Epidemiologic and Genomic Evidence for Zoonotic Transmission of SARS-CoV-2 among People and Animals on a Michigan Mink Farm, United States, 2020.

Ria R Ghai1 Anne Straily1 Nora Wineland2 Jennifer Calogero2 Mary Grace Stobierski3 Kimberly Signs3 Melissa Blievernicht2 Yaritbel Torres-Mendoza1 Michelle A Waltenburg1 Jillian A Condrey1 Heather M Blankenship3 Diana Riner3 Nancy Barr2 Michele Schalow2 Jarold Goodrich2 Cheryl Collins2 Ausaf Ahmad1 John Michael Metz1 Owen Herzegh1 Kelly Straka4 Dustin M Arsnoe5 Anthony G Duffiney5 Susan A Shriner5 Markus H Kainulainen1 Ann Carpenter1 Florence Whitehill1 Natalie M Wendling1 Robyn A Stoddard1 Adam C Retchless1 Anna Uehara1 Ying Tao1 Yan Li1 Jing Zhang1 Suxiang Tong1 Casey Barton Behravesh1
Affiliations 5 institutions
  1. U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
  2. Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA.
  3. Michigan Department of Health and Human Services, Lansing, MI 48909, USA.
  4. Michigan Department of Natural Resources, Lansing, MI 48909, USA.
  5. U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA.

Abstract

Farmed mink are one of few animals in which infection with SARS-CoV-2 has resulted in sustained transmission among a population and spillback from mink to people. In September 2020, mink on a Michigan farm exhibited increased morbidity and mortality rates due to confirmed SARS-CoV-2 infection. We conducted an epidemiologic investigation to identify the source of initial mink exposure, assess the degree of spread within the facility's overall mink population, and evaluate the risk of further viral spread on the farm and in surrounding wildlife habitats. Three farm employees reported symptoms consistent with COVID-19 the same day that increased mortality rates were observed among the mink herd. One of these individuals, and another asymptomatic employee, tested positive for SARS-CoV-2 by real-time reverse transcription PCR (RT-qPCR) 9 days later. All but one mink sampled on the farm were positive for SARS-CoV-2 based on nucleic acid detection from at least one oral, nasal, or rectal swab tested by RT-qPCR (99%). Sequence analysis showed high degrees of similarity between sequences from mink and the two positive farm employees. Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink. However, the specific source of virus introduction onto the farm was not identified. Three companion animals living with mink farm employees and 31 wild animals of six species sampled in the surrounding area were negative for SARS-CoV-2 by RT-qPCR. Results from this investigation support the necessity of a One Health approach to manage the zoonotic spread of SARS-CoV-2 and underscores the critical need for multifaceted public health approaches to prevent the introduction and spread of respiratory viruses on mink farms.

Supporting text Virus Host Location
animal 6 coronavirus 195 COVID-19 467 mink 58 Neogale vison 3 One Health 98 SARS-CoV-2 550 zoonotic disease 19 COVID-19 425 Nucleic Acids 2 Animals 1948 Animals, Wild 187 Farms 30 Genomics 32 Humans 1440 Michigan 2 Mink 48 SARS-CoV-2 453

Evidence records

7 total
Zoonotic Surveillance
3 records · 1 evidence types
Evidence type
3 records
OVE7657
Key finding

Nearly all mink sampled on the Michigan farm were positive for SARS-CoV-2 by nucleic acid detection using RT-qPCR.

Virus
Host
Location
Supporting text

All but one mink sampled on the farm were positive for SARS-CoV-2 based on nucleic acid detection from at least one oral, nasal, or rectal swab tested by RT-qPCR (99%).

Method
RT-qPCR
Sample type
oral swab | nasal swab | rectal swab
Geographic raw
Michigan farm
OVE7658
Key finding

Three companion animals and 31 wild animals sampled in the surrounding area near the Michigan mink farm were negative for SARS-CoV-2 by RT-qPCR.

Virus
Host
Not specified
Location
Supporting text

Three companion animals living with mink farm employees and 31 wild animals of six species sampled in the surrounding area were negative for SARS-CoV-2 by RT-qPCR.

Method
RT-qPCR
Sample type
unspecified animal samples
Geographic raw
surrounding area | Michigan
Country inferred
USA
OVE7656
Key finding

Two farm employees tested positive for SARS-CoV-2 by RT-qPCR nine days after mink mortality was observed on the Michigan farm.

Virus
Host
Location
Not specified
Supporting text

One of these individuals, and another asymptomatic employee, tested positive for SARS-CoV-2 by real-time reverse transcription PCR (RT-qPCR) 9 days later.

Method
real-time reverse transcription PCR (RT-qPCR)
Sample type
diagnostic specimen
Transmission Evidence
2 records · 2 evidence types
Evidence type
1 records
OVE7660
Key finding

Epidemiologic and genomic data indicate a mink-to-human spillover of SARS-CoV-2 at a Michigan mink farm, with infected employees acquiring COVID-19 from mink.

Virus
Host
Location
Supporting text

Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink.

Method
RT-qPCR | genomic sequencing
Study design
epidemiologic investigation with genomic comparison
Transmission direction
animal-to-human
Geographic raw
Michigan farm | Michigan mink farm
Evidence type
1 records
OVE7655
Key finding

An outbreak of SARS-CoV-2 infection occurred among farmed mink in Michigan, United States, in September 2020, with increased morbidity and mortality confirmed by RT-qPCR testing.

Virus
Host
Location
Supporting text

In September 2020, mink on a Michigan farm exhibited increased morbidity and mortality rates due to confirmed SARS-CoV-2 infection.

Method
epidemiologic investigation | RT-qPCR | genomic sequencing
Transmission direction
same-species transmission
Geographic raw
Michigan, United States
Outbreak setting
Michigan mink farm
Outbreak time
September 2020
Outbreak scale
increased morbidity and mortality across herd; 99% of sampled mink positive by RT-qPCR
Functional Mechanism
1 records · 1 evidence types
Evidence type
1 records
OVE7661
Key finding

SARS-CoV-2 genomes from mink and farm workers carried F486L and N501T mutations believed to arise through mink adaptation.

Virus
Host
Location
Not specified
Supporting text

Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink.

Genes or proteins
spike protein
Mutations
F486L | N501T
Mechanism types
host-range expansion | receptor binding
Genomic Evolution
1 records · 1 evidence types
Evidence type
1 records
OVE7659
Key finding

SARS-CoV-2 sequences from mink and the two positive farm employees were highly similar, indicating a close viral lineage relationship on the Michigan mink farm.

Virus
Host
Location
Not specified
Supporting text

Sequence analysis showed high degrees of similarity between sequences from mink and the two positive farm employees. Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink.

Genes or proteins
F486L | N501T
Analysis methods
sequence analysis