Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil

ABSTRACT We identified seven distinct coronaviruses (CoVs) in bats from Brazil, classified into 229E‐related (Alpha‐CoV), Nobecovirus, Sarbecovirus, and Merbecovirus (Beta‐CoV), including one closely related to MERS‐like CoV with 82.8% genome coverage. To accomplish this, we screened 423 oral and rectal swabs from 16 different bat species using molecular assays, RNA sequencing, and evolutionary analysis. Notably, gaps in the spike‐encoding gene led us to design new primers and perform Sanger sequencing, which revealed high similarities to MERS‐related (MERSr) CoV strains found in humans and camels. Additionally, we identified key residues in the receptor‐binding domain (RBD) of the spike protein, suggesting potential interactions with DPP4, the receptor for MERSr‐CoV. Our analyses also revealed evidence of recombination involving our laboratory‐produced sequences. These findings highlight the extensive genetic diversity of CoVs, the presence of novel viral lineages, and the occurrence of recombination events among bat CoVs circulating in Brazil, underscoring the critical role bats play as reservoirs for emerging viruses and emphasizing the necessity of ongoing surveillance to monitor the public health risks associated with CoV spillover events.