Molecular evolution of the capsid (VP1) region in human norovirus genogroup II genotype 3

Mariko Saito; Hiroyuki Tsukagoshi; Hirotaka Ishigaki; Jumpei Aso; Haruyuki Ishii; Kaori Okayama; Akihide Ryo; Taisei Ishioka; Makoto Kuroda; Nobuhiro Saruki; Kazuhiko Katayama; Hirokazu Kimura

doi:10.1016/j.heliyon.2020.e03835

Molecular evolution of the capsid (VP1) region in human norovirus genogroup II genotype 3

Heliyon. 2020 May 3;6(5):e03835. doi: 10.1016/j.heliyon.2020.e03835. eCollection 2020 May.

Authors

Affiliations

¹ Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
² Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan.
³ Kyorin University Hospital, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan.
⁴ Department of Microbiology, Yokohama City University School of Medicine, 3-9 Fukuura, Yokohama-shi, Kanagawa 236-0004, Japan.
⁵ Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
⁶ Laboratory of Viral Infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.

Abstract

Norovirus GII.3 has been suggested to be a prevalent genotype in patients with acute gastroenteritis. However, the genetic properties of the VP1 region encoding the major GII.3 antigen remain unclear. Here, we performed molecular evolutionary analyses of the GII.3 VP1 region detected in various countries. We performed time-scaled phylogenetic analyses, selective pressure analyses, phylogenetic distance analyses, and conformational epitope analyses. The time-scaled phylogenetic tree showed that an ancestor of the GII.3 VP1 region diverged from the common ancestors of the GII.6, GII.11, GII.18, and GII.19 approximately 70 years ago with relatively low divergence. The evolutionary rate of the GII.3 VP1 region was rapid (4.82 × 10^-3 substitutions/site/year). Furthermore, one positive site and many negative selection sites were observed in the capsid protein. These results suggest that the GII.3 VP1 region rapidly evolved with antigenic variations.

Keywords: Bioinformatics; GII.3; Microbiology; Molecular evolution; Norovirus; VP1; Viral disease; Viral genetics; Virology.