OmniVira

An Opportunistic Survey Reveals an Unexpected Coronavirus Diversity Hotspot in North America.

Hon S Ip1 Kathryn M Griffin1 Jeffrey D Messer1 Megan E Winzeler1 Susan A Shriner2 Mary Lea Killian3 Mia K Torchetti3 Thomas J DeLiberto2 Brian R Amman4 Caitlin M Cossaboom4 R Reid Harvey4 Natalie M Wendling4 Hannah Rettler5 Dean Taylor6 Jonathan S Towner4 Casey Barton Behravesh4 David S Blehert1
Affiliations 6 institutions
  1. United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch, Madison, WI 53711, USA.
  2. Wildlife Services, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA.
  3. National Veterinary Services Laboratories, Diagnostic Virology Laboratory, United States Department of Agriculture, Ames, IA 50010, USA.
  4. Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA 30329, USA.
  5. Utah Department of Health, Salt Lake City, UT 84114, USA.
  6. Utah Department of Agriculture and Food, Salt Lake City, UT 84116, USA.
PMID34696445 DOI10.3390/v13102016 Year2021 Journal Viruses Languageeng Statusepublish

Abstract

In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus. Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified. Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus. Our findings indicate an unexpectedly high prevalence of coronavirus among the domestic and wild free-roaming animals tested on mink farms. These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses.

Supporting text Virus Host Location
coronavirus 195 mink 58 mink farm 2 pandemic 15 SARS-CoV-2 550 spill-over 5 zoonosis 116 Alphacoronavirus 29 Animals 1948 Animals, Domestic 35 Animals, Wild 187 Cats 120 COVID-19 425 Disease Hotspot 1 Female 289 Male 224 Mephitidae 10 Mice 253 Mink 48 Raccoons 12 SARS-CoV-2 453 Utah 4

Evidence records

8 total
Zoonotic Surveillance
7 records · 1 evidence types
Evidence type Viral Detection
7 records
OVE5280 Viral Detection
Key finding

Seventy-four detections of SARS-CoV-2 were identified in mink.

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

Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified.

Method
viral identification | sequencing or classification
Sample type
characterized samples
OVE5278 Viral Detection
Key finding

SARS-CoV-2 was detected in animals sampled on or near affected mink farms.

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

An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses.

Method
testing | viral detection assay
Sample type
animal samples
OVE5279 Viral Detection
Key finding

Non-SARS coronaviruses were detected in animals sampled on or near affected mink farms.

Virus
Coronaviridae
Host
American mink Neogale vison Natural host
Location
Not specified
Supporting text

An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses.

Method
testing | viral detection assay
Sample type
animal samples
OVE5283 Viral Detection
Key finding

Coronaviruses were detected in 261 out of 365 animals, including domestic cats, mink, rodents, raccoons, and skunks, sampled on mink farms.

Virus
Coronaviridae
Host
domestic cat Felis catus Natural host American mink Neogale vison Natural host rodents Rodentia Natural host raccoon Procyon lotor Natural host skunks Mephitidae Natural host
Location
Not specified
Supporting text

Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus.

Method
viral detection assay
Sample type
animal samples
OVE5281 Viral Detection
Key finding

Alphacoronaviruses were identified among mink samples.

Virus
Alphacoronavirus
Host
American mink Neogale vison Natural host
Location
Not specified
Supporting text

Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified.

Method
viral identification | sequencing or classification
Sample type
characterized samples
OVE5282 Viral Detection
Key finding

Betacoronaviruses were identified among mink samples.

Virus
Betacoronavirus
Host
American mink Neogale vison Natural host
Location
Not specified
Supporting text

Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified.

Method
viral identification | sequencing or classification
Sample type
characterized samples
OVE5284 Viral Detection
Key finding

At least 27 coronavirus-positive animals were co-infected with more than one coronavirus.

Virus
Coronaviridae
Host
American mink Neogale vison Natural host
Location
Not specified
Supporting text

Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus.

Method
viral detection assay
Sample type
animal samples
Transmission Evidence
1 records · 1 evidence types
Evidence type Outbreak Investigation
1 records
OVE5277 Outbreak Investigation
Key finding

An interagency One Health outbreak investigation was initiated after SARS-CoV-2 was detected on mink farms in Utah in summer 2020.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
American mink Neogale vison Natural host
Location
United States
Supporting text

In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak.

Method
field sampling | virus detection | One Health outbreak response
Transmission direction
same-species transmission
Geographic raw
Utah
Country inferred
USA
Outbreak setting
mink farms
Outbreak time
summer 2020
Outbreak scale
extent of the outbreak (not quantified)