OmniVira

White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern.

Leonardo C Caserta1,2 Mathias Martins1 Salman L Butt1 Nicholas A Hollingshead3 Lina M Covaleda1,2 Sohel Ahmed3 Mia R R Everts2 Krysten L Schuler2,3 Diego G Diel1,2
Affiliations 3 institutions
  1. Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca 14853, NY.
  2. Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca 14853, NY.
  3. Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca 14853, NY.
PMID36719912 DOI10.1073/pnas.2215067120 Year2023 Journal Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A Languageeng Statusppublish

Abstract

The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT-PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD is warranted, and measures to minimize virus transmission between humans and animals are urgently needed.

Supporting text Virus Host Location
one health 98 SARS-CoV-2 550 spillover 105 white-tailed deer 11 wildlife reservoir 4 COVID-19 425 Deer 46 Animals 1948 Animals, Wild 187 Cross-Sectional Studies 35 Humans 1440 RNA, Viral 193 SARS-CoV-2 453 Odocoileus virginianus 11 SARS-CoV-2 variants 86

Evidence records

5 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE6703 Viral Detection
Key finding

SARS-CoV-2 RNA was detected in retropharyngeal lymph node samples from free-ranging white-tailed deer in New York during the 2020 and 2021 hunting seasons.

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

SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2.

Method
real-time RT-PCR (rRT-PCR)
Sample type
retropharyngeal lymph node samples
Geographic raw
State of New York (NY)
Country inferred
USA
Evidence type Reservoir Ecology
1 records
OVE6707 Reservoir Ecology
Key finding

White-tailed deer in New York maintained Alpha and Gamma variants of SARS-CoV-2 after these variants had disappeared from humans, indicating that deer populations may act as a wildlife reservoir.

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

Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans.

Method
SARS-CoV-2 real-time RT-PCR (rRT-PCR) | genomic sequence analysis
Sample type
retropharyngeal lymph node samples
Geographic raw
State of New York (NY)
Country inferred
USA
Transmission Evidence
2 records · 2 evidence types
Evidence type Outbreak Investigation
1 records
OVE6706 Outbreak Investigation
Key finding

SARS-CoV-2 variants Alpha and Delta were transmitted among white-tailed deer following initial human-to-deer spillover events in New York.

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

Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD in the State of New York (NY).

Method
real-time RT-PCR | genome sequencing | phylogenetic inference
Geographic raw
State of New York (NY)
Evidence type Cross-species Transmission
1 records
OVE6705 Cross-species Transmission
Key finding

Genomic analysis indicated multiple human-to-deer spillover events involving the Alpha and Delta lineages of SARS-CoV-2 in white-tailed deer in New York.

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

Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses.

Method
real-time RT-PCR | sequence analysis
Study design
genomic surveillance and sequence analysis of deer samples
Transmission direction
human-to-animal
Geographic raw
State of New York (NY)
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE6704 Phylogenetic Evolution
Key finding

Phylogenetic analysis of SARS‑CoV‑2 genomes from white‑tailed deer in New York revealed multiple viral lineages and cocirculation of the Alpha, Gamma, and Delta variants of concern.

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

Sequence analysis of SARS‑CoV‑2 genomes from 164 samples demonstrated the presence of multiple SARS‑CoV‑2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD.

Analysis methods
sequence analysis | phylogenetic analysis