OmniVira

SARS-CoV-2 Delta variant re-emerges in US farmed mink and free-ranging white-tailed deer in 2022-2023.

Alvin Crespo-Bellido1,2 Madison C Owsiany1 Natalie N Chillson1 Devra Huey1 Dillon S McBride1 Phillippe Lemey3 Steven I Rekant4 John Korslund4 Michael Neafsey4 Mary Lea Killian5 Jeffrey C Chandler6 Challis Hobbs7 Hugh H Hildebrandt8 John Easley7 Jacob S Yount9 Martha I Nelson2 Andrew S Bowman10
Affiliations 10 institutions
  1. Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA.
  2. Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  3. Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
  4. Veterinary Services, Animal and Plant Health Inspection Service, Beltsville, MD, USA.
  5. National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA.
  6. National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA.
  7. Fur Commission USA, Preston, ID, USA.
  8. Fur Care LLC, Medford, WI, USA.
  9. Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH, USA.
  10. Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA. [email protected].
PMID42425991 DOI10.1038/s41467-026-75363-4 Year2026 Journal Nature communications Nat Commun Languageeng Statusaheadofprint

Abstract

American mink (Neogale vison) are susceptible to SARS-CoV-2, but little is known about virus circulation in mink since 2021. Here, in the first active surveillance study of SARS-CoV-2 in apparently healthy farmed mink in the United States, we find a ~0.9% (760/85,656) RT-PCR positivity rate among nasal swabs collected in 18 farms across six states during 2022-2023. Phylogenetic analysis of 293 viral genome sequences shows that human-adapted SARS-CoV-2 variants (e.g., Omicron) repeatedly spill over into mink. Surprisingly, the detection of a Delta lineage virus (AY.39) on a mink farm four months after its last detection in humans within the same state suggests prolonged unsampled transmission. The spread of mink-adapted AY.39 viruses from a mink farm to neighboring free-ranging white-tailed deer represents a rare instance of SARS-CoV-2 transmission between livestock and wildlife. These findings demonstrate the value of active surveillance for identifying subclinical infections and interspecies transmission between humans, mink, and wildlife.

Supporting text Virus Host Location

Evidence records

5 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE11727 Viral Detection
Key finding

RT-PCR detected SARS-CoV-2 in nasal swabs from farmed mink in the United States with ~0.9% positivity (760/85,656) across 18 farms in six states during 2022-2023.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
weasel, mink, badger, martens and others Mustelidae Natural host American mink Neogale vison Natural host
Location
United States six states
Supporting text

Here, in the first active surveillance study of SARS-CoV-2 in apparently healthy farmed mink in the United States, we find a ~0.9% (760/85,656) RT-PCR positivity rate among nasal swabs collected in 18 farms across six states during 2022-2023.

Method
RT-PCR
Sample type
nasal swabs
Geographic raw
United States | six states
Country inferred
USA
Transmission Evidence
2 records · 2 evidence types
Evidence type Outbreak Investigation
1 records
OVE11731 Outbreak Investigation
Key finding

Active surveillance in US farmed mink during 2022–2023 detected subclinical SARS-CoV-2 infections and interspecies transmission involving humans, mink, and wildlife.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
American mink Neogale vison Natural host white-tailed deer Odocoileus virginianus Natural host weasel, mink, badger, martens and others Mustelidae Natural host human Homo sapiens Natural host
Location
United States
Supporting text

Here, in the first active surveillance study of SARS-CoV-2 in apparently healthy farmed mink in the United States, we find a ~0.9% (760/85,656) RT-PCR positivity rate among nasal swabs collected in 18 farms across six states during 2022-2023. The spread of mink-adapted AY.39 viruses from a mink farm to neighboring free-ranging white-tailed deer represents a rare instance of SARS-CoV-2 transmission between livestock and wildlife.

Method
active surveillance | RT-PCR | phylogenetic analysis | viral genome sequencing
Transmission direction
cross-species transmission
Geographic raw
United States
Country inferred
USA
Outbreak setting
farmed mink in the United States; neighboring free-ranging wildlife
Outbreak time
2022–2023
Outbreak scale
RT-PCR positivity ~0.9% (760/85,656) among nasal swabs from 18 farms across six states; detection of Delta lineage virus (AY.39) on a mink farm; spread to neighboring free-ranging white-tailed deer
Evidence type Cross-species Transmission
1 records
OVE11730 Cross-species Transmission
Key finding

Mink-adapted SARS-CoV-2 Delta lineage AY.39 spread from a mink farm to neighboring free-ranging white-tailed deer.

Virus
AY.39 Severe acute respiratory syndrome coronavirus 2
Host
white-tailed deer Odocoileus virginianus Natural host American mink Neogale vison Natural host mink farm Natural host
Location
Not specified
Supporting text

The spread of mink-adapted AY.39 viruses from a mink farm to neighboring free-ranging white-tailed deer represents a rare instance of SARS-CoV-2 transmission between livestock and wildlife.

Method
RT-PCR | phylogenetic analysis | viral genome sequencing
Study design
active surveillance with phylogenetic analysis
Transmission direction
animal-to-animal
Genomic Evolution
2 records · 1 evidence types
Evidence type Phylogenetic Evolution
2 records
OVE11728 Phylogenetic Evolution
Key finding

Phylogenetic analysis of 293 SARS-CoV-2 genomes indicates repeated spillovers of human-adapted variants, including Omicron, into mink.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
American mink Neogale vison Natural host
Location
Not specified
Supporting text

Phylogenetic analysis of 293 viral genome sequences shows that human-adapted SARS-CoV-2 variants (e.g., Omicron) repeatedly spill over into mink.

Genes or proteins
genome | viral genome sequences
Analysis methods
Phylogenetic analysis
OVE11729 Phylogenetic Evolution
Key finding

Detection of SARS-CoV-2 Delta lineage AY.39 in mink four months after its last detection in humans in the same state supports prolonged unsampled transmission.

Virus
Delta lineage virus AY.39
Host
American mink Neogale vison Natural host human Homo sapiens Natural host
Location
Not specified
Supporting text

the detection of a Delta lineage virus (AY.39) on a mink farm four months after its last detection in humans within the same state suggests prolonged unsampled transmission.

Genes or proteins
genome
Analysis methods
Phylogenetic analysis | Temporal comparison of lineage detection