Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms

Abstract Several studies have documented reverse zoonotic transmission of SARS-CoV-2, including in farmed mink which are susceptible to human respiratory viruses and are known for serving as a reservoir capable of generating new virus variants in densely populated farms. Here, we present the genomic investigation launched in response to detection of human infections with mink-origin SARS-CoV-2 lineages, and show evidence of at least 14 high-confidence introductions of SARS-CoV-2 from humans into farmed mink in Lithuania where sustained transmission in farmed mink lasted up to a year. We estimated the most likely timeframes for these introductions encompassing at least six SARS-CoV-2 lineages, some of which were already extinct in humans, with Bayesian phylogenetic and molecular clock analyses. This study highlights the public health risks posed by fur farms and underscores that passive genomic surveillance systems are ineffective without the active involvement and expertise of responsible institutions.