Complete genome sequence analysis of Sarbecovirus (severe acute respiratory syndrome-related coronaviruses) from Zimbabwean insectivorous bats.

Abstract

Bat-borne severe acute respiratory syndrome-related coronaviruses (bat SARSr-CoVs), belonging to the Sarbecovirus subgenus of the Betacoronavirus genus pose a potential risk for zoonotic spillover. This study reports the complete genome sequences of bat sarbecoviruses from Nycteris macrotis and Rhinolophus simulator insectivorous bat species in Zimbabwe. Using genome walking and nested PCR approaches, six full viral genomes were amplified, sequenced and assembled: one from Nycteris macrotis (MAG1042) and five from Rhinolophus simulator bats species (MAG388, MAG562, MAG575, MAG850, and MAG859). Comparative genomic analysis revealed a high degree of sequence conservation (99.6-99.9%) among the Rhinolophus simulator-characterised sequences, while the Nycteris macrotis characterised sequence exhibited 96.7% identity with the Rhinolophus simulator consensus (MAG Cons) genomes, suggesting genus-specific evolution. Furthermore, the spike region exhibited notable divergence, with only 88% sequence identity between the two genera. A complete absence of ORF8, and truncation of ORF7b genes were observed, while the RNA dependent RNA polymerase genes were highly conserved across all strains. Phylogenetic analysis demonstrated distinct continental clustering, with the Zimbabwean genomic sequences forming a well-supported clade within the African lineage (Lineage 4). These newly characterized Zimbabwean sarbecoviruses sequences represent the most recent evolutionary branches within the Lineage 4-African clade, indicating ongoing viral diversification in local bat populations. These findings expand understanding of SARSr-CoV diversity in African bats and underscore the importance of geographical isolation in viral evolution.