Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020
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The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. A detailed analysis of the changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants that had the Y435F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early on during the outbreak. However, further introductions of the virus, with variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of the available viral genome data, we estimate that there were a minimum of about 17 separate examples of mink to human transmission of the virus in Denmark, using a conservative approach, but up to 60 such events (95% credible interval: (35-77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using a Bayesian method. Using the latter approach, it was estimated that there were 136 jumps (95% credible interval: (112-164)) from humans to mink. Thus, transmission of these viruses from humans to mink, mink to mink, from mink to humans and between humans were all observed.
Author summary
In addition to causing a pandemic in the human population, SARS-CoV-2 also infected farmed mink. In Denmark, after the first identification of infection in mink during June 2020, a decision was made in November 2020 to cull all the farmed mink. Within this outbreak, mink on 290 farms (out of about 1100 in the country) were found to have been infected. We showed, by analysis of the viruses from the mink, that the viruses on the farms were mainly of three different, but closely related, types (termed Clusters 2, 3 and 4) that shared certain distinctive features. Thus, we found that many outbreaks in mink resulted from transmission of the virus between mink farms. However, we identified that new introductions of other virus variants, presumably from infected humans, also occurred. Furthermore, we showed that spread of the virus from infected mink to humans also happened on multiple occasions. Thus, transmission of these viruses from humans to mink, mink to mink, from mink to humans and between humans were all observed.
