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic
https://www.mdpi.com/1999-4915/16/2/221
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
https://www.science.org/doi/full/10.1126/sciadv.adj4163
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
https://www.mdpi.com/1999-4915/16/2/207
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 2.3.2.1c from domestic poultry in China
https://essopenarchive.org/doi/full/10.22541/au.170665082.26537579
Detection of clade 2.3.2.1 H5N6 virus in China, against expectation of 2.3.4.4. Result of complex pattern of reassortment among clade 2.3.2.1 and clade 2.3.4.4 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
https://www.biorxiv.org/content/10.1101/2024.01.29.577768v1.abstract
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
https://www.authorea.com/users/470420/articles/712817-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 2.3.4.4b in great skuas in Great Britain
https://www.techrxiv.org/doi/full/10.22541/au.170670066.67459333
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
https://www.woah.org/en/document/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
https://www.biorxiv.org/content/10.1101/2024.01.11.574333v1

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
https://www.researchgate.net/publication/377366536_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/references

“Smart markets”: harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets
https://journals.asm.org/doi/epub/10.1128/jvi.01683-23

Veterinarians’ knowledge and experience of avian influenza and perspectives on control measures in the UK
https://bvajournals.onlinelibrary.wiley.com/doi/10.1002/vetr.3713

Genetic properties and pathogenicity of a novel reassortant H10N5 influenza virus from wild birds
https://link.springer.com/article/10.1007/s00705-017-3234-3

Transmission dynamics and pathogenesis differ between pheasants and partridges infected with clade 2.3.4.4b H5N8 and H5N1 high-pathogenicity avian influenza viruses
https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001946

Complete Genome Sequence of an H10N5 Avian Influenza Virus Isolated from Pigs in Central China
https://journals.asm.org/doi/10.1128/jvi.02687-12

New Patterns for Highly Pathogenic Avian Influenza and Adjustment of Prevention, Control and Surveillance Strategies: The Example of France
https://www.mdpi.com/1999-4915/16/1/101

Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats
https://journals.asm.org/doi/10.1128/aem.00842-23

Markets as drivers of selection for highly virulent poultry pathogens
https://www.nature.com/articles/s41467-024-44777-3

Molecular evolution of avian influenza A (H9N2) virus in external environment in Anhui, 2019-2021
http://www.jbjc.org/cn/article/doi/10.3784/jbjc.202303150100

Public Health Implications of Antimicrobial Resistance in Wildlife at the One Health Interface
https://www.mdpi.com/2673-9992/25/1/1

Differing Expression and Potential Immunological Role of C-Type Lectin Receptors of Two Different Chicken Breeds against Low Pathogenic H9N2 Avian Influenza Virus
https://www.mdpi.com/2076-0817/13/1/95

Detection of Influenza A viruses and Avian H5 Subtype using a triplex qRT-PCR assay on the ABI Quantstudio 7 PCR system
https://www.protocols.io/view/detection-of-influenza-a-viruses-and-avian-h5-subt-crdjv24n.html

Multifaceted analysis of temporal and spatial distribution and risk factors of global poultry HPAI-H5N1, 2005-2023
https://www.sciencedirect.com/science/article/pii/S1751731124000168

Farm biosecurity practices affecting avian influenza virus circulation in commercial chicken farms in Bangladesh
https://www.sciencedirect.com/science/article/pii/S2352771424000077

Genetic Analysis of H5N1 High-Pathogenicity Avian Influenza Virus following a Mass Mortality Event in Wild Geese on the Solway Firth
https://www.mdpi.com/2076-0817/13/1/83

Avian influenza virus cross-infections as test case for pandemic preparedness: From epidemiological hazard models to sequence-based early viral warning systems
https://ami-journals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.14389

Emergence of a triple reassortment avian influenza virus (A/H5N6) from wild birds
https://www.journalofinfection.com/article/S0163-4453(24)00024-0/fulltext

Differential Protection of Chickens against Highly Pathogenic H5 Avian Influenza Virus Using Polybasic Amino Acids with H5 Cleavage Peptide
https://www.imrpress.com/journal/FBL/29/1/10.31083/j.fbl2901011/htm

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland
https://www.biorxiv.org/content/10.1101/2024.01.17.575746v1.abstract

Transboundary Determinants of Avian Zoonotic Infectious Diseases: Challenges for Strengthening Research Capacity and Connecting Surveillance Networks
https://www.frontiersin.org/articles/10.3389/fmicb.2024.1341842/abstract

The risks and consequences of a high pathogenicity avian influenza outbreak in Aotearoa New Zealand
https://www.tandfonline.com/doi/full/10.1080/00480169.2023.2294915

A Comprehensive Analysis of H5N1 Evolution: Phylogenetic Insights and Emerging Mutations in Turkey’s Avian Influenza Landscape
https://www.researchsquare.com/article/rs-3831007/v1

Running the gauntlet; flyway-wide patterns of pollutant exposure in blood of migratory shorebirds
https://www.sciencedirect.com/science/article/abs/pii/S0013935124000276

Lesions and viral antigen distribution in bald eagles, red-tailed hawks, and great horned owls naturally infected with H5N1 clade 2.3.4.4b highly pathogenic avian influenza virus
https://journals.sagepub.com/doi/abs/10.1177/03009858231222227

A case-control study of the infection risk of H5N8 highly pathogenic avian influenza in Japan during the winter of 2020–2021
https://www.sciencedirect.com/science/article/abs/pii/S0034528824000158

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022
https://www.biorxiv.org/content/10.1101/2024.01.05.574233v1.abstract

Efficacy of an inactivated influenza vaccine adjuvanted with Toll-like receptor ligands against transmission of H9N2 avian influenza virus in chickens
https://www.sciencedirect.com/science/article/abs/pii/S0165242724000011

Simultaneous Differential Detection of H5, H7, H9 and Nine NA Subtypes of Avian Influenza Viruses via a GeXP Assay
https://www.mdpi.com/2076-2607/12/1/143

Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea, 2022-2023.
https://europepmc.org/article/med/38215495

HA N193D substitution in the HPAI H5N1 virus alters receptor binding affinity and enhances virulence in mammalian hosts
https://www.tandfonline.com/doi/full/10.1080/22221751.2024.2302854

Catastrophic mortality of southern elephant seals caused by H5N1 avian influenza
https://doi.org/10.1111/mms

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022
https://www.biorxiv.org/content/10.1101/2024.01.05.574233v1

Evolution and biological characteristics of the circulated H8N4 avian influenza viruses
https://www.sciencedirect.com/science/article/pii/S209531192300480X

Meta-analysis of RNA Seq Datasets in Duck Lungs Infected with Highly Pathogenic Avian Influenza Viruses
https://www.indianjournals.com/ijor.aspx?target=ijor:jar&volume=13&issue=4&article=004

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
https://link.springer.com/article/10.1186/s12864-023-09908-y

Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck 
https://academic.oup.com/glycob/advance-article/doi/10.1093/glycob/cwad098/7486526

Mortality in Sea Lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil, October 2023: Whole genome sequencing and phylogenetic analysis
https://www.researchsquare.com/article/rs-3793926/v1

Avian Influenza A(H5N1) Neuraminidase Inhibition Antibodies in Healthy Adults after Exposure to Influenza A(H1N1)pdm09
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10756388/

Neu5Gc binding loss of subtype H7 influenza A virus facilitates adaptation to gallinaceous poultry following transmission from waterbirds but restricts spillback
https://www.biorxiv.org/content/10.1101/2024.01.02.573990v1.abstract

H5N1 avian influenza virus PB2 antagonizes duck IFN-β signaling pathway by targeting mitochondrial antiviral signaling protein
https://www.sciencedirect.com/science/article/pii/S2095311923004872

The role of PB1-F2 in adaptation of high pathogenicity avian influenza virus H7N7 in chickens
https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-023-01257-8

Identification of specific neutralising antibodies for highly pathogenic avian influenza H5 2.3.4.4b clades to facilitate vaccine design and therapeutics
https://www.tandfonline.com/doi/full/10.1080/22221751.2024.2302106

Human behaviors driving disease emergence
https://onlinelibrary.wiley.com/doi/epdf/10.1002/evan.22015

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
https://academic.oup.com/glycob/advance-article/doi/10.1093/glycob/cwad098/7486526

Highly pathogenic H5n1 avian influenza in free-living griffon vultures
https://digital.csic.es/handle/10261/341041

Trends and Spatiotemporal Patterns of Avian Influenza Outbreaks in Italy: A Data-Driven Approach
https://www.mdpi.com/2036-7449/16/1/1

Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus
https://www.biorxiv.org/content/10.1101/2023.12.20.572711v1

Avian influenza overview September–December 2023
https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2023.8539

Antigenic Architecture of the H7N2 Influenza Virus Hemagglutinin Belonging to the North American Lineage
https://www.researchgate.net/publication/376802173_Antigenic_Architecture_of_the_H7N2_Influenza_Virus_Hemagglutinin_Belonging_to_the_North_American_Lineage/references

Highly pathogenic avian influenza virus H5N1 infection in skua and gulls in the United Kingdom, 2022
https://journals.sagepub.com/doi/10.1177/03009858231217224

The risk of highly pathogenic avian influenza in the Southern Ocean: a practical guide for operators and scientists interacting with wildlife
https://www.cambridge.org/core/journals/antarctic-science/article/risk-of-highly-pathogenic-avian-influenza-in-the-southern-ocean-a-practical-guide-for-operators-and-scientists-interacting-with-wildlife/6AC82C37924D61552C96D3BF61510F5A

Continued expansion of high pathogenicity avian influenza H5 in wildlife in South America and incursion into the Antarctic region
https://www.offlu.org/wp-content/uploads/2023/12/OFFLU-wildlife-statement-no.-II.pdf

Active surveillance for influenza virus and coronavirus infection in Antarctic birds and mammals in environmental fecal samples, South Shetland Islands
https://www.scielo.br/j/aabc/a/SBM8z7V9VhkrrCtV3tQpt4F/?lang=en

Detection and Phylogenetic Analysis of Contemporary H14N2 Avian Influenza A Virus in Domestic Ducks in Southeast Asia (Cambodia) 
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2297552

Environmental Surveillance and Detection of Infectious Highly Pathogenic Avian Influenza Virus in Iowa Wetlands 
https://pubs.acs.org/doi/10.1021/acs.estlett.3c00668

A naturally occurring HA-stabilizing amino acid (HA1-Y17) in an A(H9N2) low-pathogenic influenza virus contributes to airborne transmission 
https://journals.asm.org/doi/10.1128/mbio.02957-23

Development and application of a triplex real-time PCR assay for the detection of H3, H4, and H5 subtypes of avian influenza virus 
https://www.sciencedirect.com/science/article/pii/S0032579123008532

Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice 
https://www.sciencedirect.com/science/article/pii/S1995820X23001554

Efficacy of recombinant H5 vaccines delivered in ovo or day of age in commercial broilers against the 2015 U.S. H5N2 clade 2.3.4.4c highly pathogenic avian Influenza virus 
https://virologyj.biomedcentral.com/articles/10.1186/s12985-023-02254-1

Highly pathogenic avian influenza H5N1 virus infection of companion animals
https://www.tandfonline.com/doi/full/10.1080/21505594.2023.2289780

Virulence and transmission characteristics of clade 2.3.4.4b H5N6 subtype avian influenza viruses possessing different internal gene constellations
https://www.tandfonline.com/doi/full/10.1080/21505594.2023.2250065

Characterization of Highly Pathogenic Avian Influenza A (H5N1) Viruses isolated from Cats in South Korea, 2023
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2290835

Low Pathogenic Avian Influenza H9N2 Viruses in Morocco: Antigenic and Molecular Evolution from 2021 to 2023
https://www.mdpi.com/1999-4915/15/12/2355

Genetically Related Avian Influenza H7N9 Viruses Exhibit Different Pathogenicity in Mice
https://www.mdpi.com/2076-2615/13/23/3680

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
https://www.mdpi.com/1999-4915/15/12/2374

Highly pathogenic avian influenza: Unprecedented outbreaks in Canadian wildlife and domestic poultry
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10697099/

Highly Pathogenic Avian Influenza and its Complex Patterns of Reassortment
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4655071

Responding to avian influenza A H5N1 detection on a hospital property in Maine—An interdisciplinary approach
https://onlinelibrary.wiley.com/doi/full/10.1111/zph.13097

Author response: Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation
https://folia.unifr.ch/global/documents/282060

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
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1309156/abstract

Mapping genetic markers associated with antigenicity and host range in H9N2 Influenza A viruses infecting poultry in Pakistan 
https://doi.org/10.1637/aviandiseases-D-23-00029

Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021/2022
https://www.biorxiv.org/content/10.1101/2023.11.23.565566v1.abstract

Detection of Clade 2.3.4.4 Highly Pathogenic Avian Influenza H5 Viruses in Healthy Wild Birds in the Hadeji-Nguru Wetland, Nigeria, 2022
https://www.authorea.com/doi/full/10.22541/au.170055188.85169956

Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species
https://journals.asm.org/doi/10.1128/mbio.02649-23

Baloxavir marboxil use for critical human infection of avian influenza A H5N6 virus
https://www.cell.com/med/fulltext/S2666-6340(23)00361-6

H7 influenza A viruses bind sialyl-LewisX, a potential intermediate receptor between species
https://www.biorxiv.org/content/10.1101/2023.12.15.571923v1

Connectivity of marine predators over the Patagonian Shelf during the highly pathogenic avian influenza (HPAI) outbreak
https://www.biorxiv.org/content/10.1101/2023.12.12.570574v1

A broad antibody class engages the influenza virus hemagglutinin head at its stem interface
https://www.biorxiv.org/content/10.1101/2023.12.13.571543v1

Rapid detection of H5 subtype avian influenza virus using CRISPR Cas13a based-lateral flow dipstick
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1283210/full

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
https://www.sciencedirect.com/science/article/pii/S0042682223002738

Low Pathogenic Avian Influenza H9N2 Viruses in Morocco: Antigenic and Molecular Evolution from 2021 to 2023
https://www.mdpi.com/1999-4915/15/12/2355

Effect of 2020–21 and 2021–22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands
https://wwwnc.cdc.gov/eid/article/30/1/23-0970_article

Native and invasive bird interactions increase the spread of Newcastle disease in urban environments
https://link.springer.com/article/10.1007/s10530-023-03213-1

Epidemiological Disclosing and Molecular Subtyping for the Highly Pathogenic Avian Influenza Viruses H5N8 in Commercial Broilers and Layer Chickens in some Egyptian Governorates
https://ejvs.journals.ekb.eg/article_329440.html

Utility of Feathers for Avian Influenza Virus Detection in Commercial Poultry
https://www.mdpi.com/2076-0817/12/12/1425

Effect of avian influenza scare on transmission of zoonotic avian influenza: A case study of influenza A (H7N9)
https://www.sciencedirect.com/science/article/abs/pii/S0025556423001657

Highly pathogenic avian influenza H5N1 virus infection of companion animals
https://www.tandfonline.com/doi/full/10.1080/21505594.2023.2289780

Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies
https://link.springer.com/article/10.1007/s10393-023-01659-2

Different routes of infection of H5N1 lead to changes in infecting time
https://www.sciencedirect.com/science/article/abs/pii/S0025556423001694

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
https://www.medrxiv.org/content/10.1101/2023.12.13.23298992v1

Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice
https://www.sciencedirect.com/science/article/pii/S1995820X23001554

Pigs are highly susceptible to but do not transmit mink-derived highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b
https://www.biorxiv.org/content/10.1101/2023.12.13.571575v1.abstract

Efficacy of recombinant H5 vaccines delivered in ovo or day of age in commercial broilers against the 2015 U.S. H5N2 clade 2.3.4.4c highly pathogenic avian Influenza virus
https://virologyj.biomedcentral.com/articles/10.1186/s12985-023-02254-1

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America
https://www.biorxiv.org/content/10.1101/2023.12.14.571746v1.abstract

Annual report on surveillance for avian influenza in poultry and wild birds in Member States of the European Union in 2022
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10719745/

Has avian influenza virus H9 originated from a bat source?
https://www.frontiersin.org/articles/10.3389/fvets.2023.1332886/abstract

Unraveling molecular basis for reduced neuraminidase inhibitors susceptibility in highly pathogenic avian influenza A (H5N1) viruses isolated from chickens in India
https://www.biorxiv.org/content/10.1101/2023.12.15.571865v1.abstract

Survey of exposure to stranded dolphins in Japan to investigate an outbreak of suspected infection with highly pathogenic avian influenza (H5N1) clade 2.3.4.4(b) in humans
https://www.sciencedirect.com/science/article/pii/S2052297523001336

Identification of Pre-Emptive Biosecurity Zone Areas for Highly Pathogenic Avian Influenza Based on Machine Learning-Driven Risk Analysis
https://www.mdpi.com/2076-2615/13/23/3728
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
https://www.mdpi.com/2076-2615/13/23/3680
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1286758/abstract
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
https://wwwnc.cdc.gov/eid/article/30/1/23-0970_article
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
https://vetsci.org/pdf/10.4142/jvs.23141
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
https://www.biorxiv.org/content/10.1101/2023.11.23.568045v1
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 2.3.4.4b Wild Bird Virus Compared to Two Previous H5N8 Clade 2.3.4.4 Viruses
https://www.mdpi.com/1999-4915/15/11/2273
In comparing 2.3.4.4b H5N1 to previous 2.3.4.4 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
https://www.sciencedirect.com/science/article/pii/S2352771423001751
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
https://www.biorxiv.org/content/10.1101/2023.11.16.567398v1.abstract
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
https://www.biorxiv.org/content/10.1101/2023.11.23.565566v1.full.pdf
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 2.3.4.4b Highly Pathogenic Avian Influenza Virus Isolated in Japan in the 2022–2023 Season Using Classical Serological and Molecular Methods
https://www.mdpi.com/1999-4915/15/11/2274
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
https://www.researchsquare.com/article/rs-3606932/v1
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
https://www.preprints.org/manuscript/202211.0545/v1
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
https://journals.asm.org/doi/10.1128/spectrum.03055-23
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
https://www.sciencedirect.com/science/article/pii/S0032579123007496
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
https://journals.asm.org/doi/10.1128/spectrum.02059-23
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
https://doi.org/10.1675/063.046.0113
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2287682
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2287683
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 2.3.4.4b Infections in Wild Terrestrial Mammals, United States, 2022
https://wwwnc.cdc.gov/eid/article/29/12/23-0464_article
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
https://wwwnc.cdc.gov/eid/article/29/12/23-0938_article
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
https://wwwnc.cdc.gov/eid/article/29/12/23-0505_article
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2284301
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
https://pubs.acs.org/doi/full/10.1021/acs.estlett.3c00668
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 2.3.4.4b H5N1 high pathogenicity viruses in chickens
https://link.springer.com/article/10.1007/s11259-023-10258-z
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 2.3.2.1 hemagglutinin gene
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2284294
HPAI 2.3.2.1 viruses in China, 2017-2020. Subclades 2.3.2.1a to 2.3.2.1f 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
https://www.biorxiv.org/content/10.1101/2023.11.10.566573v1.abstract
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 2.3.4.4b) in Germany
https://www.biorxiv.org/content/10.1101/2023.11.19.567176v1
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
https://www.sciencedirect.com/science/article/pii/S037811352300264X
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 2.3.4.4b virus in Bosnia and Herzegovina
https://www.frontiersin.org/articles/10.3389/fvets.2023.1255213/full
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
https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01421-3
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 2.3.4.4 Hemagglutinin Gene
https://www.mdpi.com/1999-4915/15/11/2249
Amino acid changes at position 120, 126, 141, 156, 185, or 189 (H5 numbering) may be important in antigenic changes within 2.3.4.4. 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
https://journals.uct.ac.za/index.php/ABB/article/view/v3_7/v3_7
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
https://www.mdpi.com/1999-4915/15/11/2214
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
https://www.sciencedirect.com/science/article/pii/S0042682223002453
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
https://www.sciencedirect.com/science/article/pii/S2095311923003702
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 2.3.4.4 H5 chimeric cold-adapted attenuated influenza vaccines induced cross-reactive protection in mice and ferrets
https://journals.asm.org/doi/epub/10.1128/jvi.01101-23
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 2.3.4.4b in 2020.
https://jglobalbiosecurity.com/articles/10.31646/gbio.218
Summary of human cases.

Molecular detection and characterization of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses among hunter-harvested wild birds provides evidence for three independent introductions into Alaska
https://www.sciencedirect.com/science/article/pii/S004268222300257X
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
https://www.sciencedirect.com/science/article/pii/S2095311923003908
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
https://www.biorxiv.org/content/10.1101/2023.11.08.565892v1.full.pdf
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
https://www.researchgate.net/profile/Mohamed-Amer-49/publication/375520037_Molecular_diagnosis_and_identification_of_avian_influenza_H5N8_in_Pekin_ducks_Molekulare_Diagnose_und_Identifizierung_der_Geflugelpest_H5N8_bei_Peking-Enten/links/654d4ac7b1398a779d747411/Molecular-diagnosis-and-identification-of-avian-influenza-H5N8-in-Pekin-ducks-Molekulare-Diagnose-und-Identifizierung-der-Gefluegelpest-H5N8-bei-Peking-Enten.pdf
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
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4611782
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
https://wwwnc.cdc.gov/eid/article/29/12/23-0192_article
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
https://www.sciencedirect.com/science/article/pii/S0032579123007496
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
https://wwwnc.cdc.gov/eid/article/29/12/23-0330_article#:~:text=In%20May%202022%2C%20we%20observed,b%20virus.
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
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1283210/abstract
full article isn’t available yet.

Serological exposure to influenza A in cats from an area with wild birds positive for avian influenza
https://onlinelibrary.wiley.com/doi/abs/10.1111/zph.13085
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 2.3.4.4b from Geese in Northeastern China
https://journals.asm.org/doi/10.1128/aem.01572-22
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 2.3.4.4b virus.

High pathogenicity avian influenza (H5N1) in Northern Gannets (Morus bassanus): Global spread, clinical signs and demographic consequences
https://onlinelibrary.wiley.com/doi/10.1111/ibi.13275
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
https://www.preprints.org/manuscript/202310.1557/v1
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
https://www.nature.com/articles/s41467-023-42738-w

High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020–2022
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2270068
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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.42.2300526
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
https://onlinelibrary.wiley.com/doi/10.1111/irv.13208
Five mammals tested positive for clade 2.3.4.4b 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
https://www.nature.com/articles/s41586-023-06631-2
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
https://journals.asm.org/doi/10.1128/jvi.00906-23
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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.41.2200871
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011685
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
https://www.nature.com/articles/s41467-023-41476-3
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
https://journals.asm.org/doi/10.1128/spectrum.02186-23
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
https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/j.efsa.2023.8328
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)
https://journals.asm.org/doi/10.1128/jvi.00743-23
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
https://rs.yiigle.com/cmaid/1474489
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
https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-023-01204-7
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 2.3.4.4b virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022
https://www.biorxiv.org/content/10.1101/2023.10.19.563114v1?rss=1&s=03
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
https://www.biomedcentral.com/epdf/10.1186/s13567-023-01219-0
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
https://link.springer.com/referenceworkentry/10.1007/978-3-031-27164-9_18
hefty book chapter. 

Prevention of zoonotic spillover: From relying on response to reducing the risk at source
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011504

No evidence for highly pathogenic avian influenza virus H5N1 (clade 2.3.4.4b) in the Antarctic region during the austral summer 2022/23
https://www.biorxiv.org/content/10.1101/2023.10.24.563692v1.full.pdf
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
https://jsmcah.org/index.php/jasv/article/view/61/59
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
https://www.biorxiv.org/content/10.1101/2023.10.03.558847v1.abstract

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
https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2023.8271
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
https://www.sciencedirect.com/science/article/pii/S2352771423001635
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
https://www.sciencedirect.com/science/article/abs/pii/S0163445323005339
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
https://academic.oup.com/jtm/advance-article/doi/10.1093/jtm/taad130/7295310
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 2.3.4.4b H5N1 mink influenza viruses
https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00393-6/fulltext
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
https://link.springer.com/article/10.1007/s10393-023-01649-4
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
https://link.springer.com/article/10.1186/s13567-023-01221-6
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
https://www.mdpi.com/2076-2607/11/10/2601
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
https://www.mdpi.com/2073-4425/14/10/1973
Distinct characteristics of the Malaysian LPAI H5N2, compared to HPAI H5N2 or H5N1 from ducks or chickens

Many potential pathways to future pandemic influenza
https://www.science.org/doi/10.1126/scitranslmed.adj2379
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
https://www.mdpi.com/2076-393X/11/11/1628
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
https://www.biorxiv.org/content/10.1101/2023.09.30.560331v1
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
https://doi.org/10.1093/infdis/jiad418
Phenotypic testing of 2.3.2.1a and 2.3.4.4b 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
https://www.sciencedirect.com/science/article/pii/S128645792300134X
Over-expression of the interferon-stimulated gene IFITM3 protects chicks from HPAI clade 2.2.1.2. Is the future virus-resistant chickens?

Modeling long-distance airborne transmission of highly pathogenic avian influenza carried by dust particles
https://www.nature.com/articles/s41598-023-42897-2

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
https://wwwnc.cdc.gov/eid/article/29/10/23-0536_article
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
https://www.science.org/content/article/changing-bird-migrations-threaten-bring-new-infectious-diseases-humans

HPAI reports in waders from IWSG2023
https://x.com/ScottoftheMarsh/status/1708072283137298761?s=20

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
https://www.jstage.jst.go.jp/article/jvms/advpub/0/advpub_23-0121/_article/-char/ja/
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
https://journals.asm.org/doi/10.1128/mbio.00862-23
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.
https://www.tandfonline.com/doi/full/10.1080/01652176.2023.2265173
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
https://onlinelibrary.wiley.com/doi/10.1002/vms3.1281
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
https://www.science.org/content/article/deadly-avian-flu-reaches-galapagos-islands

Influenza A(H5N1) Virus Infections in 2 Free-Ranging Black Bears (Ursus americanus), Quebec, Canada
https://wwwnc.cdc.gov/eid/article/29/10/23-0548-f1
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 2.3.4.4b H5N8 and H5N1 high-pathogenicity avian influenza viruses
https://www.biorxiv.org/content/10.1101/2023.09.22.558959v1.abstract
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 2.3.4.4b Viruses in Grebes in Inner Mongolia and Ningxia, China, 2021
https://www.sciencedirect.com/science/article/pii/S209531192300326X
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
https://www.preprints.org/manuscript/202309.1224/v1
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
https://www.sciencedirect.com/science/article/pii/S0006320723003737
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 2.3.4.4b Virus in Wild Birds, Chile
https://wwwnc.cdc.gov/eid/article/29/9/23-0067_article
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?
https://www.mdpi.com/2076-0817/12/9/1183
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
https://onlinelibrary.wiley.com/doi/epdf/10.1111/ibi.13275
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
https://doi.org/10.1016/j.cell.2023.08.014
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1250952/full
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
https://www.nature.com/articles/s41598-023-42660-7
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
https://www.sciencedirect.com/science/article/pii/S0163445323005054
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
https://www.mdpi.com/1999-4915/15/9/1865
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1229008/full
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
https://www.mdpi.com/2076-2607/11/9/2263
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 2.3.4.4b)
https://www.mdpi.com/1999-4915/15/9/1909
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
https://www.sciencedirect.com/science/article/pii/S0006320723003701?dgcid=coauthor#f0005
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 2.3.4.4b into Uruguay
https://www.mdpi.com/1999-4915/15/9/1906
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
https://www.sciencedirect.com/science/article/pii/S0378113523002043
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2257810
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
https://journals.lww.com/ijmr/abstract/9900/spatio_temporal_distribution___seasonality_of.40.aspx
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
https://www.sciencedirect.com/science/article/pii/S0882401023003637
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
https://www.mdpi.com/1999-4915/15/9/1865
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
https://www.journalofinfection.com/article/S0163-4453(23)00505-4/fulltext
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
https://www.nature.com/articles/s41467-023-41182-0
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
https://www.sciencedirect.com/science/article/pii/S016622362300190X
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
https://www.sciencedirect.com/science/article/pii/S2589004223019077
Model for humans. 

Baloxavir marboxil use for critical human infection of avian influenza A H5N6 virus
https://www.medrxiv.org/content/10.1101/2023.09.03.23294799v1
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 2.3.4.4b highly pathogenic avian influenza A(H5N1) in carnivore pets, Italy, April 2023
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.35.2300441
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 2.3.4.4b H5N6 subtype avian influenza viruses possessing different internal gene constellations
https://www.tandfonline.com/doi/full/10.1080/21505594.2023.2250065
Genome constellations have differential outcomes of HPAI. 2.3.4.4b 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
https://doi.org/10.1016/j.cub.2023.07.061
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 2.3.4.4b H5N1 Viruses by Long Distance Migratory Birds from Northern Europe to Canada in 2022/2023
https://doi.org/10.3390/v15091836
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
https://rs.yiigle.com/cmaid/1175653
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
https://rs.yiigle.com/cmaid/1447498
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
https://rs.yiigle.com/cmaid/1257603
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?
https://www.sciencedirect.com/science/article/pii/S1201971223007063
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
https://www.nature.com/articles/s41564-023-01457-0
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?
https://www.science.org/doi/full/10.1126/science.adk4500

Key amino acid position 272 in neuraminidase determines the replication and virulence of H5N6 avian influenza virus in mammals
https://doi.org/10.1016/j.isci.2022.105693
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2251600
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
https://www.sciencedirect.com/science/article/pii/S0145305X23010741
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 2.3.4.4b) Vaccine against Co-Circulating Influenza A/H5Nx Viruses
https://www.mdpi.com/2076-393X/11/9/1397
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
https://www.preprints.org/manuscript/202308.1579/v1
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 2.3.4.4.b viruses implicated.

Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? 
https://doi.org/10.1093/femsre/fuad048
“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 2.3.4.4b H5N1 highly pathogenic avian influenza A viruses in Bangladesh
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2252510
Novel clade 2.3.4.4b 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
https://onlinelibrary.wiley.com/doi/full/10.1111/irv.13187
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
https://www.biorxiv.org/content/10.1101/2023.08.23.554491v1.full.pdf
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
https://www.cell.com/heliyon/pdf/S2405-8440(23)06419-8.pdf
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
https://onlinelibrary.wiley.com/doi/epdf/10.1111/ele.14294?saml_referrer
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

BAITING AND BANDING: EXPERT OPINION ON HOW BAIT TRAPPING MAY INFLUENCE THE OCCURRENCE OF HIGHLY PATHOGENIC AVIAN INFLUENZA (HPAI) AMONG DABBLING DUCKS
https://doi.org/10.7589/JWD-D-22-00163
no access ☹

Infection and tissue distribution of Highly Pathogenic Avian Influenza A type H5N1 (clade 2.3.4.4b) in Red Fox kits (Vulpes vulpes)
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2249554
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2022.2048971
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2022.2122584
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2249558
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
https://www.tandfonline.com/doi/abs/10.1080/03079457.2023.2239191
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
https://www.sciencedirect.com/science/article/pii/S0032579123004765
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
https://ncceh.ca/resources/evidence-briefs/avian-influenza-ah5n1-and-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
https://www.sciencedirect.com/science/article/pii/S0048969723049343
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
https://www.gov.scot/publications/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
https://www.nature.com/articles/s41559-023-02182-x
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
https://www.medrxiv.org/content/10.1101/2023.08.08.23293833v1
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
https://www.sciencedirect.com/science/article/pii/S003257912300531X
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
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciad462/7239858
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
https://www.biorxiv.org/content/10.1101/2023.08.08.549695v1.abstract
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1250952/abstract
ahead of print, no details yet.

Diagnostic Detection of H7N3 Low Pathogenicity Avian Influenza in a Commercial Game Bird Flock
https://doi.org/10.1637/aviandiseases-D-22-00055
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2246582
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
https://www.mdpi.com/2076-393X/11/8/1318
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
https://doi.org/10.1016/j.cimid.2023.102039
A duck is not a duck is not a duck. Differential disease outcomes when comparing Muscovy, Pekin and Mallard ducks infected with HPAI 2.3.4.4b 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
https://www.sciencedirect.com/science/article/pii/S0147957122001667?via%3Dihub
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
https://wwwnc.cdc.gov/eid/article/28/8/21-2241_article
Description of clade 2.3.4.4b HPAI H5N6 in China. These viruses havestrong immune-escape capacity and complex genetic reassortment, suggesting further transmission risk

H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021–April 2022
https://www.sciencedirect.com/science/article/pii/S0042682223001733?via%3Dihub
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
https://www.sciencedirect.com/science/article/pii/S0264410X23009222
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
https://www.mdpi.com/2076-2607/11/8/1961
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 2.3.4.4b virus in cats, Poland, June to July 2023
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.31.2300366
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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.31.2300390
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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.31.2300400
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2244091
Detailed work on the HPAI viruses [2.3.2.1c] 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
https://esajournals.onlinelibrary.wiley.com/doi/10.1002/eap.2906
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
https://www.mdpi.com/1999-4915/15/7/1547
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
https://www.mdpi.com/1999-4915/15/7/1596
Between 2018-2021 (prior to the start of the panzootic), 2.3.4.4g and 2.3.4.4h H5N6 dominated in live bird markets of Vietnam. In 2016-17, 2.3.2.1c also present.

Evolution of Prevalent H9N2 Subtype of Avian Influenza Virus during 2019-2022 for the Development of a Control Strategy in China
https://www.sciencedirect.com/science/article/pii/S0032579123004765
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 2.3.4.4b H5 High Pathogenicity Avian Influenza Virus in Ducks
https://www.biorxiv.org/content/10.1101/2023.07.26.550633v1.abstract
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
2.3.4.4.b 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
https://www.sciencedirect.com/science/article/pii/S0032579123004674
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 2.3.2.1 H5N1 high pathogenicity avian influenza virus: an experimental infection study
https://www.jstage.jst.go.jp/article/jvms/advpub/0/advpub_23-0122/_pdf/-char/en
Observations from previous outbreaks have suggested that diving ducks are hard hit when infected with HPAI. Experimental infections (with 2.3.2.1) confirm this, with higher titres and mortality in Tufted ducks compared to wigeons mallards and pintails.

Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, Chile
https://pubmed.ncbi.nlm.nih.gov/37487166/
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 2.3.4.4
https://meridian.allenpress.com/jwd/article-abstract/doi/10.7589/JWD-D-22-00161/494554/Mortality-in-Wild-Turkey-Meleagris-gallopavo?redirectedFrom=PDF
No access ☹

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh
https://www.frontiersin.org/articles/10.3389/fpubh.2023.1168613/full
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
https://www.hindawi.com/journals/tbed/2023/8834913/
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
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01609-8
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 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses isolated from birds and mammals in the United States, 2022
https://doi.org/10.1016/j.antiviral.2023.105679
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
https://www.science.org/doi/10.1126/sciadv.adg5175
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
https://europepmc.org/article/ppr/ppr694871
HPAI H5N6 causes numerous human cases in China. Comparison of 3 strains from birds shows 2.3.4.4h. 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
https://www.mdpi.com/1999-4915/14/9/1849
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
https://www.sciencedirect.com/science/article/pii/S0378113523001840
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
https://www.researchsquare.com/article/rs-3065313/v1
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
https://link.springer.com/article/10.1007/s10393-023-01643-w
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
https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-023-01183-9
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1229008/abstract
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
https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiad276/7226356
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
https://www.mdpi.com/2076-0817/12/7/952
Chemical inactivation works well. Heat does so, when done properly. Some SOPs provided also.

Avian Influenza: A Potential Threat to Human Health
https://link.springer.com/chapter/10.1007/978-981-99-2820-0_3
book chapter

Mink farming poses risks for future viral pandemics
https://www.pnas.org/doi/abs/10.1073/pnas.2303408120
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)
https://www.mdpi.com/2076-2615/13/14/2338
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1148615/full
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
https://www.sciencedirect.com/science/article/pii/S0166093423000988
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2184177
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!

SCIENTIFIC TASK FORCE ON AVIAN INFLUENZA AND WILD BIRDS STATEMENT – JULY 2023
https://www.cms.int/sites/default/files/publication/CMS-FAO-TF_avian_influenza_statement_July2023.pdf

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
https://journals.asm.org/doi/10.1128/msphere.00200-23
Also, the mammalian mutation D701N was positively selected for.

Highly pathogenic avian influenza A(H5N1) virus clade 2.3.4.4b in domestic ducks, Indonesia, 2022
https://www.biorxiv.org/content/10.1101/2023.07.10.548369v1.full.pdf
HPAI 2.3.4.4b 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
https://www.mdpi.com/2079-7737/12/7/969
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
https://rjab.journals.ekb.eg/article_306838_0.html
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
https://www.mdpi.com/2674-1164/2/3/26
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
https://www.biorxiv.org/content/10.1101/2023.06.30.547205v1.full.pdf
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011489
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
https://animal.law.harvard.edu/wp-content/uploads/Animal-Markets-and-Zoonotic-Disease-in-the-United-States.pdf
A report commissioned to understand the zoonotic risk from mass produced animals.

Summary of Influenza Risk Assessment Tool (IRAT) Results (4 July 2023)
https://www.cdc.gov/flu/pandemic-resources/monitoring/irat-virus-summaries.htm
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
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1211355/full
Since 2013 2.3.4.4h 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
https://onlinelibrary.wiley.com/doi/10.1002/jmv.28912
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
https://journals.asm.org/doi/epub/10.1128/spectrum.04776-22
Virus genomic data from the UK eloquently demonstrate the shift to 2.3.4.4b 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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2231561
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
https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2023.0090
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]
https://www.researchgate.net/publication/372051755_Vogelgriep_panzootie_leidt_tot_massastrandingen_van_Jan-van-genten_Morus_bassanus_in_Nederland_april-oktober_2022
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
https://journals.asm.org/doi/epub/10.1128/spectrum.02586-22
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
https://www.frontiersin.org/articles/10.3389/fvets.2023.1157984/full
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
https://www.mdpi.com/1999-4915/15/6/1387
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 2.3.4.4b Virus in Domestic Cat, France, 2022
https://wwwnc.cdc.gov/eid/article/29/8/23-0188_article
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
https://www.nature.com/articles/s41586-023-06261-8
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
https://www.bbc.com/news/uk-scotland-highlands-islands-66051875

Healthy adults possess cross-reactive neuraminidase inhibition antibodies to an A(H5N1) clade 2.3.4.4b avian influenza virus A/Black Faced Spoonbill/Hong Kong/AFCD-HKU-22-21429-01012/2022
https://www.medrxiv.org/content/10.1101/2023.06.23.23291839v1
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 2.3.4.4b in 2020
https://jglobalbiosecurity.com/articles/10.31646/gbio.218
List of 2.3.4.4b H5N1 cases. Doesn’t delineate bona fide infection from those “Environmental carriers”.

Influenza A in Shorebirds in the Tropical Landscape of Guatemala
https://doi.org/10.1675/063.045.0315
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
https://www.gov.uk/government/publications/hairs-risk-assessment-avian-influenza-ah5n1-in-non-avian-uk-wildlife/hairs-risk-assessment-avian-influenza-ah5n1-in-non-avian-uk-wildlife
Assessment of the risk of infection in the UK
Probability
General UK population: Very Low
The probability of infection would be considered Low for those exposed to infected live or dead non-avian wildlife.
Impact
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
Satisfactory.

Newly emerged genotypes of highly pathogenic H5N8 avian influenza viruses in Kagoshima prefecture, Japan during winter 2020/21
https://doi.org/10.1099/jgv.0.001870
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 2.3.4.4b Introduced by Wild Birds, China, 2021
https://wwwnc.cdc.gov/eid/article/29/7/22-1149_article
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
https://www.mdpi.com/1999-4915/15/6/1403
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 2.3.4.4b
https://wwwnc.cdc.gov/eid/article/29/7/23-0296_article
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
https://doi.org/10.1080/20477724.2023.2228055
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
https://journals.sagepub.com/doi/epub/10.1177/10406387231182385
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
https://rupress.org/jem/article/220/8/e20230447/214173/Mammalian-infections-with-highly-pathogenic-avian
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 2.3.4.4 H5Nx highly pathogenic avian influenza viruses in chickens
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2218945
Comparative pathology of seven HPAI 2.3.4.4 lineages in chickens. Clade 2.3.4.4b 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
https://pubmed.ncbi.nlm.nih.gov/37310882/
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
https://journals.asm.org/doi/full/10.1128/spectrum.04351-22?af=R
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2225645
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
https://www.jstage.jst.go.jp/article/jvms/advpub/0/advpub_23-0124/_article
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 2.3.4.4b Clade Virus
https://www.mdpi.com/2076-2607/11/5/1162
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 2.3.4.4) High-Pathogenicity Avian Influenza Outbreaks in the United Kingdom
https://www.mdpi.com/1999-4915/15/6/1344
APHA have published a new qPCR based assay for confirmation of HPAI.

The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022
https://www.mdpi.com/1999-4915/15/6/1383
Great summary of HPAI in Southern Africa since 2021. clade 2.3.4.4B 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
https://www.mdpi.com/1660-4601/20/11/6030
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
https://www.nature.com/articles/s41467-023-38415-7
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
https://rr-europe.woah.org/en/Events/the-first-meeting-of-the-sge-hpai/
> Conclusions and recommendations (draft)
https://rr-europe.woah.org/wp-content/uploads/2023/05/09_draft-recommendations_sge-hpai-1st-meeting_v02.pdf
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
https://www.nature.com/articles/d41586-023-01760-0
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
https://www.ecdc.europa.eu/sites/default/files/documents/Avian-influenza-overview-March-April-2023_0.pdf
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
https://www.biorxiv.org/content/10.1101/2023.05.12.540493v1.full.pdf
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
https://www.biorxiv.org/content/10.1101/2023.05.12.540367v1.full.pdf
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 2.3.4.4b into South America
https://doi.org/10.1016/j.tmaid.2023.102591
More evidence of at least 4 incursions into South America.

Novel Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea
https://wwwnc.cdc.gov/eid/article/29/7/22-1893_article
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
https://www.preprints.org/manuscript/202305.1027/v1
Between 2021-22, 467 outbreaks of HPAI detected in Nigeria. Widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses detected in Europe since late 2020. Detection of reassortant with H9N2.

Novel Avian Influenza Virus (H5N1) Clade 2.3.4.4b Reassortants in Migratory Birds, China
https://wwwnc.cdc.gov/eid/article/29/6/22-1723_article
HPAI viruses from swans in China in 2021 fall into 2.3.4.4b2 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
https://www.researchsquare.com/article/rs-2948767/v1
Tracking of HPAI in Egypt from 2006-2017 demonstrates 6 waves through poultry. Includes clade 2.2.1.1a, 2.2.1.2. 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
https://repo.niv.ns.ac.rs/xmlui/handle/123456789/614
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
https://www.nature.com/articles/s41598-023-35365-4
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
https://www.biorxiv.org/content/10.1101/2023.05.15.538689v1.full.pdf
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
https://journals.asm.org/doi/full/10.1128/spectrum.04946-22
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 2.3.4.4b avian influenza viruses
https://www.biorxiv.org/content/10.1101/2023.05.14.540682v1.full.pdf
Rapid detection of HPAI with LAMP. “specific detection of HPAIV H5Nx clade 2.3.4.4b within 30 minutes with a sensitivity of 86.11%” .

Avian influenza, new aspects of an old threat
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.19.2300227?crawler=true
“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
https://www.nature.com/articles/s41598-023-33814-8
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 2.3.2.1.a (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
https://www.researchsquare.com/article/rs-2944417/v1
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
https://www.sciencedirect.com/science/article/pii/S0163445323002967
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
https://www.biorxiv.org/content/10.1101/2023.05.22.541648v1.full.pdf
Seasonal bird migration can explain salient features of the global dispersal of 2.3.4.4. – 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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2214255
“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).
https://www.biorxiv.org/content/10.1101/2023.05.18.541344v1.full.pdf
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
https://www.researchsquare.com/article/rs-2937503/v1
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
https://www.biorxiv.org/content/10.1101/2023.05.01.538918v1
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
https://www.preprints.org/manuscript/202305.0199/v1
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 2.3.4.4b in highly diverse wild bird species from Peru
https://www.researchsquare.com/article/rs-2814674/v1
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 2.3.4.4b H5 highly pathogenic avian influenza virus
https://www.biorxiv.org/content/10.1101/2023.04.30.538854v1.full.pdf
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
https://www.biorxiv.org/content/10.1101/2023.05.02.539182v1

Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203411/pdf/fgene-14-1172048.pdf
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
https://www.authorea.com/users/607294/articles/636040-hpaiv-outbreak-triggers-long-distance-movements-in-breeding-northern-gannets-implications-for-disease-spread?commit=554c9f0238d40f35cddaddcf16dce1ed97f98543

Environmental Samples Test Negative for Avian Influenza Virus H5N1 Four Months after Mass Mortality at A Seabird Colony
https://www.mdpi.com/2076-0817/12/4/584
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
https://elifesciences.org/articles/86051
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 2.3.4.4b) Strain Isolated from a Pelican in Peru
https://journals.asm.org/doi/10.1128/mra.00199-23
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
https://www.sciencedirect.com/science/article/pii/S0378113523001128
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
https://www.mdpi.com/1999-4915/15/5/1093
# 2344f. 2344g and 2321c

Potential Effects of Habitat Change on Migratory Bird Movements and Avian Influenza Transmission in the East Asian-Australasian Flyway
https://www.mdpi.com/1424-2818/15/5/601
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 2.3.4.4b Clade Virus
https://www.mdpi.com/2076-2607/11/5/1162
Pigs reared on same property as infected birds showed extensive seroconversion to 2.3.4.4b: 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 2.3.4.4b avian influenza in ferrets
https://www.researchsquare.com/article/rs-2842567/v1
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
https://wwwnc.cdc.gov/eid/article/29/6/22-1680_article
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
https://wwwnc.cdc.gov/eid/article/29/6/23-0103_article
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
https://doi.org/10.1016/j.jinf.2023.04.007
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
https://www.biorxiv.org/content/10.1101/2023.04.24.538139v1.full.pdf
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 2.3.4.4b
https://doi.org/10.1016/j.ijid.2023.04.403
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
https://wwwnc.cdc.gov/eid/article/29/3/22-1079_article

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
https://wwwnc.cdc.gov/eid/article/29/6/22-1786_article

Human Infection with highly pathogenic avian influenza A(H5N1) virus in Chile
https://www.cdc.gov/flu/avianflu/spotlights/2022-2023/chile-first-case-h5n1-addendum.htm
## 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
https://www.nature.scot/doc/naturescot-scientific-advisory-committee-sub-group-avian-influenza-report-h5n1-outbreak-wild-birds

Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human–live bird market interface in China
https://www.pnas.org/doi/10.1073/pnas.2215610120

Efficacy of multivalent recombinant herpesvirus of turkey vaccines against high pathogenicity avian influenza, infectious bursal disease, and Newcastle disease viruses
https://www.sciencedirect.com/science/article/pii/S0264410X23003493

Emergence and rapid dissemination of highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b in wild birds, Chile
https://www.biorxiv.org/content/10.1101/2023.04.07.535949v1

Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b
https://pubmed.ncbi.nlm.nih.gov/37014781/

Targeted genomic sequencing of avian influenza viruses in wetlands sediment from wild bird habitats
https://www.biorxiv.org/content/10.1101/2023.03.30.534984v1.abstract

The pathogenesis of a 2022 North American highly pathogenic clade 2.3.4.4b H5N1 avian influenza virus in mallards (Anas platyrhynchos)
https://www.tandfonline.com/doi/abs/10.1080/03079457.2023.2196258?journalCode=cavp20

Using integrated wildlife monitoring to prevent future pandemics through one health approach
https://www.sciencedirect.com/science/article/pii/S2352771422001112

41% of Pelicans in Peru now dead due to HPAI
https://www.actualidadambiental.pe/el-41-de-la-poblacion-de-pelicanos-ha-muerto-desde-el-inicio-de-la-gripe-aviar-en-peru/

Prevalence, evolution, replication and transmission of H3N8 avian influenza viruses isolated from migratory birds in eastern China from 2017 to 2021
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2184178
## highly relevant given the recent human case of avian H3

H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks
https://academic.oup.com/ve/article/9/1/vead014/7057897?login=false

Human influenza A virus H1N1 in marine mammals in California, 2019
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0283049

Gradual adaptation of animal influenza A viruses to human-type sialic acid receptors
https://www.sciencedirect.com/science/article/pii/S1879625723000147

The role of airborne particles in the epidemiology of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in commercial poultry production units
https://www.biorxiv.org/content/10.1101/2023.03.16.532935v1

Avian influenza H5N1 in a great white pelican (Pelecanus onocrotalus), Mauritania 2022
https://link.springer.com/article/10.1007/s11259-023-10100-6

Welcome on EURL Avian Flu Data Portal
https://eurlaidata.izsvenezie.it/

The changing dynamics of highly pathogenic avian influenza H5N1: Next steps for management & science in North America
https://doi.org/10.1016/j.biocon.2023.110041

Active wild bird surveillance of avian influenza viruses, a report
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2022.EN-7791
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
https://www.sciencedirect.com/science/article/abs/pii/S0042682223000764

Protective efficacy of a bivalent H5 influenza vaccine candidate against both clades 2.3.2.1 and 2.3.4.4 high pathogenic avian influenza viruses in SPF chickens
https://www.sciencedirect.com/science/article/pii/S0264410X23003110

How human ecology landscapes shape the circulation of H5N1 avian influenza: A case study in Indonesia
https://www.sciencedirect.com/science/article/pii/S2352771423000575

Highly pathogenic avian influenza (HPAI A H5N1) outbreak in Spain: its mitigation through the One Health approach – a short communication
https://journals.lww.com/annals-of-medicine-and-surgery/Abstract/9900/Highly_pathogenic_avian_influenza__HPAI_A_H5N1_.195.aspx

A protective measles virus-derived vaccine inducing long-lasting immune responses against influenza A virus H7N9
https://www.nature.com/articles/s41541-023-00643-9

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
https://www.mdpi.com/1999-4915/15/4/823

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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.7.2300085;jsessionid=YScPi6NkUoXrgPSFgxKwpMTyCSlRWt6lNkuGTx7q.i-0b3d9850f4681504f-ecdclive
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
https://journals.asm.org/doi/epub/10.1128/spectrum.01798-22

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
https://peerj.com/articles/14917/

Influenza A(H5N1) detection in two asymptomatic poultry farm workers in Spain, September to October 2022: suspected environmental contamination
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.8.2300107?TRACK=RSS

Letter to the Editor: Knowledge gap in assessing the risk of a human pandemic via mammals’ infection with highly pathogenic avian influenza A(H5N1)
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.9.2300134?crawler=true

Characterization of neurotropic HPAI H5N1 viruses with novel genome constellations and mammalian adaptive mutations in free-living mesocarnivores in Canada
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2186608

Infection of wild rats with H5N6 subtype highly pathogenic avian influenza virus in China
https://www.journalofinfection.com/article/S0163-4453(23)00136-6/fulltext

First case of human infection with highly pathogenic H5 avian influenza a virus in South America: a new zoonotic pandemic threat for 2023?
https://pubmed.ncbi.nlm.nih.gov/36881656/

Being ready for the next influenza pandemic?
https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00117-2/fulltext

Virological and Genetic Characterization of the Unusual Avian Influenza H14Nx Viruses in the Northern Asia
https://www.mdpi.com/1999-4915/15/3/734
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011214
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
https://www.sciencedirect.com/science/article/pii/S0163445323001366
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?
https://academic.oup.com/jtm/advance-article/doi/10.1093/jtm/taad032/7070564?login=false
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2186608
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
https://peerj.com/articles/14917/
Great to see some HPAI genomes from Indonesia, albeit lineage 2.3.2.1c, and not the same as 2.3.4.4b. Reassortment between 2.3.2.1c, and H3 virus, and an H5N1 Indonesian endemic virus

Characterization of an H7N9 Influenza Virus Isolated from Camels in Inner Mongolia, China
https://journals.asm.org/doi/epub/10.1128/spectrum.01798-22
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
https://www.mdpi.com/1999-4915/15/3/591
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 2.3.4.4b in wild terrestrial mammals in the United States in 2022
https://www.biorxiv.org/content/10.1101/2023.03.10.532068v1
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
https://www.sciencedirect.com/science/article/pii/S1567134823000217?via%3Dihub
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
https://www.bto.org/sites/default/files/publications/rr752_pearce-higgins_et_al_2023_hpai_workshop_final_web_0.pdf
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?
https://www.sciencenews.org/article/bird-flu-mammals-influenza-pandemic

Avian influenza spread and seabird movements between colonies
https://doi.org/10.1016/j.tree.2023.02.002
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
https://www.hindawi.com/journals/tbed/2023/2708458/
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
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.8.2300107#html_fulltext
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
https://www.mdpi.com/1999-4915/15/2/483
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
https://www.mdpi.com/1999-4915/15/1/3
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
https://www.biorxiv.org/content/10.1101/2023.02.17.528990v1
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
https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.4432
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
https://edepot.wur.nl/569551
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
https://www.frontiersin.org/articles/10.3389/fmicb.2022.1007350/full
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 2.3.4.4e

Zoonotic Mutation of Highly Pathogenic Avian Influenza H5N1 Virus Identified in the Brain of Multiple Wild Carnivore Species
https://www.mdpi.com/2076-0817/12/2/168
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
https://journals.asm.org/doi/10.1128/spectrum.02867-22
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
https://www.biorxiv.org/content/10.1101/2023.02.08.527769v1.full.pdf
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 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) from the 2021/22 epizootic is highly duck adapted and poorly adapted to chickens
https://www.biorxiv.org/content/10.1101/2023.02.07.527270v1.full.pdf
Lots of questions abt why we have seen 2.3.4.4 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
https://www.woah.org/en/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 2.3.4.4b incursion into Australia in 2022
https://onlinelibrary.wiley.com/doi/10.1111/irv.13118
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
https://www.preprints.org/manuscript/202301.0480/v1
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
https://www.ijidonline.com/article/S1201-9712(23)00029-2/fulltext
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 2.3.4.4b Virus in Chile, 2022
https://www.biorxiv.org/content/10.1101/2023.02.01.526205v1
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 2.3.4.4.b in Captive Mallards (Anas platyrhynchos)
https://www.mdpi.com/2076-0817/12/2/217
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
https://academic.oup.com/mbe/article/40/2/msad019/7005671?login=false
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
https://www.researchgate.net/publication/367268355_Avian_influenza_leads_to_mass_mortality_of_adult_Great_Skuas_in_Foula_in_summer_2022/references
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
https://www.biorxiv.org/content/10.1101/2023.01.18.524666v1
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
https://www.science.org/doi/10.1126/science.adg2271
– 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
https://science.org/doi/10.1126/science.adg2271

In Vitro and In Vivo Characterization of H5N8 High-Pathogenicity Avian Influenza Virus Neurotropism in Ducks and Chickens
https://journals.asm.org/doi/10.1128/spectrum.04229-22
Why are there differences in disease between chickens and ducks infected with 2.3.4.4b 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
https://royalsocietypublishing.org/doi/10.1098/rspb.2022.2237
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
https://www.tandfonline.com/doi/full/10.1080/22221751.2023.2167610
In January 2022, more than 6500 Cape cormorants died due to HPAI on Bird Island, Walvis Bay. Phylogenetics indicate clade 2.3.4.4b, 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 2.3.4.4b Avian Influenza A(H5N8) Virus in Cambodia, 2021
https://wwwnc.cdc.gov/eid/article/29/1/22-0934_article
Avian influenza H5 viruses have been routinely detected in Cambodia for a number of years, particularly 2.3.2.1c since 2014. Here 2.3.4.4b was first detected in late 2021.

Emergence of Highly Pathogenic Avian Influenza A Virus (H5N1) of Clade 2.3.4.4b in Egypt, 2021–2022
https://www.mdpi.com/2076-0817/12/1/90
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 2.3.4.4 highly pathogenic H5N1 influenza a virus
https://www.nature.com/articles/s41598-023-27446-1
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
https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-022-01125-x
Gulls are highly susceptible to 2.3.4.4b 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
https://wwwnc.cdc.gov/eid/article/28/12/22-1086_article
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
https://www.researchsquare.com/article/rs-2136604/v1
Different genotypes of 2.3.4.4b 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
https://dataverse.nioz.nl/file.xhtml?fileId=2735&version=4.0
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
https://wwwnc.cdc.gov/eid/article/28/12/22-1292_article
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 2.3.4.4b
https://wwwnc.cdc.gov/eid/article/28/12/22-1292_article

The impact of avian influenza 2022 on Dalmatian pelicans was the worst ever wildlife disaster in Greece
https://doi.org/10.1017/S0030605322001041
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
https://bvajournals.onlinelibrary.wiley.com/doi/epdf/10.1002/vetr.2399
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
https://onlinelibrary.wiley.com/doi/10.1111/tbed.14728
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
https://onlinelibrary.wiley.com/doi/10.1111/mec.16738
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
https://bvajournals.onlinelibrary.wiley.com/doi/epdf/10.1002/vetr.2311
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 2.3.4.4b Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021
https://www.mdpi.com/1999-4915/14/9/1901/htm
New paper from Burkina Faso, with H5N1 viruses detected in clade 2.3.4.4b, 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
https://journals.asm.org/doi/10.1128/jvi.01233-22
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
https://journals.asm.org/doi/10.1128/mbio.00609-22
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009973
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
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010605
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
https://academic.oup.com/ve/article/8/2/veac073/6671198?login=false
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
https://journals.asm.org/doi/epub/10.1128/jvi.00776-22
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
https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2022.1312
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
https://journals.asm.org/doi/pdf/10.1128/spectrum.01427-22
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
https://academic.oup.com/ve/article/8/2/veac074/6700668?searchresult=1

A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways
https://doi.org/10.1093/ve/veac077
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
https://doi.org/10.1093/ve/veac073

Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America
https://wildlife.onlinelibrary.wiley.com/doi/10.1002/jwmg.22171
For wild birds, lineage 2.3.4.4 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