Bottleneck Size-Dependent Changes in the Genetic Diversity of Rotavirus

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.