Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States

Abstract

SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses

“…While the 7% wild-type SARS-CoV-2 neutralizing antibody seroprevalence observed among white-tailed deer in our study ( Figure 1B ) was lower than the 14-40% neutralizing antibody positivity found in other locations 10,23,28,30,32 , it was surprisingly high given the semi-restricted nature of the sampling sites. All six seropositive deer samples tested positive in duplicate.…”

“…Few examples of secondary spillover of any pathogen have been reported, likely in part due to the many behavioral and host barriers a pathogen must overcome combined with the challenges of observing such dynamics 2 . Despite this, potentially due to broad susceptibility and substantial exposure opportunities, several instances of SARS-CoV-2 secondary spillover have been reported including from farmed mink ( Neovison vison ) to workers in the Netherlands, imported golden hamsters ( Mesocricetus auratus ) to pet shop workers in Hong Kong, and white-tailed deer ( Odocoileus virginianus ) to human contacts in Canada and the United States 7–10 . Not all animals are equally likely to experience viral spillback, sustained transmission, and/or secondary spillover.…”

“…SARS-CoV-2 surveillance in rodents remains highly limited despite these occasional detections. While rodents are the focus of our study, we also evaluated white-tailed deer, a species with extensive evidence of infection and exposure across the United States and Canada to provide a comparison 8,10,22–32 . Experimental challenge studies further confirm the SARS-CoV-2 infection and transmission capacity of deer, and note that the disease presents subclinically 33–35 .…”

Widespread exposure to SARS-CoV-2 in wildlife communities

“…Diluted serum samples were mixed in a 1:1 v/v ratio with a solution containing 1300 plaque-forming units per mL (PFU/mL) of SARS-CoV-2 Delta virus strain USA-GNL-1205/2021 (a generous gift from the World Reference Center for Emerging Viruses and Arboviruses), or approximately 40 PFU’s per well. Our serum samples were collected in June and July of 2022, following the Delta wave in fall of 2021, and given the life expectancy of the animal species (Supplementary Table 12) we were sampling, we assumed Delta would have been the most likely recent variant they were exposed to 54 . Each sample was tested in triplicate.…”

Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection

“…Newly emergent VOCs generally perch atop a long ancestral phylogenetic branch, rooted in a historic lineage absent from the current variant landscape [6] . While SARS-CoVspillover/spillback to and from an animal host could potentially generate similar long phylogenetic branches [10] , recent evidence suggests that immunocompromised individuals with persistent infections are the main source of these divergent lineages [2,11] . Since the early stages of the pandemic, long-term replication has been documented in chronically infected immunocompromised individuals, accelerating intrahost viral evolution and leading to the acquisition of amino acid changes that often overlap with those identified in VOCs [12][13][14] .…”