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Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two ‘Florida’ clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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1 Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University , Ithaca, NY 14853, USA
2 Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky , Lexington, KY 40546, USA
3 MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G61 1QH, Scotland
4 Department of Medicine & Epidemiology, School Veterinary Medicine, University of California , Davis, CA 95616, USA
5 Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University , Ithaca, NY 14853, USA
6 Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney , Sydney, NSW 2006, Australia
7 Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA