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

• Published in: Nature communications Vol. 12; no. 1; p. 6802
• Main Authors: Lu, Lu, Sikkema, Reina S., Velkers, Francisca C., Nieuwenhuijse, David F., Fischer, Egil A. J., Meijer, Paola A., Bouwmeester-Vincken, Noortje, Rietveld, Ariene, Wegdam-Blans, Marjolijn C. A., Tolsma, Paulien, Koppelman, Marco, Smit, Lidwien A. M., Hakze-van der Honing, Renate W., van der Poel, Wim H. M., van der Spek, Arco N., Spierenburg, Marcel A. H., Molenaar, Robert Jan, Rond, Jan de, Augustijn, Marieke, Woolhouse, Mark, Stegeman, J. Arjan, Lycett, Samantha, Oude Munnink, Bas B., Koopmans, Marion P. G.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.11.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/47; 45/77; 49/91; 631/181/735; 631/326/421; 631/326/596/2562; 631/326/596/4130; 692/700/478/174; Amino Acid Sequence; Amino acid substitution; Amino acids; Animal Diseases - epidemiology; Animal Diseases - transmission; Animal Diseases - virology; Animals; Bayes Theorem; Bayesian analysis; COVID-19; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; Disease Outbreaks; Dispersal; Epidemiology; Evolution, Molecular; Farms; Farmworkers; Humanities and Social Sciences; Humans; Mink - virology; multidisciplinary; Mustela; Netherlands - epidemiology; Outbreaks; Pandemics; Personnel; Phylogeny; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - physiology; Science; Science (multidisciplinary); Sequence Analysis, Protein; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - classification; Spike Glycoprotein, Coronavirus - genetics; Spike protein; Statistical analysis; Viral diseases; Viruses; Netherlands
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27096-9

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. SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.