Background: Bats have been implicated as the main reservoir of coronavirus (CoV). Thus the role of these hosts on the evolution and spread of Co. Vs currently deserve the attention of emerging diseases surveillance programs. On the view of the interest on and importance of Co. Vs in bats the occurrence and molecular characterization of CoV were conducted in bats from Brazil. Findings: Three hundred five enteric contents of 29 bat species were tested using a panCoV nested RT-PCR. Nine specimens were positive and eight was suitable for Rd. Rp gene sequencing. Rd. Rp gene phylogeny showed that all Co. Vs strains from this study cluster in Alphacoronavirus genus, with one Molossidae and one Phlyllostomidae-CoV specific groups. Phylogenetic analyses of two S gene sequences showed a large diversity within the Alphacoronavirus genus. Conclusions: This study indicated a CoV-to-host specificity and draws attention for CoV detection in Cynomops sp, a potential new reservoir. The phylogenetic analyses indicate that diversity of CoV in bats is higher than previously known.
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