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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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Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [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: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
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Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
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Sapoviruses detected from acute gastroenteritis outbreaks and hospitalized children in Taiwan. J Formos Med Assoc 2021; 120:1591-1601. [DOI: 10.1016/j.jfma.2020.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/11/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
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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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Mancini P, Bonanno Ferraro G, Iaconelli M, Suffredini E, Valdazo-González B, Della Libera S, Divizia M, La Rosa G. Molecular characterization of human Sapovirus in untreated sewage in Italy by amplicon-based Sanger and next-generation sequencing. J Appl Microbiol 2018; 126:324-331. [DOI: 10.1111/jam.14129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/12/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022]
Affiliation(s)
- P. Mancini
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - G. Bonanno Ferraro
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - M. Iaconelli
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - E. Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health; Istituto Superiore di Sanità; Rome Italy
| | - B. Valdazo-González
- The National Institute for Biological Standards and Control; The Medicines and Healthcare Products Regulatory Agency; Hertfordshire UK
| | - S. Della Libera
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - M. Divizia
- Department of Biomedicine and Prevention; University of Rome “Tor Vergata”; Rome Italy
| | - G. La Rosa
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
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Oka T, Iritani N, Yamamoto SP, Mori K, Ogawa T, Tatsumi C, Shibata S, Harada S, Wu FT. Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes. J Med Virol 2018; 91:370-377. [PMID: 30320885 DOI: 10.1002/jmv.25334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022]
Abstract
Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader-range sapovirus real-time RT-PCR assay. The assay can detect 2.5 × 107 and 2.5 × 10 1 copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1-7, GII.1-8, GIV.1, and GV.1, 2. No cross-reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.
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Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nobuhiro Iritani
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Seiji P Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kohji Mori
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Tomoko Ogawa
- Division of Virology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Chika Tatsumi
- Division of Virology, Shimane Prefectural Institute of Public Health and Environmental Science, Shimane, Japan
| | - Shinichiro Shibata
- Microbiology Department, Nagoya City Public Health Research Institute, Aichi, Japan
| | - Seiya Harada
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Kumamoto, Japan
| | - Fang-Tzy Wu
- Center for Research, Diagnostics and Vaccine Development, Taiwan Centers for Disease Control, Taipei, Taiwan
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