Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Abstract

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ∼75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer

“…To determine the identity and genetic relatedness of the circulating strains, whole-genome sequencing (WGS) was applied on four of the seven positive samples (tags 102-104 and 2067) using a recently described pipeline 6 . Sequencing of 3 RT-PCR positive samples (numbers 2089, 2108 and 2125) is currently underway.…”

SARS-CoV-2 has not emerged in roe, red or fallow deer in Germany or Austria during the COVID 19 pandemic

“…In some cases, the result was the spillback of a novel SARS-CoV-2 variant to humans, making new wildlife reservoirs a clear threat to human health. Spillover is of particular concern in North America where there is strong evidence that white tailed deer ( Odocoileus virginianus ) have been infected in the U.S. and Canada with prevalences reaching 82.5% (3). White tailed deer may now represent a reservoir in which SARS-CoV-2 may evolve and potentially spill back to humans with unpredictable health consequences.…”

Novel pathogen introduction rapidly alters evolved movement strategies, restructuring animal societies

“…Whether such sharp, temporally restricted outbreaks result in substantial evolutionary pressure against sociality is unclear. Comparing sociality before and after an unexpected pathogen spillover (as in Kuchipudi et al, 2022) is likely to be challenging, not least because data on past and ongoing host-pathogen introduction events is sparse. Our model then is especially suited to longer-term outbreaks in which populations are repeatedly exposed to novel pathogens (or strains), such as wild boar swine fever outbreaks (Scherer et al, 2020), avian influenza in Arctic migratory birds (The Global Consortium for H5N8 and Related Influenza Viruses, 2016), or the recent introduction of Covid-19 to deer (Kuchipudi et al, 2022).…”

“…This is also realistic, as populations may repeatedly acquire pathogens through external sources, such as infected individuals of other, spatially overlapping species (e.g. Kuchipudi et al, 2022).…”