Data and code from: Viral outbreak dynamics and evolution in wildlife at the interface with humans

In this study, we used a multi-faceted approach to understand patterns of
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission
and persistence in a wild white-tailed deer population. Serology data
indicated transmission of SARS-CoV-2 and persistence during the
seven-month sampling period. Traditional disease modeling based on
deer-to-deer transmission indicated relatively low prevalence with an R 0
of 1.2 and recovery period of 5 days; however, individual-based modeling
informed by GPS tracked-movement data captured a potential transmission
event. Phylogenetic analyses revealed a recurring pattern of divergent
groups of deer-derived sequences with human-derived sequences falling
close to each deer-derived cluster.Further, human-derived sequences were
frequently sampled months prior to the deer-derived sequences, indicating
repeated human to deer spillover. Using multiple types of data as well as
both fine and broad scale analyses, we have characterized a pattern of
localized outbreaks of SARS-CoV-2 within white-tailed deer populations
that are likely recurring due to frequent spillover events. Our results
suggest that while deer-to-deer transmission occurs over small
spatiotemporal scales, SARS-CoV-2 persistence over longer periods and
across larger regions is likely driven by repeated spillover from human
populations.