Alphacoronaviruses detected in fecal samples of bats captured in Moscow and Rostov-on-Don in 2021

BACKGROUND: Bats are a reservoir of a large number of viruses, including coronaviruses. Monitoring viruses in bats is an important task. AIM: To detect viruses belonging to Coronaviridae family in bats which habitat in European part of Russia. MATERIALS AND METHODS: We used PCR amplification of viral genome fragments, followed by high-throughput sequencing. RESULTS: RdRp gene fragments of at least two different alphacoronaviruses (Bat coronavirus, Coronaviridae) were revealed in four bats of three species. CONCLUSIONS: Our results demonstrate the presence of viruses of the Alphacoronavirus genus in 4 of 17 bats. Coronavirus-positive animals were captured in 2021 in Moscow, Moscow Region and Rostov-on-Don, these four animals have been found to be carriers of different isolates of the same alphacoronavirus, which allows us to suggest the possibility of transmission of this virus between animals between different species. One animal was found as carrier of genome fragments of two different alphacoronaviruses.