Bottleneck Size-Dependent Changes in the Genetic Diversity of Rotavirus. Simian rotavirus A strain RRV

RNA viruses form a dynamic distribution of mutant swarm due to the accumulation in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck. Human-to-human transmission exemplifies a bottleneck effect in that only part of a viral population can reach the next susceptible hosts. In the present study, the rhesus rotavirus (RRV) strain of Rotavirus A was serially passaged five times under at a multiplicity of infection (MOI) of 0.001 in duplicate. Using next generation sequencing, we obtained SNPs information of RRV populations, and then estimated a nucleotide diversity, synonymous/non-synonymous substitution rate and evolutionary rate.

RNA病毒因在病毒基因组中累积突变，形成动态分布的突变群（mutant swarm）。病毒种群的遗传多样性受多种因素影响，其中包括瓶颈效应（bottleneck）。人际传播即为瓶颈效应的典型实例：仅有部分病毒种群能够抵达下一批易感宿主。本研究选取A组轮状病毒的恒河猴轮状病毒（rhesus rotavirus, RRV）毒株，以感染复数（multiplicity of infection, MOI）为0.001的条件开展5次连续传代，并设置双份生物学重复。本研究借助下一代测序（next generation sequencing）技术获取了RRV种群的单核苷酸多态性（single nucleotide polymorphisms, SNPs）信息，进而估算了其核苷酸多样性、同义/非同义替换率以及进化速率。