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Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania
10.1128/mbio.02101-22
Andrew D. Marques
Scott Sherrill-Mix
John K. Everett
Hriju Adhikari
Shantan Reddy
Julie C. Ellis
Haley Zeliff
Sabrina S. Greening
Carolyn C. Cannuscio
Katherine M. Strelau
Ronald G. Collman
Brendan J. Kelly
Kyle G. Rodino
Frederic D. Bushman
Roderick B. Gagne
Eman Anis
Research Article
Research Article
SARS-CoV-2
coronavirus
white-tail deer
Odocoileus virginianus
animal reservoir
zoonosis
American Society for Microbiology
Marques et al.
Copyright © 2022 Marques et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
20220824
2022
ABSTRACT
The SARS-CoV-2 pandemic began by viral spillover from animals to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus, are infected in North America at substantial levels, and genomic data suggests that a variant in deer may have spilled back to humans. Here, we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole genome sequences were obtained, together with six more partial spike gene sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.
IMPORTANCE Coronaviruses have been documented to replicate in numerous species of vertebrates, and multiple spillovers of coronaviruses from animals into humans have founded human epidemics. The COVID-19 epidemic likely derived from a spillover of SARS-CoV-2 from bats into humans, possibly via an intermediate host. There are now several examples of SARS-CoV-2 jumping from humans into other mammals, including mink and deer, creating the potential for new animal reservoirs from which spillback into humans could occur. For this reason, data on formation of new animal reservoirs is of great importance for understanding possible sources of future infection. Here, we identify extensive infection in white-tailed deer in Pennsylvania, including what appear to be multiple independent transmissions. Data further suggests possible transmission among deer. These data thus help identify a potential new animal reservoir and provide background information relevant to its management.
20220726
20220808
2150-7511
Adobe LiveCycle PDF Generator; modified using iText® 5.5.13.2 ©2000-2020 iText Group NV (AGPL-version)2022-10-24T10:00:09-07:00
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