Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P strains circulating in Africa
Nyaga MM, Tan Y, Seheri ML, Halpin RA, Akopov A, Stucker KM, Fedorova NB, Shrivastava S, Duncan Steele A, Mwenda JM, Pickett BE, Das SR, Jeffrey Mphahlele M
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P VP4 sequences. Phylogenetic analyses on 167 P VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P VP4 full-length sequences downloaded from GenBank. The strength of association between the phenotypic features and the phylogeny was also determined. A number of reassortment and mixed infections of RVA genotype P strains were observed in this study. Phylogenetic analyses demostrated the extensive genetic diversity that exists among human P strains, porcine-like strains, their concomitant clades/subclades and estimated that P VP4 gene has a higher substitution rate with the mean of 1.05E-3 substitutions/site/year. Further, the phylogenetic analyses indicated that genotype P strains were endemic in Africa, characterised by an extensive genetic diversity and long-time local evolution of the viruses. This was also supported by phylogeographic clustering and G-genotype clustering of the P strains when Bayesian Tip-association Significance testing (BaTS) was applied, clearly supporting that the viruses evolved locally in Africa instead of spatial mixing among different regions. Overall, the results demonstrated that multiple mechanisms such as reassortment events, various mutations and possibly interspecies transmission account for the enormous diversity of genotype P strains in Africa. These findings highlight the need for continued global surveillance of rotavirus diversity.