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The RNA-dependent RNA polymerase ( RdRp ) and capsid ( VP1 ) genes of 51 GII.2 human norovirus (HuNoV) strains collected during the period of 2004–2015 in Japan were analyzed. Full-length analyses of the genes were performed using next-generation sequencing. Based on the gene sequences, we constructed the time-scale evolutionary trees by Bayesian Markov chain Monte Carlo methods. Time-scale phylogenies showed that the  RdRp  and  VP1  genes evolved uniquely and independently. Four genotypes of GII.2 (major types: GII.P2-GII.2 and GII.P16-GII.2) were detected. A common ancestor of the GII.2  VP1  gene existed until about 1956. The evolutionary rates of the genes were high (over 10 −3  substitutions/site/year). Moreover, the  VP1  gene evolution may depend on the  RdRp  gene. Based on these results, we hypothesized that transfer of the  RdRp  gene accelerated the  VP1  gene evolution of HuNoV genotype GII.2. Consequently, recombination between ORF1 (polymerase) and ORF2 (capsid) might promote changes of GII.2 antigenicity.

Molecular Evolution of the RNA-Dependent RNA Polymerase and Capsid Genes of Human Norovirus Genotype GII.2 in Japan during 2004–2015