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

  1. Lu Lu
  2. Reina S. Sikkema
  3. Francisca C. Velkers
  4. David F. Nieuwenhuijse
  5. Egil A.J. Fischer
  6. Paola A. Meijer
  7. Noortje Bouwmeester-Vincken
  8. Ariene Rietveld
  9. Marjolijn C.A. Wegdam-Blans
  10. Paulien Tolsma
  11. Marco Koppelman
  12. Lidwien A.M. Smit
  13. Renate W. Hakze-van der Honing
  14. Wim H. M. van der Poel
  15. Arco N. van der Spek
  16. Marcel A. H. Spierenburg
  17. Robert Jan Molenaar
  18. Jan de Rond
  19. Marieke Augustijn
  20. Mark Woolhouse
  21. J. Arjan Stegeman
  22. Samantha Lycett
  23. Bas B. Oude Munnink
  24. Marion P. G. Koopmans

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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 related humans on farms. High number of farm infections (68/126) in minks and farm related personnel (>50% of farms) were detected, with limited spread to the general human population. Three of five initial introductions of SARS-CoV-2 lead to subsequent spread between mink farms until November 2020. The largest cluster acquired a mutation in the receptor binding domain of the Spike protein (position 486), evolved faster and spread more widely and longer. 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 combing genetic information with epidemiological information at the animal-human interface.

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  1. ScreenIT

    SciScore for 10.1101/2021.07.13.452160: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    For the mandatory serological screening in mink, blood on filter paper was eluated and approximately 2 µL of serum was tested for SARS-CoV-2 antibodies using an in-house indirect ELISA based on the RBD antigen.
    SARS-CoV-2
    suggested: None
    Software and Algorithms
    SentencesResources
    Genomes were aligned with MAFFT 30 and edited by partitioning into coding regions and non-coding intergenic regions with a final alignment length of 29,508 nucleotides.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    To determine if our sequence data exhibited temporal qualities, we used TempEst v1.5 32 to measure the root-to-tip divergence for ML trees.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    To analyse fluctuations in SARS-COV-2 epidemic spread in mink farms in the Netherlands per individual cluster, we estimated the changes of viral effective population size (Ne) over time using the skygrid model 34 in BEAST version 1.10.4, and the effective reproductive number (Re) during the course of the outbreak in mink farms, using the Birth-death skyline (BDSKY) model 37 in BEAST2 version 2.6.3 38.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    BEAST2
    suggested: (BEAST2, RRID:SCR_017307)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.07.13.452160 on bioRxiv