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Volume 13
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10.3390/microorganisms13020322
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Article

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2

by
Fuminori Mizukoshi
1,*,
Ryusuke Kimura
2,3,
Tatsuya Shirai
1,
Asumi Hirata-Saito
4,
Eri Hiraishi
5,
Kosuke Murakami
6,
Yen Hai Doan
7,
Hiroyuki Tsukagoshi
8,
Nobuhiro Saruki
8,
Takeshi Tsugawa
9,
Kana Kidera
10,
Yoshiyuki Suzuki
11,
Naomi Sakon
12,
Kazuhiko Katayama
10,
Tsutomu Kageyama
7,
Akihide Ryo
1 and
Hirokazu Kimura
3,5,*
1
Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
2
Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Japan
3
Advanced Medical Science Research Center, Gunma Paz University, Takasaki-shi 370-0006, Japan
4
Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi 329-1196, Japan
5
Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki-shi 370-0006, Japan
6
Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
7
Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
8
Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan
9
Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo-shi 060-8543, Japan
10
Laboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku, Tokyo 108-8641, Japan
11
Division of Biological Science, Department of Information and Basic Science, Graduate School of Sciences, Nagoya City University, Nagoya-shi 467-8501, Japan
12
Department of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan
 
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*
Authors to whom correspondence should be addressed.
Microorganisms 2025, 13(2), 322; https://doi.org/10.3390/microorganisms13020322
Submission received: 27 December 2024 / Revised: 17 January 2025 / Accepted: 24 January 2025 / Published: 1 February 2025
(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)
Versions Notes

Abstract

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen.
Keywords: human sapovirus; molecular evolutionary analyses; RNA-dependent RNA polymerase (RdRp); capsid (VP1) human sapovirus; molecular evolutionary analyses; RNA-dependent RNA polymerase (RdRp); capsid (VP1)

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MDPI and ACS Style

Mizukoshi, F.; Kimura, R.; Shirai, T.; Hirata-Saito, A.; Hiraishi, E.; Murakami, K.; Doan, Y.H.; Tsukagoshi, H.; Saruki, N.; Tsugawa, T.; et al. Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2. Microorganisms 2025, 13, 322. https://doi.org/10.3390/microorganisms13020322

AMA Style

Mizukoshi F, Kimura R, Shirai T, Hirata-Saito A, Hiraishi E, Murakami K, Doan YH, Tsukagoshi H, Saruki N, Tsugawa T, et al. Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2. Microorganisms. 2025; 13(2):322. https://doi.org/10.3390/microorganisms13020322

Chicago/Turabian Style

Mizukoshi, Fuminori, Ryusuke Kimura, Tatsuya Shirai, Asumi Hirata-Saito, Eri Hiraishi, Kosuke Murakami, Yen Hai Doan, Hiroyuki Tsukagoshi, Nobuhiro Saruki, Takeshi Tsugawa, and et al. 2025. "Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2" Microorganisms 13, no. 2: 322. https://doi.org/10.3390/microorganisms13020322

APA Style

Mizukoshi, F., Kimura, R., Shirai, T., Hirata-Saito, A., Hiraishi, E., Murakami, K., Doan, Y. H., Tsukagoshi, H., Saruki, N., Tsugawa, T., Kidera, K., Suzuki, Y., Sakon, N., Katayama, K., Kageyama, T., Ryo, A., & Kimura, H. (2025). Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2. Microorganisms, 13(2), 322. https://doi.org/10.3390/microorganisms13020322

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