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Swine are critical hosts for influenza A viruses (IAV) because they can be co-infected with IAV from multiple host species (1). Swine also have close proximity with humans through agricultural [...]

Aims: Swine are a mixing vessel for the emergence of novel reassortant influenza A viruses (IAV). Interspecies transmission of swine‐origin IAV poses a public health and pandemic risk. In the United States, the majority of zoonotic IAV transmission events have occurred in association with swine exposure at agricultural fairs. Accordingly, this human‐animal interface necessitates mitigation strategies informed by understanding of interspecies transmission mechanisms in exhibition swine. Likewise, the diversity of IAV in swine can be a source for novel reassortant or mutated viruses that pose a risk to both swine and human health. Methods and Results: In an effort to better understand those risks, here we investigated the epidemiology of IAV in exhibition swine and subsequent transmission to humans by performing phylogenetic analyses using full genome sequences from 272 IAV isolates collected from exhibition swine and 23 A(H3N2)v viruses from human hosts during 2013–2015. Sixty‐seven fairs (24.2%) had at least one pig test positive for IAV with an overall estimated prevalence of 8.9% (95% CI: 8.3–9.6, Clopper‐Pearson). Of the 19 genotypes found in swine, 5 were also identified in humans. There was a positive correlation between the number of human cases of a genotype and its prevalence in exhibition swine. Additionally, we demonstrated that A(H3N2)v viruses clustered tightly with exhibition swine viruses that were prevalent in the same year. Conclusions: These data indicate that multiple genotypes of swine‐lineage IAV have infected humans, and highly prevalent IAV genotypes in exhibition swine during a given year are also the strains detected most frequently in human cases of variant IAV. Continued surveillance and rapid characterization of IAVs in exhibition swine can facilitate timely phenotypic evaluation and matching of candidate vaccine strains to those viruses present at the human‐animal interface which are most likely to spillover into humans. [ABSTRACT FROM AUTHOR]

Understanding pathogen emergence in new host species is fundamental for developing prevention and response plans for human and animal health. We leveraged a large-scale surveillance dataset coordinated by United States Department of Agriculture, Animal and Plant Health Inspection Service and State Natural Resources Agencies to quantify the outbreak dynamics of SARS-CoV-2 in North American white-tailed deer (Odocoileus virginianus; WTD) throughout its range in the United States. Local epidemics in WTD were well approximated by a single-outbreak peak followed by fade out. Outbreaks peaked early in the northeast and mid-Atlantic. Local effective reproduction ratios of SARS-CoV-2 were between 1 and 2.5. Ten percent of variability in peak prevalence was explained by human infection pressure. This, together with the similar peak infection prevalence times across many counties and single-peak outbreak dynamics followed by fade out, suggest that widespread transmission via human-to-deer spillover may have been an important driver of the patterns and persistence. We provide a framework for inferring population-level epidemiological processes through joint analysis of many sparsely observed local outbreaks (landscape-scale surveillance data) and linking epidemiological parameters to ecological risk factors. The framework combines mechanistic and statistical models that can identify and track local outbreaks in long-term infection surveillance monitoring data. [ABSTRACT FROM AUTHOR]