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Panizzolo M, Gea M, Carraro E, Gilli G, Bonetta S, Pignata C. Occurrence of human pathogenic viruses in drinking water and in its sources: A review. J Environ Sci (China) 2023; 132:145-161. [PMID: 37336605 DOI: 10.1016/j.jes.2022.07.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/21/2023]
Abstract
Since many waterborne diseases are caused by human pathogenic viruses, virus monitoring of drinking water (DW) and DW sources is crucial for public health. Therefore, the aim of this review was to describe the occurrence of human pathogenic viruses in DW and DW sources; the occurrence of two viruses proposed as novel indicators of human faecal contamination (Pepper mild mottle virus and Tobacco mosaic virus) was also reported. This research was focused on articles that assessed viral occurrence using molecular methods in the surface water used for DW production (SW-D), groundwater used for DW production (GW-D), DW and bottled-DW (BW). A total of 1544 studies published in the last 10 years were analysed, and 79 were ultimately included. In considering the detection methods, filtration is the most common concentration technique, while quantitative polymerase chain reaction is the most common quantification technique. Regarding virus occurrence in SW-D, GW-D, and DW, high percentages of positive samples were reported for adenovirus, polyomavirus and Pepper mild mottle virus. Viral genomes were frequently detected in SW-D and rarely in GW-D, suggesting that GW-D may be a safe DW source. Viral genomes were also detected in DW, posing a possible threat to human health. The lowest percentages of positive samples were found in Europe, while the highest were found in Asia and South America. Only three articles assessed viral occurrence in BW. This review highlights the lack of method standardization and the need for legislation updates.
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Affiliation(s)
- Marco Panizzolo
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Marta Gea
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy.
| | - Elisabetta Carraro
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Giorgio Gilli
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
| | - Silvia Bonetta
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
| | - Cristina Pignata
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126, Torino, Italy
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Dinu S, Oprea M, Iordache RI, Rusu LC, Usein CR. Genome characterisation of norovirus GII.P17-GII.17 detected during a large gastroenteritis outbreak in Romania in 2021. Arch Virol 2023; 168:116. [PMID: 36947248 DOI: 10.1007/s00705-023-05741-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023]
Abstract
Norovirus (NoV) is one of the leading causes of acute gastroenteritis worldwide. Genotype GII.P17-G.II.17 emerged in Asia between 2013 and 2015 and transiently replaced the GII.4 Sydney 2012 variant circulating at that time. We present the genome characterisation of a GII.P17-GII.17 strain causing a large outbreak in Romania in 2021. Our study shows that the 2021 strain belongs to a novel cluster of genotype GII.17, different from the two previously recognised P.17 clusters. Distinctive substitutions in predicted conformational epitopes of VP1 were identified for this new cluster. Also, our phylogenetic analysis showed the existence of another P.17 cluster grouping strains from France and Canada.
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Affiliation(s)
- Sorin Dinu
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania.
| | - Mihaela Oprea
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
| | - Ramona-Ionela Iordache
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
| | - Lavinia-Cipriana Rusu
- National Institute of Public Health, National Center for Surveillance and Control of Communicable Diseases, 1-3 Doctor Leonte Anastasievici, Bucharest, 050463, Romania
| | - Codruța-Romanița Usein
- Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development, 103 Splaiul Independenței, Bucharest, 050096, Romania
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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Opere WM, John M, Ombori O, Kiulia NM. Identification of enteroviruses along Lake Victoria shoreline - a potential indicator of sewage pollution. Access Microbiol 2022; 4:000334. [PMID: 35812714 PMCID: PMC9260088 DOI: 10.1099/acmi.0.000334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022] Open
Abstract
Enteric viruses are mainly transmitted by the faecal-oral route and have been linked to several diseases including gastroenteritis and respiratory infections. Their presence in surface waters has been exacerbated by pollution from a variety of point sources such as sewage discharge. We studied the occurrence of enteroviruses in water samples from Lake Victoriain Kenya to investigate if there was a link between sewage pollution and detection of enteroviruses (EVs) to build a baseline for an enteric viruses monitoring platform for this region. We analysed 216 samples collected over 6 months from six different locations along the Homa Bay Pier. The six sampling locations comprised of three sites (P3, P5, P6) located <500 m from a local sewage treatment plant and pit latrines while three other sites (P1, P2, P4) were located at approximately 0.5 to 3 Km. EVs were concentrated using glass wool adsorption elution protocol and identified using the nested reverse transcription-polymerase chain reaction. The odds ratio was performed to determine whether the location of the sources of sewage pollution near the lake was associated with the EVs contamination. Five out of 108 (5 %) samples collected from the sites (P3, P5 and P6 were EV positive, while 2 % (2/108) of samples from P1, P2 and P4 were EV positive. The presence of the EVs was associated with the distance from the possible sources of faecal contamination (odds ratio 20.28 and 4.86, confidence interval 2.42, and 0.95) for pit latrines and the sewage treatment plant respectively. The result from this study indicates that sewage discharge at the shoreline of Lake Victoria may have been the source of EVs contamination. Data from this study could significantly contribute to informing risk management on sewage pollution in Lake Victoria and it is important to continue monitoring this lake for potentially pathogenic enteric viruses.
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Affiliation(s)
- Wasonga M. Opere
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Maingi John
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Omwoyo Ombori
- Department of Plant Sciences, Kenyatta University, Nairobi, Kenya
| | - Nicholas M. Kiulia
- Enteric pathogens & Water Research Laboratory, Institute of Primate Research (IPR), Nairobi, Kenya
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Kittigul L, Pombubpa K, Rupprom K, Thasiri J. Detection of Norovirus Recombinant GII.2[P16] Strains in Oysters in Thailand. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:59-68. [PMID: 35075605 DOI: 10.1007/s12560-022-09508-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Human norovirus causes sporadic and epidemic acute gastroenteritis worldwide, and the predominant strains are genotype GII.4 variants. Recently, a novel GII.17[P17] and a recombinant GII.2[P16] strain have been reported as the causes of gastroenteritis outbreaks. Outbreaks of norovirus are frequently associated with foodborne illness. In this study, each of 75 oyster samples processed by a proteinase K extraction method and an adsorption-elution method were examined for noroviruses using RT-nested PCR with capsid primers. Thirteen (17.3%) samples processed by either method tested positive for norovirus genogroup II (GII). PCR amplicons were characterized by DNA sequencing and phylogenetic analysis as GII.2 (n = 6), GII.4 (n = 1), GII.17 (n = 3), and GII.unclassified (n = 3). Norovirus-positive samples were further amplified by semi-nested RT-PCR targeting the polymerase-capsid genes. One nucleotide sequence revealed GII.17[P17] Kawasaki strain. Five nucleotide sequences were identified as belonging to the recombinant GII.2[P16] strains by recombination analysis. The collected oyster samples were quantified for norovirus GII genome copy number by RT-quantitative PCR. Using the proteinase K method, GII was found in 13/75 (17.3%) of samples with a range of 8.83-1.85 × 104 genome copies/g of oyster. One sample (1/75, 1.3%) processed by the adsorption-elution method was positive for GII at 5.00 × 101 genome copies/g. These findings indicate the circulation of a new variant GII.17 Kawasaki strain and the recombinant GII.2[P16] in oyster samples corresponding to the circulating strains reported at a global scale during the same period of time. The detection of the recombinant strains in oysters emphasizes the need for continuing systematic surveillance for control and prevention of norovirus gastroenteritis.
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Affiliation(s)
- Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand.
| | - Kannika Pombubpa
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Kitwadee Rupprom
- Department of Clinical Pathology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Jinthapha Thasiri
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
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Nagarajan V, Chen J, Hsu B, Hsu G, Wang J, Hussain B. Prevalence, Distribution, and Genotypes of Adenovirus and Norovirus in the Puzi River and Its Tributaries and the Surrounding Areas in Taiwan. GEOHEALTH 2021; 5:e2021GH000465. [PMID: 34977444 PMCID: PMC8686652 DOI: 10.1029/2021gh000465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 05/04/2023]
Abstract
This study investigated the prevalence, distribution, and genotypes of adenoviruses (AdVs) and noroviruses (NoVs) in the Puzi River and surrounding areas in Taiwan. The viruses in the water samples were isolated using the membrane filtration method and the viral nucleic acids were extracted. The RNA of NoVs was reverse-transcribed into complementary DNA using reverse transcriptase-polymerase chain reaction. AdVs and NoVs were detected using nested PCR. Genotyping and phylogenetic analyses were performed to identify the various viral genotypes in the water samples. Human adenovirus (HAdVs) and porcine adenovirus (PAdVs) were the predominant genotypes in the water samples. The prevalence of F species HAdVs serotype 41 (79.2%) and C species PAdVs serotype 5 (18.1%) was higher than that of other serotypes. Among NoVs, genogroup GII was more prevalent than GI. In particular, GII.4 (21.2%) and GII.17 (18.2%) were the predominant genotypes, which was consistent with the clinical findings. The prevalence of both AdVs and NoVs was higher in the winter than spring, summer and autumn seasons. AdVs and NoVs detection results were statistically analyzed by investigating their association with water quality indicators. The results revealed that the presence of AdVs was significantly correlated with the heterotrophic bacterial count, total coliform Escherichia coli, turbidity, salinity, and dissolved oxygen. Meanwhile, the presence of NoVs was only significantly correlated with temperature, pH, and dissolved oxygen. Microbial pollution sources may include urban runoff and discharge of water from livestock farms situated near the river and tributaries within this region of Taiwan. Future studies should include comparisons of the presence of AdVs and NoVs in these known pollution sources and water quality monitoring of these watersheds, as this will allow potential identification of pollution sources. Additionally, remediation strategies must be developed to minimize viral contamination in the river ecosystem.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
| | | | - Bing‐Mu Hsu
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
| | - Gwo‐Jong Hsu
- Division of Infectious DiseasesDitmanson Medical FoundationChia‐Yi Christian HospitalChiayi CountyTaiwan
| | - Jiun‐Ling Wang
- Department of Internal MedicineNational Cheng Kung University HospitalTainanTaiwan
| | - Bashir Hussain
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
- Department of Biomedical SciencesNational Chung Cheng UniversityChiayi CountyTaiwan
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Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon. Viruses 2021; 13:v13040545. [PMID: 33805214 PMCID: PMC8064335 DOI: 10.3390/v13040545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.
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Upfold NS, Luke GA, Knox C. Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:1-31. [PMID: 33501612 PMCID: PMC7837882 DOI: 10.1007/s12560-020-09456-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/16/2020] [Indexed: 05/02/2023]
Abstract
Enteric viruses are a diverse group of human pathogens which are primarily transmitted by the faecal-oral route and are a major cause of non-bacterial diarrhoeal disease in both developed and developing countries. Because they are shed in high numbers by infected individuals and can persist for a long time in the environment, they pose a serious threat to human health globally. Enteric viruses end up in the environment mainly through discharge or leakage of raw or inadequately treated sewage into water sources such as springs, rivers, dams, or marine estuaries. Human exposure then follows when contaminated water is used for drinking, cooking, or recreation and, importantly, when filter-feeding bivalve shellfish are consumed. The human health hazard posed by enteric viruses is particularly serious in Africa where rapid urbanisation in a relatively short period of time has led to the expansion of informal settlements with poor sanitation and failing or non-existent wastewater treatment infrastructure, and where rural communities with limited or no access to municipal water are dependent on nearby open water sources for their subsistence. The role of sewage-contaminated water and bivalve shellfish as vehicles for transmission of enteric viruses is well documented but, to our knowledge, has not been comprehensively reviewed in the African context. Here we provide an overview of enteric viruses and then review the growing body of research where these viruses have been detected in association with sewage-contaminated water or food in several African countries. These studies highlight the need for more research into the prevalence, molecular epidemiology and circulation of these viruses in Africa, as well as for development and application of innovative wastewater treatment approaches to reduce environmental pollution and its impact on human health on the continent.
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Affiliation(s)
- Nicole S Upfold
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Scotland, KY16 9ST, UK
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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Wainaina E, Otieno CA, Kamau J, Nyachieo A, Lowther SA. Norovirus infections and knowledge, attitudes and practices in food safety among food handlers in an informal urban settlement, Kenya 2017. BMC Public Health 2020; 20:474. [PMID: 32276622 PMCID: PMC7146951 DOI: 10.1186/s12889-020-8401-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/24/2020] [Indexed: 01/18/2023] Open
Abstract
Introduction A leading cause of acute gastroenteritis, norovirus can be transmitted by infected food handlers but norovirus outbreaks are not routinely investigated in Kenya. We estimated norovirus prevalence and associated factors among food handlers in an informal urban settlement in Nairobi, Kenya. Methods We conducted a cross-sectional survey among food handlers using pretested questionnaires and collected stool specimens from food handlers which were analyzed for norovirus by conventional PCR. We observed practices that allow norovirus transmission and surveyed respondents on knowledge, attitudes, and practices in food safety. We calculated odd ratios (OR) with 95% confidence intervals (CI) to identify factors associated with norovirus infection. Variables with p < 0.05 were included in multivariate logistic regression analysis to calculate adjusted OR and 95% CI. Results Of samples from 283 respondents, 43 (15.2%) tested positive for norovirus. Factors associated with norovirus detection were: reporting diarrhea and vomiting within the previous month (AOR = 5.7, 95% CI = 1.2–27.4), not knowing aerosols from infected persons can contaminate food (AOR = 6.5, 95% CI = 1.1–37.5), not knowing that a dirty chopping board can contaminate food (AOR = 26.1, 95% CI = 1.6–416.7), observing respondents touching food bare-handed (AOR = 3.7, 95% CI = 1.5–11.1), and working in premises without hand washing services (AOR = 20, 95% CI = 3.4–100.0). Conclusion The norovirus infection was prevalent amongst food handlers and factors associated with infection were based on knowledge and practices of food hygiene. We recommend increased hygiene training and introduce more routine inclusion of norovirus testing in outbreaks in Kenya.
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Affiliation(s)
- Eliud Wainaina
- Moi University, Eldoret, Kenya. .,Field Epidemiology and Laboratory Training Program, Ministry of Health Program, Kenyatta National Hospital Grounds, P.O Box 22313-00100, Nairobi, Kenya.
| | | | - Joseph Kamau
- Institute of Primate Research, Karen, Kenya.,University of Nairobi, Nairobi, Kenya
| | - Atunga Nyachieo
- Institute of Primate Research, Karen, Kenya.,University of Nairobi, Nairobi, Kenya
| | - Sara A Lowther
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Goh SG, Saeidi N, Gu X, Vergara GGR, Liang L, Fang H, Kitajima M, Kushmaro A, Gin KYH. Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use. WATER RESEARCH 2019; 150:200-215. [PMID: 30528917 PMCID: PMC7112093 DOI: 10.1016/j.watres.2018.11.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 05/21/2023]
Abstract
Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.
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Affiliation(s)
- Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | | | - Liang Liang
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Haoming Fang
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, Singapore
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore.
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11
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Fumian TM, Fioretti JM, Lun JH, Dos Santos IAL, White PA, Miagostovich MP. Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing. ENVIRONMENT INTERNATIONAL 2019; 123:282-291. [PMID: 30553201 DOI: 10.1016/j.envint.2018.11.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 05/23/2023]
Abstract
Noroviruses are a leading cause of epidemic and pandemic acute gastroenteritis (AGE) worldwide, and contaminated food and water are important routes for its transmission. Raw sewage has been used for viral surveillance to monitor the emergence of new norovirus strains with the potential to cause epidemics. In this study, we investigated norovirus occurrence and norovirus RNA levels in 156 samples collected from May 2013 to May 2014, across three different stages (52 samples each) of a wastewater treatment plant (WWTP) in Rio de Janeiro, Brazil. We also explored norovirus GII diversity in raw sewage samples by next-sequencing generation (NGS). In addition, we examined norovirus prevalence and molecular epidemiology from acute gastroenteritis cases. Using RT-qPCR, norovirus GI and GII was detected in 38.5% and 96.1% of raw sewage samples, 40.4% and 96.1% of primary effluent samples and 1.9% and 5.8% of final effluent samples, respectively. Norovirus RNA levels varied from 4 to 6.2 log10 genome copies per litre (gc L-1) for GI and from 4.4 to 7.3 log10 gc L-1 for GII. Using MiSeq NGS, we identified 13 norovirus genotypes over the one-year period, with six dominant capsid genotypes, including GII.4, GII.17, GII.5, GII.2, GII.3 and GII.1. GII.4 noroviruses were the most prevalent in wastewater samples (68.5%), and a similar trend was observed in AGE cases (71%). The emergent GII.17 was the second most prevalent genotype (14.3%) identified in the raw sewage samples, however, it was not detected in clinical cases. Due to the high burden of norovirus outbreaks and the lack of vaccine and antiviral drugs, it is essential to understand the genotypic diversity of norovirus at the population level. Complementary data obtained from both clinical and environmental (sewage) samples proved to be an effective strategy to monitor the circulation and emergence of norovirus epidemic genotypes.
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Affiliation(s)
- Tulio M Fumian
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil.
| | - Julia M Fioretti
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil
| | - Jennifer H Lun
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ingrid A L Dos Santos
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil
| | - Peter A White
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marize P Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil
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12
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The prevalence of non-GII.4 norovirus genotypes in acute gastroenteritis outbreaks in Jinan, China. PLoS One 2018; 13:e0209245. [PMID: 30592717 PMCID: PMC6310239 DOI: 10.1371/journal.pone.0209245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 12/03/2018] [Indexed: 01/01/2023] Open
Abstract
Noroviruses (NoVs) are the leading cause of acute viral gastroenteritis outbreaks. From June 2015 to March 2017, fifteen outbreaks of acute gastroenteritis (AGE) were reported to the Jinan Center for Disease Control and Prevention in China. To identify the circulating NoV genotypes associated with outbreaks in Jinan, China, 414 specimens from the 15 outbreaks were collected and analyzed for the causative viruses, and phylogenetic analysis was performed on the NoV-positive strains. The NoV detection rate was 57.5% (238/414), and a total of 14 outbreaks were caused by NoVs (eight by infection with genogroup II (GII), five by mixed infection with GI and GII, and one by mixed infection with GII and rotavirus (RoV)-A). A total of 75 NoV sequences were obtained from 13 NoV-positive outbreaks and classified into seven genotypes (38 GII.17, 13 GII.2, 4 GII.3, 4 GII.1, 10 GI.6, 5 GI.5 and 1 GI.3), while GII.4 was not identified. The most prevalent genotype changed yearly during the 2015–2017 period. Phylogenetic analysis demonstrated that these NoV genotypes had high homology with the strains circulating worldwide, especially strains from Asian countries and cities. Our study illustrated that multiple non-GII.4 NoV genotypes were prevalent in outbreaks of AGE in Jinan, China. Year-round surveillance of multiple NoV genotypes could help health authorities reduce the impact of NoV outbreaks on public health.
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Ji L, Chen L, Xu D, Wu X, Han J. Nearly complete genome sequence of one GII.17 Norovirus identified by direct sequencing from HuZhou, China. Mol Genet Genomic Med 2018; 6:796-804. [PMID: 29992776 PMCID: PMC6160709 DOI: 10.1002/mgg3.446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/23/2018] [Accepted: 06/12/2018] [Indexed: 01/29/2023] Open
Abstract
Background Human norovirus is the leading cause of acute gastroenteritis worldwide. However, in vitro culture system is complicated for human norovirus. Sequence analysis became more useful for norovirus research, particularly when using complete genomic sequences. Methods Real‐time RT‐PCR (qPCR) was performed for norovirus detection. Three modified paris of PCR primes were designed based on the alignment of the novel GII.17 norovirus complete sequence available in Genbank., which could amplify three overlapping fragments cover the whole genome. The PCR fragments were sequencing by Sanger sequence with Primer walking methods. Genogroup and genotype were assigned using the Norovirus Noronet typing tool and the strains were named according to the time of isolation. The phylogenetic analysis was conducted using MEGA software (ver. 6.06). Results One nearly complete genome sequence were obtained from sample collected from Huzhou, China. The partial genome sequence of the HuzhouNS2014603 strain is composed of 7556 nucleotides (nt).The strain was classified as GII.17 genotype both in ORF1 and ORF2, and was most closely related to the LC037415.1/Hu/GII.17/Kawasaki308 strain. Within the GII.17 cluster, the 2013/14 season strains were grouped separately from the GII.17 strains detected in 2014/15. HuzhouNS2014603 was clustered with the 2014/15 season strains. Compared with other strains selected, there are 98 variable residues across the VP1 domain. Among the 98 variable amino acids, 13 (13.3%) were observed in the shell domain and 22 (22.4%) in the P1domain; most of the substitutions and insertions were located in the P2 domain, account for 63 (64.3%). Conclusions This is the first report of the nearly complete genome of the novel GII.17 by direct sequencing method in the Huzhou area. The results of this study could be helpful for the study of the genetic evolution of the virus, the development of rapid diagnostic reagents and the design of vaccine.
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Affiliation(s)
- Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, China
| | - Jiankang Han
- Huzhou Center for Disease Control and Prevention, Huzhou, China
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14
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Suffredini E, Iaconelli M, Equestre M, Valdazo-González B, Ciccaglione AR, Marcantonio C, Della Libera S, Bignami F, La Rosa G. Genetic Diversity Among Genogroup II Noroviruses and Progressive Emergence of GII.17 in Wastewaters in Italy (2011-2016) Revealed by Next-Generation and Sanger Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:141-150. [PMID: 29185203 DOI: 10.1007/s12560-017-9328-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/24/2017] [Indexed: 05/28/2023]
Abstract
Noroviruses (NoV) are a major cause of gastroenteritis worldwide. Recently, a novel variant of NoV GII.17 (GII.P17_GII.17 NoV), termed Kawasaki 2014, has been increasingly reported in NoV outbreaks in Asia, and has also been described in Europe and North America. In this study, sewage samples were investigated to study the occurrence and genetic diversity of NoV genogroup II (GII) along a 6-year period. Moreover, the spread of GII.17 strains (first appearance and occurrence along time) was specifically assessed. A total of 122 sewage samples collected from 2011 to 2016 from four wastewater treatment plants in Rome (Italy) were initially tested using real-time RT-(q)PCR for GII NoV. Positive samples were subsequently subjected to genotypic characterization by RT-nested PCRs using broad-range primes targeting the region C of the capsid gene of GII NoV, and specific primers targeting the same region of GII.17 NoV. In total, eight different genotypes were detected with the broad-range assay: GII.1 (n = 6), GII.2 (n = 8), GII.3 (n = 3), GII.4 (n = 13), GII.6 (n = 3), GII.7 (n = 2), GII.13 (n = 2), and GII.17 (n = 3), with the latter two genotypes detected only in 2016. Specific amplification of GII.17 NoV was successful in 14 out of 110 positive samples, spanned over the years 2013-2016. The amplicons of the broad-range PCR, pooled per year, were further analyzed by next-generation sequencing (NGS) for a deeper analysis of the genotypes circulating in the study period. NGS confirmed the circulation of GII.17 NoV since 2013 and detected, beyond the eight genotypes identified by Sanger sequencing, three additional genotypes regarded as globally uncommon: GII.5, GII.16, and GII.21. This study provides evidence that GII.17 NoV Kawasaki has been circulating in the Italian population before its appearance and identification in clinical cases, and has become a major genotype in 2016. Our results confirm the usefulness of wastewater surveillance coupled with NGS to study the molecular epidemiology of NoV and to monitor the emergence of NoV strains.
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Affiliation(s)
- E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Equestre
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - B Valdazo-González
- The National Institute for Biological Standards and Control, The Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, UK
| | - A R Ciccaglione
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - C Marcantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - S Della Libera
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - F Bignami
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
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15
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Waterborne outbreak of gastroenteritis on the KwaZulu-Natal Coast, South Africa, December 2016/January 2017. Epidemiol Infect 2018; 146:1318-1325. [PMID: 29781418 DOI: 10.1017/s095026881800122x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
An unexpected increase in gastroenteritis cases was reported by healthcare workers on the KwaZulu-Natal Coast, South Africa, January 2017 with >600 cases seen over a 3-week period. A case-control study was conducted to identify the source and risk factors associated with the outbreak so as to recommend control and prevention measures. Record review identified cases and controls and structured-telephonic interviews were conducted to obtain exposure history. Stool specimens were collected from 20 cases along with environmental samples and both screened for enteric pathogens. A total of 126 cases and 62 controls were included in the analysis. The odds of developing gastroenteritis were 6.0 times greater among holiday makers than residents (95% confidence interval (CI) 2.0-17.7). Swimming in the lagoon increased the odds of developing gastroenteritis by 3.3 times (95% CI 1.06-10.38). Lagoon water samples tested positive for norovirus (NoV) GI.6, GII.3 and GII.6, astrovirus and rotavirus. Eleven (55%) stool specimens were positive for NoV with eight genotyped as GI.1 (n = 2), GI.5 (n = 3), GI.6 (n = 2), and GI.7 (n = 1). A reported sewage contamination event impacting the lagoon was the likely source with person-to-person spread perpetuating the outbreak. Restriction to swimming in the lagoon was apparently ineffective at preventing the outbreak, possibly due to inadequate enforcement, communication and signage strategies.
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16
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Mabasa VV, Meno KD, Taylor MB, Mans J. Environmental Surveillance for Noroviruses in Selected South African Wastewaters 2015-2016: Emergence of the Novel GII.17. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:16-28. [PMID: 28779481 DOI: 10.1007/s12560-017-9316-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
Norovirus (NoV) GII.4 is the predominant genotype associated with gastroenteritis pandemics and new strains emerge every 2-3 years. Between 2008 and 2011, environmental studies in South Africa (SA) reported NoVs in 63% of the sewage-polluted river water samples. The aim of this study was to assess whether wastewater samples could be used for routine surveillance of NoVs, including GII.4 variants. From April 2015 to March 2016, raw sewage and effluent water samples were collected monthly from five wastewater treatment plants in SA. A total of 108 samples were screened for NoV GI and GII using real-time RT-qPCR. Overall 72.2% (78/108) of samples tested positive for NoVs with 4.6% (5/108) GI, 31.5% (34/108) GII and 36.1% (39/108) GI + GII strains being detected. Norovirus concentrations ranged from 1.02 × 102 to 3.41 × 106 genome copies/litre for GI and 5.00 × 103 to 1.31 × 106 genome copies/litre for GII. Sixteen NoV genotypes (GI.2, GI.3, GI.4, GI.5, GI.6, GII.2, GII.3, GII.4, GII.7, GII.9, GII.10, GII.14, GII.16, GII.17, GII.20, and GII.21) were identified. Norovirus GII.2 and GII.17 co-dominated and the majority of GII.17 strains clustered with the novel Kawasaki 2014 variant. Sewage surveillance facilitated detection of Kawasaki 2014 in SA, which to date has not been detected with surveillance in children with gastroenteritis <5 years of age. Combined surveillance in the clinical setting and environment appears to be a valuable strategy to monitor emergence of NoV strains in countries that lack NoV outbreak surveillance.
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Affiliation(s)
- V V Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - K D Meno
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - M B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa.
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17
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Abstract
Background During the winter of 2014–2015, a rarely reported norovirus (NoV) genotype GII.17 was found to have increased its frequency in norovirus outbreaks in East Asia, surpassing the GII.4 NoV infections. GII.17 genotype has been detected for over three decades in the world. The aim of this study is to examine the evolutionary dynamics of GII.17 over the last four decades. Methods NoV GII.17 sequences with complete or nearly complete VP1 were downloaded from GenBank and the phylogenetic analyses were then conducted. Results The maximum likelihood analysis showed that GII.17 genotype could be divided into four different clades (Clades A–D). The strains detected after 2012, which could be the cause of the outbreaks, were separated into Clades C–D with their mean amino acid distance being 4.5%. Bayesian Markov chain Monte Carlo analyses indicated that the rate of nucleotide substitution per sites was 1.68 × 10−3 nucleotide substitutions/site/year and the time of the most recent common ancestor was 1840. The P2 subdomain of GII.17 was highly variable with 44% (56/128) amino acids variations including two insertions at positions 295–296 and one deletion at position 385 (Clades C and D) and one insertion at position 375 (Clade D). Variations existed in Epitopes A, B and D corresponding to GII.4 and human histo-blood group antigens binding site I in P2 subdomain. Conclusion The novel GII.17 strains that caused outbreaks in 2013–2015 may have two new variants. The evolvement of HBGAs binding site and epitopes in P2 subdomain might contribute to the novel GII.17 strains predominance in some regions.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaoyun Yang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
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18
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Cheng HY, Hung MN, Chen WC, Lo YC, Su YS, Wei HY, Chen MY, Tuan YC, Lin HC, Lin HY, Liu TY, Wang YY, Wu FT. Ice-associated norovirus outbreak predominantly caused by GII.17 in Taiwan, 2015. BMC Public Health 2017; 17:870. [PMID: 29116002 PMCID: PMC5688813 DOI: 10.1186/s12889-017-4869-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022] Open
Abstract
Background On 5 March 2015, Taiwan Centers for Disease Control was notified of more than 200 students with gastroenteritis at a senior high school during excursion to Kenting. We conducted an outbreak investigation to identify the causative agent and possible vehicle of the pathogen. Methods We conducted a retrospective cohort study by using a structured questionnaire to interview all students for consumed food items during their stay at the resort. Students were defined as a gastroenteritis case while having vomiting or diarrhea after the breakfast on 4 March. We inspected the environment to identify possible contamination route. We collected stool or vomitus samples from ill students, food handlers and environmental specimens for bacterial culture for common enteropathogens, reverse transcription polymerase chain reaction (RT-PCR) for norovirus and enzyme-linked immunosorbent assay (ELISA) for rotavirus. Norovirus PCR-positive products were then sequenced and genotyped. Results Of 267 students enrolled, 144 (54%) met our case definition. Regression analysis revealed elevated risk associated with iced tea, which was made from tea powder mixed with hot water and self-made ice (risk ratio 1.54, 95% confidence interval 1.22–1.98). Ice used for beverages, water before and after water filter of the ice machine and 16 stool and vomitus samples from ill students were tested positive for norovirus; Multiple genotypes were identified including GI.2, GI.4 and GII.17. GII.17 was the predominant genotype and phylogenetic analyses showed that noroviruses identified in ice, water and human samples were clustered into the same genotypes. Environmental investigation revealed the ice was made by inadequate-filtered and un-boiled water. Conclusions We identified the ice made by norovirus-contaminated un-boiled water caused the outbreak and the predominant genotype was GII.17. Adequately filtered or boiled water should be strongly recommended for making ice to avoid possible contamination.
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Affiliation(s)
- Hao-Yuan Cheng
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Min-Nan Hung
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Wan-Chin Chen
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Yi-Chun Lo
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Ying-Shih Su
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Hsin-Yi Wei
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Meng-Yu Chen
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Yen-Chang Tuan
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Hui-Chen Lin
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan
| | - Hsu-Yang Lin
- Taiwan Food and Drug Administration, No.161-2, Kunyang St, Nangang District, Taipei, Taiwan
| | - Tsung-Yen Liu
- Taiwan Food and Drug Administration, No.161-2, Kunyang St, Nangang District, Taipei, Taiwan
| | - Yu-Ying Wang
- Taiwan Food and Drug Administration, No.161-2, Kunyang St, Nangang District, Taipei, Taiwan
| | - Fang-Tzy Wu
- Taiwan Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei, Taiwan. .,Research and Diagnostic Center, Taiwan Centers for Disease Control, No.161, Kunyang St., Nangang Dist, Taipei City, 115, Taiwan.
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19
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Van Abel N, Mans J, Taylor MB. Quantitative microbial risk assessment to estimate the health risk from exposure to noroviruses in polluted surface water in South Africa. JOURNAL OF WATER AND HEALTH 2017; 15:908-922. [PMID: 29215355 DOI: 10.2166/wh.2017.305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study assessed the risks posed by noroviruses (NoVs) in surface water used for drinking, domestic, and recreational purposes in South Africa (SA), using a quantitative microbial risk assessment (QMRA) methodology that took a probabilistic approach coupling an exposure assessment with four dose-response models to account for uncertainty. Water samples from three rivers were found to be contaminated with NoV GI (80-1,900 gc/L) and GII (420-9,760 gc/L) leading to risk estimates that were lower for GI than GII. The volume of water consumed and the probabilities of infection were lower for domestic (2.91 × 10-8 to 5.19 × 10-1) than drinking water exposures (1.04 × 10-5 to 7.24 × 10-1). The annual probabilities of illness varied depending on the type of recreational water exposure with boating (3.91 × 10-6 to 5.43 × 10-1) and swimming (6.20 × 10-6 to 6.42 × 10-1) being slightly greater than playing next to/in the river (5.30 × 10-7 to 5.48 × 10-1). The QMRA was sensitive to the choice of dose-response model. The risk of NoV infection or illness from contaminated surface water is extremely high in SA, especially for lower socioeconomic individuals, but is similar to reported risks from limited international studies.
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Affiliation(s)
- Nicole Van Abel
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
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La Rosa G, Della Libera S, Iaconelli M, Proroga YTR, De Medici D, Martella V, Suffredini E. Detection of Norovirus GII.17 Kawasaki 2014 in Shellfish, Marine Water and Underwater Sewage Discharges in Italy. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:326-333. [PMID: 28258477 DOI: 10.1007/s12560-017-9290-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
Norovirus (NoV) is a major cause of non-bacterial acute gastroenteritis worldwide, and the variants of genotype GII.4 are currently the predominant human strains. Recently, a novel variant of NoV GII.17 (GII.P17_GII.17 NoV), termed Kawasaki 2014, has been reported as the cause of gastroenteritis outbreaks in Asia, replacing the pandemic strain GII.4 Sydney 2012. The GII.17 Kawasaki 2014 variant has also been reported sporadically in patients with gastroenteritis outside of Asia, including Italy. In this study, 384 shellfish samples were subjected to screening for human NoVs using real-time PCR and 259 (67.4%) tested positive for Genogroup II (GII) NoV. Of these, 52 samples, selected as representative of different areas and sampling dates, were further amplified by conventional PCR targeting the capsid gene, using broad-range primers. Forty shellfish samples were characterized by amplicon sequencing as GII.4 (n = 29), GII.2 (n = 4), GII.6 (n = 2), GII.12 (n = 2), and GII.17 (n = 3). Sixty-eight water samples (39 seawater samples from the corresponding shellfish production areas and 29 water samples from nearby underwater sewage discharge points) were also tested using the above broad-range assay: eight NoV-positive samples were characterized as GII.1 (n = 3), GII.2 (n = 1), GII.4 (n = 2), and GII.6 (n = 2). Based on full genome sequences available in public databases, a novel RT-PCR nested assay specific for GII.17 NoVs was designed and used to re-test the characterized shellfish (40) and water (8) samples. In this second screening, the RNA of GII.17 NoV was identified in 17 additional shellfish samples and in one water sample. Upon phylogenetic analysis, these GII.17 NoV isolates were closely related to the novel GII.17 Kawasaki 2014. Interestingly, our findings chronologically matched the emergence of the Kawasaki 2014 variant in the Italian population (early 2015), as reported by hospital-based NoV surveillance. These results, showing GII.17 NoV strains to be widespread in shellfish samples collected in 2015 in Italy, provide indirect evidence that this strain has started circulating in the Italian population. Notably, using a specific assay, we were able to detect many more samples positive for GII.17 NoV, indicating that, in food and water matrices, broad-range assays for NoV may grossly underestimate the prevalence of some, less common, NoVs. The detection of the GII.17 strain Kawasaki 2014 in clinical, water and food samples in Italy highlights the need for more systematic surveillance for future disease control and prevention.
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Affiliation(s)
- G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy.
| | - S Della Libera
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - Y T R Proroga
- Department of Food Inspection, Istituto Zooprofilattico Sperimentale del Mezzogiorno, via della Salute 2, 80055, Portici, Italy
| | - D De Medici
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
| | - V Martella
- Faculty of Veterinary Medicine, University of Bari "Aldo Moro", Valenzano, BA, Italy
| | - E Suffredini
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, viale Regina Elena 299, 00161, Rome, Italy
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21
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Iaconelli M, Muscillo M, Della Libera S, Fratini M, Meucci L, De Ceglia M, Giacosa D, La Rosa G. One-year Surveillance of Human Enteric Viruses in Raw and Treated Wastewaters, Downstream River Waters, and Drinking Waters. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:79-88. [PMID: 27682315 DOI: 10.1007/s12560-016-9263-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/23/2016] [Indexed: 05/22/2023]
Abstract
Human enteric viruses are a major cause of waterborne diseases, and can be transmitted by contaminated water of all kinds, including drinking and recreational water. The objectives of the present study were to assess the occurrence of enteric viruses (enterovirus, norovirus, adenovirus, hepatitis A and E virus) in raw and treated wastewaters, in rivers receiving wastewater discharges, and in drinking waters. Wastewater treatment plants' (WWTP) pathogen removal efficiencies by adenovirus quantitative real-time PCR and the presence of infectious enterovirus, by cell culture assays, in treated wastewaters and in surface waters were also evaluated. A total of 90 water samples were collected: raw and treated wastewaters (treated effluents and ultrafiltered water reused for industrial purposes), water from two rivers receiving treated discharges, and drinking water. Nested PCR assays were used for the identification of viral DNA/RNA, followed by direct amplicon sequencing. All raw sewage samples (21/21), 61.9 % of treated wastewater samples (13/21), and 25 % of ultrafiltered water samples (3/12) were contaminated with at least one viral family. Multiple virus families and genera were frequently detected. Mean positive PCRs per sample decreased significantly from raw to treated sewage and to ultrafiltered waters. Moreover, quantitative adenovirus data showed a reduction in excess of 99 % in viral genome copies following wastewater treatment. In surface waters, 78.6 % (22/28) of samples tested positive for one or more viruses by molecular methods, but enterovirus-specific infectivity assays did not reveal infectious particles in these samples. All drinking water samples tested negative for all viruses, demonstrating the effectiveness of treatment in removing viral pathogens from drinking water. Integrated strategies to manage water from all sources are crucial to ensure water quality.
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Affiliation(s)
- M Iaconelli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - M Muscillo
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - S Della Libera
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - M Fratini
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - L Meucci
- Centro Ricerche SMAT, Società Metropolitana Acque Torino, Turin, Italy
| | - M De Ceglia
- Centro Ricerche SMAT, Società Metropolitana Acque Torino, Turin, Italy
| | - D Giacosa
- Centro Ricerche SMAT, Società Metropolitana Acque Torino, Turin, Italy
| | - G La Rosa
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy.
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22
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Jung S, Hwang BM, Jung H, Chung G, Yoo CK, Lee DY. Emergence of Norovirus GII.17-associated Outbreak and Sporadic Cases in Korea from 2014 to 2015. Osong Public Health Res Perspect 2017; 8:86-90. [PMID: 28443229 PMCID: PMC5402847 DOI: 10.24171/j.phrp.2017.8.1.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Human norovirus are major causative agent of nonbacterial acute gastroenteritis. In general, genogroup (G) II.4 is the most prominent major genotype that circulate in human population and the environment. However, a shift in genotypic trends was observed in Korea in December 2014. In this study, we investigated the trend of norovirus genotype in detail using the database of Acute Diarrhea Laboratory Surveillance (K-EnterNet) in Korea. GII.17 has since become a major contributor to outbreaks of norovirus-related infections and sporadic cases in Korea, although the reason for this shift remain unknown.
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Affiliation(s)
- Sunyoung Jung
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
| | - Bo-Mi Hwang
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
| | - HyunJu Jung
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
| | - GyungTae Chung
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
| | - Cheon-Kwon Yoo
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
| | - Deog-Yong Lee
- Division of Enteric Diseases, Center for Infectious Diseases, National Research Institute of Health, Osong, Korea
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Huang XY, Su J, Lu QC, Li SZ, Zhao JY, Li ML, Li Y, Shen XJ, Zhang BF, Wang HF, Mu YJ, Wu SY, Du YH, Liu LC, Chen WJ, Klena JD, Xu BL. A large outbreak of acute gastroenteritis caused by the human norovirus GII.17 strain at a university in Henan Province, China. Infect Dis Poverty 2017; 6:6. [PMID: 28143569 PMCID: PMC5286658 DOI: 10.1186/s40249-017-0236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 01/03/2017] [Indexed: 12/31/2022] Open
Abstract
Background Human noroviruses are a major cause of viral gastroenteritis and are the main etiological agents of acute gastroenteritis outbreaks. An increasing number of outbreaks and sporadic cases of norovirus have been reported in China in recent years. There was a large acute gastroenteritis outbreak at a university in Henan Province, China in the past five years. We want to identify the source, transmission routes of the outbreak by epidemiological investigation and laboratory testing in order to provide the effective control measures. Methods The clinical cases were investigated, and analysed by descriptive epidemiological methods according to factors such as time, department, grade and so on. Samples were collected from clinical cases, healthy persons, the environment, water, and food at the university. These samples were tested for potential bacteria and viruses. The samples that tested positive for norovirus were selected for whole genome sequencing and the sequences were then analysed. Results From 4 March to 3 April 2015, a total of 753 acute diarrhoea cases were reported at the university; the attack rate was 3.29%. The epidemic curve showed two peaks, with the main peak occurring between 10 and 20 March, accounting for 85.26% of reported cases. The rates of norovirus detection in samples from confirmed cases, people without symptoms, and environmental samples were 32.72%, 17.39%, and 9.17%, respectively. The phylogenetic analysis showed that the norovirus belonged to the genotype GII.17. Conclusions This is the largest and most severe outbreak caused by genotype GII.17 norovirus in recent years in China. The GII.17 viruses displayed high epidemic activity and have become a dominant strain in China since the winter of 2014, having replaced the previously dominant GII.4 Sydney 2012 strain. Electronic supplementary material The online version of this article (doi:10.1186/s40249-017-0236-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue-Yong Huang
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Jia Su
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Qian-Chao Lu
- Nanyang City Center for Disease Control and Prevention, Nanyang, China
| | - Shi-Zheng Li
- Nanyang City Center for Disease Control and Prevention, Nanyang, China
| | - Jia-Yong Zhao
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Meng-Lei Li
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Yi Li
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Xiao-Jing Shen
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Bai-Fan Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Hai-Feng Wang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Yu-Jiao Mu
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Shu-Yu Wu
- Program of Global Disease Detection, US Centers for Disease Control and Prevention, Beijing, China
| | - Yan-Hua Du
- Henan Center for Disease Control and Prevention, Zhengzhou, China.,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China
| | - Li-Cheng Liu
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wei-Jun Chen
- State Key Laboratory of Pathogens and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - John David Klena
- Program of Global Disease Detection, US Centers for Disease Control and Prevention, Beijing, China.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, USA
| | - Bian-Li Xu
- Henan Center for Disease Control and Prevention, Zhengzhou, China. .,Henan Key Laboratory of Pathogenic Microorganisms, Zhengzhou, China.
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Zhang P, Chen L, Fu Y, Ji L, Wu X, Xu D, Han J. Clinical and molecular analyses of norovirus-associated sporadic acute gastroenteritis: the emergence of GII.17 over GII.4, Huzhou, China, 2015. BMC Infect Dis 2016; 16:717. [PMID: 27894272 PMCID: PMC5126990 DOI: 10.1186/s12879-016-2033-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/15/2016] [Indexed: 11/11/2022] Open
Abstract
Background Noroviruses (NoVs) are the most common cause of non-bacterial acute gastroenteritis (AGE) in all age groups worldwide. The NoVs circulating in Huzhou over the past 7 years were predominantly GII.4 genotypes. In the winter of 2014–2015, a novel variant of NoV GII.17 emerged and became predominant. We report the epidemiological patterns and genetic characteristics of NoV after the appearance of GII.17 in Huzhou City, Zhejiang, China. Methods Between January and December 2015, 746 stool specimens collected from patients with acute gastroenteritis were screened for NoV. Real-time RT-PCR (qPCR) was performed for NoV detection. RT-PCR was used for genomic amplification and sequencing. Genogroups and genotypes were assigned using an online NoV typing tool (http://www.rivm.nl/mpf/norovirus/typingtool). Phylogenetic analyses were conducted using MEGA (ver. 6.06). Results In total, 196 (26.3%) specimens were identified as NoV-positive. NoV infection was found in all age groups tested (≤5, 6–15, 16–40, 41–60, and ≥60 years), with the 16–40-year age group having the highest detection rate (117/196, 59.7%). Of the 196 NoV-positive specimens, 191 (97.5%) viruses belonged to GII, and 4 (2.0%) to GI; one sample showed GI and GII co-infection. Overall, 117 (59.7%) viruses were sequenced, and new GII.P17/GII.17 variants were the dominant genotype, accounting for 75.2%, followed by GII.Pe/GII.4 Sydney 2012 strains (11.11%). AGE patients infected with the GII.P17/GII.17 genotypes almost all had abdominal pain and watery stools. Conclusions We report the epidemiological patterns and genetic characteristics of the emergence GII.17 over the GII.4 in Huzhou between January and December 2015. After the emergence of GII.17 in October 2014, it steadily replaced the previously circulating GII.4 Sydney 2012 strain, and continued to be dominant in 2015. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2033-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Yun Fu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China
| | - Jiankang Han
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, China. .,Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
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26
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Wang X, Du X, Yong W, Qiao M, He M, Shi L, Guo B, Hong L, Jiang Y, Xie G, Ding J. Genetic characterization of emergent GII.17 norovirus variants from 2013 to 2015 in Nanjing, China. J Med Microbiol 2016; 65:1274-1280. [DOI: 10.1099/jmm.0.000363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xuan Wang
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Xuefei Du
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Wei Yong
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Mengkai Qiao
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Min He
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Limin Shi
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Baofu Guo
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Lei Hong
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Yun Jiang
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Guoxiang Xie
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
| | - Jie Ding
- Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, Zizhulin 2, Nanjing 210003, PR China
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Kim MS, Koo ES, Choi YS, Kim JY, Yoo CH, Yoon HJ, Kim TO, Choi HB, Kim JH, Choi JD, Park KS, Shin Y, Kim YM, Ko G, Jeong YS. Distribution of Human Norovirus in the Coastal Waters of South Korea. PLoS One 2016; 11:e0163800. [PMID: 27681683 PMCID: PMC5040428 DOI: 10.1371/journal.pone.0163800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023] Open
Abstract
The presence of human norovirus in the aquatic environment can cause outbreaks related to recreational activities and the consumption of norovirus-contaminated clams. In this study, we investigated the prevalence of norovirus genogroups I (GI) and II (GII) in the coastal aquatic environment in South Korea (March 2014 to February 2015). A total of 504 water samples were collected periodically from four coastal areas (total sites = 63), of which 44 sites were in estuaries (clam fisheries) and 19 were in inflow streams. RT-PCR analysis targeting ORF2 region C revealed that 20.6% of the water samples were contaminated by GI (13.3%) or GII (16.6%). The prevalence of human norovirus was higher in winter/spring than in summer/fall, and higher in inflow streams (50.0%) than in estuaries (7.9%). A total of 229 human norovirus sequences were identified from the water samples, and phylogenetic analysis showed that the sequences clustered into eight GI genotypes (GI.1, 2, 3, 4, 5, 6, 7, and 9) and nine GII genotypes (GII.2, 3, 4, 5, 6, 11, 13, 17, and 21). This study highlighted three issues: 1) a strong correlation between norovirus contamination via inflow streams and coastal areas used in clam fisheries; 2) increased prevalence of certain non-GII.4 genotypes, exceeding that of the GII.4 pandemic variants; 3) seasonal shifts in the dominant genotypes of both GI and GII.
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Affiliation(s)
- Man Su Kim
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Eung Seo Koo
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Yong Seon Choi
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Ji Young Kim
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Chang Hoon Yoo
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Hyun Jin Yoon
- Department of Seafood Science and Technology, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Gyeongnam, South Korea
| | - Tae-Ok Kim
- Department of Food Science and Biotechnology, College of Ocean Science and Technology, Kunsan National University, Kunsan, South Korea
| | - Hyun Bae Choi
- Department of Environmental Engineering & Biotechnology, Mokpo National Maritime University, Mokpo, South Korea
| | - Ji Hoon Kim
- Department of Food Science and Technology, Pukyong National University, Busan, South Korea
| | - Jong Deok Choi
- Department of Seafood Science and Technology, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Gyeongnam, South Korea
| | - Kwon-Sam Park
- Department of Food Science and Biotechnology, College of Ocean Science and Technology, Kunsan National University, Kunsan, South Korea
| | - Yongsik Shin
- Department of Environmental Engineering & Biotechnology, Mokpo National Maritime University, Mokpo, South Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, South Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Yong Seok Jeong
- Department of Biology and Research Institute of Basic Sciences, Kyung Hee University, Seoul, South Korea
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28
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Qin M, Dong XG, Jing YY, Wei XX, Wang ZE, Feng HR, Yu H, Li JS, Li J. A Waterborne Gastroenteritis Outbreak Caused by Norovirus GII.17 in a Hotel, Hebei, China, December 2014. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:180-6. [PMID: 27084118 DOI: 10.1007/s12560-016-9237-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/31/2016] [Indexed: 05/06/2023]
Abstract
Norovirus (NoV) is responsible for an estimated 90 % of all epidemic nonbacterial outbreaks of gastroenteritis worldwide. Waterborne outbreaks of NoV are commonly reported. A novel GII.17 NoV strain emerged as a major cause of gastroenteritis outbreaks in China during the winter of 2014/2015. During this time, an outbreak of gastroenteritis occurred at a hotel in a ski park in Hebei Province, China. Epidemiological investigations indicated that one water well, which had only recently been in use, was the probable source. GII.17 NoV was detected by real-time reverse-transcription polymerase chain reaction from samples taken from cases, from concentrated water samples from water well, and from the nearby sewage settling tank. Nucleotide sequences of NoV extracted from clinical and water specimens were genetically identical and had 99 % homology with Beijing/CHN/2015. All epidemiological data indicated that GII.17 NoV was responsible for this outbreak. This is the first reported laboratory-confirmed waterborne outbreak caused by GII.17 NoV genotype in China. Strengthening management of well drinking water and systematica monitoring of NoV is essential for preventing future outbreaks.
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Affiliation(s)
- Meng Qin
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Xiao-Gen Dong
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Yan-Yan Jing
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Xiu-Xia Wei
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Zhao-E Wang
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Hui-Ru Feng
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Hong Yu
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China
| | - Jin-Song Li
- China CDC, National Institute for Viral Disease Control and Prevention, 100 Ying-Xin St., Xuan-Wu District, Beijing, 100052, China.
| | - Jie Li
- Fengtai District Center for Disease Control and Prevention of Beijing, 3 Xi An St., Feng-Tai District, Beijing, 100071, China.
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A novel norovirus GII.17 lineage contributed to adult gastroenteritis in Shanghai, China, during the winter of 2014–2015. Emerg Microbes Infect 2016; 4:e67. [PMID: 26975060 PMCID: PMC4661427 DOI: 10.1038/emi.2015.67] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Norovirus (NoV) is now recognized as a leading cause of nonbacterial acute gastroenteritis; however, the NoV GII.17 genotype has rarely been reported as the predominant genotype in clinical diarrhea cases. During the winter of 2014–2015, the GII.17 genotype, together with the NoV GII.4 genotype, dominated in sporadic adult patients with gastroenteritis in Shanghai. Phylogenetic analysis based on full-length VP1 amino acid sequences showed that the GII.17 strains that emerged in Shanghai have close evolutionary relationships with strains recently collected in the Hong Kong area, Guangdong province of China, and Japan during the same period. This cluster in the phylogenetic tree may represent a novel NoV GII.17 lineage recently circulating in East Asia. Pairwise distances between clusters also revealed the evolution of the NoV GII.17 genotype in previous decades. Our study emphasizes the importance of combined surveillance of NoV-associated infections.
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30
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Jin M, Zhou YK, Xie HP, Fu JG, He YQ, Zhang S, Jing HB, Kong XY, Sun XM, Li HY, Zhang Q, Li K, Zhang YJ, Zhou DQ, Xing WJ, Liao QH, Liu N, Yu HJ, Jiang X, Tan M, Duan ZJ. Characterization of the new GII.17 norovirus variant that emerged recently as the predominant strain in China. J Gen Virol 2016; 97:2620-2632. [PMID: 27543110 DOI: 10.1099/jgv.0.000582] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Human noroviruses are the most important viral pathogens causing epidemic acute gastroenteritis, in which the GII.4 viruses have been predominant worldwide for the past decades. During 2014-2015 winter season, a new GII.17 variant emerged as the predominant virus in China surpassing the GII.4 virus in causing significantly increased acute gastroenteritis outbreaks. Genome sequences of the new GII.17 variant was determined and compared with other GII.17 noroviruses, revealing residue substitutions at specific locations, including the histo-blood group antigen-binding site and the putative antigenic epitopes. Further study of GII.17 outbreaks focusing on host susceptibility showed that the new GII.17 variant infected secretor individuals of A, B, O and Lewis types. Accordingly, the P particles of the new GII.17 variant bound secretor saliva samples of A, B, O and Lewis types with significantly higher binding signals than those of the P particles of the previous GII.17 variants. In addition, human sera collected from the outbreaks exhibited stronger blockade against the binding of the new GII.17 P particles to saliva samples than those against the binding between the P particles of previous GII.17 variants and saliva samples. Taken together, our data strongly suggested that the new GII.17 variant gained new histo-blood group antigen-binding ability and antigenic features, which may contribute to its predominance in causing human norovirus epidemics.
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Affiliation(s)
- Miao Jin
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Yong-Kang Zhou
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.,The First Clinical Medical College of Lanzhou University, Lanzhou, PR China
| | - Hua-Ping Xie
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong Province, PR China
| | - Jian-Guang Fu
- Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu Province, PR China
| | - Ya-Qing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong Province, PR China
| | - Shuang Zhang
- Beijing Shunyi Center for Disease Control and Prevention, Shunyi District, Beijing, PR China
| | - Hong-Bo Jing
- Beijing Shunyi Center for Disease Control and Prevention, Shunyi District, Beijing, PR China
| | - Xiang-Yu Kong
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xiao-Man Sun
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Hui-Ying Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Qing Zhang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Kai Li
- Guangzhou Huadu Center for Disease Control and Prevention, Huadu District, Guangzhou, Guangdong Province, PR China
| | - Ying-Jun Zhang
- Guangzhou Huadu Center for Disease Control and Prevention, Huadu District, Guangzhou, Guangdong Province, PR China
| | - De-Qian Zhou
- Guangzhou Yuexiu Center for Disease Control and Prevention, Yuexiu District, Guangzhou, Guangdong Province, PR China
| | - Wei-Jia Xing
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Qiao-Hong Liao
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Na Liu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Hong-Jie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ming Tan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Zhao-Jun Duan
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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Dinu S, Nagy M, Negru DG, Popovici ED, Zota L, Oprișan G. Molecular identification of emergent GII.P17-GII.17 norovirus genotype, Romania, 2015. ACTA ACUST UNITED AC 2016; 21:pii=30141. [PMID: 26924169 DOI: 10.2807/1560-7917.es.2016.21.7.30141] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/18/2016] [Indexed: 11/20/2022]
Abstract
The novel GII.P17-GII.17 norovirus genotype has been reported as cause of gastroenteritis outbreaks in China and Japan since the winter season 2014/15, replacing the pandemic strain GII.4 Sydney 2012. These emergent strains have also been sporadically reported on other continents than Asia. GII.P17-GII.17 isolates, similar to Kawasaki308 2015, were identified in three patients during a large outbreak of acute gastroenteritis affecting 328 people in Romania, in neighbouring localities, in 2015.
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Affiliation(s)
- Sorin Dinu
- Molecular Epidemiology Laboratory, Cantacuzino National Institute of Research, Bucharest, Romania
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Sisay Z, Djikeng A, Berhe N, Belay G, Gebreyes W, Abegaz WE, Njahira MN, Wang QH, Saif LJ. Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia. Arch Virol 2016; 161:2169-82. [PMID: 27193022 DOI: 10.1007/s00705-016-2887-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/03/2016] [Indexed: 01/02/2023]
Abstract
Viral gastroenteritis is a major public health problem worldwide. In Ethiopia, very limited studies have been done on the epidemiology of enteropathogenic viruses. The aim of this study was to detect and characterize noroviruses (NoVs) and sapoviruses (SaVs) from acute gastroenteritis patients of all ages. Fecal samples were collected from diarrheic patients (n = 213) in five different health centers in Addis Ababa during June-September 2013. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. Of the clinical samples, 25.3 % and 4.2 % were positive for NoV and SaV RNA, respectively. Among the norovirus positives, 22 were sequenced further, and diverse norovirus strains were identified: GI (n = 4), GII (n = 17) and GIV (n = 1). Most strains were GII (n = 17/22: 77.2 %), which were further divided into three different genotypes (GII.4, GII.12/GII.g recombinant-like and GII.17), with GII.17 being the dominant (7/17) strain detected. GI noroviruses, in particular GI.4 (n = 1), GI.5 (n = 2) and GI.8 (n = 1), were also detected and characterized. The GIV strain detected is the first from East Africa. The sapoviruses sequenced were also the first reported from Ethiopia. Collectively, this study showed the high burden and diversity of noroviruses and circulation of sapoviruses in diarrheic patients in Ethiopia. Continued surveillance to assess their association with diarrhea is needed to define their epidemiology, disease burden, and impact on public health.
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Affiliation(s)
- Zufan Sisay
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia. .,Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia.
| | - Appolinaire Djikeng
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Nega Berhe
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Wondwossen Gebreyes
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Woldaregay Erku Abegaz
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Moses N Njahira
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Q H Wang
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA.
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Abstract
Norovirus (NoV) is recognised as a leading cause of gastroenteritis worldwide across all age groups. The prevalence and diversity of NoVs in many African countries is still unknown, although early sero-prevalence studies indicated widespread early infection. Reports on NoVs in Africa vary widely in terms of study duration, population groups and size, inclusion of asymptomatic controls, as well as genotyping information. This review provides an estimate of NoV prevalence and distribution of genotypes of NoVs in Africa. Inclusion criteria for the review were study duration of at least 6 months, population size of >50 and diagnosis by RT-PCR. As regions used for genotyping varied, or genotyping was not always performed, this was not considered as an inclusion criteria. A literature search containing the terms norovirus+Africa yielded 74 publications. Of these 19 studies from 14 out of the 54 countries in Africa met the inclusion criteria. Data from studies not meeting the inclusion criteria, based on sample size or short duration, were included as discussion points. The majority of studies published focused on children, under five years of age, hospitalised with acute gastroenteritis. The mean overall prevalence was 13.5% (range 0.8–25.5%) in children with gastroenteritis and 9.7% (range 7–31%) in asymptomatic controls, where tested. NoV GII.4 was the predominant genotype identified in most of the studies that presented genotyping data. Other prevalent genotypes detected included GII.3 and GII.6. In conclusion, NoV is a common pathogen in children with diarrhoea in Africa, with considerable carriage in asymptomatic children. There is however, a paucity of data on NoV infection in adults.
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Affiliation(s)
- Janet Mans
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - George E. Armah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - A. Duncan Steele
- MRC Diarrhoeal Pathogens Research Unit, University of Limpopo, Pretoria, South Africa
| | - Maureen B. Taylor
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
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Lu J, Sun L, Fang L, Yang F, Mo Y, Lao J, Zheng H, Tan X, Lin H, Rutherford S, Guo L, Ke C, Hui L. Gastroenteritis Outbreaks Caused by Norovirus GII.17, Guangdong Province, China, 2014-2015. Emerg Infect Dis 2016; 21:1240-2. [PMID: 26080037 PMCID: PMC4480401 DOI: 10.3201/eid2107.150226] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past decade, the most prevalent norovirus genotype causing viral gastroenteritis outbreaks worldwide, including China, has been GII.4. In winter 2014–15, norovirus outbreaks in Guangdong, China, increased. Sequence analysis indicated that 82% of the outbreaks were caused by a norovirus GII.17 variant.
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Gao Z, Liu B, Huo D, Yan H, Jia L, Du Y, Qian H, Yang Y, Wang X, Li J, Wang Q. Increased norovirus activity was associated with a novel norovirus GII.17 variant in Beijing, China during winter 2014-2015. BMC Infect Dis 2015; 15:574. [PMID: 26678989 PMCID: PMC4683961 DOI: 10.1186/s12879-015-1315-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 12/10/2015] [Indexed: 12/19/2022] Open
Abstract
Background Norovirus (NoV) is a leading cause of sporadic cases and outbreaks of acute gastroenteritis (AGE). Increased NoV activity was observed in Beijing, China during winter 2014–2015; therefore, we examined the epidemiological patterns and genetic characteristics of NoV in the sporadic cases and outbreaks. Methods The weekly number of infectious diarrhea cases reported by all hospitals in Beijing was analyzed through the China information system for disease control and prevention. Fecal specimens were collected from the outbreaks and outpatients with AGE, and GI and GII NoVs were detected using real time reverse transcription polymerase chain reaction. The partial capsid genes and RNA-dependent RNA polymerase (RdRp) genes of NoV were both amplified and sequenced, and genotyping and phylogenetic analyses were performed. Results Between December 2014 and March 2015, the number of infectious diarrhea cases in Beijing (10,626 cases) increased by 35.6 % over that of the previous year (7835 cases), and the detection rate of NoV (29.8 %, 191/640) among outpatients with AGE was significantly higher than in the previous year (12.9 %, 79/613) (χ2 = 53.252, P < 0.001). Between November 2014 and March 2015, 35 outbreaks of AGE were reported in Beijing, and NoVs were detected in 33 outbreaks, all of which belonged to the GII genogroup. NoVs were sequenced and genotyped in 22 outbreaks, among which 20 were caused by a novel GII.17 strain. Among outpatients with AGE, this novel GII.17 strain was first detected in an outpatient in August 2014, and it replaced GII.4 Sydney_2012 as the predominant variant between December 2014 and March 2015. A phylogenetic analysis of the capsid genes and RdRp genes revealed that this novel GII.17 strain was distinct from previously identified GII variants, and it was recently designated as GII.P17_GII.17. This variant was further clustered into two sub-groups, named GII.17_2012 and GII.17_2014. During winter 2014–2015, GII.17_2014 caused the majority of AGE outbreaks in China and Japan. Conclusions During winter 2014–2015, a novel NoV GII.17 variant replaced the GII.4 variant Sydney 2012 as the predominant strain in Beijing, China and caused increased NoV activity.
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Affiliation(s)
- Zhiyong Gao
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Baiwei Liu
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Da Huo
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Hanqiu Yan
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Lei Jia
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Yiwei Du
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Haikun Qian
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Yang Yang
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Xiaoli Wang
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Jie Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
| | - Quanyi Wang
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, No.16 Hepingli Middle Street, Dongcheng District, Beijing, 100013, China.
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An outbreak caused by GII.17 norovirus with a wide spectrum of HBGA-associated susceptibility. Sci Rep 2015; 5:17687. [PMID: 26639056 PMCID: PMC4671059 DOI: 10.1038/srep17687] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/04/2015] [Indexed: 01/23/2023] Open
Abstract
During the past norovirus (NoV) epidemic season, a new GII.17 variant emerged as a predominant NoV strain, surpassed the GII.4 NoVs, causing outbreaks of acute gastroenteritis (AGE) in China. Here we report a study of an AGE outbreak in an elementary school in December 2014 caused by the new GII.17 NoV to explore the potential mechanism behind the sudden epidemics of the GII.17 NoV. A total of 276 individuals were sick with typical NoV infection symptoms of vomiting (93.4%), abdominal pain (90.4%), nausea (60.0%), and diarrhea (10.4%) at an attack rate of 5.7–16.9%. Genotyping of the symptomatic patients showed that individuals with a secretor positive status, including those with A, B, and O secretors and Lewis positive blood types, were sensitive to the virus, while the non-secretors and the Lewis negative individual were not. Accordingly, the recombinant capsid P protein of the GII.17 isolate showed a wide binding spectrum to saliva samples of all A, B, and O secretors. Thus, the broad binding spectrum of the new GII.17 variant could explain its widely spread nature in China and surrounding areas in the past two years.
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Chan MCW, Lee N, Hung TN, Kwok K, Cheung K, Tin EKY, Lai RWM, Nelson EAS, Leung TF, Chan PKS. Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014. Nat Commun 2015; 6:10061. [PMID: 26625712 PMCID: PMC4686777 DOI: 10.1038/ncomms10061] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/29/2015] [Indexed: 12/11/2022] Open
Abstract
Norovirus genogroup II genotype 4 (GII.4) has been the predominant cause of viral gastroenteritis since 1996. Here we show that during the winter of 2014-2015, an emergent variant of a previously rare norovirus GII.17 genotype, Kawasaki 2014, predominated in Hong Kong and outcompeted contemporary GII.4 Sydney 2012 in hospitalized cases. GII.17 cases were significantly older than GII.4 cases. Root-to-tip and Bayesian BEAST analyses estimate GII.17 viral protein 1 (VP1) evolves one order of magnitude faster than GII.4 VP1. Residue substitutions and insertion occur in four of five inferred antigenic epitopes, suggesting immune evasion. Sequential GII.4-GII.17 infections are noted, implicating a lack of cross-protection. Virus bound to saliva of secretor histo-blood groups A, B and O, indicating broad susceptibility. This fast-evolving, broadly recognizing and probably immune-escaped emergent GII.17 variant causes severe gastroenteritis and hospitalization across all age groups, including populations who were previously less vulnerable to GII.4 variants; therefore, the global spread of GII.17 Kawasaki 2014 needs to be monitored.
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Affiliation(s)
- Martin C W Chan
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Nelson Lee
- Department of Medicine and Therapeutics, Faculty of Medicine, 9/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Tin-Nok Hung
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Kirsty Kwok
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Kelton Cheung
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Edith K Y Tin
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Raymond W M Lai
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - E Anthony S Nelson
- Department of Paediatrics, Faculty of Medicine, 6/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Ting F Leung
- Department of Paediatrics, Faculty of Medicine, 6/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, 1/F Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
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Tao Z, Xu M, Lin X, Wang H, Song L, Wang S, Zhou N, Zhang D, Xu A. Environmental Surveillance of Genogroup I and II Noroviruses in Shandong Province, China in 2013. Sci Rep 2015; 5:17444. [PMID: 26616566 PMCID: PMC5378908 DOI: 10.1038/srep17444] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/29/2015] [Indexed: 02/05/2023] Open
Abstract
Noroviruses are the most common cause of epidemic gastroenteritis. However, the
case-based surveillance is limited in China. In this study, we analyzed the results
of environmental surveillance conducted in two cities of Shandong Province, China
from January to December in 2013. Twenty-four sewage samples were collected and
concentrated via membrane absorption/elution method. After reverse
transcription-PCR, cloning and sequencing on ORF2 region, norovirus nucleic acid was
detected in all 24 sewage samples. A total of 403 norovirus sequences of 16
genotypes were detected, among which GII.3 (22.6%), GI.2 (17.1%), GI.5 (13.4%), GI.3
(11.9%), GII.4 (7.7%), and GII.6 (6.7%) were the 6 most common genotypes.
Phylogenetic analysis revealed multiple lineages within most common genotypes,
especially in GI.3, whereas all GII.4 sequences belonged to Sydney 2012 strain.
Recombination events were observed in 5 GI and 4 GII sequences within or near the
ORF1/ORF2 overlap. This is the first report on systematic environmental surveillance
on norovirus in China. The data presented here reveal co-circulation and high
genetic diversity of multiple norovirus genotypes in the two cities, and suggest
continued environmental surveillance can provide valuable information on norovirus
circulation in the population.
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Affiliation(s)
- Zexin Tao
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Minglei Xu
- Qingdao Medical College, Qingdao University, No. 38 Dengzhou Road Qingdao, 266021, china
| | - Xiaojuan Lin
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Haiyan Wang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Lizhi Song
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Suting Wang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Nan Zhou
- School of Public Health, Shandong University, Jinan, People's Republic of China
| | - Dongfeng Zhang
- Qingdao Medical College, Qingdao University, No. 38 Dengzhou Road Qingdao, 266021, china
| | - Aiqiang Xu
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China.,School of Public Health, Shandong University, Jinan, People's Republic of China
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Han J, Ji L, Shen Y, Wu X, Xu D, Chen L. Emergence and predominance of norovirus GII.17 in Huzhou, China, 2014-2015. Virol J 2015; 12:139. [PMID: 26362650 PMCID: PMC4566299 DOI: 10.1186/s12985-015-0370-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/01/2015] [Indexed: 12/01/2022] Open
Abstract
Background Norovirus (NoV) has been recognized as the leading cause of both outbreaks and sporadic cases of acute gastroenteritis in children and adults worldwide. Stool samples collected from outpatients with clinical symptoms of acute gastroenteritis in all age groups at the First People’s Hospital in Huzhou, Huzhou, China between March 2014 and February 2015 were analyzed to gain insight into the epidemiology and genetic variation in NoV strains circulating in China. Method Real-time RT-PCR (qPCR) was performed for Norovirus detection. RT-PCR were used for genomic amplification and sequencing. Genogroup and genotype were assigned using the NoV Noronet typing tool and the strains were named according to the time of isolation. The phylogenetic analysis was conducted using MEGA 5. Results Of the 809 specimens, 193 (23.9 %) were positive for NoV, with GII.4 and GII.17 the most commonly identified strains. Phylogenetic analysis confirmed the presence of five recombinant strains in Huzhou. Recombinants GII.P13/GII.17 and GII.P12/GII.4 were newly detected in China. The GII.P13/GII.17 recombinant was first identified in October 2014 and steadily replaced GII.Pe/GII.4 (GII.4 Sydney 2012) as the predominant circulating NoV genotype. Conclusion This is the first report of the detection of GII.17 in the Huzhou area and of a NoV genotype being detected in greater numbers than GII.4. Furthermore, our results indicated that following the emergence of GII.17 in October 2014, it steadily replaced the previous circulating GII.4 Sydney2012 strain, which was the dominant circulating genotype for the past 2 years. As norovirus are the important cause of nonbacterial gastroenteritis, continuous and comprehensive study of the norovirus strains involved in large and cost-effective acute gastroenteritis would help understanding the molecular epidemiology of norovirus infections and development of improved prevention and control measures.
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Affiliation(s)
- Jiankang Han
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Yuehua Shen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.
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40
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Lee CC, Feng Y, Chen SY, Tsai CN, Lai MW, Chiu CH. Emerging norovirus GII.17 in Taiwan. Clin Infect Dis 2015; 61:1762-4. [PMID: 26306886 DOI: 10.1093/cid/civ647] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Chung-Chan Lee
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ye Feng
- Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ming-Wei Lai
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
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de Graaf M, van Beek J, Vennema H, Podkolzin AT, Hewitt J, Bucardo F, Templeton K, Mans J, Nordgren J, Reuter G, Lynch M, Rasmussen LD, Iritani N, Chan MC, Martella V, Ambert-Balay K, Vinjé J, White PA, Koopmans MP. Emergence of a novel GII.17 norovirus – End of the GII.4 era? ACTA ACUST UNITED AC 2015; 20. [PMID: 26159308 DOI: 10.2807/1560-7917.es2015.20.26.21178] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the winter of 2014/15 a novel GII.P17-GII.17 norovirus strain (GII.17 Kawasaki 2014) emerged, as a major cause of gastroenteritis outbreaks in China and Japan. Since their emergence these novel GII.P17-GII.17 viruses have replaced the previously dominant GII.4 genotype Sydney 2012 variant in some areas in Asia but were only detected in a limited number of cases on other continents. This perspective provides an overview of the available information on GII.17 viruses in order to gain insight in the viral and host characteristics of this norovirus genotype. We further discuss the emergence of this novel GII.P17-GII.17 norovirus in context of current knowledge on the epidemiology of noroviruses. It remains to be seen if the currently dominant norovirus strain GII.4 Sydney 2012 will be replaced in other parts of the world. Nevertheless, the public health community and surveillance systems need to be prepared in case of a potential increase of norovirus activity in the next seasons caused by this novel GII.P17-GII.17 norovirus.
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Affiliation(s)
- M de Graaf
- Erasmus MC, Department of Viroscience, Rotterdam, the Netherlands
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