Abstract
In November 2021, an A/Goose/Guangdong/1/96 lineage highly pathogenic avian influenza virus (HPAIV) bearing the hemagglutinin (HA) gene of clade 2.3.4.4b (subtype A(H5N1)) was detected for the first time in North America. This initial incursion led to an outbreak that spread across the continent, was detected in >80 wildlife species and affected >90 million domestic birds in Canada and the USA. From samples collected in Canada during this outbreak, the National Centre for Foreign Animal Disease has sequenced >3000 complete A(H5N1) genomes. These data, in conjunction with previously published data, were used to perform multifaceted phylodynamic and genome-wide evolutionary analyses. By jointly analyzing whole-genome sequences, collection dates, locations and host information, we provide substantial insights into the emergence, evolution, spatiotemporal spread and host dynamics of A(H5N1) in North America. Our analyses reveal significant viral diversification, as more than 60 distinct A(H5N1) genotypes have been detected in Canada since November 2021. Phylogeographic reconstructions reveal successive lineage replacement by descendant reassortants, which is suggestive of compounding fitness increases. Genome-wide association studies and estimates of molecular selection pressure were employed to identify genomic motifs associated with phenotypic variation and host specificity of A(H5N1) genotypes. These insights into the diversification, host dynamics, spatiotemporal diffusion, and genome evolution of A(H5N1) HPAI virus will inform ongoing surveillance efforts to minimize damages to ecological, animal and human health as these viruses continue to circulate throughout North America.
Co-Author(s)
Jolene Giacintib, Megan E.B. Jonesc,d, Cassidy N.G. Erdelyana, Angela McLaughlinb,e, Tamiru N. Alkiea, Sherri Coxf, Stéphane Lairg, Claire M. Jardineh, Brian Stevensh, Maria Bravo-Arayai, Neil Poplej, Margo J. Pybusk,l, Tamiko Hisanagaa, Wanhong Xua, Janice Koziuka, Oliver Lunga, Peter Kruczkiewicza, Mathew Fishera, Jordan Wightm, Ishraq Rahmanm, Kathryn E. Harganm, Andrew S. Langm, Orie Hochmana, Davor Ojkicn, Carmencita Yasono, British Columbia Wildlife AIV Surveillance Programp, Laura Bourquec, Trent K. Bollingerq, Jennifer F. Provencherr, Sarah Ogilvieo, Amanda Clarks, Robyn MacPheeo, Hazel Eaglesomet, Sayrah Gilbertu, Kelsey Saborakiv, Richard Davisv, Alexandra Jeraow, Matthew Ginnx, Catherine Soosb, Yohannes Berhanea,q,y
aNational Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
bEnvironment and Climate Change Canada, Saskatoon, Canada;
cCanadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, Canada
dNova Scotia Department of Natural Resources and Renewables, Kentville, Canada
eBioinformatics, University of British Columbia, Vancouver, BC, Canada
fCollege of Biological Science, University of Guelph, Guelph, Canada
gCanadian Wildlife Health Cooperative, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
hCanadian Wildlife Health Cooperative, University of Guelph, Guelph, Canada
iUniversity of Saskatchewan, Saskatoon, Canada
jVeterinary Diagnostic Services, Manitoba Agriculture, Winnipeg, Canada
kFish and Wildlife, Alberta Environment and Protected Areas, Edmonton, Canada
lDepartment of Biological Sciences, University of Alberta, Edmonton, Canada
mDepartment of Biology, Memorial University of Newfoundland, St. John’s, Canada
nAnimal Health Laboratory, University of Guelph, Guelph, Canada
oRegional Diagnostic Virology Services, Atlantic Veterinary College, University of Prince Edward Island
pBritish Columbia Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
qDepartment of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
rEnvironment and Climate Change Canada, Ottawa, Canada
sDepartment of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
tNational Wildlife Centre, Caledon, Canada
uWildlife Haven Rehabilitation Centre, Île-des-Chênes, Canada
vWildlife Branch, Manitoba Economic Development, Investment, Trade and Natural Resources, Dauphin, Canada
wOffice of the Chief Veterinarian, Manitoba Agriculture, Winnipeg, Canada
xPrince Edward Island Department of Environment, Energy and Climate Action, Charlottetown, Canada
yDepartment of Animal Science, University of Manitoba, Winnipeg, Canada
Abstract Category
Notable outbreaks, field and molecular epidemiology, and surveillance in wild birds