SARS-CoV-2 infection in free-ranging white-tailed deer

Abstract

Humans have infected a wide range of animals with SARS-CoV-2^1-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.

Figure 1.. SARS-CoV-2 viral RNA in white-tailed deer across the study locations.

(A) The nine study sites were spread across a 1000 km² landscape of varying population density in Northeast Ohio. Darker shading corresponds to higher human population density (people per square mile). Sampling sites one, two, five, seven, and nine are in close proximity to human populations and are indicated as urban sites with an asterisk in panels B and C. (B) Nasal swabs from white-tailed deer were tested for the presence of SARS-CoV-2 viral RNA using real-time reverse transcriptase PCR (rRT-PCR). Estimates of SARS-CoV-2 viral RNA are represented by the Ct value of the N1 rRT-PCR target subtracted from 40. Negative samples are represented with a value of zero. (C) The prevalence of SARS-CoV-2 in the white-tailed deer at each study site was estimated using rRT-PCR. Proportion of positive samples is shown with Clopper-Pearson exact 95% confidence interval bars. Number of samples collected for each site is indicated in parentheses.

Figure 2.. Three SARS-CoV-2 lineages identified in white-tailed deer.

(A) The number of weekly COVID-19 cases in humans in Ohio is presented from October 2020 – September 2021, shaded by the proportion of viruses sequenced each week in Ohio that belong to one of five Pango lineages (or “Other”). (B) Summary of six human-to-deer transmission events observed in Ohio, with putative deer-to-deer transmission. (C) Maximum likelihood tree inferred for SARS-CoV-2 viruses in humans and white-tailed deer in Ohio during January – March 2021. Tips are shaded by Pango lineage and major lineages are boxed, labeled, and shaded similar to Figure 2B. Viruses found in white-tailed deer (clusters or singletons) are shaded red and labeled by location (the B.1.2 virus identified at site 4 not shown due to lower sequence coverage). All branch lengths drawn to scale.

Figure 3.. Evolution of B.1.596 viruses in white-tailed deer.

(A) Bayesian time-scale MCC tree inferred for the cluster of 7 B.1.596 viruses identified in white-tailed deer at site 1, the 46 most closely related human B.1.596 viruses, and a random sampling of other B.1.596 viruses observed in the United States during November 2020 – March 2021. Tips are shaded by location state (host species + geography). Branches are shaded by the location state inferred from an ancestral reconstruction. Posterior probabilities are provided for key nodes. Cartoons indicate the host-switch branch where human-to-deer transmission may have occurred, followed by putative deer-to-deer transmission within site 1. The estimated timing and location state probability is provided for key nodes defining the host-switch branch. (B) Clade-defining amino acid changes observed in all 7 B.1.596 deer viruses are listed. (C) The E484D substitution in the spike protein’s receptor binding motif (RBM) is shown in one of the B.1.596 deer viruses (OH-OSU-340).