1
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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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2
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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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3
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Hoque SA, Pham NTK, Onda-Shimizu Y, Nishimura S, Sugita K, Kobayashi M, Islam MT, Okitsu S, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Sapovirus infections in Japan before and after the emergence of the COVID-19 pandemic: An alarming update. J Med Virol 2023; 95:e29023. [PMID: 37543991 DOI: 10.1002/jmv.29023] [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: 01/17/2023] [Revised: 06/19/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
An increasing trend of sapovirus (SaV) infections in Japanese children during 2009-2019, particularly after the introduction of the voluntary rotavirus (RV)-vaccination program has been observed. Herein, we investigated the epidemiological situation of SaV infections from 2019 to 2022 when people adopted a precautionary lifestyle due to the emergence of the COVID-19 pandemic, and RV vaccines had been implemented as routine vaccines. Stool samples were collected from children who attended outpatient clinics with acute gastroenteritis and analyzed by reverse transcriptase-polymerase chain reaction to determine viral etiology. Among 961 stool samples, 80 (8.3%) were positive for SaV: 2019-2020 (6.5%), 2020-2021 (0%), and 2021-2022 (12.8%). The trend of SaV infection in Japanese children yet remained upward with statistical significance (p = 0.000). The major genotype was GI.1 (75%) which caused a large outbreak in Kyoto between December 2021 and February 2022. Phylogenetic, gene sequence and deduced amino acid sequence analyses suggested that these GI.1 strains detected in the outbreak and other places during 2021-2022 or 2019-2020 remained genetically identical and widely spread. This study reveals that SaV infection is increasing among Japanese children which is a grave concern and demands immediate attention to be paid before SaV attains a serious public health problem.
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Affiliation(s)
- Sheikh Ariful Hoque
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Ngan Thi Kim Pham
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Yuko Onda-Shimizu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shuichi Nishimura
- Cell and Tissue Culture Research, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Kumiko Sugita
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | - Masaaki Kobayashi
- Division of Microbiology, Nihon University School of Medicine, Japanese Viral Gastritis Group, Tokyo, Japan
| | | | - Shoko Okitsu
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Thailand
| | - Satoshi Hayakawa
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Wei R, Shang R, Cheng K, Wang S, Wu J, Yu Z. A novel recombinant porcine sapovirus infection in piglets with diarrhea in Shandong Province, China, 2022. Braz J Microbiol 2023; 54:1309-1314. [PMID: 37036658 PMCID: PMC10235293 DOI: 10.1007/s42770-023-00963-x] [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: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 04/11/2023] Open
Abstract
Sapporo virus (SaV) is an emerging enteric virus causing acute gastroenteritis in animals. Here, we found a novel porcine SaV (PoSaV) strain (named SD2202) from the piglets with diarrhea in China in 2022. The highest nucleotide homology of SD2202 with other PoSaV strains is only 90.67%, and there are four amino acids insertion in the viral capsid protein and minor structural protein compared to other PoSaV; furthermore, we found that SD2202 belongs to a new GIII genogroup clade (GIII-6 clade). Interestingly, we found that SD2202 may be an intra-genogroup recombinant strain. Taken together, we found a novel PoSaV implicated in the piglet diarrhea epidemic and emphasized the importance of continuous surveillance of PoSaV.
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Affiliation(s)
- Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Rui Shang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Kaihui Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Song Wang
- Medical Integration and Practice Center, Shandong University, Jinan, 250012, China
| | - Jiaqiang Wu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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5
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Phengma P, Khamrin P, Jampanil N, Yodmeeklin A, Ushijima H, Maneekarn N, Kumthip K. The emergence of recombinant norovirus GII.12[P16] and predominance of GII.3[P12] strains in pediatric patients with acute gastroenteritis in Thailand, 2019-2020. J Med Virol 2023; 95:e28321. [PMID: 36397269 DOI: 10.1002/jmv.28321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/17/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Norovirus (NoV) and sapovirus (SaV) are important pathogens that cause acute gastroenteritis (AGE) in all age groups, commonly in children worldwide. Recently, a number of studies have reported a wide variety of NoV recombinant strains. This study aimed to investigate the distribution of NoV and SaV recombinant strains circulating in Chiang Mai, Thailand, during 2019-2020. One hundred and twenty-four NoV and seven SaV strains detected in children admitted to the hospital with AGE were included in this study. The partial RNA-dependent RNA-polymerase (RdRp)/VP1 regions of these NoV and SaV strains were analyzed by phylogenetic analysis, Simplot, and RDP software. Overall, eight recombination patterns of NoV were detected. NoV GII.4[P16] was the most common strain detected (39.1%), followed by GII.3[P12] (25.0%), GII.4[P31] (17.2%), and other recombinant strains were detected at a lower rate. NoV GII.12[P16] strains were detected for the first time in Thailand. For SaV, none of the recombinant strains was detected. All SaV strains, GI.1/GI.1, GI.2/GI.2, and GII.5/GII.5, exhibited VP1 genotype corresponded to RdRp genotype. In conclusion, this study demonstrates the distribution and diversity of NoV and SaV recombinant strains circulating in pediatric patients with AGE in Chiang Mai, during 2019-2020 with the emergence of NoV GII.3[P12] and GII.12[P16].
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Affiliation(s)
- Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Division of Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence (Emerging and Re-Emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
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Colito DA, Dorta-Guerra R, Da Costa Lima HS, Pina C, Gonçalves D, Valladares B, Foronda P. Epidemiological investigations of diarrhea in children in Praia city, Cape Verde. Front Microbiol 2022; 13:1059431. [PMID: 36619987 PMCID: PMC9814011 DOI: 10.3389/fmicb.2022.1059431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Diarrheal disease is a major cause of infant mortality and morbidity in Africa and results primarily from contaminated food and water sources, but its prevalence predictors in Cape Verde are not completely known. For this reason, this study aimed to identify the etiological agents of diarrhea in Cape Verdean children and assess its associated risk factors. Methods A survey questionnaire was used, and a total of 105 stool samples from children with diarrhea aged 0-12 years at the Central Hospital of Praia (Santiago, Cape Verde) were analyzed. The analyses were carried out using Biofire FilmArray Gastrointestinal Panels. Possible risk factors for these pathogens were analyzed using logistic regression, chi-square tests, or Fisher's exact test. Results Among the bacteria, enteroaggregative Escherichia coli (45.71%; 95% CI: 36.71-56.70), enteropathogenic E. coli (40%; 95% CI: 30.56-50.02), Shigella/enteroinvasive E. coli (29.52%; 95% CI: 21.02-39.22), E. coli enterotoxigenic (12.38%; 95% CI: 6.76-20.24), Campylobacter sp. (10.48%; 95% CI: 5.35-1.97), Vibrio sp. (4.76%; 95% CI: 1.56-10.76), Clostridioides difficile (3.81%; 95% CI: 1.05-9.47), Vibrio cholerae (2.86%; 0.59-8.12), Shiga-like toxin-producing E. coli (2.86%; 0.59-8.12) and Salmonella sp. (0.95%; 0.02-5.19) were identified; four viruses, Rotavirus A (28.57%; 95% CI: 20.18-38.21), Sapovirus I. II. IV and V (11.43%; 95% CI: 6.05-19.11), Norovirus GI.GII (6.67%; 95% CI: 2.72-13.25) and Adenovirus F 40.41 (6.67%; 95% CI: 2.72-13.25) were also observed. All the pathogens detected in this study were found in coinfections. Significant associations with risk factors were found; specifically, having a bathroom at home reduced the risk of Campylobacter sp., having animals at home increased the risk of Shigella/EIEC infection, and drinking bottled water reduced the risk of Sapovirus infection. Discussion From the findings of this study, it can be concluded that, in Cape Verde, there is a high prevalence and diversity of pathogens among children. Our results could help to establish an adequate diagnosis and effective treatments for diarrheal disease.
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Affiliation(s)
| | - Roberto Dorta-Guerra
- Departamento de Matemáticas, Estadística e IO, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Carine Pina
- Faculty of Science and Technology, University of Cape Verde, Palmarejo, Cape Verde
| | - Deisy Gonçalves
- Faculty of Science and Technology, University of Cape Verde, Palmarejo, Cape Verde
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Pilar Foronda
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,*Correspondence: Pilar Foronda,
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7
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Shen H, Zhang J, Gauger PC, Burrough ER, Zhang J, Harmon K, Wang L, Zheng Y, Petznick T, Li G. Genetic characterization of porcine sapoviruses identified from pigs during a diarrhoea outbreak in Iowa, 2019. Transbound Emerg Dis 2022; 69:1246-1255. [PMID: 33780163 DOI: 10.1111/tbed.14087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
Porcine sapovirus (SaV) was first identified by electron microscopy in the United States in 1980 and has since been reported from both asymptomatic and diarrhoeic pigs usually in mixed infection with other enteric pathogens. SaV as the sole aetiological agent of diarrhoea in naturally infected pigs has not previously been reported in the United States. Here, we used four independent lines of evidence including metagenomics analysis, real-time RT-PCR (rRT-PCR), histopathology, and in situ hybridization to confirm porcine SaV genogroup III (GIII) as the sole cause of enteritis and diarrhoea in pigs. A highly sensitive and specific rRT-PCR was established to detect porcine SaV GIII. Examination of 184 faecal samples from an outbreak of diarrhoea on a pig farm showed that pigs with clinical diarrhoea had significantly lower Ct values (15.9 ± 0.59) compared to clinically unaffected pigs (35.8 ± 0.71). Further survey of 336 faecal samples from different states in the United States demonstrated that samples from pigs with clinical diarrhoea had a comparable positive rate (45.3%) with those from asymptomatic pigs (43.1%). However, the SaV-positive pigs with clinical diarrhoea had significantly higher viral loads (Ct = 26.0 ± 0.5) than the SAV-positive but clinically healthy pigs (Ct = 33.2 ± 0.9). Phylogenetic analysis of 20 field SaVs revealed that all belonged to SaV GIII and recombination analysis indicated that intragenogroup recombination had occurred within the field isolates of SaV GIII. These results suggest that porcine SaV GIII plays an important aetiologic role in swine enteritis and diarrhoea and rRT-PCR is a reliable method to detect porcine SaV. Our findings provide significant insights to better understand the epidemiology and pathogenicity of porcine SaV infection.
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Affiliation(s)
- Huigang Shen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianfeng Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Eric R Burrough
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, USA
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Makhaola K, Lechiile K, Moyo S, Goldfarb DM, Pernica JM, Kebaabetswe LP. Molecular Characterization of Sapovirus from Children with Gastroenteritis in Botswana. JOURNAL OF CLINICAL VIROLOGY PLUS 2022. [DOI: 10.1016/j.jcvp.2022.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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9
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Hoque SA, Nishimura K, Thongprachum A, Khamrin P, Thi Kim Pham N, Islam MT, Khandoker N, Okitsu S, Onda-Shimizu Y, Dey SK, Maneekarn N, Kobayashi T, Hayakawa S, Ushijima H. An Increasing Trend of Human Sapovirus Infection in Japan, 2009 to 2019: An Emerging Public Health Concern. J Infect Public Health 2022; 15:315-320. [DOI: 10.1016/j.jiph.2022.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
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10
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Razizadeh MH, Khatami A, Zarei M. Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis. Rev Med Virol 2021; 32:e2302. [PMID: 34626019 DOI: 10.1002/rmv.2302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.
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Affiliation(s)
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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11
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Song K, Lin X, Liu Y, Ji F, Zhang L, Chen P, Zhao C, Song Y, Tao Z, Xu A. Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:270-280. [PMID: 33755873 PMCID: PMC7985922 DOI: 10.1007/s12560-021-09469-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.
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Affiliation(s)
- Ke Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Yao Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Li Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Peng Chen
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, 44-1 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Chenxu Zhao
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Yanyan Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China.
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China.
| | - Aiqiang Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
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Abstract
PURPOSE OF REVIEW Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen. RECENT FINDINGS Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied. SUMMARY Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.
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Cilli A, Luchs A, Morillo SG, Carmona RDCC, Dos Santos FCP, Maeda AY, Primo D, Pacheco GT, Souza EV, Medeiros RS, Timenetsky MDCST. Surveillance and molecular characterization of human sapovirus in patients with acute gastroenteritis in Brazil, 2010 to 2017. J Clin Virol 2021; 140:104844. [PMID: 33971579 DOI: 10.1016/j.jcv.2021.104844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/06/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Human sapoviruses (HuSaV) are associated with acute gastroenteritis (AGE), causing sporadic cases and outbreaks in patients worldwide. In Brazil, however, there are few reports describing the prevalence of HuSaV in patients with AGE. OBJECTIVE Describing the diversity of HuSaV in Brazil by detecting and molecularly characterizing HuSaV among patients with AGE during an 8-year period (2010-2017). STUDY DESIGN A total of 3974 stool samples, testing negative for rotavirus (RVA), norovirus (NoV) and human adenovirus (HAdV), were selected and screened for the presence of HuSaV. Nested RT-PCR were performed for a partial region of VP1, sequenced and genetic analyzed for genotyping the positive samples. RESULTS In the current study, the HuSaV prevalence was determined to be 3.7% (149/3974). A higher prevalence, 5.7% (118/2074), was observed in children under 2 years of age. During the surveillance period, 13 outbreaks were detected: 12 outbreaks in children under 3 years old and one outbreak in adults. Among the 149 HuSaV positive cases, 106 samples (71%) were successfully sequenced. The most prevalent genotype found was GI.1 (44.3%), followed by GI.2 (21.7%), GI.3 (3.8%), GI.6 (2.8%), GII.1 (5.7%), GII.2 (8.5%), GII.3 (2.8%), GII.4 (2.8%), GII.5 (5.7%) and GIV.1 (1.9%). Two GIV.1 strains characterized in this study are, to date, the only strains of this genotype reported in Brazil. CONCLUSIONS The present study elucidated the circulation of HuSaV in Brazil and highlight that HuSaV has not assumed an epidemiological importance in the country after the introduction of the RVA vaccine.
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Affiliation(s)
- Audrey Cilli
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil.
| | - Adriana Luchs
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Simone G Morillo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | | | | | - Adriana Y Maeda
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Dieli Primo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Gabriela T Pacheco
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Ellen V Souza
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Roberta S Medeiros
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
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Okitsu S, Khamrin P, Thongprachum A, Hikita T, Kumthip K, Pham NTK, Takanashi S, Hayakawa S, Maneekarn N, Ushijima H. Diversity of human sapovirus genotypes detected in Japanese pediatric patients with acute gastroenteritis, 2014-2017. J Med Virol 2021; 93:4865-4874. [PMID: 33704833 DOI: 10.1002/jmv.26934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 11/09/2022]
Abstract
Sapovirus (SaV) is one of the pathogens related to acute gastroenteritis (AGE) in adults and children worldwide. This study reported the diversity of SaV genotypes in children with AGE in Japan from July 2014 to June 2017. Of a total of 2259 stool samples tested by using reverse transcription-PCR method and further analyzed by nucleotide sequencing, 114 (5.0%) were positive for SaV and GI.1 (83.3%) was the most predominant genotype, followed by GII.1, GIV.1, GI.2, GI.3, and GII.3 genotypes. Monthly distribution analysis demonstrated two epidemic peaks from July to December 2015 and February to May 2017. However, no detection peak was observed in 2014 and 2016. Phylogenetic analysis of the complete VP1 nucleotide sequences of these GI.1 strains revealed two major clusters of GI.1 and each of which contained GI.1 strains of both 2015 and 2017. This study suggests that the continuous surveillance of SaV is needed to monitor high genetic diversity in Japanese children with AGE.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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de Oliveira-Tozetto S, Santiso-Bellón C, Ferrer-Chirivella JM, Navarro-Lleó N, Vila-Vicent S, Rodríguez-Díaz J, Buesa J. Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain). Viruses 2021; 13:v13020184. [PMID: 33530573 PMCID: PMC7911121 DOI: 10.3390/v13020184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023] Open
Abstract
Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.
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Affiliation(s)
- Sibele de Oliveira-Tozetto
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Cristina Santiso-Bellón
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Correspondence: (C.S.-B.); (J.B.)
| | - Josep M. Ferrer-Chirivella
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Noemi Navarro-Lleó
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Susana Vila-Vicent
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Correspondence: (C.S.-B.); (J.B.)
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Yan Y, Li Y, Shi W, Kong X, Li H, Zhang Q, Pang L, Jiang L, Liu J, Jin M, Li Y, Duan Z. An outbreak of gastroenteritis associated with a novel GII.8 sapovirus variant-transmitted by vomit in Shenzhen, China, 2019. BMC Infect Dis 2020; 20:911. [PMID: 33261582 PMCID: PMC7706173 DOI: 10.1186/s12879-020-05643-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022] Open
Abstract
Background Human Sapoviruses (SaVs) has been reported as one of the causative agents of acute gastroenteritis (AGE) worldwide. An outbreak of SaVs affected 482 primary school students during spring activities from February 24 to March 11, 2019 in Shenzhen City, China. Our study was aimed at determining the epidemiology of the outbreak, investigating its origins, and making a clear identification of the SaVs genetic diversity. Methods Epidemiological investigation was conducted for this AGE outbreak. Stool samples were collected for laboratory tests of causative agents. Real-time reverse-transcription polymerase chain reaction (rRT-PCR) and conventional RT-PCR were used for detecting and genotyping of SaVs. The nearly complete genome of GII.8 SaV strains were amplified and sequenced by using several primer sets designed in this study. Phylogenetic analysis was performed to characterize the genome of GII.8 SaV strains. Results The single factor analysis showed that the students who were less than 1.5 m away from the vomitus in classroom or playgroundwere susceptible (P < 0.05). Seven of 11 fecal samples from patients were positive for GII.8 SaV genotype. In this study, we obtained the genome sequence of a SaV GII.8 strain Hu/SaV/2019008Shenzhen/2019 /CHN (SZ08) and comprehensively analyzed the genetic diversity. The phylogenetic analysis showed that the GII.8 strain SZ08 formed an independent branch and became a novel variant of GII.8 genotype. Strain SZ08 harbored 11 specific amino acid variations compared with cluster A-D in full-length VP1. Conclusions This study identified SaVs as the causative agents for the AGE outbreak. Strain Hu SZ08 was clustered as independent branch and there was no recombination occurred in this strain SZ08. Further, it might become the predominant strain in diarrhea cases in the near future. Constant surveillance is required to monitor the emerging variants which will improve our knowledge of the evolution of SaVs among humans.
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Affiliation(s)
- Yuxiao Yan
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, 730000, Gansu, China.,Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Yuan Li
- Shenzhen Baoan Center for Disease Control and Prevention, Baoan District, Shenzhen, Guangdong Province, China
| | - Wen Shi
- Yingkou Center for Disease Control and Prevention, Yingkou, Liaoning, China
| | - Xiangyu Kong
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Huiying Li
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Qing Zhang
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Lili Pang
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
| | - Li Jiang
- The First Hospital of Lanzhou University, Donggang-xi Rd, Cheng-guan District, Lanzhou, 730000, Gansu, China
| | - Junying Liu
- Central Hospital of Zhoukou, Zhoukou, 466000, Henan, China
| | - Miao Jin
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China.
| | - Yuning Li
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, 730000, Gansu, China. .,The First Hospital of Lanzhou University, Donggang-xi Rd, Cheng-guan District, Lanzhou, 730000, Gansu, China.
| | - Zhaojun Duan
- Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Chang-ping District, Beijing, 102206, China
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Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions. Viruses 2020; 12:v12050516. [PMID: 32392864 PMCID: PMC7290424 DOI: 10.3390/v12050516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.
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