Data from the article “An opportunistic survey reveals an unexpected coronavirus diversity hotspot in North America”

In summer 2020, 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 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 at the time. Among the samples which could be further characterized, 126 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2) were identified. Moreover, at least 10% (n=27) of the corona-virus-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 animals tested on mink farms and raise the possibility that commercial animal husbandry operations could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses.
Figure 1. Phylogenetic relationships of the identified coronaviruses from mink and other animals from mink farms in Utah. The four genera of coronaviruses are highlighted in different colors. AlphaCoV, alkphacoronavirus; BetaCoV, betacoronavirus; DeltaCoV, deltacoronaviruses; and GammaCoV, gammacoronavirus. Type species for the currently recognized subgenera are annotated according to the nomenclature scheme used in this manuscript with the addition of the ICTV subgenus. Additional viruses, including the closest GenBank entry as identified by the BLAST tool, were included to help delineate relationship. Red circles are viruses identified in this study. Panel A. Full phylogenetic tree (A full-size image is included in Supplementary Figure 1). Red arrows designate the group of nearly identical Utah mink coronavirus strains collapsed into the colored triangle in Panel B.
Table 1. Coronavirus distribution among species tested. The species are listed by their common names; Total, the total number of animals of each species tested; Negative, number of each species with no coronavirus detected among the tissues tested; Positive, number of animals positive for coronavirus in at least one tissue; % Pos, percentage of coronavirus positives in each species.
Table 2. Detailed tissue panel tested for SARS-CoV-2. The distribution of SARS-CoV-2 RNA detection in the first 96 animals is listed. Tissue, tissue or tissue pools received; Total, total number tested in each category; Negative, number of N1 RT-PCR negatives; Posi-tives, number of N1 RT-PCR positives; % Pos, percentage of tissues positive for corona-virus.
Table 3. Summary of coronaviruses identified. The distribution of coronaviruses detected and characterized according to their host is listed. Species, common name of animal species tested; AlphaCoV, number of alphacoronaviruses identified; BetaCoV, number of betacoronaviruses identified; Sequenced, number of viruses identified by sequencing, Unchar, number of coronavirus-positive samples not further characterized.
Table 4. SARS-CoV-2 coinfections identified in Utah mammals. The individual animals that are both SARS-CoV-2 positive and infected with a second coronavirus are listed. Animal ID, Unique animal identification number; Common name, common name of animal; Scientific name, scientific name of animal; Sex, F, female, M, male. Unk, un-known; Age, A adult, J juvenile, Unk, unknown; SARS-CoV-2, Neg-N1 RT-PCR nega-tive, Pos-N1 RT-PCR positive, Second strain, genus and common name of the coronavirus, Pan-CoV RT-PCR Equivocal, sample is PCR positive but not further characterized.
Supplementary Figure 1. Phylogenetic relationships of the identified coronaviruses from mink farms in Utah. The four genera of coronaviruses are highlighted in different colors. AlphaCoV, alkphacoronavirus; BetaCoV, betacoronavirus; DeltaCoV, deltacoronaviruses; and GammaCoV, gammacoronavirus. Type species for the currently recognized subgenera are annotated according to the nomenclature scheme used in this manuscript with the addition of the ICTV subgenus. Additional viruses, including the closest GenBank entry as identified by the BLAST tool were included to help delineate relationship. Red circles are viruses identified in this study.
Supplementary Table 1. List of animals and tissues sampled and RT-PCR test results. Animal ID, unique identifier for each animal; Specimen ID, unique identifier for each tissue; Common name, common name of the animal species; Scientific name, scientific name of the animal species, Sex, F-female, M-male, UNK-unknown; Age, J-juvenile, A-adult, UNK-unknown; Tissue, organ or organ pools tested; Tissue study, X denotes the animals and tissues used in the tissue distribution sub-study; N1 PCR, Ct values from the CDC N1 assay; Pan-CoV PCR, Neg, negative, Pos, positive, Equiv, equivocal; * wild mink.
Supplementary Table 2. Summary of coronavirus test results. Animal ID, unique identifier for each animal; Common name, common name of the animal species; Scientific name, scientific name of the animal species, Sex, F-female, M-male, UNK-unknown; Age, J-juvenile, A-adult, UNK-unknown; CoV, Neg-negative, Pos-positive on either one or both RT-PCR tests; SARS-CoV-2, animals positive in the CDC N1 test; AlphaCoV, the tissues positive for alphacoronavirus for each animal is listed; BetaCoV, the tissues positive for betacoronavirus for each animal is listed; C-colon, C/R-colon/rectum pool, H-heart, L-lung, L/S-live/spleen pool, S int-small intestine; Co-infections, Y-yes; PCR only, Y-yes; Virus identified by sequencing, brief name of virus identified.

Tags: alphacoronavirus, betacoronavirus, biota, coronavirus, deer-mouse, domestic-cat, house-mouse, mink, mink-farm, raccoon, sars-cov-2, striped-skunk, usgs-6113f248d34ed11898f82a94
Organization: Department of the Interior