OmniVira

Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA.

Hannah W Despres1 Margaret G Mills2 Madaline M Schmidt1 Jolene Gov2 Yael Perez2 Mars Jindrich2 Allison M L Crawford2 Warren T Kohl2 Elias Rosenblatt3 Hannah C Kubinski1 Benjamin C Simmons4 Miles C Nippes4 Anne J Goldenberg4 Kristina E Murtha4 Samantha Nicoloro4 Mia J Harris4 Avery C Feeley4 Taylor K Gelinas4 Maeve K Cronin4 Robert S Frederick4 Matthew Thomas4 Meaghan E Johnson4 James Murphy4 Elle B Lenzini4 Peter A Carr4 Danielle H Berger4 Soham P Mehta4 Christopher J Floreani4 Amelia C Koval4 Aleah L Young4 Jess H Fish4 Jack Wallace4 Ella Chaney4 Grace Ushay4 Rebecca S Ross4 Erin M Vostal4 Maya C Thisner4 Kyliegh E Gonet4 Owen C Deane4 Kari R Pelletiere4 Vegas C Rockafeller4 Madeline Waterman4 Tyler W Barry4 Catriona C Goering4 Sarah D Shipman4 Allie C Shiers4 Claire E Reilly4 Alanna M Duff4 Sarah L Madruga4 David J Shirley5 Keith R Jerome2,6 Ailyn C Pérez-Osorio2 Alexander L Greninger2,6 Nick Fortin7 Brittany A Mosher8 Emily A Bruce9
Affiliations 9 institutions
  1. Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
  2. Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
  3. Rubenstein School of Environment and Natural Resources, University of Vermont, 81 Carrigan Dr, Burlington, VT, 05405, USA.
  4. Wildlife and Fisheries Society, Wildlife Society Chapter, University of Vermont, Burlington, VT, 05405, USA.
  5. Department of Engineering, Faraday, Inc., Burlington, VT, 05405, USA.
  6. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
  7. Fish and Wildlife Department, Vermont Agency of Natural Resources, Rutland, VT, 05701, USA.
  8. Rubenstein School of Environment and Natural Resources, University of Vermont, 81 Carrigan Dr, Burlington, VT, 05405, USA. [email protected].
  9. Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA. [email protected].
PMID37674004 DOI10.1038/s41598-023-39232-0 Year2023 Journal Scientific reports Sci Rep Languageeng Publication statusActive
Active Last checked 2026-10-02 03:30:39 Source: NCBI PubMed

Abstract

Previous studies have documented natural infections of SARS-CoV-2 in various domestic and wild animals. More recently, studies have been published noting the susceptibility of members of the Cervidae family, and infections in both wild and captive cervid populations. In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Surprisingly, we initially detected a number of N1 and/or N2 positive samples with high cycle threshold values, though after conducting environmental swabbing of the laboratory and verifying with a second independent primer set (WHO-E) and PCR without reverse transcriptase, we showed that these were false positives due to plasmid contamination from a construct expressing the N gene in the general laboratory environment. Our final results indicate that no sampled wildlife were positive for SARS-CoV-2 RNA, and highlight the importance of physically separate locations for the processing of samples for surveillance and experiments that require the use of plasmid DNA containing the target RNA sequence. These negative findings are surprising, given that most published North America studies have found SARS-CoV-2 within their deer populations. The absence of SARS-CoV-2 RNA in populations sampled here may provide insights in to the various environmental and anthropogenic factors that reduce spillover and spread in North American's wildlife populations.

Supporting text Virus Host Location
COVID-19 427 Coyotes 3 Deer 47 Lynx 7 Otters 3 Animals 1981 Animals, Wild 193 Foxes 17 RNA, Viral 194 SARS-CoV-2 456 Vermont 1 Odocoileus virginianus 11

Evidence records

1 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE7326 Viral Detection
Key finding

Quantitative RT-qPCR testing of 739 wildlife samples in Vermont detected no SARS-CoV-2 RNA after confirming initial positives were due to plasmid contamination.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
red fox Vulpes vulpes Natural host gray fox Urocyon cinereoargenteus Natural host fisher Pekania pennanti Natural host Northern American river otter Lontra canadensis Natural host coyote Canis latrans Natural host bobcat Lynx rufus Natural host American black bear Ursus americanus Natural host white-tailed deer Odocoileus virginianus Natural host
Location
United States
Supporting text

In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Our final results indicate that no sampled wildlife were positive for SARS-CoV-2 RNA.

Method
quantitative RT-qPCR | CDC N1/N2 primer set | WHO-E gene primer set
Sample type
nasal samples | throat samples
Geographic raw
Vermont
Country inferred
USA