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

Abstract

The RNA-dependent RNA polymerase (<i>RdRp</i>) and capsid (<i>VP1</i>) 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 <i>RdRp</i> and <i>VP1</i> 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 <i>VP1</i> gene existed until about 1956. The evolutionary rates of the genes were high (over 10^-3 substitutions/site/year). Moreover, the <i>VP1</i> gene evolution may depend on the <i>RdRp</i> gene. Based on these results, we hypothesized that transfer of the <i>RdRp</i> gene accelerated the <i>VP1</i> gene evolution of HuNoV genotype GII.2. Consequently, recombination between ORF1 (polymerase) and ORF2 (capsid) might promote changes of GII.2 antigenicity.