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Sun Z, Niu P, Jin M, Zhang R, Gao Q, Wang H, Ma X, Wang J. Genotyping and traceability analysis of norovirus in Yantai between 2017 and 2019. J Med Virol 2023; 95:e29220. [PMID: 37947460 DOI: 10.1002/jmv.29220] [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: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
To investigate the diversity and evolution of noroviruses in Yantai in recent years, this study focused on the coat protein regions of norovirus-positive samples with nucleic acid detection (cycle threshold) values below 30 between 2017 and 2019. A total of 81 sequences were obtained for genotyping. Initially, a high-throughput sequencing approach was established to perform the whole-genome sequencing of multiple typical diarrheal strains. Using bioinformatics software such as BEAST, recombinant variant analysis was performed for each genotype of the norovirus strains, and genetic evolutionary analysis was conducted for the dominant strain GII.4, as well as the rare variant GII.21. The results showed that there were multiple genotypes such as GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.13, GII.17, GII.21, and GIX.1 in the positive samples of norovirus from 2017 to 2019. GII.4 is characterized by diverse genotypes, with new changes in antigenic epitopes occurring during the course of the epidemic. This may have led to the emergence of a new pandemic. This suggests a need to strengthen surveillance. The results of this study suggest that attention should be paid to the predominant genotypes prevalent in neighboring countries and regions, and the safety supervision of imported food should be strengthened to aid in the prevention and control of related viruses.
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Affiliation(s)
- Zhenlu Sun
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Peihua Niu
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Miao Jin
- Department of Viral Diarrhea, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Qiao Gao
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Hongtao Wang
- Yantai Center for Disease Control and Prevention, Yantai, Shandong, China
| | - Xuejun Ma
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Ji Wang
- Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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Satter SM, Abdullah Z, Cardemil CV, Flora MS, Gurley ES, Rahman M, Talha M, Islam MD, Hossain ME, Balachandran N, Lopman B, Rahman M, Vinjé J, Hall AJ, Parashar UD. Hospital-based Surveillance for Pediatric Norovirus Gastroenteritis in Bangladesh, 2012-2016. Pediatr Infect Dis J 2021; 40:215-219. [PMID: 33264214 PMCID: PMC9006183 DOI: 10.1097/inf.0000000000002989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Globally, noroviruses are recognized as an important cause of acute gastroenteritis (AGE), but data from low and middle-income countries are limited. AIMS To examine the epidemiology and strain diversity of norovirus infections among children hospitalized for AGE in Bangladesh. METHODS We implemented active surveillance of children <5 years of age hospitalized with AGE at 8 geographically dispersed tertiary care hospitals in Bangladesh from July 2012 to June 2016. We tested random samples of AGE cases stratified by site and age group for norovirus by real-time RT-PCR. Noro-positive specimens were genotyped. Coinfection with rotavirus was assessed based on prior EIA testing. RESULTS We enrolled 5622 total AGE cases, of which 1008 were tested for norovirus. Total of 137 (14%) AGE cases tested positive for norovirus (range, 11%-17% by site). Most (94%) norovirus-associated hospitalizations were among children less than 2 years of age. Norovirus was detected year-round, with higher detection from March to June (20%-38%) and November to January (9%-18%). Genogroup II (GII) noroviruses were detected in 96% of cases, and the most frequent genotypes were GII.4 Sydney [P4 New Orleans] (33%), GII.3 [P16] (20%), and GII.4 Sydney [P16] (11%). The proportion of norovirus-positive specimens was significantly greater among rotavirus-negative AGE patients compared with rotavirus-positive AGE patients (27% vs. 5%, P < 0.001). As measured by the Vesikari severity score, a similar proportion of norovirus and rotavirus positive AGE patients were considered severe (68% vs. 70%, P = 0.86). CONCLUSIONS Norovirus is an important cause of AGE hospitalization in Bangladeshi children with most infections caused by GII viruses.
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Affiliation(s)
- Syed M. Satter
- icddr,b, Mohakhali, Dhaka, Bangladesh
- Programme for Emerging Infections, Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Zarin Abdullah
- icddr,b, Mohakhali, Dhaka, Bangladesh
- Programme for Emerging Infections, Infectious Diseases Division, icddr,b, Mohakhali, Dhaka, Bangladesh
| | | | - Meerjady S. Flora
- Institute of Epidemiology, Disease Control & Research, Dhaka, Bangladesh
| | - Emily S. Gurley
- icddr,b, Mohakhali, Dhaka, Bangladesh
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | | | | | | | - Neha Balachandran
- Centers for Disease Control and Prevention, Atlanta, GA
- Cherokee Nation Assurance, Arlington, VA
| | - Benjamin Lopman
- Rollins School of Public Health, Emory University, Atlanta, GA
| | | | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Aron J. Hall
- Centers for Disease Control and Prevention, Atlanta, GA
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Ludwig-Begall LF, Mauroy A, Thiry E. Norovirus recombinants: recurrent in the field, recalcitrant in the lab - a scoping review of recombination and recombinant types of noroviruses. J Gen Virol 2018; 99:970-988. [PMID: 29906257 DOI: 10.1099/jgv.0.001103] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are recognized as the major global cause of sporadic and epidemic non-bacterial gastroenteritis in humans. Molecular mechanisms driving norovirus evolution are the accumulation of point mutations and recombination. Intragenotypic recombination has long been postulated to be a driving force of GII.4 noroviruses, the predominant genotype circulating in humans for over two decades. Increasingly, emergence and re-emergence of different intragenotype recombinants have been reported. The number and types of norovirus recombinants remained undefined until the 2007 Journal of General Virology research article 'Norovirus recombination' reported an assembly of 20 hitherto unclassified intergenotypic norovirus recombinant types. In the intervening decade, a host of novel recombinants has been analysed. New recombination breakpoints have been described, in vitro and in vivo studies supplement in silico analyses, and advances have been made in analysing factors driving norovirus recombination. This work presents a timely overview of these data and focuses on important aspects of norovirus recombination and its role in norovirus molecular evolution. An overview of intergenogroup, intergenotype, intragenotype and 'obligatory' norovirus recombinants as detected via in silico methods in the field is provided, enlarging the scope of intergenotypic recombinant types to 80 in total, and notably including three intergenogroup recombinants. A recap of advances made studying norovirus recombination in the laboratory is given. Putative drivers and constraints of norovirus recombination are discussed and the potential link between recombination and norovirus zoonosis risk is examined.
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Affiliation(s)
- Louisa F Ludwig-Begall
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
| | - Axel Mauroy
- 2Staff direction for risk assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Blv du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Etienne Thiry
- 1Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, B-4000 Liège, Belgium
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Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea. Epidemiol Infect 2017; 145:2231-2240. [PMID: 28651680 DOI: 10.1017/s0950268817001273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noroviruses (NoVs) are major causal agents of acute gastroenteritis in humans. NoV GII.4 is the predominant genotype globally. However, uncommon and minor types of NoVs are consistently detected and some have been shown to dominate over GII.4. Therefore, the prevalence of dominant and uncommon NoVs makes the identification of these viruses important for the prediction and prevention of pandemics. In this study, the full-genome sequence of a NoV (strain JW) detected in Korea was extensively characterized. The full-length genome was 7510 nucleotides long, and phylogenetic analysis based on the whole-genome sequences, including open reading frame (ORF)1, ORF2, and ORF3, indicated that it belonged to the GII.21 genotype. Strain JW showed maximum identity with strain YO284; however, comparison of the amino acid sequence of ORF2, which functions as an antigen, showed substitutions in several amino acids. GII.21 is not a prevalent epidemiological agent of acute gastroenteritis in humans, but it is consistently found in gastroenteritis patients from several countries. The present study provides the first full-genome sequence analysis of NoV GII.21 isolated from a patient in Korea. Our findings provide not only valuable genome information but also data for epidemiology studies, epidemic prevention, and vaccine development strategies.
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Rahman M, Rahman R, Nahar S, Hossain S, Ahmed S, Golam Faruque AS, Azim T. Norovirus diarrhea in Bangladesh, 2010-2014: prevalence, clinical features, and genotypes. J Med Virol 2016; 88:1742-50. [PMID: 27003679 DOI: 10.1002/jmv.24530] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2016] [Indexed: 01/22/2023]
Abstract
Norovirus infections in diarrhea patients attending an urban and a rural hospital in Bangladesh were investigated. A total of 953 fecal specimens from both children and adults collected during 2010-2014 were tested for the presence of norovirus using real time PCR. One fourth (25%) of the specimens were positive for norovirus RNA which was identified both in children and adults. Norovirus was associated with short duration of diarrhea, high abdominal pain, and more moderate to severe dehydration when compared with rotavirus infections. Norovirus GII (69%) was the most prevalent genogroup followed by GI (18%), mixed GI/GII/GIV (11%), and GIV (2%). Among GII genogroup, GII.4 (42%) was the most prevalent genotype followed by GII.3 (21%), GII.6 (7%), GII.7 (6%), and GII.21 (6%). GII.4 and GII.3 strains were frequently identified (82% and 75%, respectively) in children <2 years of age and less commonly (16% and 15%) in adults more than 18 years of age. The present study reinforces the importance of norovirus-associated hospitalizations both in children and adults. The dynamic molecular epidemiology of norovirus requires routine strain surveillance to identify changes in prevailing strains. J. Med. Virol. 88:1742-1750, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Rajibur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Shakhaowat Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Tasnim Azim
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
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Yahiro T, Wangchuk S, Wada T, Dorji C, Matsumoto T, Mynak ML, Tshering KP, Nishizono A, Ahmed K. Norovirus GII.21 in children with Diarrhea, Bhutan. Emerg Infect Dis 2015; 21:732-4. [PMID: 25811105 PMCID: PMC4378497 DOI: 10.3201/eid2104.141856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Pringle K, Lopman B, Vega E, Vinje J, Parashar UD, Hall AJ. Noroviruses: epidemiology, immunity and prospects for prevention. Future Microbiol 2015; 10:53-67. [PMID: 25598337 DOI: 10.2217/fmb.14.102] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In recent years, noroviruses have become recognized as an important cause of both sporadic and epidemic acute gastroenteritis (AGE), largely due to the improved availability of broadly reactive real-time RT-PCR (TaqMan-based RT-PCR) assays. While there is substantial diversity among noroviruses, one specific genotype, GII.4, is the most common etiology in sporadic and epidemic AGE. Outbreaks of norovirus AGE most commonly occur in healthcare facilities and restaurants and result in significant morbidity and mortality and substantial healthcare costs. Norovirus vaccine development is progressing, and Phase I and II human trials have shown proof-of-principle that norovirus vaccines can reduce illness and infection.
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Affiliation(s)
- Kimberly Pringle
- Division of Viral Diseases, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, 1600 Clifton Road, Mailstop A-34, Atlanta, GA, 30333, USA
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Altay A, Yahiro T, Bozdayi G, Matsumoto T, Sahin F, Ozkan S, Nishizono A, Söderlund-Venermo M, Ahmed K. Bufavirus genotype 3 in Turkish children with severe diarrhoea. Clin Microbiol Infect 2015; 21:965.e1-4. [PMID: 26086570 DOI: 10.1016/j.cmi.2015.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 05/31/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Recently a parvovirus called bufavirus (BuV) has been implicated as a causative agent of diarrhoea. To further reveal the epidemiology and genetic characteristics of BuV, this study was performed in Turkish children with diarrhoea. BuV was detected in 1.4% (8/583) of stool samples. All stool samples from healthy children (n = 148) were negative for BuV. Diarrhoea in BuV-positive patients was severe and occurred mainly during the colder months of the year. Complete genome sequences were generated from four BuVs. Only BuV3 was found, which was genetically and phylogenetically similar to Bhutanese BuV3, indicating that BuV3 is prevalent in Asian countries.
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Affiliation(s)
- A Altay
- Department of Medical Microbiology, Gazi University, Ankara, Turkey
| | - T Yahiro
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - G Bozdayi
- Department of Medical Microbiology, Gazi University, Ankara, Turkey
| | - T Matsumoto
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | - F Sahin
- Department of Paediatrics, Turkey
| | - S Ozkan
- Department of Public Health, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - A Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan
| | | | - K Ahmed
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia; Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Japan; Research Promotion Institute, Oita University, Yufu, Japan.
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9
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Lee L, Ison M. Diarrhea caused by viruses in transplant recipients. Transpl Infect Dis 2014; 16:347-58. [DOI: 10.1111/tid.12212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 12/11/2013] [Accepted: 12/21/2013] [Indexed: 01/25/2023]
Affiliation(s)
- L.Y. Lee
- Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Northwestern University Transplant Outcomes Research Collaborative; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
| | - M.G. Ison
- Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Northwestern University Transplant Outcomes Research Collaborative; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Division of Infectious Diseases Northwestern University Feinberg School of Medicine; Chicago Illinois USA
- Division of Organ Transplantation; Northwestern University Feinberg School of Medicine; Chicago Illinois USA
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Nahar S, Afrad MH, Matthijnssens J, Rahman MZ, Momtaz Z, Yasmin R, Jubair M, Faruque ASG, Choudhuri MSK, Azim T, Rahman M. Novel intergenotype human norovirus recombinant GII.16/GII.3 in Bangladesh. INFECTION GENETICS AND EVOLUTION 2013; 20:325-9. [PMID: 24080167 DOI: 10.1016/j.meegid.2013.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 11/15/2022]
Abstract
Noroviruses (NoVs) are one of the major etiological agents of acute gastroenteritis in all age groups. In this study, we identified an intergenotype NoV recombinant strain in the fecal specimens of two male infants with acute diarrhea in Bangladesh. Phylogenetic analysis showed that the identified strains were recombinant NoV strains with a GII.3 capsid and a GII.16 polymerase gene. The recombination breakpoint was located in the ORF1/ORF2 overlap region. To the best of our knowledge this is the first report of a NoV recombinant GII.16/GII.3 strain worldwide.
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Affiliation(s)
- Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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