Phylogeography and Evolutionary analysis of African Rotavirus A genotype G12 reveals district genetic diversification within Lineage III

Abstract

Significance of the studyRotavirus genotype G12 has a recent history, and has spread rapidly causing outbreaks of acute gastroenteritis across Africa. To further understand the mechanisms behind its rapid spread, we investigated the Evolutionary dynamics, Phylogeny and population demography of the VP7 gene among African strains. Our study revealed that African G12 rotaviruses have diversified into 3 potential clades within their parental lineage III based on geographic boundaries. We also discovered that they have a constant demographic profile. Our findings reveal the potential for rapid genetic diversity of Rotavirus G12 and highlight the importance of molecular surveillance in Rotavirus control effort. AbstractObjective: 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. Methods: 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. Results: 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 T MRC, was 16.8,). 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. Conclusions: 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.

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

“…Interestingly, a possible common geographical origin was identified for lineage-III, whose members come mainly from China, with the exception of one isolate from the USA. The heterogeneous geographical origin of this last member of lineage-III and of the members of the other two lineages (I and II) could be attributed to human population migration, as has been identified for other pathogens [69]. However, the limited sample size is not enough to elucidate this hypothesis; further work with an increased number of individuals from different geographical origins will allow a more accurate picture of the population genetic structure of this species.…”

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

“…Our results show a coincident decline in the relative diversities and effective population sizes of all RVA segments after 2006. Supporting this analysis, several studies, including an analysis of G12 strains in Africa, G12 strains in Spain, and a lineage of P [8] strains also show a general decline in diversity/effective population size after 2008 (108)(109)(110).…”

The origins of G12P[6] rotavirus strains detected in Lebanon

“…Continued constellation, commonly detected worldwide [9,37]. Another, less prevalent G12P [6] lineage within the DS-1-like genogroup has also been reported in many countries including Bangladesh, Malawi and Thailand [8,37,38]. G12 strains has spread globally showing a steady mutation rate with the potential to diversify rapidly [39].…”

“…In Europe, G12 strains were identified in the UK, Belgium and Spain [52]. Moreover, G12P [8] and G12P [6] were the most prevalent genotypes being responsible for over 43 % of all rotavirus infections in Ivorian children [38,53]. In the MENA region, G12 was reported in Saudi Arabia (7 %) [10], Yemen (2 %) [11], Iraq (7 %) [12], Iran (9.4 %) [13], Egypt (9.2 %) [16], Tunisia (5.2 %) [14,15], Pakistan (12.85 %) [17,54] and Turkey (15.6 %) [18].…”