South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Next Generation Sequencing Unit, Department of Medical Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Infect Genet Evol. 2018 Sep;63:79-88. doi: 10.1016/j.meegid.2018.05.013. Epub 2018 May 18.
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] 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[6] 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[6] strains were observed in this study. Phylogenetic analyses demostrated the extensive genetic diversity that exists among human P[6] strains, porcine-like strains, their concomitant clades/subclades and estimated that P[6] 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[6] 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[6] 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[6] strains in Africa. These findings highlight the need for continued global surveillance of rotavirus diversity.
轮状病毒 A（RVA）在全球范围内表现出广泛的基因型多样性。关于来自非洲的基因型 P[6]的遗传组成知之甚少。本研究调查了导致基因型 P[6] VP4 序列遗传多样性的可能进化机制。对 167 个 P[6] VP4 全长序列进行了系统发育分析，其中包括 6 个猪源序列。在 167 个序列中，有 57 个是通过全基因组测序获得的，这是本研究的一部分。其他 110 个序列均来自 GenBank 下载的全球公开 P[6] VP4 全长序列。还确定了表型特征与系统发育之间的关联强度。本研究观察到 RVA 基因型 P[6] 株存在许多重组和混合感染。系统发育分析表明，人类 P[6] 株、猪样株及其伴随的枝系/亚枝系之间存在广泛的遗传多样性，并估计 P[6] VP4 基因的替代率较高，平均为 1.05E-3 个替代/位点/年。此外，系统发育分析表明，基因型 P[6] 株在非洲流行，其特点是病毒具有广泛的遗传多样性和长时间的本地进化。当应用贝叶斯尖端关联显著性检验（BaTS）时，P[6] 株的系统地理聚类和 G 基因型聚类也支持这一观点，这清楚地表明病毒是在非洲本地进化的，而不是不同地区之间的空间混合。总的来说，结果表明，多种机制，如重组事件、各种突变和可能的种间传播，导致了非洲基因型 P[6] 株的巨大多样性。这些发现强调了需要继续对轮状病毒的多样性进行全球监测。
