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Hoque SA, Akari Y, Khamrin P, Phan T, Onda Y, Okitsu S, Komoto S, Hayakawa S, Komine-Aizawa S, Yuki Y, Kiyono H, Ushijima H. Epidemiology and molecular evolution of GI.1 sapovirus in the recent era. J Med Virol 2024; 96:e29904. [PMID: 39264064 DOI: 10.1002/jmv.29904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 08/25/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, including the largest SaV outbreak in 2021-2022, were caused by the GI.1 genotype. Therefore, to get insight into the underlying molecular mechanism behind this rising trend of the SaV GI.1 type, we selected 15 SaV GI.1 outbreak strains for complete genome analysis through next-generation sequencing. Phylogenetically, our strains remained clustered in different branches in lineages I and II among the GI.1 genotype. We showed all amino acid (aa) substitutions in different open reading frames (ORFs) in these strains. Importantly, we have demonstrated that the strains involved in the largest SaV outbreak in Japan in 2021-2022 belonged to lineage II and possessed the third ORF. We have identified some unique aa mutations in these major outbreak strains in the NS1 and NS6-NS7 regions that are thought to be associated with viral pathogenicity, cell tropism, and epidemiological competence. Thus, in addition to enriching the database of SaV's complete sequences, this study provides insights into its important mutations.
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Affiliation(s)
- Sheikh A Hoque
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, and Emerging and Re-emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai, Thailand
| | - Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuko Onda
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Shoko Okitsu
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
- Research Center for GLOBAL and LOCAL Infectious Diseases, Division of One Health, Oita University, Yufu, Japan
| | - Satoshi Hayakawa
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Shihoko Komine-Aizawa
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Yoshikazu Yuki
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
- Research Institute of Disaster Medicine, Institute for Global Prominent Research, Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Division of Gastroenterology, University of California, San Diego, California, USA
| | - Hiroshi Kiyono
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
- Research Institute of Disaster Medicine, Institute for Global Prominent Research, Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Division of Gastroenterology, University of California, San Diego, California, USA
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
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Yokoyama M, Doan YH, Motomura K, Sato H, Oka T. Strong evolutionary constraints against amino acid changes in the P2 subdomain of sapovirus GI.1 capsid protein VP1. Biochem Biophys Res Commun 2024; 710:149878. [PMID: 38608492 DOI: 10.1016/j.bbrc.2024.149878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Sapovirus (SaV) is a nonenveloped RNA virus that causes acute gastroenteritis in humans. Although SaV is a clinically important pathogen in children, an effective vaccine is currently unavailable. The capsid protein VP1 of SaVs forms the outer shell of the virion and is highly diverse, as often seen in the virion-surface proteins of RNA viruses, creating an obstacle for vaccine development. We here report a unique phenomenon pertaining to the variation of SaV VP1. Phylogenetic and information entropy analyses using full-length VP1 sequences from a public database consistently showed that the amino acid sequences of the VP1 protein have been highly conserved over more than 40 years in the major epidemic genotype GI.1 but not in GI.2. Structural modeling showed that even the VP1 P2 subdomain, which is arranged on the outermost shell of the virion and presumably exposed to anti-SaV antibodies, remained highly homogeneous in GI.1 but not in GI.2. These results suggest strong evolutionary constraints against amino acid changes in the P2 subdomain of the SaV GI.1 capsid and illustrate a hitherto unappreciated mechanism, i.e., preservation of the VP1 P2 subdomain, involved in SaV survival. Our findings could have important implications for the development of an anti-SaV vaccine.
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Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazushi Motomura
- Osaka Institute of Public Health, Osaka, Japan; Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Thailand; Research Institute of Microbial Diseases, Osaka University, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
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Ji X, Guo C, Dai Y, Chen L, Chen Y, Wang S, Sun Y. Genomic Characterization and Molecular Evolution of Sapovirus in Children under 5 Years of Age. Viruses 2024; 16:146. [PMID: 38275956 PMCID: PMC10819405 DOI: 10.3390/v16010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area.
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Affiliation(s)
- Xiaolei Ji
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Chen Guo
- Department of Laboratory Medicine, Nantong Chongchuan Center for Disease Control and Prevention, 47 Zhongxiu Middle Road, Nantong 226001, China;
| | - Yaoyao Dai
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Lu Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yujia Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Shifang Wang
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yihua Sun
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
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