Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria

• Published in: Virus research 2023-09, Vol.334, p.199174-199174, Article 199174
• Main Authors: George, Uwem, George, Oluwadamilola, Oguzie, Judith, Osasona, Oluwadamilola, Motayo, Babatunde, Kamani, Joshua, Eromon, Philomena, Folarin, Onikepe, Happi, Anise, Komolafe, Isaac, Happi, Christian
• Format: Article
• Language: English
• Subjects: Alphacoronavirus; Alphacoronavirus - genetics; Animals; Chiroptera; Coronavirus - genetics; Coronavirus Infections - epidemiology; Coronavirus Infections - genetics; Coronavirus Infections - veterinary; Genome, Viral; Genomics; Metagenomics; Molossidae; Nigeria; Phylogeny; Recombination
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2023.199174

•First report of a near-complete genome of bat Alphacoronavirus in Nigeria.•Unique AlphaCoV subgenera circulating in the Molossidae bat family.•Evidence of Alphacoronaviruses recombination within the Molossidae bat family.•Nigerian AlphaCoV strains have a genetically distinct spike protein.•Binding sites distinct from the motifs used for ACE2 and hAPN binding. Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.