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

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

doi:10.3389/fmicb.2019.02189

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

Front Microbiol. 2019 Sep 27:10:2189. doi: 10.3389/fmicb.2019.02189. eCollection 2019.

Authors

Yuki Matsushima¹, Fuminori Mizukoshi², Naomi Sakon³, Yen Hai Doan⁴, Yo Ueki⁵, Yasutaka Ogawa⁶, Takumi Motoya⁷, Hiroyuki Tsukagoshi⁸, Noriko Nakamura⁹, Naoki Shigemoto¹⁰, Hideaki Yoshitomi¹¹, Reiko Okamoto-Nakagawa¹², Rieko Suzuki¹³, Rika Tsutsui¹⁴, Fumio Terasoma¹⁵, Tomoko Takahashi¹⁶, Kenji Sadamasu¹⁷, Hideaki Shimizu¹, Nobuhiko Okabe¹, Koo Nagasawa¹⁸, Jumpei Aso^{19

20}, Haruyuki Ishii²⁰, Makoto Kuroda²¹, Akihide Ryo²², Kazuhiko Katayama²³, Hirokazu Kimura^{19

22}

Affiliations

¹ Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan.
² Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya, Japan.
³ Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan.
⁴ Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Japan.
⁵ Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai, Japan.
⁶ Division of Virology, Saitama Institute of Public Health, Saitama, Japan.
⁷ Ibaraki Prefectural Institute of Public Health, Mito, Japan.
⁸ Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan.
⁹ Aichi Prefectural Institute of Public Health, Kita, Japan.
¹⁰ Hiroshima Prefectural Technology Research Institute Public Health and Environment Center, Hiroshima, Japan.
¹¹ Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan.
¹² Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan.
¹³ Kanagawa Prefectural Institute of Public Health, Chigasaki, Japan.
¹⁴ Aomori Prefecture Public Health and Environment Center, Aomori, Japan.
¹⁵ Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan.
¹⁶ Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan.
¹⁷ Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Japan.
¹⁸ Eastern Chiba Medical Center, Togane, Japan.
¹⁹ Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.
²⁰ Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan.
²¹ Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan.
²² Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan.
²³ Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Minato, Japan.

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.

Keywords: GII.P17-GII.17; RdRp; VP1; human norovirus; molecular evolution.

Copyright © 2019 Matsushima, Mizukoshi, Sakon, Doan, Ueki, Ogawa, Motoya, Tsukagoshi, Nakamura, Shigemoto, Yoshitomi, Okamoto-Nakagawa, Suzuki, Tsutsui, Terasoma, Takahashi, Sadamasu, Shimizu, Okabe, Nagasawa, Aso, Ishii, Kuroda, Ryo, Katayama and Kimura.