OmniVira

SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City.

Kurt J Vandegrift1,2 Michele Yon3 Meera Surendran Nair3,4 Abhinay Gontu3,4 Santhamani Ramasamy3,4 Saranya Amirthalingam3,4 Sabarinath Neerukonda5 Ruth H Nissly3,4 Shubhada K Chothe3,4 Padmaja Jakka3,4 Lindsey LaBella3,4 Nicole Levine6 Sophie Rodriguez6 Chen Chen7 Veda Sheersh Boorla7 Tod Stuber8 Jason R Boulanger9 Nathan Kotschwar9 Sarah Grimké Aucoin10 Richard Simon10 Katrina L Toal10 Randall J Olsen11,12 James J Davis13,14 Dashzeveg Bold15 Natasha N Gaudreault15 Krishani Dinali Perera15 Yunjeong Kim15 Kyeong-Ok Chang15 Costas D Maranas7 Juergen A Richt15 James M Musser11,12 Peter J Hudson1,2 Vivek Kapur2,6 Suresh V Kuchipudi2,3,4
Affiliations 15 institutions
  1. Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
  2. The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
  3. Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
  4. Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
  5. United States Department of Health and Human Services, Silver Spring, MD 20993, USA.
  6. Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA.
  7. Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
  8. National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, IA 50010, USA.
  9. White Buffalo, Inc., Chester, CT 06412, USA.
  10. City of New York Parks & Recreation, New York, NY 10029, USA.
  11. Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA.
  12. Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA.
  13. Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.
  14. Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA.
  15. Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA.
PMID36560774 DOI10.3390/v14122770 Year2022 Journal Viruses Languageeng Statusepublish

Abstract

There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.

Supporting text Virus Host Location
disease ecology 7 enzootic transmission 1 Odocoileus virginianus 14 omicron 9 reinfection 3 reservoir competence 1 SARS-CoV-2 550 spillover 105 variant of concern 5 white-tailed deer 11 zoonotic 23 COVID-19 425 Deer 46 Animals 1948 Animals, Wild 187 Humans 1440 New York City 3 RNA, Viral 193 SARS-CoV-2 453 Odocoileus virginianus 11 SARS-CoV-2 variants 86

Evidence records

5 total
Zoonotic Surveillance
4 records · 3 evidence types
Evidence type Viral Detection
2 records
OVE6624 Viral Detection
Key finding

SARS-CoV-2 RNA, including Omicron and Delta variants, was detected in nasopharyngeal swabs from wild white-tailed deer on Staten Island, New York.

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

Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta).

Method
RNA detection | RT-PCR
Sample type
nasopharyngeal swabs
Geographic raw
Staten Island, New York
Country inferred
USA
OVE6627 Viral Detection
Key finding

Humans infected wild white‑tailed deer with SARS‑CoV‑2, demonstrating a human‑to‑animal spillover event in New York City.

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

Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City.

Method
nasopharyngeal swab RT-PCR for viral RNA detection | serological antibody testing
Geographic raw
New York City | Staten Island
Evidence type Serological Evidence
1 records
OVE6625 Serological Evidence
Key finding

Antibodies to SARS-CoV-2 were detected in serum samples from wild white-tailed deer on Staten Island, New York, indicating prior viral exposure.

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

Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage.

Method
serological test | antibody detection
Sample type
serum samples
Evidence type Reservoir Ecology
1 records
OVE6628 Reservoir Ecology
Key finding

SARS-CoV-2 variants of concern were observed to continue circulating and potentially reinfecting US deer populations, suggesting establishment of enzootic transmission cycles in the wild.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
deer Cervidae Natural host
Location
United States
Supporting text

Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild.

Method
wildlife surveillance | ecological inference from observed circulation patterns
Geographic raw
US
Country inferred
USA
Transmission Evidence
1 records · 1 evidence types
Evidence type Outbreak Investigation
1 records
OVE6626 Outbreak Investigation
Key finding

SARS-CoV-2 transmission occurred between wild white-tailed deer, indicating animal-to-animal spread within this species in New York City.

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

Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants.

Method
nasopharyngeal swabs | RT-PCR | serology
Geographic raw
New York City