The genetic characterization of the first detected Bat Coronaviruses in Poland revealed SARS-related types and Alphacoronaviruses

Abstract

Bats are a major global reservoir of alphacoronaviruses (alphaCoVs) and betaCoVs. Attemptsto discover the causative agents of COVID-19 and SARS have revealed horseshoe bats(Rhinolophidae) to be the most probable source of the virus. We report the first detection of batcoronaviruses (BtCoVs) in insectivorous bats in Poland and highlight SARS-related coronavirusesfound in Rhinolophidae bats. The study included 503 (397 oral swabs and 106 fecal) samples collectedfrom 20 bat species. Genetically diverse BtCoVs (n = 20) of the Alpha- and Betacoronavirus generawere found in fecal samples of two bat species. SARS-related CoVs were in 18 out of 58 lesserhorseshoe bat (Rhinolophus hipposideros) samples (31%, 95% CI 20.6–43.8), and alphaCoVs were in 2out of 55 Daubenton’s bat (Myotis daubentonii) samples (3.6%, 95% CI 0.6–12.3). The overall BtCoVprevalence was 4.0% (95% CI 2.6–6.1). High identity was determined for BtCoVs isolated fromEuropean M. daubentonii and R. hipposideros bats. The detection of SARS-related and alphaCoVs inPolish bats with high phylogenetic relatedness to reference BtCoVs isolated in different Europeancountries but from the same species confirms their high host restriction. Our data elucidate themolecular epidemiology, prevalence, and geographic distribution of coronaviruses and particularlySARS-related types in the bat population.