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.

Keywords: One Health; SARS-CoV-2; animal reservoir; deer; spillover.

Fig. 1.

Epidemic curve showing SARS-CoV-2 weekly cases (per 100,000) in humans and the monthly change in SARS-CoV-2 positivity in white-tailed deer in Iowa. Weekly reported SARS-CoV-2 cases in humans per 100,000 population in Iowa from 30 March 2020 to 7 March 2021 (blue bars; left y axis) and monthly SARS-CoV-2 test positivity with 95% CI in white-tailed deer from September 2020 to January 2021 (red line; right y axis). The timing of the first positive sample identified in white-tailed deer on 28 September 2020 is marked, as are the start and end of the white-tailed deer hunting season on 19 September 2020 and 10 January 2021, respectively. Deer, white-tailed deer.

Fig. 2.

Temporal and spatial distribution of SARS-CoV-2 positive RPLN samples from white-tailed deer in Iowa. The 94 SARS-CoV-2 positive RPLN samples show strong temporal clustering in frequency of detection. (A) Monthly snapshots showing number and location of SARS-CoV-2 positive RPLNs from white-tailed deer. (B) Progression in number of positive cases in white-tailed deer from September through December 2020 in three exemplar regions in Iowa (Left) highlighting different sampling intensities and geographic sizes of sampling areas but similar trends of increase in incidence during November and December of 2020. Each black circle represents a negative test result, and each red circle represents a positive test result for presence of SARS-CoV-2 RNA in RPLNs. Due to geographic proximity of site of sample collection, all individual points overlaps are not visible on the state map depicted on Left and are highlighted for selected regions in Right.

Fig. 3.

Whole-genome SNP-based phylogenies of 94 SARS-CoV-2 genomes recovered from free-living and captive white-tailed deer in Iowa. Whole genome sequences of all 94 SARS-CoV-2 positive samples from RPLNs were analyzed in the context of 92 publicly available genomes from animal origin SARS-CoV-2 isolates and 312 human SARS-CoV-2 genomes circulating in Iowa during this same period (SI Appendix, Table S3). The genome sequences were screened for quality, SNP positions called against the SARS-CoV-2 reference genome (NC_045512), and SNP alignments used to generate a maximum-likelihood phylogenetic tree using RAxML. The results show several genetically distinct clusters of animal and human SARS-CoV-2 lineages circulating within Iowa white-tailed deer, with clades highlighted in salmon color, consistent with multiple spillover events from humans to deer. Six branches with shared human and white-tailed deer SARS-CoV-2 isolates circulating in Iowa are highlighted. The genome sequences from white-tailed deer were genetically distinct from isolates from outbreaks in farmed mink (periwinkle color) and otters (fern color) but were closely related to SARS-CoV-2 genomes recovered from humans in Iowa.