OmniVira

Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024.

Andrew D Marques1 Matthew Hogenauer1 Natalie Bauer2 Michelle Gibison2 Beatrice DeMarco2 Scott Sherrill-Mix3 Carter Merenstein1 Ronald G Collman4 Roderick B Gagne2 Frederic D Bushman1
Affiliations 4 institutions
  1. Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
  2. Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, United States of America.
  3. Department of Microbiology, Genetics, and Immunology, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America.
  4. Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, United States of America.
PMID39854608 DOI10.1371/journal.ppat.1012883 Year2025 Journal PLoS pathogens PLoS Pathog Languageeng Statusepublish

Abstract

SARS-CoV-2 continues to transmit and evolve in humans and animals. White-tailed deer (Odocoileus virginianus) have been previously identified as a zoonotic reservoir for SARS-CoV-2 with high rates of infection and probable spillback into humans. Here we report sampling 1,127 white-tailed deer (WTD) in Pennsylvania, and a genomic analysis of viral dynamics spanning 1,017 days between April 2021 and January 2024. To assess viral load and genotypes, RNA was isolated from retropharyngeal lymph nodes and analyzed using RT-qPCR and viral whole genome sequencing. Samples showed a 14.64% positivity rate by RT-qPCR. Analysis showed no association of SARS-CoV-2 prevalence with age, sex, or diagnosis with Chronic Wasting Disease. From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. The viral variants identified included 17 Alpha, 11 Delta, and 14 Omicron. Alpha largely stopped circulating in humans around September 2021, but persisted in WTD as recently as March of 2023. Phylodynamic analysis of pooled genomic data from Pennsylvania documents at least 12 SARS-CoV-2 spillovers from humans into WTD, including a recent series of Omicron spillovers. Prevalence was higher in WTD in regions with crop coverage rather than forest, suggesting an association with proximity to humans. Analysis of seasonality showed increased prevalence in winter and spring. Multiple examples of recurrent mutations were identified associated with transmissions, suggesting WTD-specific evolutionary pressures. These data document ongoing infections in white-tailed deer, probable onward transmission in deer, and a remarkable rate of new spillovers from humans.

Supporting text Virus Host Location
COVID-19 425 Deer 46 SARS-CoV-2 453 Animals 1948 Disease Reservoirs 149 Evolution, Molecular 176 Female 289 Genome, Viral 317 Humans 1440 Male 224 Pennsylvania 5 Phylogeny 805 Spike Glycoprotein, Coronavirus 274 Viral Load 36

Evidence records

4 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE8838 Viral Detection
Key finding

SARS-CoV-2 RNA was detected in 14.64% of white-tailed deer sampled in Pennsylvania by RT-qPCR.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host
Location
United States
Supporting text

Here we report sampling 1,127 white-tailed deer (WTD) in Pennsylvania, and a genomic analysis of viral dynamics spanning 1,017 days between April 2021 and January 2024. To assess viral load and genotypes, RNA was isolated from retropharyngeal lymph nodes and analyzed using RT-qPCR and viral whole genome sequencing. Samples showed a 14.64% positivity rate by RT-qPCR.

Method
RT-qPCR | RNA isolation
Sample type
retropharyngeal lymph nodes
Geographic raw
Pennsylvania
Country inferred
USA
Evidence type Reservoir Ecology
1 records
OVE8842 Reservoir Ecology
Key finding

SARS-CoV-2 prevalence in white-tailed deer was greater during winter and spring, revealing seasonal ecological patterns of infection.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host
Location
United States
Supporting text

Analysis of seasonality showed increased prevalence in winter and spring.

Method
seasonal prevalence analysis
Sample type
retropharyngeal lymph nodes
Geographic raw
Pennsylvania
Country inferred
USA
Transmission Evidence
1 records · 1 evidence types
Evidence type Cross-species Transmission
1 records
OVE8840 Cross-species Transmission
Key finding

Phylodynamic analysis showed at least 12 independent human-to-deer spillover events of SARS-CoV-2, including Omicron variants, in Pennsylvania.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host human Homo sapiens Natural host
Location
United States
Supporting text

Phylodynamic analysis of pooled genomic data from Pennsylvania documents at least 12 SARS-CoV-2 spillovers from humans into WTD, including a recent series of Omicron spillovers.

Method
phylodynamic analysis | whole genome sequencing | RT-qPCR
Study design
phylodynamic genomic analysis of field-collected white-tailed deer samples
Transmission direction
human-to-animal
Geographic raw
Pennsylvania
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE8839 Phylogenetic Evolution
Key finding

Phylodynamic analysis showed continued circulation and evolutionary divergence of the SARS‑CoV‑2 Alpha variant in white‑tailed deer after it disappeared from humans, with recurrent mutations indicating deer‑specific adaptive pressures.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host human Homo sapiens Natural host
Location
Not specified
Supporting text

Alpha largely stopped circulating in humans around September 2021, but persisted in WTD as recently as March of 2023. Multiple examples of recurrent mutations were identified associated with transmissions, suggesting WTD‑specific evolutionary pressures.

Genes or proteins
whole genome | spike
Analysis methods
phylodynamic analysis | phylogenetic analysis | genomic analysis