SARS-CoV-2 infection in free-ranging white-tailed deer ( Odocoileus virginianus )

Abstract

Human-to-animal spillover of SARS-CoV-2 virus has occurred in a wide range of animals, but thus far, the establishment of a new natural animal reservoir has not been detected. Here, we detected SARS-CoV-2 virus using rRT-PCR in 129 out of 360 (35.8%) free-ranging white-tailed deer ( Odocoileus virginianus ) from northeast Ohio (USA) sampled between January-March 2021. Deer in 6 locations were infected with at least 3 lineages of SARS-CoV-2 (B.1.2, B.1.596, B.1.582). The B.1.2 viruses, dominant in Ohio at the time, spilled over multiple times into deer populations in different locations. Deer-to-deer transmission may have occurred in three locations. The establishment of a natural reservoir of SARS-CoV-2 in white-tailed deer could facilitate divergent evolutionary trajectories and future spillback to humans, further complicating long-term COVID-19 control strategies.

One-sentence summary: A significant proportion of SARS-CoV-2 infection in free-ranging US white-tailed deer reveals a potential new reservoir.

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 (Clopper-Pearson exact 95% confidence interval bars).

Figure 2.. Timing of SARS-CoV-2 waves in Ohio, USA.

The number of weekly COVID-19 cases in humans in Ohio is presented from April 2020 – September 2021 (y-axis). The proportion of viruses sequenced each week in Ohio for routine surveillance that are assigned to one of five Pango lineages (or “Other”) is indicated by shading. Genomic data prior to December 2020 was too sparse to reliably estimate lineage frequency. The shading and placement of each circle indicates the timing and lineage of SARS-CoV-2 viruses found in white-tailed deer at seven time points in this study.

Figure 3.. Evolutionary relationships of SARS-CoV-2 viruses in white-tailed deer.

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 labeled and boxed. Viruses found in white-tailed deer (clusters or singletons) are shaded red and labeled by location (site 4 not shown due to lower sequence coverage). All branch lengths drawn to scale.

Figure 4.. Evolutionary relationships of B.1.596 viruses in white-tailed deer.

Maximum likelihood tree inferred for the cluster of 7 B.1.596 viruses found in white-tailed deer at site 1 and the 46 most closely related human B.1.596 viruses, all of which were observed in the United States during November 2020 – March 2021. Human viruses are shaded by month of collection. Cartoons indicate the branch where human-to-deer transmission may have occurred, followed by likely deer-to-deer transmission within site 1. Amino acid changes observed in the 7 B.1.596 deer viruses are listed. Bootstrap values are provided for key nodes and all branch lengths are drawn to scale.