Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria

Abstract

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.

Keywords: Alphacoronavirus; Metagenomics; Molossidae; Nigeria; Recombination.

Fig. 1

Maximum likelihood tree with ModelFinder based on complete ORF1ab sequences, with 1000 bootstrap replications. All AlphaCoV subgenera are colour-coded, as shown in the legend. AlphaCoV strains reported in this study are asterisked and highlighted in white. The Interactive Tree of Life (iTOL) v5 with midpoint rooting was used to visualise the tree. The Best-fit model according to BIC was GTR+F+I+G4.

Fig. 2

(A) Time scaled Maximum clade credibility tree (MCC) of ORF1ab region of AlphaCoV. Based on the legend, branch colours denote AlphaCoV subgenera, while branch lengths correspond to time in years, (B). Bayesian Skyride plot of All AlphaCoV analysed in this study showing estimates of the effective virus population size over time. The upper and lower blue lines represent the population's 95% high posterior density intervals (95% HPD), while the solid blue line depicts the median population size.

Fig. 3

Genomic analyses of putative recombinant alphacoronavirus with evidence of recombination at breakpoints 24,032–27,736. (A) Distance Plot analyses of GB013-NGR_2020 from this study predicted to be a recombinant of Chaerephon pumilus bats alphacoronavirus (OL807610-Major Parent highlighted in green) and unverified Alphacoronavirus (ON313747.1-Minor Parent highlighted in purple) while the figures below shows the Maximum likelihood tree of AlphaCoV detected in bats in Molossidae family based on B. complete ORF1ab protein, C. Spike protein, D. Envelope protein, E. Membrane protein and F. Nucleocapsid protein, with 1000 bootstrap replications. The Nigerian strains reported in this study are asterisked.

Fig. 4

Sequence alignment showing amino acid similarities and variations in A. S-RBD and B. S1 C-terminal domain of the unclassified AlphaCoV in comparison with two human Alphacoronavirus HCoV-NL63 and HCoV-229E. The highlighted red section in the alignment denotes the receptor binding motifs of HCoV-229E that contain most of the contacting residues that bind to hAPN while the highlighted section in green denotes HCoV-NL63 binding motifs (amino acid residues 573–599) that contain contacting residues that bind to ACE2. The dot in the alignment denotes amino acid similarities.