Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2
Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (<i>RdRp</i>) and capsid (<i>VP1</i>) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinforma...
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2025-02-01
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| author | Fuminori Mizukoshi Ryusuke Kimura Tatsuya Shirai Asumi Hirata-Saito Eri Hiraishi Kosuke Murakami Yen Hai Doan Hiroyuki Tsukagoshi Nobuhiro Saruki Takeshi Tsugawa Kana Kidera Yoshiyuki Suzuki Naomi Sakon Kazuhiko Katayama Tsutomu Kageyama Akihide Ryo Hirokazu Kimura |
| author_facet | Fuminori Mizukoshi Ryusuke Kimura Tatsuya Shirai Asumi Hirata-Saito Eri Hiraishi Kosuke Murakami Yen Hai Doan Hiroyuki Tsukagoshi Nobuhiro Saruki Takeshi Tsugawa Kana Kidera Yoshiyuki Suzuki Naomi Sakon Kazuhiko Katayama Tsutomu Kageyama Akihide Ryo Hirokazu Kimura |
| author_sort | Fuminori Mizukoshi |
| collection | DOAJ |
| description | Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (<i>RdRp</i>) and capsid (<i>VP1</i>) 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 <i>RdRp</i> region and <i>VP1</i> gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 <i>RdRp</i> region and <i>VP1</i> gene were divided into two clusters. Further, the MRCAs of the <i>RdRp</i> region and <i>VP1</i> gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for <i>VP1</i> 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 <i>RdRp</i> for GI.1 and in <i>VP1</i> for GI.2, respectively. These results suggest that the <i>RdRp</i> region and <i>VP1</i> gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the <i>RdRp</i> region and <i>VP1</i> gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen. |
| format | Article |
| id | doaj-art-a75f7590fc8e4915aa0f85cc64d0780f |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-a75f7590fc8e4915aa0f85cc64d0780f2025-08-20T03:12:05ZengMDPI AGMicroorganisms2076-26072025-02-0113232210.3390/microorganisms13020322Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2Fuminori Mizukoshi0Ryusuke Kimura1Tatsuya Shirai2Asumi Hirata-Saito3Eri Hiraishi4Kosuke Murakami5Yen Hai Doan6Hiroyuki Tsukagoshi7Nobuhiro Saruki8Takeshi Tsugawa9Kana Kidera10Yoshiyuki Suzuki11Naomi Sakon12Kazuhiko Katayama13Tsutomu Kageyama14Akihide Ryo15Hirokazu Kimura16Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, JapanDepartment of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, JapanDepartment of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, JapanDepartment of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya-shi 329-1196, JapanDepartment of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki-shi 370-0006, JapanCenter for Emergency Preparedness and Response, National Institute of Infectious Diseases, Shinjuku-ku 162-8640, JapanCenter for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, JapanGunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, JapanGunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, JapanDepartment of Pediatrics, Sapporo Medical University School of Medicine, Sapporo-shi 060-8543, JapanLaboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku 108-8641, JapanDivision of Biological Science, Department of Information and Basic Science, Graduate School of Sciences, Nagoya City University, Nagoya-shi 467-8501, JapanDepartment of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, JapanLaboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku 108-8641, JapanCenter for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, JapanDepartment of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, JapanAdvanced Medical Science Research Center, Gunma Paz University, Takasaki-shi 370-0006, JapanHuman sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (<i>RdRp</i>) and capsid (<i>VP1</i>) 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 <i>RdRp</i> region and <i>VP1</i> gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 <i>RdRp</i> region and <i>VP1</i> gene were divided into two clusters. Further, the MRCAs of the <i>RdRp</i> region and <i>VP1</i> gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for <i>VP1</i> 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 <i>RdRp</i> for GI.1 and in <i>VP1</i> for GI.2, respectively. These results suggest that the <i>RdRp</i> region and <i>VP1</i> gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the <i>RdRp</i> region and <i>VP1</i> gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen.https://www.mdpi.com/2076-2607/13/2/322human sapovirusmolecular evolutionary analysesRNA-dependent RNA polymerase (<i>RdRp</i>)capsid (<i>VP1</i>) |
| spellingShingle | Fuminori Mizukoshi Ryusuke Kimura Tatsuya Shirai Asumi Hirata-Saito Eri Hiraishi Kosuke Murakami Yen Hai Doan Hiroyuki Tsukagoshi Nobuhiro Saruki Takeshi Tsugawa Kana Kidera Yoshiyuki Suzuki Naomi Sakon Kazuhiko Katayama Tsutomu Kageyama Akihide Ryo Hirokazu Kimura Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 Microorganisms human sapovirus molecular evolutionary analyses RNA-dependent RNA polymerase (<i>RdRp</i>) capsid (<i>VP1</i>) |
| title | Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 |
| title_full | Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 |
| title_fullStr | Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 |
| title_full_unstemmed | Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 |
| title_short | Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (<i>RdRp</i>) Region and <i>VP1</i> Gene in Sapovirus GI.1 and GI.2 |
| title_sort | molecular evolutionary analyses of the rna dependent rna polymerase i rdrp i region and i vp1 i gene in sapovirus gi 1 and gi 2 |
| topic | human sapovirus molecular evolutionary analyses RNA-dependent RNA polymerase (<i>RdRp</i>) capsid (<i>VP1</i>) |
| url | https://www.mdpi.com/2076-2607/13/2/322 |
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