Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Human Norovirus Genotypes GII.P6-GII.6 and GII.P7-GII.6

Tomoko Takahashi; Ryusuke Kimura; Tatsuya Shirai; Mitsuru Sada; Toshiyuki Sugai; Kosuke Murakami; Kazuhiko Harada; Kazuto Ito; Yuki Matsushima; Fuminori Mizukoshi; Kaori Okayama; Yuriko Hayashi; Mayumi Kondo; Tsutomu Kageyama; Yoshiyuki Suzuki; Haruyuki Ishii; Akihide Ryo; Kazuhiko Katayama; Kiyotaka Fujita; Hirokazu Kimura

doi:10.3390/v15071497

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Human Norovirus Genotypes GII.P6-GII.6 and GII.P7-GII.6

Viruses. 2023 Jul 1;15(7):1497. doi: 10.3390/v15071497.

Authors

Tomoko Takahashi^{1

2}, Ryusuke Kimura^{3

4}, Tatsuya Shirai^{3

5}, Mitsuru Sada^{3

5}, Toshiyuki Sugai⁶, Kosuke Murakami⁷, Kazuhiko Harada³, Kazuto Ito³, Yuki Matsushima⁸, Fuminori Mizukoshi⁹, Kaori Okayama¹, Yuriko Hayashi¹, Mayumi Kondo¹⁰, Tsutomu Kageyama¹¹, Yoshiyuki Suzuki¹², Haruyuki Ishii⁵, Akihide Ryo¹³, Kazuhiko Katayama¹⁴, Kiyotaka Fujita¹, Hirokazu Kimura^{1

3

10}

Affiliations

¹ Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan.
² Iwate Prefectural Research Institute for Environmental Science and Public Health, Morioka-shi, Iwate 020-0857, Japan.
³ Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi, Gunma 377-0008, Japan.
⁴ Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi, Gunma 371-8514, Japan.
⁵ Department of Respiratory Medicine, School of Medicine, Kyorin University, Mitaka-shi, Tokyo 181-8611, Japan.
⁶ Department of Nursing Science, Graduate School of Health Science, Hiroshima University, Hiroshima-shi, Hiroshima 734-8551, Japan.
⁷ Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
⁸ Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
⁹ Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi, Tochigi 329-1196, Japan.
¹⁰ Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma 370-0006, Japan.
¹¹ Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
¹² Division of Biological Science, Department of Information and Basic Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya-shi, Aichi 467-8501, Japan.
¹³ Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
¹⁴ Laboratory of Viral Infection Control, Graduate School of Infection Control Sciences, Ōmura Satoshi Memorial Institute, Kitasato University, Minato-ku, Tokyo 108-8641, Japan.

Abstract

To understand the evolution of GII.P6-GII.6 and GII.P7-GII.6 strains, the prevalent human norovirus genotypes, we analysed both the RdRp region and VP1 gene in globally collected strains using authentic bioinformatics technologies. A common ancestor of the P6- and P7-type RdRp region emerged approximately 50 years ago and a common ancestor of the P6- and P7-type VP1 gene emerged approximately 110 years ago. Subsequently, the RdRp region and VP1 gene evolved. Moreover, the evolutionary rates were significantly faster for the P6-type RdRp region and VP1 gene than for the P7-type RdRp region and VP1 genes. Large genetic divergence was observed in the P7-type RdRp region and VP1 gene compared with the P6-type RdRp region and VP1 gene. The phylodynamics of the RdRp region and VP1 gene fluctuated after the year 2000. Positive selection sites in VP1 proteins were located in the antigenicity-related protruding 2 domain, and these sites overlapped with conformational epitopes. These results suggest that the GII.6 VP1 gene and VP1 proteins evolved uniquely due to recombination between the P6- and P7-type RdRp regions in the HuNoV GII.P6-GII.6 and GII.P7-GII.6 virus strains.

Keywords: RNA-dependent RNA polymerase (RdRp) region; VP1 gene; epitope mapping; human norovirus; molecular evolution.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Caliciviridae Infections*
Gastroenteritis*
Genotype
Humans
Norovirus* / genetics
Norovirus* / metabolism
Phylogeny
RNA-Dependent RNA Polymerase / genetics
RNA-Dependent RNA Polymerase / metabolism

Substances

RNA-Dependent RNA Polymerase

Grants and funding

This research was supported by the Japan Agency for Medical Research and Development, AMED (https://www.amed.go.jp/, accessed on 1 April 2023), under Grant Number JP23fk0108667. The funders played no role in the study design, data collection, analysis, decision to publish, or manuscript preparation.