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

Lu Lu, Reina S. Sikkema, Francisca C. Velkers, David F. Nieuwenhuijse, Egil A.J. Fischer, Paola A. Meijer, Noortje Bouwmeester-Vincken, Ariene Rietveld, Marjolijn C.A. Wegdam-Blans, Paulien Tolsma, Marco Koppelman, Lidwien A.M. Smit, Renate W. Hakze-van der Honing, Wim H.M. van der Poel, Arco N. van der Spek, Marcel A.H. Spierenburg, Robert Jan Molenaar, Jan de Rond, Marieke Augustijn, Mark WoolhouseJ. Arjan Stegeman, Samantha Lycett, Bas B. Oude Munnink, Marion P.G. Koopmans*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

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.

Original languageEnglish
Article number6802
JournalNature Communications
Volume12
Issue number1
DOIs
Publication statusPublished - 23 Nov 2021

Bibliographical note

Funding Information:
We acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCov Database on which the phylogenetic analysis was based (see Supplementary Data 1). All submitters of data may be contacted directly via the GISAID website www.gisaid.org. This work is supported by European Union’s Horizon 2020 research and innovation programme under Grant No. 874735 (VEO), received by L.L., S.L., M.W., R.S.S., B.B.O.M., M.P.G.K. and D.F.N., as well as ZonMW under Grant No.10150062010005, received by R.S.S., D.F.N., M.P.G.K. and B.B.O.M. The mink farm outbreak investigation was funded by the Dutch Ministries of Health, Welfare and Sport, and of Agriculture, Nature and Food Quality under Grant No. 1400011731, 1400011746 and 1400010752, received by R.S., F.C.V., D.F.M., E.A.J.F., P.A.M., L.A.M.S., R.W.H.H., W.H.M.P., R.J.M., J.R., M.A., J.A.S., B.O.M. and M.P.G.K.; S.L. is additionally supported by Biotechnology and Biological Sciences Research Council (BBSRC) programme grant to Roslin Institute (Award Number BBS/E/D/20002173.

Publisher Copyright:
© 2021, The Author(s).

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