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Literature detail

Transmission of SARS-CoV-2 from humans to animals and potential host adaptation.

Cedric C S Tan1,2 Su Datt Lam3,4 Damien Richard5,6 Christopher J Owen5 Dorothea Berchtold5 Christine Orengo4 Meera Surendran Nair7,8 Suresh V Kuchipudi7,8 Vivek Kapur8,9 Lucy van Dorp5 François Balloux5
Affiliations 9 institutions
  1. UCL Genetics Institute, University College London, London, UK. [email protected].
  2. Genome Institute of Singapore, A*STAR, Singapore, Singapore. [email protected].
  3. Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.
  4. Department of Structural and Molecular Biology, University College London, London, UK.
  5. UCL Genetics Institute, University College London, London, UK.
  6. Division of Infection and Immunity, University College London, London, UK.
  7. Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA, Pennsylvania, USA.
  8. Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, Pennsylvania, USA.
  9. Department of Animal Science, The Pennsylvania State University, PA, Pennsylvania, USA.
PMID 35624123 2022 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

SARS-CoV-2, the causative agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. Understanding the extent of adaptation to these animal hosts is critical for assessing the threat that the spillback of animal-adapted SARS-CoV-2 into humans poses. We compare the genomic landscapes of SARS-CoV-2 isolated from animal species to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focus on viral genomes isolated from mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported. We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V), and one in deer (NSP3a_L1035F), though they appear to confer a minimal advantage for human-to-human transmission. No considerable changes to the mutation rate or evolutionary trajectory of SARS-CoV-2 has resulted from circulation in mink and deer thus far. Our findings suggest that minimal adaptation was required for onward transmission in mink and deer following human-to-animal spillover, highlighting the 'generalist' nature of SARS-CoV-2 as a mammalian pathogen.

COVID-19 Deer Animals Host Adaptation Humans Pandemics SARS-CoV-2

Structured evidence records

Evidence records

8 total
Cross Species Transmission 2 records
Cross Species Transmission Extraction confidence 0.90
Key finding

Onward animal-to-animal transmission of SARS-CoV-2 was reported within mink populations after human-to-animal spillover.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

We focus on viral genomes isolated from mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported.

Method
genomic analysis
Study design
outbreak investigation
Transmission direction
animal-to-animal
Cross Species Transmission Extraction confidence 0.90
Key finding

Onward animal-to-animal transmission of SARS-CoV-2 was reported within white-tailed deer populations after human-to-animal spillover.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

We focus on viral genomes isolated from mink (Neovison vison) and white-tailed deer (Odocoileus virginianus) for which multiple independent outbreaks driven by onward animal-to-animal transmission have been reported.

Method
genomic analysis
Study design
outbreak investigation
Transmission direction
animal-to-animal
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.90
Key finding

Genomic comparison of SARS-CoV-2 from mink and humans revealed five candidate mutations associated with mink-specific adaptation, demonstrating limited evolutionary change during spillover.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

We compare the genomic landscapes of SARS-CoV-2 isolated from animal species to that in humans, profiling the mutational biases indicative of potentially different selective pressures in animals. We focus on viral genomes isolated from mink ... We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V).

Genes or proteins
NSP9; Spike; ORF3a
Analysis methods
genomic comparison; mutational profiling
Genomic Evolution Extraction confidence 0.90
Key finding

Analysis of SARS-CoV-2 genomes from white-tailed deer identified one mutation, NSP3a_L1035F, suggesting minimal adaptation during spillover.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

We focus on viral genomes isolated from ... white-tailed deer (Odocoileus virginianus) ... We identify one candidate mutation for animal-specific adaptation in deer (NSP3a_L1035F), though it appears to confer a minimal advantage for human-to-human transmission.

Genes or proteins
NSP3a
Analysis methods
genomic comparison; mutational profiling
Molecular Adaptation 2 records
Molecular Adaptation Extraction confidence 0.95
Key finding

Five SARS-CoV-2 mutations in mink were identified as candidates for animal-specific molecular adaptation.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

We identify five candidate mutations for animal-specific adaptation in mink (NSP9_G37E, Spike_F486L, Spike_N501T, Spike_Y453F, ORF3a_L219V).

Genes or proteins
NSP9; Spike; ORF3a
Mutations
NSP9_G37E; Spike_F486L; Spike_N501T; Spike_Y453F; ORF3a_L219V
Mechanism types
host_adaptation
Molecular Adaptation Extraction confidence 0.95
Key finding

A SARS-CoV-2 NSP3a_L1035F mutation in white-tailed deer was identified as a candidate for animal-specific molecular adaptation with minimal impact on human transmission.

Virus
SARS-CoV-2
Host
Not specified
Location
Not specified
Supporting text

We identify ... one in deer (NSP3a_L1035F), though they appear to confer a minimal advantage for human-to-human transmission.

Genes or proteins
NSP3a
Mutations
NSP3a_L1035F
Mechanism types
host_adaptation
Spillover Event 2 records
Spillover Event Extraction confidence 0.95
Key finding

SARS-CoV-2 was transmitted from humans to mink populations following initial human outbreaks.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. We focus on viral genomes isolated from mink (Neovison vison)... following human-to-animal spillover.

Method
genome sequencing; phylogenetic analysis
Study design
genomic surveillance
Transmission direction
human-to-animal
Spillover Event Extraction confidence 0.95
Key finding

SARS-CoV-2 was transmitted from humans to white-tailed deer following human outbreaks.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. We focus on viral genomes isolated from ... white-tailed deer (Odocoileus virginianus)... following human-to-animal spillover.

Method
genome sequencing; phylogenetic analysis
Study design
genomic surveillance
Transmission direction
human-to-animal