Phylodynamic and Evolutionary analysis of Rotavirus G12 in Africa

Rotavirus genotype G12 has spread globally and has caused outbreaks across Africa. It has become one of the most prevalent genotypes of rotavirus in Africa in recent years. To further understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeny, viral evolution and population demography of Rotavirus genotype G12 in Africa.We downloaded full and partial VP7 gene sequences of Rotavirus genotype G12, from twelve African countries (n=96). We aligned the African G12 sequences with seven global reference G12 sequences. Phylogenetic analysis was carried out using MEGA Vs 6, Evolutionary analysis and Bayesian Phylogeny was carried out, using Markov Chain Monte Carlo (MCMC) implemented in BEAST. 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 estimated to be 1,678×10-3, with 95% high posterior density interval (95%HPD) of 1.201×10-3 to 2.198×10-3 nucleotide substitutions/ site/ year. The time to most recent common ancestor TMRC, was 16.8, 95%HPD (15.0 -25.54). The MCMC tree topology clustered into three lineages (II, III, IV), with all the African trains falling into lineage III, and further diversified into three clusters within lineage III. The demographic history of the African G12 viruses was estimated using BSP model, and revealed a constant population dynamic. 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.