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Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands.

Lu Lu1 Reina S Sikkema2 Francisca C Velkers3 David F Nieuwenhuijse2 Egil A J Fischer3 Paola A Meijer3 Noortje Bouwmeester-Vincken4 Ariene Rietveld5 Marjolijn C A Wegdam-Blans6 Paulien Tolsma7 Marco Koppelman8 Lidwien A M Smit9 Renate W Hakze-van der Honing10 Wim H M van der Poel10 Arco N van der Spek11 Marcel A H Spierenburg11 Robert Jan Molenaar12 Jan de Rond12 Marieke Augustijn12 Mark Woolhouse1 J Arjan Stegeman3 Samantha Lycett13 Bas B Oude Munnink2 Marion P G Koopmans14
Affiliations 14 institutions
  1. Usher Institute, University of Edinburgh, Edinburgh, UK.
  2. Erasmus MC, Department of Viroscience, WHO Collaborating Centre, Rotterdam, the Netherlands.
  3. Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
  4. Municipal Health Service GGD Limburg-Noord, Venlo, the Netherlands.
  5. Municipal Health Service GGD Hart voor Brabant, Tilburg, the Netherlands.
  6. Stichting PAMM, Veldhoven, the Netherlands.
  7. Municipal Health Service GGD Brabant-Zuidoost, Eindhoven, the Netherlands.
  8. Sanquin Blood Supply Foundation, Amsterdam, the Netherlands.
  9. Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
  10. Wageningen Bioveterinary Research, Lelystad, the Netherlands.
  11. Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands.
  12. GD Animal Health, Deventer, the Netherlands.
  13. Roslin Institute, University of Edinburgh, Edinburgh, UK.
  14. Erasmus MC, Department of Viroscience, WHO Collaborating Centre, Rotterdam, the Netherlands. [email protected].
PMID 34815406 2021 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms. High number of farm infections (68/126) in minks and farm workers (>50% of farms) were detected, with limited community spread. Three of five initial introductions of SARS-CoV-2 led to subsequent spread between mink farms until November 2020. Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combining genetic information with epidemiological information when investigating outbreaks at the animal-human interface.

Evolution, Molecular Farms Amino Acid Sequence Animal Diseases Animals Bayes Theorem COVID-19 Disease Outbreaks Humans Mink Netherlands Phylogeny SARS-CoV-2 Sequence Analysis, Protein Spike Glycoprotein, Coronavirus spike protein, SARS-CoV-2

Structured evidence records

Evidence records

5 total
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.95
Key finding

SARS-CoV-2 spread between distinct mink farms, indicating animal-to-animal transmission among minks.

Virus
SARS-CoV-2
Location
Netherlands Netherlands
Supporting text

Three of five initial introductions of SARS-CoV-2 led to subsequent spread between mink farms until November 2020.

Method
genomic sequencing; Bayesian phylodynamic methods
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
Netherlands
Country inferred
Netherlands
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.90
Key finding

Bayesian phylodynamic analysis of SARS-CoV-2 genomes from minks and humans showed a Spike position 486 substitution associated with accelerated viral evolution and extended spread among mink farms.

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

Genomic sequencing was performed on mink farms and farm personnel, and sequence data with Bayesian phylodynamic methods were used to explore SARS-CoV-2 transmission. Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely.

Genes or proteins
Spike; receptor binding domain
Analysis methods
genomic sequencing; Bayesian phylodynamic analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.90
Key finding

SARS-CoV-2 strains from farmed minks developed a substitution at position 486 in the spike receptor-binding domain, indicating molecular adaptation during outbreaks.

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

Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely.

Genes or proteins
Spike protein
Mutations
position 486 substitution
Mechanism types
receptor_binding; molecular_adaptation
Outbreak Investigation 1 records
Outbreak Investigation Extraction confidence 0.95
Key finding

SARS-CoV-2 outbreaks occurred in farmed minks and associated humans, with sequence analysis showing transmission within and between farms.

Virus
SARS-CoV-2
Location
Netherlands Netherlands
Supporting text

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms.

Method
genomic sequencing; Bayesian phylodynamic methods
Transmission direction
animal-to-human
Geographic raw
Netherlands
Country inferred
Netherlands
Outbreak setting
mink farms
Outbreak time
April-November 2020
Outbreak scale
68/126 minks infected, >50% of farms affected
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

SARS-CoV-2 transmitted between minks and humans on mink farms in the Netherlands, indicating animal-human interface spillover events.

Virus
SARS-CoV-2
Location
Netherlands Netherlands
Supporting text

SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. The study describes SARS-CoV-2 transmission in minks and humans on farms in the Netherlands.

Method
genomic sequencing; Bayesian phylodynamic analysis
Study design
outbreak investigation
Transmission direction
animal-to-human
Geographic raw
Netherlands
Country inferred
Netherlands