Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013-2017.

Yuki Matsushima,Makoto Kuroda,Noriko Nakamura,Kazuhiko Katayama,Takumi Motoya,Fumio Terasoma,Rika Tsutsui,Akihide Ryo,Hideaki Shimizu,Hiroyuki Tsukagoshi,Yo Ueki,Hirokazu Kimura,Hideaki Yoshitomi,Reiko Okamoto-Nakagawa,Kenji Sadamasu,Yen Hai Doan,Tomoko Takahashi,Yasutaka Ogawa,Jumpei Aso,Naomi Sakon,Nobuhiko Okabe,Fuminori Mizukoshi,Haruyuki Ishii,Riéko Suzuki ,Norifumi Shigemoto ,Kinzo Nagasawa

doi:10.3389/fmicb.2019.02189

Abstract

Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10−3 and ~2.3 × 10−3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.

Highlights

Human norovirus (HuNoV) is a major causative pathogen of acute viral gastroenteritis (de Graaf et al, 2016)
We constructed time-scaled phylogenetic trees using the Markov Chain Monte Carlo (MCMC) method based on the full-length of the VP1 (343 strains) and RdRp (133 strains) regions in the GII.17 strains detected in the various countries (Figures 1, 2)
The MCMC tree for the VP1 region estimated that the common ancestor of the GII.17, GII.13, and GII.21 diverged in September, 1931 (95% highest posterior densities (HPDs) January, 1911–February, 1950)

Summary

Introduction

Human norovirus (HuNoV) is a major causative pathogen of acute viral gastroenteritis (de Graaf et al, 2016). HuNoV is most prevalent during autumn and winter in the northern hemisphere, the virus can be detected throughout the year (Ahmed et al, 2013). Molecular epidemiological studies have indicated that distinct GII. variants have recurrently emerged every 2–3 years in the past decade to cause pandemics of gastroenteritis in all aged individuals (Bull et al, 2010). GII.P17-GII. (Kawasaki2014 variant) has suddenly been prevalent since 2014 in various countries including Japan, China, South Korea, Italy, Romania, Argentina, Brazil, and the USA (Chan et al, 2015; Fu et al, 2015; Matsushima et al, 2015; Medici et al, 2015; Dang Thanh et al, 2016; Dinu et al, 2016; Cannon et al, 2017; Degiuseppe et al, 2017; Silva et al, 2017). The epidemiology of this virus over a long period of time is unclear at present

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Results

Conclusion