OmniVira

Literature detail

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.
PMID 34696445 2021 Viruses eng epublish
PubMed DOI Browse context

Article

Publication summary

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% (<i>n</i> = 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.

coronavirus mink mink farm pandemic SARS-CoV-2 spill-over zoonosis Alphacoronavirus Animals Animals, Domestic Animals, Wild Cats COVID-19 Disease Hotspot Female Male Mephitidae Mice

Structured evidence records

Evidence records

5 total
Zoonotic Surveillance 2 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Animals from and around Utah mink farms, including domestic cats, mink, rodents, raccoons, and skunks, were surveilled for coronaviruses, with a high overall detection rate.

Virus
SARS-CoV-2
Location
United States Utah, United States
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. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus.

Method
sampling; testing
Geographic raw
Utah
Country inferred
United States
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Surveillance of animals on and near Utah mink farms detected alphacoronaviruses and betacoronaviruses among multiple cohabiting species.

Location
United States Utah, United States
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
testing
Geographic raw
Utah
Country inferred
United States
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.80
Key finding

Domestic cats, mink, rodents, raccoons, and skunks on or near Utah mink farms harbored diverse coronaviruses, implying possible transmission between different non-human animal species.

Location
United States Utah, United States
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... These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover.

Method
sampling; testing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
Utah
Country inferred
United States
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.65
Key finding

Genetic characterization revealed multiple alphacoronaviruses and betacoronaviruses, including SARS-CoV-2, among domestic and wild animals at mink farms in Utah.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

MeSH terms list 'Alphacoronavirus / genetics' and 'SARS-CoV-2 / genetics', which explicitly support genetic analysis of coronavirus sequences detected in animals sampled near mink farms.

Genes or proteins
whole genome
Analysis methods
genetic characterization
Spillover Event 1 records
Spillover Event Extraction confidence 0.90
Key finding

SARS-CoV-2 was detected in mink on Utah farms, consistent with human-to-mink spillback of the virus.

Virus
SARS-CoV-2
Location
United States Utah, United States
Supporting text

In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah.

Method
sampling; testing; virus detection
Study design
outbreak investigation
Transmission direction
human-to-animal
Geographic raw
Utah
Country inferred
United States