Phylogeography and evolutionary analysis of African Rotavirus a genotype G12 reveals district genetic diversification within lineage III

Abstract Group A rotavirus (RVA) genotype G12 has spread globally and has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeography, viral evolution and population demography of Rotavirus G12 in Africa. We downloaded and aligned VP7 gene sequences of Rotavirus genotype G12, from thirteen African countries (n = 96). Phylogenetic analysis, Evolutionary analysis and Bayesian Phylogeography was carried out, using MEGA Vs 6, BEAST, and SPREAD3. Phylogenetic analysis revealed that all the African sequences fell into lineage III diversifying into two major clades. The evolutionary rate of the African rotavirus G12 sequences was 1.678×10−3, (95% HPD, 1.201×10−3 - 2.198×10−3) substitutions/site/year, with TMRC of 16.8 years. The Maximum clade credibility (MCC) tree clustered into three lineages (II, III, IV), African strains fell within lineage III, and diversified into three clusters. Phylogeography suggested that South Africa seemed to be the epicentre of dispersal of the genotype. The demographic history of the G12 viruses revealed a steady increase between the years1998–2007, followed by a sharp decrease in effective population size between the years 2008–2011. We have shown the potential for genetic diversification of Rotavirus genotype G12 in Africa. We recommend the adoption of Molecular surveillance across Africa to further control spread and diversification of Rotavirus.