OmniVira

Paired SARS-CoV-2 spike protein mutations observed during ongoing SARS-CoV-2 viral transfer from humans to minks and back to humans.

Scott Burkholz1 Suman Pokhrel2 Benjamin R Kraemer2 Daria Mochly-Rosen2 Richard T Carback1 Tom Hodge1 Paul Harris3 Serban Ciotlos1 Lu Wang1 C V Herst1 Reid Rubsamen4,5,6
Affiliations 6 institutions
  1. Flow Pharma, Inc., 4829 Galaxy Parkway, Suite K, Warrensville Heights, OH 44128, United States of America.
  2. Department of Chemical and Systems Biology, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, United States of America.
  3. Department of Medicine, College of Physicians and Surgeons, Columbia University, 630 W 168th St, New York, NY 10032, United States of America.
  4. Flow Pharma, Inc., 4829 Galaxy Parkway, Suite K, Warrensville Heights, OH 44128, United States of America
  5. Department of Anesthesiology and Perioperative Medicine, University Hospitals, Cleveland Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, OH 44106, United States of America
  6. Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114, United States of America. Electronic address: [email protected].
PMID33971305 DOI10.1016/j.meegid.2021.104897 Year2021 Journal Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Infect Genet Evol Languageeng Statusppublish

Abstract

A mutation analysis of SARS-CoV-2 genomes collected around the world sorted by sequence, date, geographic location, and species has revealed a large number of variants from the initial reference sequence in Wuhan. This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.

Supporting text Virus Host Location
Bioinformatics 6 Mink 58 Mutation 222 Next-generation sequencing 7 SARS-CoV-2 550 Zoonotic 23 Mutation 209 Angiotensin-Converting Enzyme 2 177 Animals 1948 Binding Sites 89 Canada 8 COVID-19 425 Denmark 7 Humans 1440 Mink 48 Netherlands 12 Phylogeny 805 SARS-CoV-2 453 Spike Glycoprotein, Coronavirus 274 United States 46 ACE2 protein, human 87 spike protein, SARS-CoV-2 157

Evidence records

3 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Reservoir Ecology
1 records
OVE4773 Reservoir Ecology
Key finding

SARS-CoV-2 has transferred from humans to mink populations and back to humans, and attention to viral transfer from humans to farm animals and pets is required to prevent formation of animal reservoirs facilitating future zoonotic transfer.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
American mink Neogale vison Natural host animals Metazoa Context pending
Location
Netherlands Denmark United States Canada
Supporting text

This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.

Method
mutation analysis
Geographic raw
Netherlands | Denmark | United States | Canada
Country inferred
NLD | DNK | USA | CAN
Transmission Evidence
2 records · 2 evidence types
Evidence type Spillover Event
1 records
OVE4771 Spillover Event
Key finding

SARS-CoV-2 variants that evolved in minks were transmitted back into humans, indicating mink-to-human spillover.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
human Homo sapiens Natural host Mustela Natural host
Location
Netherlands Denmark
Supporting text

In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer.

Method
genomic sequencing | mutation analysis | phylogenetic comparison
Study design
comparative viral genome analysis identifying reversely transmitted mink variants
Transmission direction
animal-to-human
Geographic raw
Netherlands | Denmark
Country inferred
NLD | DNK
Evidence type Cross-species Transmission
1 records
OVE4770 Cross-species Transmission
Key finding

Humans infected with SARS-CoV-2 transmitted the virus to mink populations in four countries.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
American mink Neogale vison Natural host human Homo sapiens Natural host
Location
Netherlands Denmark United States Canada
Supporting text

This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada.

Method
genomic sequencing | mutation analysis
Study design
genomic mutation analysis comparing human and animal SARS-CoV-2 sequences
Transmission direction
human-to-animal
Geographic raw
Netherlands | Denmark | United States | Canada