Genetic Analysis of Human Norovirus Strains in Japan in 2016-2017.

Kinzo Nagasawa ,Hiroto Shinomiya,Koichi Murakami,Tomomi Shimizu,Hirokazu Kimura,Nobuhiko Okabe,Komei Shirabe,Akihide Ryo,Kiyotaka Fujita,Yuki Matsushima,Kazuhiko Katayama,Yo Ueki,Naomi Sakon,Wataru Suzuki,Yoshiyuki Suzuki,Fuminori Mizukoshi,Kazunori Oishi,Tsuyoshi Sekizuka,Takumi Motoya,Noriko Nagata,Makoto Kuroda

doi:10.3389/fmicb.2018.00001

Abstract

In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their time-scale evolutionary phylogeny, positive/negative selection, conformational epitopes, and phylodynamics. The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2. The evolutionary rates of the VP1 gene and RdRp region were around 10-3 substitutions/site/year. Amino acid substitutions (position 341) in an epitope in the P2 domain of 2016 strains were not found in pre-2016 GII.2 strains. Bayesian skyline plot analyses showed that the effective population size of the VP1 gene in GII.2 strains was almost constant for those 50 years, although the number of patients with NoV GII.2 increased in 2016. The 2016 strain may be involved in future outbreaks in Japan and elsewhere.

Highlights

Human norovirus (HuNoV) is a common cause of acute gastroenteritis in humans (Matson, 2004)
The evolutionary rate of the VP1 gene in HuNoV Gll.2 strains was estimated as 3.26 × 10−3 substitutions/site/year (95% highest posterior density (HPD) interval, 2.74–3.78 × 10−3 substitutions/site/year)
We describe the evolution of the VP1 gene and RNAdependent RNA polymerase (RdRp) region in the HuNoV GII.P16-GII.2 strains detected in the 2016/2017

Summary

Introduction

Human norovirus (HuNoV) is a common cause of acute gastroenteritis in humans (Matson, 2004). HuNoV is classified into two genogroups (GI and GII), including many genotypes (Vinjé, 2015). Molecular Evolution of HuNoV GII.P16-GII. genotypes, including GII., GII., GII., and GII., were detected worldwide, including Japan (Thongprachum et al, 2017). During the 2016–2017 winter season in Japan, GII.P16GII. strains (2016 strains) suddenly appeared and caused large outbreaks of gastroenteritis in Japanese children (Thongprachum et al, 2017). The Japanese national surveillance system reported in Infectious Diseases Weekly Report (IDWR) that the outbreaks of acute gastroenteritis in children in this season were the second largest number of patients in the past 11 seasons [National Institute of Infectious Diseases, Japan, Infectious Gastroenteritis (cited 2017 February 16, in Japanese)1]. Similar findings were reported from Germany, France, China, and United States (Bidalot et al, 2017; Lu et al, 2017; Niendorf et al, 2017; Tohma et al, 2017)

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