Full genomeNobecovirussequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade

Bats are natural reservoirs for bothAlpha- andBetacoronavirusesand 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-relatedBetacoronavirusesin the subgenusSarbecovirushave been identified circulating inRhinolophidbats 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 fromBetacoronavirussubgenusNobecovirusin fecal samples from all three species and describe full genome sequences of novelNobecovirusesinP. rufusandR. madagascariensis. Phylogenetic analysis indicates the existence of five distinctNobecovirusclades, one of which is defined by the highly divergent sequence reported here fromP. rufusbats. MadagascarNobecovirusesderived fromP. rufusandR. madagascariensisdemonstrate, 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.