Evolution of SARS-CoV-2 caused infection in farmed minks: Continuous surveillance of an eleven-month outbreak at the largest Latvian mink farm

Abstract

SARS-CoV-2, responsible for the COVID-19 pandemic, can productively infect a variety of animal hosts. The evidence suggests that both wild and farmed animal populations supporting continuous transmission present us with novel concerning genotypes of SARS-CoV-2. This is especially worrisome within large and dense populations of farmed animals, such as minks, for which spillbacks of “mink genotypes” to the human population have been recorded on numerous occasions.

In this study, we present the results of continuous clinical, virological, serological, and genomic surveillance during the period of eleven months of the SARS-CoV-2 outbreak at the largest Latvian mink farm with more than 300,000 animals. Using the One Health approach, the COVID-19 status of minks and farm workers was constantly monitored during the surveillance period. The presence of the SARS-CoV-2 genome was confirmed in 299 minks and thirty-two farm workers during the outbreak. The phylogenetic analysis of 188 mink and fourteen human SARS-CoV-2 isolates linked to the farm provided insight into the evolution of the virus in situ and contributed to epidemiological investigation.

The results revealed that SARS-CoV-2 lineage B.1.177.60 was initially introduced to the mink farm by an infected farm worker between 17th of February and 23rd of March, 2021, and subsequently spread among the minks. Surveillance in the affected farm showed fluctuating virus circulation. Although the average seroprevalence in samples taken from live minks was 76.92%, a fluctuating course of infection was observed from April 2021 to March 2022. Despite the implementation of strict preventive and control measures at the farm, several additional SARS-CoV-2 strain introductions were identified during eleven months. The initial introduction of a common viral strain circulating among the people at the time soon resulted in the co-circulation of multiple sister sub-lineages that have evolved some concerning spike protein amino acid substitutions. Subsequent other lineage introductions into the farm were not able to spread among minks. Several independent cases of farm workers infected with genotypes restricted to this mink farm were documented throughout the study timeframe. However, the “Latvian mink genotypes” were not detected in the general human population beyond epidemiologic association with the given mink farm.