Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase Region in Norovirus Genogroup II

Abstract

Noroviruses are the leading cause of viral gastroenteritis in humans across the world. RNA-dependent RNA polymerase (RdRp) plays a critical role in the replication of the viral genome. Although there have been some reports on a limited number of genotypes with respect to the norovirus evolution of the RdRp region, no comprehensive molecular evolution examination of the norovirus GII genotype has yet been undertaken. Therefore, we conducted an evolutionary analysis of the 25 genotypes of the norovirus GII RdRp region (full-length), collected globally using different bioinformatics technologies. The time-scaled phylogenetic tree, generated using the Bayesian Markov Chain Monte Carlo (MCMC) method, indicated that the common ancestor of GII diverged from GIV around 1443 CE [95% highest posterior density (HPD), 1336–1542]. The GII RdRp region emerged around 1731 CE (95% HPD, 1703–1757), forming three lineages. The evolutionary rate of the RdRp region of the norovirus GII strains was estimated at over 10−3 substitutions/site/year. The evolutionary rates were significantly distinct in each genotype. The composition of the phylogenetic distances differed among the strains for each genotype. Furthermore, we mapped the negative selection sites on the RdRp protein and many of these were predicted in the GII.P4 RdRp proteins. The phylodynamics of GII.P4, GII.P12, GII.P16, and GII.Pe showed that their effective population sizes increased during the period from 2003 to 2014. Our results cumulatively suggest that the RdRp region of the norovirus GII rapidly and uniquely evolved with a high divergence similar to that of the norovirus VP1 gene.

Molecular Evolution of the Protease Region in Norovirus Genogroup II

“…The histogram of the distance of GII.P16 showed a bimodal distribution, suggesting that they contain two distinct groups within the same genotype. The trends of phylogenetic distance distribution among genotypes in the GII Pro region were analogous to that of the GII RdRp region (Ozaki et al, 2018). Thus, it appears that the GII Pro and RdRp regions might co-evolve.…”

“…This study showed that the evolutionary rate of the GII Pro region was estimated at 3.94 × 10 −3 substitutions/site/year, and that evolution at different rates occurred between the ORF1 genotypes (Figure 2). The Pro region evolved rapidly (>10 −3 substitutions/site/year) as did the VP1 region and the RdRp region (Kobayashi et al, 2016;Ozaki et al, 2018). We therefore speculate that evolutionary rates in the other regions on the NoV genome were rapid.…”

“…The years of divergence of the Pro and RdRp regions were very similar (270 vs. 290 years ago), whereas the year of divergence of the VP1 region was different by approximately 100 years. The year in divergence of each lineage was comparable between the Pro and RdRp regions (Ozaki et al, 2018). We estimated that in lineage 1 the Pro region diverged around 150 years ago (1873 CE) and the RdRp region around 170 years ago (1847 CE).…”

“…These results suggested that the Pro region of the NoV GII evolved rapidly with amino acid substitutions under no positive selection, and the evolutionary trends were different between the ORF1 genotypes. A time-scaled phylogenetic tree constructed using a Bayesian MCMC method indicated that the Pro region showed similar evolutionary process to the RdRp region, but was different from the VP1 region at post emergence of the GII cluster, including the generations of three lineages (Kobayashi et al, 2016;Ozaki et al, 2018). We estimated that the Pro region, the RdRp region and the VP1 region diverged around 270 years ago (1752 CE), around 290 years ago (1731 CE) and around 390 years ago (1630 CE), respectively, to form the GII cluster.…”

“…The statistical results for multiple comparisons are shown in Supplementary Table S2. Ozaki et al (2018) recently classified 23 ORF1 genotypes in the HuNoV GII strains into three lineages: lineage 1 (GII.P6-P8, P15 and P20), lineage 2 (GII.P1-P5, P12, P16, P17, P21, P30-P33, P35, and P37), and lineage 3 (GII.P22, P23, and P24). The phylogenetic topology in the ORF1 genotypes and the year of divergence of each lineage were almost analogous between the Pro and the RdRp regions.…”