RT Journal Article SR Electronic T1 Full genome Nobecovirus sequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.09.29.462406 DO 10.1101/2021.09.29.462406 A1 Gwenddolen Kettenburg A1 Amy Kistler A1 Hafaliana Christian Ranaivoson A1 Vida Ahyong A1 Angelo Andrianiaina A1 Santino Andry A1 Joseph L. DeRisi A1 Anecia Gentles A1 Vololoniaina Raharinosy A1 Tsiry Hasina Randriambolamanantsoa A1 Ny Anjara Fifi Ravelomanantsoa A1 Cristina M. Tato A1 Philippe Dussart A1 Jean-Michel Heraud A1 Cara E. Brook YR 2021 UL http://biorxiv.org/content/early/2021/09/29/2021.09.29.462406.abstract AB Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.Competing Interest StatementThe authors have declared no competing interest.