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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\u2010encoding gene led us to design new primers and perform Sanger sequencing, which revealed high similarities to MERS\u2010related (MERSr) CoV strains found in humans and camels. Additionally, we identified key residues in the receptor\u2010binding domain (RBD) of the spike protein, suggesting potential interactions with DPP4, the receptor for MERSr\u2010CoV. Our analyses also revealed evidence of recombination involving our laboratory\u2010produced 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.<\/jats:p>","DOI":"10.1002\/jmv.70173","type":"journal-article","created":{"date-parts":[[2025,1,18]],"date-time":"2025-01-18T11:38:55Z","timestamp":1737200335000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil"],"prefix":"10.1002","volume":"97","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-7938-3663","authenticated-orcid":false,"given":"Bruna Stefanie","family":"Silv\u00e9rio","sequence":"first","affiliation":[{"name":"Department of Morphology and Genetics Federal University of S\u00e3o Paulo S\u00e3o Paulo\u2010SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana Dias","family":"Guilardi","sequence":"additional","affiliation":[{"name":"Interunit Bioinformatics Graduate Program, Institute of Chemistry University of S\u00e3o Paulo S\u00e3o Paulo\u2010SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junior Ol\u00edmpio","family":"Martins","sequence":"additional","affiliation":[{"name":"Department of Morphology and Genetics Federal University of S\u00e3o Paulo S\u00e3o Paulo\u2010SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo Lopes Sanz","family":"Duro","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Parasitology Federal University of S\u00e3o Paulo S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larissa Le\u00e3o F.","family":"de Sousa","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Parasitology Federal University of S\u00e3o Paulo S\u00e3o Paulo Brazil"},{"name":"Rabies Diagnosis Laboratory, Central Laboratory of Public Health \u2010 LACEN Fortaleza\u2010CE Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo","family":"Cabral\u2010Miranda","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Sciences University of S\u00e3o Paulo S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz M\u00e1rio Ramos","family":"Janini","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Parasitology Federal University of S\u00e3o Paulo S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leo L. 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