Fig. 1: Distinct Clusters of SARS-Cov-2 circulating in mink farms in the Netherlands.

a Overview of SARS-CoV-2 outbreaks on mink farms in the Netherlands in relation to implementation of control measures and the mink farm cycle. The diagnosed farms per week are coloured based on virus cluster. One farm in June 2020 is indicated as half A/half D as both clusters were found. The blue arrows above the graph point to the starting week of implementation of more strict hygiene protocols with regard to people working on or visiting farms. Orange arrows point to the start of other control measures including obligation for notification of clinical signs and mortality (Not.), first and second serological screening (SER1 and 2), early warning system with weekly sending in of carcasses (EW) and culling of infected farms. Below the graph important periods in the farmed mink production cycle are indicated. These include mating (March), whelping (April/May), vaccination (June) and weaning (June and July). Also, the start of the pelting season is shown. The 5 viral clusters are in unique colour (A in red, B in yellow, C in green, D in blue and E in pink) and are consistently used in (a–d). b The location of each infected mink farm. The node size represents the number of sequences obtained from minks in each farm. The locations of farms on the map have been jittered for privacy reasons. c Time-scaled maximum clade credibility (MCC) tree of SARS-CoV-2 sequences isolated from humans and minks in the Netherlands (n = 673). Human sequences are highlighted in red and mink sequences in green, the subsampled human samples (n = 72) isolated from the same four-digit postal code are highlighted as triangle, and 3 samples (1 escaped mink and 2 un-associated human sequences) which fell within mink clusters are highlighted as diamond and indicated by arrows. Clusters of sequences from minks and associated humans are indicated on the right with unique colours. d The number of samples in time for each cluster. The estimated TMRCAs of each cluster are indicated via dotted line (mean) and grey shade (95% highest posterior density (HPD) intervals).