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The prevalence, genetic diversity, and evolution of SARS-CoV-2 in white-tailed deer in New York

In a recent study posted to bioRxiv*, researchers investigated the prevalence, genomic diversity, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among white-tailed deers (WTD) in New York (NY).

Study: White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Image Credit: Jim Cumming/Shutterstock


Studies have reported SARS-CoV-2 spillover from human beings into WTD and the capability of SARS-CoV-2 to transmit among deers, raising concerns about the role of WTD in SARS-CoV-2 ecology and epidemiology. Continued surveillance programs for monitoring SARS-CoV-2 dynamics in WTD and developing measures to curtail SARS-CoV-2 transmission between animals and humans are required.

About the study

In the present study, researchers investigated WTD susceptibility to SARS-CoV-2 infections.

Retropharyngeal lymph node (RPLN, n=5462) specimens were obtained from WTD under the NY State’s chronic wasting disease (CWD) surveillance program for two seasons of hunting. The first season was between September and December 2020, and the second season was during the same period of the consecutive year.

In total, 2700 and 2762 specimens were obtained from the first and second seasons, respectively, and subjected to real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis to detect the presence of SARS-CoV-2 ribonucleic acid (RNA) and obtain the cycle threshold (Ct) values for viral load assessment.

Virus isolation experiments using Vero-E6 transmembrane serine protease 2 (TMPRRSS2) cells and whole genome sequencing (WGS) of SARS-CoV-2 sequences were performed for RPLN specimens with Ct values <30 (11 and 205 specimens from the first and second seasons, respectively). SARS-CoV-2 genomes that crossed the Pangolin threshold for length and content (n=164) were analyzed further.  

Phylogenetic relationships of the 164 WTD SARS-CoV-2 samples were compared to 159 other WTD-derived sequences of the GISAID (global initiative on sharing all influenza data) EpiCoV database. The genetic relationship between SARS-CoV-2 sequences of WTD and humans was investigated, and sites with potential strong host adaptive mutations of the SARS-CoV-2 VOCs in WTD were identified.

Specimens were obtained from 57 NY counties and subjected to spatial cluster analysis to identify hotspots of SARS-CoV-2 infections. In addition, the distribution of SARS-CoV-2-positive cases by age and sex of WTD was investigated. The age and sex of WTD from both seasons and categorized as fawns aged < 1.5 years, yearlings aged 1.5 to 2.5 years, and adults aged equal to or above 2.5 years.


In the first season, SARS-CoV-2 was detected among October to November 2020 samples, whereas in the second season, the virus was detected among October to December 2021 samples, and the peak of SARS-CoV-2 positivity was identified in the first half of November 2021. SARS-CoV-2 RNA was identified among 17 and 583 specimens from the first and second seasons, respectively.

SARS-CoV-2 RNA loads varied marginally between the two seasons, with average Ct values of 29.8 and 30.8 for the first and second seasons, respectively. However, there were no statistically significant differences in the Ct values for the two hunting seasons. In the virus isolation experiments, infectious SARS-CoV-2 was detected among seven specimens obtained in the second season.

A 35-fold increase in SARS-CoV-2 prevalence in one year i.e., by 2021, with a broad SARS-CoV-2 circulation among WTD in NY. The number of SARS-CoV-2-positive male WTD was higher than female WTD by two-fold to three-fold across ages [odds ratio (OR) = 1.95], with higher odds of adult males being SARS-CoV-2 positive than male yearlings (OR = 1.9).

In the first and second seasons, SARS-CoV-2-positive samples were identified from 10 and 48 NY counties, respectively, and 19 spatial clusters (C1 to C19) denoting seven hotspots of SARS-CoV-2 infections among WTD [relative risk (RR) >1.8)]. Most of the hotspots overlapped with geographical regions with the greatest deer population densities and the highest rates of deer harvesting in NY.

Most of the clusters (C2,7, 13, and 18) were located in NY’s South Tier region, of which cluster 2 comprised the Allegany and Cattaraugus counties (RR = 2.7) and all Gamma VOC sequences, whereas C7, C13, and C18 involved a single county each, with RR values of 2.6, 2.9 and 2.7, respectively. C7 and C18 mainly comprised the Alpha and Delta VOCs, respectively. Cluster 1 was the largest in the analysis comprising the Ulster, Sullivan, and Orange counties of Hudson Valley.

WGS analysis showed the concomitant circulation of three main SARS-CoV-2 variants of concern (VOCs), i.e., Alpha, Gamma, and Delta, in WTD in 2021. The closest phylogenetic relationship (with a monophyletic cluster) was observed for the Gamma VOC sequences with 99.9% nucleotide similarity, whereas Alpha and Delta formed several small clusters.

There was no direct association between SARS-CoV-2 sequences detected in WTD and humans. The WTD SARS-CoV-2 Alpha and Gamma VOC sequences showed multiple mutations (50 to 80) compared to the Wuhan-Hu-1 strain reference sequence. WTD SARS-CoV-2 Delta VOC sequences showed similar but lesser genetic divergence from human Delta VOC sequences.

Among the SARS-CoV-2 spike (S) receptor binding domain (RBD) mutations, S:Q564L was identified in 41% (n= 11) Gamma VOC sequences and S1252F in 16% (n=9) Alpha sequences, whereas no mutations were detected in Delta S RBD. The open reading frame 1a (ORF1a) L4111F, S:T29I, ORF1a:T3150I, and S:P25S were identified as targets for strong host-adaptive SARS-CoV-2 VOC mutations in WTD.


Overall, the study findings showed that WTD (Odocoileus virginianus) could be a potential reservoir for nearly extinct SARS-CoV-2 VOCs.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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