To date, my research has focused on the following themes:

Avian virome ecology

We have made great strides in understanding virus ecology utilizing the “one host-one parasite” model. This is, of course, not realistic as multihost viruses such as influenza utilize many species within the Anseriformes and Charadriiformes as hosts, and these individuals may in turn be infected with a multitude of viruses (and bacteria, fungi, nematodes, etc). Using meta-transcriptomics, we can now characterize the entire RNA virome of birds, and test which factors play a role in abundance, diversity and structure of these viromes. This expansion is crucial if we are to better understand viral ecology. Collaborators: Eddie Holmes (University of Sydney) and Marcel Klaassen (Deakin University). This work is supported by an Australian Research Council DECRA fellowship.

Ecology and evolution of avian influenza in Australia

Very little is known about the ecology of influenza A in Australia. Overall, prevalence is very low and doesn’t follow seasonal patterns as demonstrated from Northern Hemisphere datasets. Low prevalence in Australia is attributed to the fact that waterfowl do not migrate beyond the continent, this is left to the millions of migratory shorebirds. This project is twofold. First, we are trying to understand the host range, ecology, and seasonal patterns of this virus in Australia, and importantly trying to ascertain whether some species of migratory shorebird may play a role in potential incursions of influenza into Australia. Second, using sequence data generated by our work in addition to those kindly provided by state laboratories, we aim to disentangle the phylogeography of these viruses on the Australian continent. Collaborators: Aeron Hurt  (previously WHOCCRI), Eddie Holmes (University of Sydney) and Marcel Klaassen (Deakin University). This work has been supported by an ARC Discovery Project (2016-2019 to ECH), the Australian Government Department of Agriculture and Water Resources as part of its Agricultural Competitiveness White Paper, and National Avian Influenza Wild Bird (NAIWB) Surveillance Program Special Project Funding.

Ecology and evolution of avian influenza A viruses in the Mallard model

Mallards are the main reservoir host for influenza A viruses in the Northern Hemisphere, with >20% of populations infected during the autumnal prevalence peak. Given the high prevalence in a single species, it is a great model in which to better disentangle the ecology and evolution of this virus. We have begun to disentangle reassortment, have demonstrated critical features of long term viral maintenance, revealed features of viral subtypes only very rarely isolated globally, assessed individual host variation and effect of prior infection on future infection probability. Experimental infection work using Mallards has further allowed us to assess host immunity, antiviral resistance, transmission patterns, and reassortment patterns. Work using this Mallard model continues to be crucial to our understanding of low pathogenic influenza A in the host reservoir. Collaborators: Jonas Waldenström (Linnaeus Unvieristy), Björn Olsen (Uppsala University), Josef Järhult (Uppsala University). My PhD was in part supported by an NSERC PGS-D2 fellowship award.

Reassortment of avian influenza at continental margins

With few exceptions, birds migrate within continental margins. That is, birds tend to move on an annual cycle northwards and southwards within the Americas or Eurasia. As such, the genetic structure of avian influenza A reflects this, wherein genes from viruses isolated in the Americas is very different from those isolated in Eurasia. Contiental margins and birds that move across these, such as gulls, have viruses with geographic mosacism, and may play an important role in the movement of viruses or genes across these continental margins. The ramification for this is huge, as demonstrated by the recent incursion of highly pathogenic H5Nx into North America through the Bering Sea corridor. Collaborators: Andrew Lang (Memorial University) and Hugh Whitney (retired, NL Department of Natural Resources). I was supported by an NSERC-CGS-M fellowship.