Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation using whole genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced from humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. Despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, transmission occurred between mink farms in three big transmission clusters with unknown modes of transmission. Sixty-eight percent (68%) of the tested mink farm residents, employees and/or contacts had evidence of SARS-CoV-2 infection. Where whole genomes were available, these persons were infected with strains with an animal sequence signature, providing evidence of animal to human transmission of SARS-CoV-2 within mink farms.

The zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms.One sentence summarySARS-CoV-2 transmission on mink farms.

Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula).In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. this analyses further suggest some extent of circulation of USUV between the netherlands, Germany and Belgium, as well as likely overwintering of USUV in the netherlands.Usutu virus (USUV) is a mosquito-borne arbovirus of the genus Flavivirus. The virus has a positive-stranded RNA genome with a genome length of around 11,000 nucleotides which encodes a single polyprotein. The polyprotein is processed by viral and host proteases into structural and non-structural proteins 1 . The life cycle of USUV involves mosquitoes (mainly Culex sp. 2,3 ) as vectors and wild birds as the main amplifying hosts. Humans and other mammals can be infected by mosquito bites and are generally considered dead-end hosts. Recent studies revealed that USUV can also be detected in small mammals such as bats 4 , rodents and shrews 5 .USUV was first identified from a Culex neavei mosquito in South Africa in 1959 6 . Over subsequent decades, it was sporadically reported in several mosquito and bird species, and twice in a human patient with fever and rash in African countries 7 . USUV was for first identified in Europe in 2001, when it was determined to be the causative agent of a mass mortality event in several bird species in Austria 8 . This prompted retrospective analysis of archived tissue samples from dead wild birds in Italy in 1996, which revealed an earlier presence of the virus in Europe 9 . Our understanding of the USUV geographical range has since expanded to include the majority of European countries 10 , where outbreaks are marked by mass die-offs of wild birds, with the heaviest toll on common blackbird (Turdus merula) populations. In Germany, it has been demonstrated that five years after the first detection of USUV in the southwest of the country, circulation of the virus was associated with a 15.7% decline in the common blackbird population in USUV-suitable areas 11 .The recent emergence of USUV epizootics among wild bird populations in Europe has been accompanied by reports of USUV infections in humans. Pathogenicity in humans appears to range from asymptomatic or mild symptoms, as shown in seroprevalence studies among healthy blood donors in Italy 12 , Germany 13 , Austria 14 and the Netherlands 15 to neuroinvasive infections associated with encephalitis or meningo-encephalitis, m...