Speaker
Description
A widespread outbreak of H5N1 avian influenza A virus was detected in U.S. dairy cattle in 2024, causing significant illness in cattle, reduced milk production, and economic damage. We analyze 537 H5N1 genomes from birds and non-human mammals leading up to the emergence of H5N1 in cattle, and 1,739 genomes from cattle, poultry, humans, and other mammals involved in the 2024 outbreak for which metadata is available. We show that the H5N1 genotype is a reassortant between the Eurasian panzootic H5N1 genotype and low pathogenicity North American genotypes first seen in late 2023. Maximum likelihood trees for each segment reveal that the cattle viruses form a monophyletic clade, consistent with a single introduction followed by cattle-to-cattle transmission. Reconstructing a time-resolved phylogeny using HA segments sampled from cattle and a background set of genomes from wild birds and other mammals sampled in North America after 1 January 2023 indicates the jump from the avian reservoir into cattle occurred in late 2023 or early 2024, with the virus potentially circulating for a few months before detection. Through a phylogeographic inference of H5N1 in cattle, we find that the dispersal of H5N1 can be explained by an underlying cattle movement network, with limited evidence for wild bird movement resulting in later spillover into cattle. Our inference indicates that the outbreak originated in Texas, where the first human and cattle cases were reported, and that Texas was an early source of virus dissemination across the U.S. Lastly, we find support for H5N1 spilling over from cattle into humans, wild birds, poultry, and mammals, and moderate support for transmission from poultry into humans, cattle, and mammals. Our findings highlight the need for ongoing monitoring of dairy cattle to track H5N1 evolution and the role of animal movement in virus dissemination more broadly.
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