Usutu virus is an RNA virus which was introduced into Europe from Africa at the end of the 20th century. It has been causing increasingly more zootics in Europe, and infections have been diagnosed in humans. As in previous studies, we also noted that the virus is circulating in Slovenia. Antibodies have already been detected in various animal species of a zoological garden in Ljubljana and USUV associated deaths of wild birds have been reported in 2018. Two Culex mosquito pools sampled in 2018, six in 2019 and one in 2020 tested positive for USUV. In the season of 2021 no USUV positive mosquito pools were sampled. Our study is the first to investigate the genetic diversity of Slovenian USUV strains. Nine strains were confirmed in mosquitoes sampled at different Slovenian sites between 2018 and 2020. The complete genomes of eight strains were amplicon sequenced using Illumina technology and phylogenetic analysis was performed. All eight strains belong to the Europe 2 lineage, which all the while has been and continues to prevail in neighbouring countries. Two phylogenetic groups were demonstrated in Slovenia. Phylogenetic comparison with strains from neighbouring countries suggests multiple introductions of the virus into Slovenia, mainly from Italy, but probably also from Austria and Hungary. It is possible that the virus has overwintered in Slovenia and is becoming endemic. There are many data gaps on the epidemiology of USUV. Our research on virus circulation and changing could be more accurate, if more USUV complete genome sequences from Europe were publicly available. A multidisciplinary approach involving virologists, health personnel, ornithologists and entomologists is needed, as well as closer collaboration between the health, agricultural and environmental sectors to better identify the main risk factors in order to implement appropriate USUV monitoring and prevention methods.
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