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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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2
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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Loeb SK, Jennings WC, Wigginton KR, Boehm AB. Sunlight Inactivation of Human Norovirus and Bacteriophage MS2 Using a Genome-Wide PCR-Based Approach and Enzyme Pretreatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8783-8792. [PMID: 34101449 DOI: 10.1021/acs.est.1c01575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Human norovirus (hNoV) is an important etiology of gastrointestinal illness and can be transmitted via ingestion of contaminated water. Currently impractical to culture, hNoV detection is reliant on real-time polymerase chain reaction (RT-PCR)-based methods. This approach cannot distinguish between infective and inactivated viruses because intact regions of the RNA genome can amplify even if the damage is present in other regions of the genome or because intact genetic material is not contained within an infectious virion. Herein, we employ a multiple long-amplicon RT-qPCR extrapolation approach to assay genome-wide damage and an enzymatic pretreatment to study the impact of simulated sunlight on the infectivity of hNoV in clear, sensitizer-free water. Using MS2 coliphage as an internal control, the genome-wide damage extrapolation approach, previously successfully applied for UV-254 inactivation, vastly overestimated sunlight inactivation, suggesting key differences in photoinactivation under different spectral conditions. hNoV genomic RNA was more susceptible to simulated sunlight degradation per base compared to MS2 genomic RNA, while enzymatic pretreatment indicated that hNoV experienced more capsid damage than MS2. This work provides practical and mechanistic insight into the endogenous sunlight inactivation of single-stranded RNA bacteriophage MS2, a widely used surrogate, and hNoV GII.4 Sydney, an important health-relevant virus, in clear sensitizer-free water.
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Affiliation(s)
- Stephanie K Loeb
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California 94305, United States
- Engineering Research Center (ERC) for Re-inventing the Nation's Urban Water Infrastructure (ReNUWIt), Stanford, California 94305, United States
| | - Wiley C Jennings
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Krista Rule Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexandria B Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California 94305, United States
- Engineering Research Center (ERC) for Re-inventing the Nation's Urban Water Infrastructure (ReNUWIt), Stanford, California 94305, United States
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Mohapatra S, Menon NG, Mohapatra G, Pisharody L, Pattnaik A, Menon NG, Bhukya PL, Srivastava M, Singh M, Barman MK, Gin KYH, Mukherji S. The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142746. [PMID: 33092831 PMCID: PMC7536135 DOI: 10.1016/j.scitotenv.2020.142746] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/08/2020] [Accepted: 09/27/2020] [Indexed: 04/14/2023]
Abstract
The contagious SARS-CoV-2 virus, responsible for COVID-19 disease, has infected over 27 million people across the globe within a few months. While literature on SARS-CoV-2 indicates that its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of alternate routes of transmission and/or reinfection via the environment requires considerable scientific attention. This review aims to collate information on possible transmission routes of this virus, to ascertain its fate in the environment. Concomitant with the presence of SARS-CoV-2 viral RNA in faeces and saliva of infected patients, studies also indicated its occurrence in raw wastewater, primary sludge and river water. Therefore sewerage system could be a possible route of virus outbreak, a possible tool to assess viral community spread and future surveillance technique. Hence, this review looked into detection, occurrence and fate of SARS-CoV-2 during primary, secondary, and tertiary wastewater and water treatment processes based on published literature on SARS-CoV and other enveloped viruses. The review also highlights the need for focused research on occurrence and fate of SARS-CoV-2 in various environmental matrices. Utilization of this information in environmental transmission models developed for other enveloped and enteric viruses can facilitate risk assessment studies. Preliminary research efforts with SARS-CoV-2 and established scientific reports on other coronaviruses indicate that the threat of virus transmission from the aquatic environment may be currently non-existent. However, the presence of viral RNA in wastewater provides an early warning that highlights the need for effective sewage treatment to prevent a future outbreak of SARS-CoV-2.
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Affiliation(s)
- Sanjeeb Mohapatra
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, India; NUS Environmental Research Institute, National University of Singapore (NUS), Singapore
| | - N Gayathri Menon
- Centre for Research in Nanotechnology and Science (CRNTS), Indian Institute of Technology Bombay, India; nEcoTox GmbH, An der Neümuhle 2, Annweiler am Trifels, Germany
| | | | - Lakshmi Pisharody
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, India
| | - Aryamav Pattnaik
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln (UNL), USA
| | - N Gowri Menon
- Department of Veterinary Epidemiology and Preventive Medicine, Kerala Veterinary and Animal Sciences University (KVASU), Wayanad, Kerala, India
| | | | | | | | | | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore (NUS), Singapore.
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, India; Centre for Research in Nanotechnology and Science (CRNTS), Indian Institute of Technology Bombay, India.
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Pairing of Parental Noroviruses with Unequal Competitiveness Provides a Clear Advantage for Emergence of Progeny Recombinants. Appl Environ Microbiol 2021; 87:AEM.02015-20. [PMID: 33187997 PMCID: PMC7848925 DOI: 10.1128/aem.02015-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher-competitiveness parents) and LP (relatively lower-competitiveness parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP-type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness.IMPORTANCE Novel recombinants, generated from inter- and intraspecies recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remain largely unknown. Therefore, current investigations on these recombinants are inevitably limited to postepidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we provide a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide an additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.
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Rosiles-González G, Ávila-Torres G, Moreno-Valenzuela OA, Cháidez-Quiroz C, Hernández-Flores CI, Acosta-González G, Brown JK, Betancourt WQ, Gerba CP, Hernández-Zepeda C. Norovirus and human adenovirus occurrence and diversity in recreational water in a karst aquifer in the Yucatan Peninsula, Mexico. J Appl Microbiol 2019; 127:1255-1269. [PMID: 31309647 DOI: 10.1111/jam.14385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/17/2019] [Accepted: 07/01/2019] [Indexed: 11/29/2022]
Abstract
AIMS To determine the seasonal occurrence and diversity of norovirus (NoV) and human adenovirus (HAdV) in groundwater from sinkholes, and brackish water used for recreational activities in the karst aquifer of the Yucatan Peninsula, Mexico. METHODS AND RESULTS Hollow fibre ultrafiltration was used to concentrate viruses and standard plaque assay methods were used to enumerate somatic and F+ specific coliphages as viral indicators. Real-time quantitative polymerase chain reaction assays were used to estimate the number of genome copies for NoV strains GI, and GII, and HAdVs. The predominant NoV genotypes and HAdV serotypes were identified by comparative sequence analysis. Somatic and male F+ specific coliphages were detected at concentrations up to 94 and 60 plaque-forming units per 100 ml respectively. The NoV genogroup I (GI) was associated with 50% of the sampled sites during the rainy season only, at concentrations ranging from 120 to 1600 genome copies per litre (GC l-1 ). The NoV genogroup II (GII) was detected in 30 and 40% of the sampled sites during the rainy and dry seasons, respectively, at concentrations ranging from 10 to 290 GC l-1 . During the rainy and dry seasons, HAdVs were detected in 20% of the sites, at concentrations ranging from 24 to 690 GC l-1 . Identification of viral types revealed the presence of NoV GI.2, GII.Pe, GII.P16 and GII.P17, and HAdV F serotypes 40 and 41. CONCLUSIONS These findings demonstrate that NoVs and HAdVs are prevalent as virus contaminants in the karst aquifer, representing potential health risks particularly during the rainy season, in one of the most important areas used for tourism in Mexico. SIGNIFICANCE AND IMPACT OF THE STUDY This is one of the few studies conducted in karst aquifers that provide a foundational baseline of the distribution, concentrations and diversity of NoVs and HadVs in these particular environments.
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Affiliation(s)
- G Rosiles-González
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Ciencias del Agua, Cancún, Quintana Roo, México
| | - G Ávila-Torres
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Ciencias del Agua, Cancún, Quintana Roo, México
| | - O A Moreno-Valenzuela
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Yucatán, México
| | - C Cháidez-Quiroz
- Centro de Investigación en Alimentación y Desarrollo A.C., Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, Sinaloa, México
| | - C I Hernández-Flores
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Ciencias del Agua, Cancún, Quintana Roo, México
| | - G Acosta-González
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Ciencias del Agua, Cancún, Quintana Roo, México
| | - J K Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - W Q Betancourt
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona, Tucson, AZ, USA
| | - C P Gerba
- Water and Energy Sustainable Technology (WEST) Center, The University of Arizona, Tucson, AZ, USA
| | - C Hernández-Zepeda
- Centro de Investigación Científica de Yucatán, A.C., Unidad de Ciencias del Agua, Cancún, Quintana Roo, México
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7
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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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Hata A, Hanamoto S, Ihara M, Shirasaka Y, Yamashita N, Tanaka H. Comprehensive Study on Enteric Viruses and Indicators in Surface Water in Kyoto, Japan, During 2014-2015 Season. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:353-364. [PMID: 30151619 DOI: 10.1007/s12560-018-9355-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Certain enteric viruses that are present in the water environment are potential risk factors of waterborne infections. To better understand the impact of viruses in water, both enteric viruses and their potential indicators should be comparatively investigated. In this study, occurrences of GI- and GII-noroviruses (NoVs), sapovirus (SaV), rotavirus (RoV), Aichi virus 1 (AiV-1), enterovirus (EV), and pepper mild mottle virus (PMMoV) were quantitatively determined in surface water samples in Japan. Additionally, the genotype distribution of GI- and GII-NoVs was determined using a next-generation amplicon sequencing. PMMoV was the most abundant virus regardless of season and location, indicating its usefulness as an indicator for the viral contamination of water. Other potential indicators, AiV and EV, were less abundant than GII-NoV. Viruses other than PMMoV showed seasonality, i.e., EV and other viruses (NoVs, SaV, RoV, and AiV-1) became prevalent during summer and winter, respectively. SaV showed a relatively high abundance at a location that was affected by untreated wastewater. Regarding NoV genotypes, GI.1, GI.2, GI.4, GI.5, GI.6, GII.3, GII.4, GII.6, and GII.17 were found from the surface water samples. GII.4 and GII.17 seemed to have contributed to the high abundance of GII-NoV in the samples. Interestingly, GII.17 strains became prevalent in the water samples before becoming prevalent among gastroenteritis patients in Japan. These findings provide further insights into the properties of viruses as contaminants in the water environment.
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Affiliation(s)
- Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan.
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Seiya Hanamoto
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Water Quality Research Team, Public Works Research Institute, 1-6 Minamihara, Tsukuba, Ibaraki, 305-8516, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Yuya Shirasaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Naoyuki Yamashita
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Course of Rural Engineering, Department of Science and Technology for Biological Resources and Environment, Faculty of Agriculture, Graduate School of Agriculture Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
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Gu X, Tay QXM, Te SH, Saeidi N, Goh SG, Kushmaro A, Thompson JR, Gin KYH. Geospatial distribution of viromes in tropical freshwater ecosystems. WATER RESEARCH 2018; 137:220-232. [PMID: 29550725 PMCID: PMC7112100 DOI: 10.1016/j.watres.2018.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 05/05/2023]
Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | | | - Shu Harn Te
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, 637819, Singapore
| | | | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore.
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10
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Haramoto E, Kitajima M, Hata A, Torrey JR, Masago Y, Sano D, Katayama H. A review on recent progress in the detection methods and prevalence of human enteric viruses in water. WATER RESEARCH 2018; 135:168-186. [PMID: 29471200 DOI: 10.1016/j.watres.2018.02.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/17/2023]
Abstract
Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.
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Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Akihiko Hata
- Integrated Research System for Sustainability Science, Institutes for Advanced Study, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Jason R Torrey
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Yoshifumi Masago
- Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan.
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Vietnam Japan University, Luu Huu Phuoc Road, My Dinh 1 Ward, Nam Tu Liem District, Ha Noi, Vietnam.
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11
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Oshiki M, Miura T, Kazama S, Segawa T, Ishii S, Hatamoto M, Yamaguchi T, Kubota K, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Kobayashi N, Araki N, Sano D. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters. Front Microbiol 2018; 9:830. [PMID: 29755444 PMCID: PMC5934477 DOI: 10.3389/fmicb.2018.00830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023] Open
Abstract
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan); genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Shinobu Kazama
- Center for Simulation Sciences and Informational Biology, Ochanomizu University, Bunkyô, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Kofu, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, Minneapolis, MN, United States
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
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12
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Waldman P, Meseguer A, Lucas F, Moulin L, Wurtzer S. Interaction of Human Enteric Viruses with Microbial Compounds: Implication for Virus Persistence and Disinfection Treatments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:13633-13640. [PMID: 29116763 DOI: 10.1021/acs.est.7b03875] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Although the interaction between phages and bacteria has already been well described, it only recently emerged that human viruses also interact with bacteria in the mammalian gut. We studied whether this interaction could occur in tap water and thus confer enteric viruses protection against temperature and the classical disinfection treatments used in drinking water production. We demonstrated that the addition of lipopolysaccharide or peptidoglycan of bacterial origin to enterovirus provides thermal protection through stabilization of the viral capsid. This interaction plays a role when viruses are exposed to disinfection that targets the capsid, but less so when the virus genome is directly targeted. The interaction seems to be serotype-specific, suggesting that the capsid protein sequence could be important. The protection is linked to a direct association between viral particles and bacterial compounds as observed by microscopy. These results show that bacterial compounds present in the environment can affect virus inactivation.
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Affiliation(s)
- Prunelle Waldman
- Laboratoire Eau Environnement et Systèmes Urbains (LEESU UMR MA 102), Faculté des Sciences et Technologie, Université Paris-Est , 61 avenue du Général de Gaulle, 94000 Créteil, France
| | - Alba Meseguer
- Eau de Paris, DRDQE, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
| | - Françoise Lucas
- Laboratoire Eau Environnement et Systèmes Urbains (LEESU UMR MA 102), Faculté des Sciences et Technologie, Université Paris-Est , 61 avenue du Général de Gaulle, 94000 Créteil, France
| | - Laurent Moulin
- Eau de Paris, DRDQE, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
| | - Sébastien Wurtzer
- Eau de Paris, DRDQE, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
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13
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Tian P, Yang D, Shan L, Wang D, Li Q, Gorski L, Lee BG, Quiñones B, Cooley MB. Concurrent Detection of Human Norovirus and Bacterial Pathogens in Water Samples from an Agricultural Region in Central California Coast. Front Microbiol 2017; 8:1560. [PMID: 28871242 PMCID: PMC5566579 DOI: 10.3389/fmicb.2017.01560] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/02/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial pathogens and human norovirus (HuNoV) are major cause for acute gastroenteritis caused by contaminated food and water. Public waterways can become contaminated from a variety of sources and flood after heavy rain events, leading to pathogen contamination of produce fields. We initiated a survey of several public watersheds in a major leafy green produce production region of the Central California Coast to determine the prevalence of HuNoV as well as bacterial pathogens. Moore swabs were used to collect environmental samples bi-monthly at over 30 sampling sites in the region. High prevalence of HuNoV and bacterial pathogens were detected in environmental water samples in the region. The overall detection rates of HuNoV, O157 Shiga toxin-producing Escherichia coli (STEC), non-O157 STEC, Salmonella, and Listeria were 25.58, 7.91, 9.42, 59.65, and 44.30%, respectively. The detection rates of Salmonella and L. monocytogenes were significantly higher in the spring. Fall and spring had elevated detection rates of O157 STEC. The overall detection rates of non-O157 STEC in the fall were lower than the other seasons but not significant. The overall detection rates of HuNoV were highest in fall, followed by spring and winter, with summer being lowest and significantly lower than other seasons. This study presented the first study of evaluating the correlation between the detection rate of HuNoV and the detection rates of four bacterial pathogens from environmental water. Overall, there was no significant difference in HuNoV detection rates between samples testing positive or negative for the four bacterial pathogens tested. Pathogens in animal-impacted and human-impacted areas were investigated. There were significant higher detection rates in animal-impacted areas than that of human-impacted areas for bacterial pathogens. However, there was no difference in HuNoV detection rates between these two areas. The overall detection levels of generic E. coli and detection rate of HuNoV showed no correlation.
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Affiliation(s)
- Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - David Yang
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Lei Shan
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Dapeng Wang
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States.,MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Qianqian Li
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States.,Department of Bioengineering, Shanghai Institute of TechnologyShanghai, China
| | - Lisa Gorski
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Bertram G Lee
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
| | - Michael B Cooley
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, AlbanyCA, United States
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14
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Gupta N, Lainson JC, Belcher PE, Shen L, Mason HS, Johnston SA, Diehnelt CW. Cross-Reactive Synbody Affinity Ligands for Capturing Diverse Noroviruses. Anal Chem 2017. [DOI: 10.1021/acs.analchem.7b01337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nidhi Gupta
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - John C. Lainson
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Paul E. Belcher
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Luhui Shen
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Hugh S. Mason
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Stephen Albert Johnston
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Chris W. Diehnelt
- Biodesign
Institute Center for Innovations in Medicine, and ‡Biodesign Institute
Center for Immunotherapy, Vaccines, and Virotherapy, and School of
Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
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15
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Boonchan M, Motomura K, Inoue K, Ode H, Chu P, Lin M, Iwatani Y, Ruchusatsawat K, Guntapong R, Tacharoenmuang R, Chantaroj S, Tatsumi M, Takeda N, Sangkitporn S. Distribution of norovirus genotypes and subtypes in river water by ultra-deep sequencing-based analysis. Lett Appl Microbiol 2017; 65:98-104. [DOI: 10.1111/lam.12750] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022]
Affiliation(s)
- M. Boonchan
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI); Nonthaburi Thailand
| | - K. Motomura
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI); Nonthaburi Thailand
- Research Institute of Microbial Diseases; Osaka University; Suita Japan
| | - K. Inoue
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI); Nonthaburi Thailand
- Research Institute of Microbial Diseases; Osaka University; Suita Japan
| | - H. Ode
- National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - P.Y. Chu
- Department of Medical Laboratory Science and Biotechnology; Kaohsiung Medical University; Kaohsiung Taiwan
| | - M. Lin
- Department of Medical Laboratory Science and Biotechnology; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Y. Iwatani
- National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - K. Ruchusatsawat
- National Institute of Health; Department of Medical Science; Ministry of Public Health; Nonthaburi Thailand
| | - R. Guntapong
- National Institute of Health; Department of Medical Science; Ministry of Public Health; Nonthaburi Thailand
| | - R. Tacharoenmuang
- National Institute of Health; Department of Medical Science; Ministry of Public Health; Nonthaburi Thailand
| | - S. Chantaroj
- National Institute of Health; Department of Medical Science; Ministry of Public Health; Nonthaburi Thailand
| | - M. Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI); Nonthaburi Thailand
- Research Institute of Microbial Diseases; Osaka University; Suita Japan
| | - N. Takeda
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI); Nonthaburi Thailand
- Research Institute of Microbial Diseases; Osaka University; Suita Japan
| | - S. Sangkitporn
- National Institute of Health; Department of Medical Science; Ministry of Public Health; Nonthaburi Thailand
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16
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Rupprom K, Chavalitshewinkoon-Petmitr P, Diraphat P, Kittigul L. Evaluation of real-time RT-PCR assays for detection and quantification of norovirus genogroups I and II. Virol Sin 2017; 32:139-146. [PMID: 28224385 DOI: 10.1007/s12250-016-3863-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022] Open
Abstract
Noroviruses are the leading cause of acute gastroenteritis in humans. Real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) is a promising molecular method for the detection of noroviruses. In this study, the performance of three TaqMan real-time RT-PCR assays was assessed, which were one commercially available real-time RT-PCR kit (assay A: Norovirus Real Time RT-PCR kit) and two in-house real-time RT-PCR assays (assay B: LightCycler RNA Master Hybprobe and assay C: RealTime ready RNA Virus Master). Assays A and B showed higher sensitivity than assay C for norovirus GI, while they all had the same sensitivity (103 DNA copies/mL) for GII DNA standard controls. Assay B had the highest efficiency for both genogroups. No cross-reactivity was observed among GI and GII noroviruses, rotavirus, hepatitis A virus, and poliovirus. The detection rates of these assays in GI and GII norovirus-positive fecal samples were not significantly different. However, the mean quantification cycle (Cq) value of assay B for GII was lower than assays A and C with statistical significance (P-value, 0.000). All three real-time RT-PCR assays could detect a variety of noroviruses including GI.2, GII.2, GII.3, GII.4, GII.6, GII.12, GII.17, and GII.21. This study suggests assay B as a suitable assay for the detection and quantification of noroviruses GI and GII due to good analytical sensitivity and higher performance to amplify norovirus on DNA standard controls and clinical samples.
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Affiliation(s)
- Kitwadee Rupprom
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pornphan Diraphat
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | - Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand.
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17
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Koo ES, Kim MS, Choi YS, Park KS, Jeong YS. Occurrence of novel GII.17 and GII.21 norovirus variants in the coastal environment of South Korea in 2015. PLoS One 2017; 12:e0172237. [PMID: 28199388 PMCID: PMC5310787 DOI: 10.1371/journal.pone.0172237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Human norovirus (HNoV), a positive-sense RNA virus, is the main causative agent of acute viral gastroenteritis. Multiple pandemic variants of the genogroup II genotype 4 (GII.4) of NoV have attracted great attention from researchers worldwide. However, novel variants of GII.17 have been overtaking those pandemic variants in some areas of East Asia. To investigate the environmental occurrence of GII in South Korea, we collected water samples from coastal streams and a neighboring waste water treatment plant in North Jeolla province (in March, July, and December of 2015). Based on capsid gene region C analysis, four different genotypes (GII.4, GII.13, GII.17, and GII.21) were detected, with much higher prevalence of GII.17 than of GII.4. Additional sequence analyses of the ORF1-ORF2 junction and ORF2 from the water samples revealed that the GII.17 sequences in this study were closely related to the novel strains of GII.P17-GII.17, the main causative variants of the 2014-2015 HNoV outbreak in China and Japan. In addition, the GII.P21-GII.21 variants were identified in this study and they had new amino acid sequence variations in the blockade epitopes of the P2 domain. From these results, we present two important findings: 1) the novel GII.P17-GII.17 variants appeared to be predominant in the study area, and 2) new GII.21 variants have emerged in South Korea.
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Affiliation(s)
- Eung Seo Koo
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Man Su Kim
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Yong Seon Choi
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Kwon-Sam Park
- Department of Food Science and Biotechnology, Kunsan National University, Gunsan, Republic of Korea
| | - Yong Seok Jeong
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
- * E-mail:
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18
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Jacxsens L, Stals A, De Keuckelaere A, Deliens B, Rajkovic A, Uyttendaele M. Quantitative farm-to-fork human norovirus exposure assessment of individually quick frozen raspberries and raspberry puree. Int J Food Microbiol 2016; 242:87-97. [PMID: 27914323 DOI: 10.1016/j.ijfoodmicro.2016.11.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/12/2016] [Accepted: 11/19/2016] [Indexed: 01/14/2023]
Abstract
A quantitative human norovirus (NoV) exposure model describing transmission of NoV during pre-harvest, harvest and further processing of soft red fruits exemplified by raspberries is presented. The outcomes of the model demonstrate the presence of NoV in raspberry puree or individual quick frozen (IQF) raspberry fruits and were generated by Monte Carlo simulations by combining GoldSim® and @Risk® software. Input data were collected from scientific literature, observational studies and assumptions. NoV contamination of soft red fruits is assumed to take place at farms by application of contaminated water for pesticides dilution or by berries' pickers shedding NoV. The model was built simulating that a collection center received berries from ten farms with a total of 245 food handlers picking soft red fruits during a 10-hour day shift. Given 0, 5 and 20 out of 245 berries' pickers were shedding NoV, these conditions were calculated to result in a mean NoV contamination of respectively 0.47, 14.1 and 36.2 NoV particles per kg raspberries in case all raspberries are mixed to one day-batch of 11tons. The NoV contamination of the fruits was mainly driven by the route of NoV shedding food pickers (95.8%) rather than by spraying contaminated pesticide water (4.2%) (baseline scenario with 5 shedding pickers and contaminated pesticide water). Inclusion of appropriate hand washing procedures or hand washing followed by hand disinfection resulted in estimated reductions of the mean NoV levels from 14.1 to 0.16 and 0.17 NoV particles per kg raspberries, respectively, for the baseline scenario with 5 out of 245 food pickers shedding NoV. The use of a mild heat treatment (30s at 75°C) during further processing of berries to purees was noted to reduce mean NoV levels substantially from 14.1 to 0.2 NoV particles per kg raspberry puree. For IQF raspberries, the NoV contamination is heterogeneously distributed and resulted in a mean contamination of 3.1 NoV particles per 250g package containing approximately 115 berries. This farm-to-fork model is a useful tool for evaluating NoV mitigation strategies in the soft red fruit supply chain.
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Affiliation(s)
- L Jacxsens
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - A Stals
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - A De Keuckelaere
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - B Deliens
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - A Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium; Department of Food Safety and Food Quality Management, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia
| | - M Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Ghent University, Coupure links 653, 9000 Gent, Belgium
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19
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Vergara GGRV, Rose JB, Gin KYH. Risk assessment of noroviruses and human adenoviruses in recreational surface waters. WATER RESEARCH 2016; 103:276-282. [PMID: 27472908 DOI: 10.1016/j.watres.2016.07.048] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/01/2016] [Accepted: 07/20/2016] [Indexed: 05/07/2023]
Abstract
In the interest of public health and safety, this study aimed to quantify risks associated with the presence of noroviruses (NoV) and human adenoviruses (HAdV) in an urban catchment area in Singapore. Enteric viruses were quantified using QPCR. NoV were more prevalent in water samples than HAdV, and presented higher associated illness risks across all exposure scenarios. For primary contact recreation of adults and children, mean probability of illness were 0.0061 and 0.0089 for NoV, and 0.0028 and 0.0048 for HAdV. For secondary contact recreation, mean probability of illness were 0.0016 for NoV and 0.00068 for HAdV. Therefore, owing to their prevalence and associated risks, NoV are better suited as reference pathogens in recreational waters in Singapore.
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Affiliation(s)
- G G R V Vergara
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - J B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - K Y H Gin
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore.
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20
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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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21
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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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Kazama S, Masago Y, Tohma K, Souma N, Imagawa T, Suzuki A, Liu X, Saito M, Oshitani H, Omura T. Temporal dynamics of norovirus determined through monitoring of municipal wastewater by pyrosequencing and virological surveillance of gastroenteritis cases. WATER RESEARCH 2016; 92:244-53. [PMID: 26874777 DOI: 10.1016/j.watres.2015.10.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 10/14/2015] [Accepted: 10/17/2015] [Indexed: 05/21/2023]
Abstract
Norovirus is a leading etiological agent of viral gastroenteritis. Because of relatively mild disease symptoms and frequent asymptomatic infections, information on the ecology of this virus is limited. Our objective was to examine the genetic diversity of norovirus circulating in the human population by means of genotyping the virus in municipal wastewater. We investigated norovirus genogroups I and II (GI and GII) in municipal wastewater in Japan by pyrosequencing and quantitative PCR (qPCR) from November 2012 to March 2013. Virological surveillance for gastroenteritis cases was concurrently conducted in the same area. A total of fourteen distinct genotypes in total (GI.1, 3, 4, 6, 7, GII.2, 4, 5, 6, 7, 12, 13, 14, and 17), with up to eight genotypes detected per sample, were observed in wastewater using pyrosequencing; only four genotypes (GI.6, GII.4, 5, and 14) were obtained from clinical samples. Seventy-eight percent of norovirus-positive stool samples contained GII.4, but this genotype was not dominant in wastewater. The norovirus GII.4 Sydney 2012 variant, which appeared and spread during our study period, was detected in both the wastewater and clinical samples. These results suggest that an environmental approach using pyrosequencing yields a more detailed distribution of norovirus genotypes/variants. Thus, wastewater monitoring by pyrosequencing is expected to provide an effective analysis of the distribution of norovirus genotypes causing symptomatic and asymptomatic infections in human populations.
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Affiliation(s)
- Shinobu Kazama
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8479, Japan
| | - Yoshifumi Masago
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8479, Japan; Institute for the Advanced Study of Sustainability, United Nations University, Shibuya-ku, Tokyo 150-8925, Japan.
| | - Kentaro Tohma
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Nao Souma
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Toshifumi Imagawa
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Akira Suzuki
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai, Miyagi, 983-8520, Japan
| | - Xiaofang Liu
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Tatsuo Omura
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8479, Japan
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Tran NH, Gin KYH, Ngo HH. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 538:38-57. [PMID: 26298247 DOI: 10.1016/j.scitotenv.2015.07.155] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 07/31/2015] [Accepted: 07/31/2015] [Indexed: 05/24/2023]
Abstract
The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater.
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Affiliation(s)
- Ngoc Han Tran
- NUS Environmental Research Institute, National University of Singapore, T-Lab Building, #02-01, 5A Engineering Drive 1, 117411, Singapore.
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore.
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
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Alternative fecal indicators and their empirical relationships with enteric viruses, Salmonella enterica, and Pseudomonas aeruginosa in surface waters of a tropical urban catchment. Appl Environ Microbiol 2014; 81:850-60. [PMID: 25416765 DOI: 10.1128/aem.02670-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions.
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Rezaeinejad S, Vergara GGRV, Woo CH, Lim TT, Sobsey MD, Gin KYH. Surveillance of enteric viruses and coliphages in a tropical urban catchment. WATER RESEARCH 2014; 58:122-31. [PMID: 24747143 DOI: 10.1016/j.watres.2014.03.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 05/13/2023]
Abstract
An assessment of the occurrence and concentration of enteric viruses and coliphages was carried out in highly urbanized catchment waters in the tropical city-state of Singapore. Target enteric viruses in this study were noroviruses, adenoviruses, astroviruses and rotaviruses. In total, 65 water samples were collected from canals and the reservoir of the Marina catchment on a monthly basis over a period of a year. Quantitative PCR (qPCR) and single agar layer plaque assay (SAL) were used to enumerate target enteric viruses and coliphages in water samples, respectively. The most prevalent pathogen were noroviruses, detected in 37 samples (57%), particularly norovirus genogroup II (48%), with a mean concentration of 3.7 × 10(2) gene copies per liter. Rotavirus was the second most prevalent virus (40%) with a mean concentration of 2.5 × 10(2) GC/L. The mean concentrations of somatic and male-specific coliphages were 2.2 × 10(2) and 1.1 × 10(2) PFU/100 ml, respectively. The occurrence and concentration of each target virus and the ratio of somatic to male-specific coliphages varied at different sampling sites in the catchment. For sampling sites with higher frequency of occurrence and concentration of viruses, the ratio of somatic to male-specific coliphages was generally much lower than other sampling sites with lower incidences of enteric viruses. Overall, higher statistical correlation was observed between target enteric viruses than between enteric viruses and coliphages. However, male-specific coliphages were positively correlated with norovirus concentrations. A multi-level integrated surveillance system, which comprises the monitoring of bacterial indicators, coliphages and selected enteric viruses, could help to meet recreational and surface water quality criteria in a complex urbanized catchment.
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Affiliation(s)
- S Rezaeinejad
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - G G R V Vergara
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - C H Woo
- Technology and Water Quality Office, Public Utilities Board, Singapore
| | - T T Lim
- Technology and Water Quality Office, Public Utilities Board, Singapore
| | - M D Sobsey
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K Y H Gin
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore.
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26
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Matsushita T, Shirasaki N, Tatsuki Y, Matsui Y. Investigating norovirus removal by microfiltration, ultrafiltration, and precoagulation-microfiltration processes using recombinant norovirus virus-like particles and real-time immuno-PCR. WATER RESEARCH 2013; 47:5819-27. [PMID: 23880217 DOI: 10.1016/j.watres.2013.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 05/03/2023]
Abstract
The removal of microorganisms by drinking water treatment processes has been widely investigated in laboratory-scale experiments using artificially propagated microorganisms. However, this approach cannot be applied to norovirus removal, because this virus does not grow in cell or organ culture, and this fact has hampered our ability to investigate its behavior during drinking water treatment. To overcome this difficulty, our research group previously used recombinant norovirus virus-like particles (rNV-VLPs), which consist of an artificially expressed norovirus capsid protein, in laboratory-scale drinking water treatment experiments. However, the enzyme-linked immunosorbent assay (ELISA) method generally used to detect rNV-VLPs is not sensitive enough to evaluate high removal ratios such as those obtained by ultrafiltration (UF). We therefore developed and applied a real-time immuno-polymerase chain reaction (iPCR) assay for rNV-VLP quantification to investigate norovirus removal by microfiltration (MF), UF, and hybrid precoagulation-MF processes. The rNV-VLP detection limit with the developed iPCR assay was improved at least 1000-fold compared with ELISA. Whereas MF with a nominal pore size of 0.1 μm could not eliminate NV-VLPs, a 4-log reduction was achieved by UF with a molecular weight cutoff of 1 kDa. When MF was combined with precoagulation (≥10 μmol-Fe/L for ferric chloride; ≥20 μmol-Al/L for polyaluminum chloride; ≥40 μmol-Al/L for alum), the performance of the hybrid process in eliminating rNV-VLPs was greater than that achieved by the 1 kDa UF. For all processes, the removal ratios of the bacteriophages MS2 and Qβ were greater than the rNV-VLP removal ratios by 1-2 logs, so neither bacteriophage can be recommended as a possible conservative surrogate for predicting the behavior of native NV during these processes.
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Affiliation(s)
- Taku Matsushita
- Graduate School of Engineering, Hokkaido University, N13W8, Sapporo 060-8628, Japan.
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27
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Chaimongkol N, Khamrin P, Malasao R, Thongprachum A, Kongsricharoern T, Ukarapol N, Ushijima H, Maneekarn N. Molecular characterization of norovirus variants and genetic diversity of noroviruses and sapoviruses in Thailand. J Med Virol 2013; 86:1210-8. [DOI: 10.1002/jmv.23781] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Natthawan Chaimongkol
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Pattara Khamrin
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Rungnapa Malasao
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences; Institute of International Health, Graduate School of Medicine, The University of Tokyo; Tokyo Japan
| | | | - Nuthapong Ukarapol
- Department of Pediatrics; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences; Institute of International Health, Graduate School of Medicine, The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University; Tokyo Japan
| | - Niwat Maneekarn
- Department of Microbiology; Faculty of Medicine; Chiang Mai University; Chiang Mai Thailand
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28
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Lim KL, Eden JS, Oon LL, White PA. Molecular epidemiology of norovirus in Singapore, 2004-2011. J Med Virol 2013; 85:1842-51. [DOI: 10.1002/jmv.23669] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | | | - Lynette L.E. Oon
- Molecular Laboratory, Department of Pathology; Singapore General Hospital; Singapore
| | - Peter A. White
- Faculty of Science; School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney; NSW; Australia
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Lee BR, Lee SG, Park JH, Kim KY, Ryu SR, Rhee OJ, Park JW, Lee JS, Paik SY. Norovirus contamination levels in ground water treatment systems used for food-catering facilities in South Korea. Viruses 2013; 5:1646-54. [PMID: 23820792 PMCID: PMC3738952 DOI: 10.3390/v5071646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022] Open
Abstract
This study aimed to inspect norovirus contamination of groundwater treatment systems used in food-catering facilities located in South Korea. A nationwide study was performed in 2010. Water samples were collected and, for the analysis of water quality, the temperature, pH, turbidity, and residual chlorine content were assessed. To detect norovirus genotypes GI and GII, RT-PCR and semi-nested PCR were performed with specific NV-GI and NV-GII primer sets, respectively. The PCR products amplified from the detected strains were then subjected to sequence analyses. Of 1,090 samples collected in 2010, seven (0.64%) were found to be norovirus-positive. Specifically, one norovirus strain was identified to have the GI-6 genotype, and six GII strains had the GII, GII-3, GII-4, and GII-17 genotypes. The very low detection rate of norovirus most likely reflects the preventative measures used. However, this virus can spread rapidly from person to person in crowded, enclosed places such as the schools investigated in this study. To promote better public health and sanitary conditions, it is necessary to periodically monitor noroviruses that frequently cause epidemic food poisoning in South Korea.
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Affiliation(s)
- Bo-Ram Lee
- Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul 137-701, Korea; E-Mail:
| | - Sung-Geun Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Jeonju 561-756, Korea; E-Mail:
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Kyungwon University, Seongnam 461-701, Korea; E-Mail:
| | - Kwang-Yup Kim
- Department of Food Science and Technology, Chungbuk National University Korea, Chongju 361-763, Korea; E-Mail:
| | - Sang-Ryeol Ryu
- Department of Food Science and Biotechnology, Seoul National University Korea, Seoul 151-742, Korea; E-Mail:
| | - Ok-Jae Rhee
- DK EcoV Environmental Microbiology Lab, Biotechnology Business Incubating Center, Dankook University, Chungnam 330-714, Korea; E-Mail:
| | - Jeong-Woong Park
- Sanigen Co. Ltd., Juan-dong, Gwacheon-si, Gyeonggi-do 427-070, Korea; E-Mail:
| | - Jeong-Su Lee
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Osong 363-700, Korea; E-Mail:
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul 137-701, Korea; E-Mail:
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Li Y, Guo H, Xu Z, Zhou X, Zhang H, Zhang L, Miao J, Pan Y. An outbreak of norovirus gastroenteritis associated with a secondary water supply system in a factory in south China. BMC Public Health 2013; 13:283. [PMID: 23537289 PMCID: PMC3679847 DOI: 10.1186/1471-2458-13-283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 03/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Between September 17 and October 3, 2009, hundreds of workers employed in a manufacturing factory in Shenzhen, a city in south China developed a sudden onset of acute gastroenteritis. A retrospective cohort study is designed to identify the risk factors and control this outbreak. METHODS Information on demographic characteristics, working place, the history of contact with a person having diarrhea and/or vomiting, drink water preference and frequency, eating in the company cafeteria or outside the company, hand-washing habits and eating habits is included. Furthermore, in order to find the contamination source, we investigated the environment around the underground reservoir and collected water samples from the junction between municipal supply water system and underground reservoir to test potential bacteria and virus, examine the seepage tracks on the wall of the underground reservoir from the side of septic tank, and check the integrity and attitude of this lid. Relative risk was presented and Chi-square test was performed. All the analyses were performed with OpenEpi software version 2.3.1 online. RESULTS The cohort study demonstrated that the workers who had direct drink water were 3.0 fold more likely to suffer from acute gastroenteritis than those who consumed commercial bottled water. The direct drinking water, water of the tank of buildings, and the underground reservoir were positive only for norovirus. Norovirus was also detected from stool and rectal swab samples from patients with acute gastroenteritis. The underground reservoir was found to be the primary contamination source. Further environmental investigation showed that the norovirus contaminated substance entered into the underground reservoir via access holes in lid covering this underground reservoir. CONCLUSION This acute gastroenteritis outbreak was caused by the secondary supply system contaminated by norovirus in this factory. The outbreak of gastroenteritis cases caused by norovirus frequently occurred in China due to a lack of surveillance and supervision, and due to faults in the construction of such water systems. Therefore, more attentions should pay to the secondary supply water system in China.
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Affiliation(s)
- Yuan Li
- Department of infectious disease prevention and control, Shenzhen bao’an center for disease control and prevention, 116 Longjinger Road, Shenzhen 51810, China
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31
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Marine and Freshwater Fecal Indicators and Source Identification. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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32
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Mathijs E, Stals A, Baert L, Botteldoorn N, Denayer S, Mauroy A, Scipioni A, Daube G, Dierick K, Herman L, Van Coillie E, Uyttendaele M, Thiry E. A review of known and hypothetical transmission routes for noroviruses. FOOD AND ENVIRONMENTAL VIROLOGY 2012; 4:131-52. [PMID: 23412887 DOI: 10.1007/s12560-012-9091-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 10/06/2012] [Indexed: 05/04/2023]
Abstract
Human noroviruses (NoVs) are considered a worldwide leading cause of acute non-bacterial gastroenteritis. Due to a combination of prolonged shedding of high virus levels in feces, virus particle shedding during asymptomatic infections, and a high environmental persistence, NoVs are easily transmitted pathogens. Norovirus (NoV) outbreaks have often been reported and tend to affect a lot of people. NoV is spread via feces and vomit, but this NoV spread can occur through several transmission routes. While person-to-person transmission is without a doubt the dominant transmission route, human infective NoV outbreaks are often initiated by contaminated food or water. Zoonotic transmission of NoV has been investigated, but has thus far not been demonstrated. The presented review aims to give an overview of these NoV transmission routes. Regarding NoV person-to-person transmission, the NoV GII.4 genotype is discussed in the current review as it has been very successful for several decades but reasons for its success have only recently been suggested. Both pre-harvest and post-harvest contamination of food products can lead to NoV food borne illness. Pre-harvest contamination of food products mainly occurs via contact with polluted irrigation water in case of fresh produce or with contaminated harvesting water in case of bivalve molluscan shellfish. On the other hand, an infected food handler is considered as a major cause of post-harvest contamination of food products. Both transmission routes are reviewed by a summary of described NoV food borne outbreaks between 2000 and 2010. A third NoV transmission route occurs via water and the spread of NoV via river water, ground water, and surface water is reviewed. Finally, although zoonotic transmission remains hypothetical, a summary on the bovine and porcine NoV presence observed in animals is given and the presence of human infective NoV in animals is discussed.
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Affiliation(s)
- Elisabeth Mathijs
- Department of Infectious and Parasitic diseases, Virology and Viral diseases, Faculty of Veterinary Medicine, University of Liège, Boulevard du Colonster 20, 4000, Liège, Belgium
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Ji Z, Wang X, Zhang C, Miura T, Sano D, Funamizu N, Okabe S. Occurrence of hand-foot-and-mouth disease pathogens in domestic sewage and secondary effluent in Xi'an, China. Microbes Environ 2012; 27:288-92. [PMID: 22446307 PMCID: PMC4036047 DOI: 10.1264/jsme2.me11352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hand, foot and mouth disease (HFMD), caused by a group of enteric viruses such as Enterovirus 71 (EV71), Coxsackievirus A16 (CVA16) and Coxsackievirus A10 (CVA10), is heavily epidemic in East Asia. This research focused on investigating the occurrence of HFMD pathogens in domestic sewage and secondary effluent before disinfection in a wastewater treatment plant (WWTP) in Xi’an, the largest megacity in northwest China. In order to simultaneously detect all three HFMD pathogens, a semi-nested RT-PCR assay was constructed with a newly designed primer set targeting conservative gene regions from the 5′ untranslated region (UTR) to VP2. As a result, 86% of raw sewage samples and 29% of the secondary effluent samples were positive for the HFMD viral gene, indicating that HFMD pathogens were highly prevalent in domestic wastewater and that they could also persist, even with lower probability, in the secondary effluent before disinfection. Of the three HFMD pathogens, CVA10 was positive in 48% of the total samples, while the occurrences of CVA16 and EV71 were 12% and 2%, respectively. It could thus be stated that CVA10 is the main HFMD pathogen prevailing in the study area, at least during the investigation period. High genetic diversity in the conservative gene region among the same serotype of the HFMD pathogen was identified by phylogenetic analysis, implying that this HFMD pathogen replicates frequently among the population excreting the domestic sewage.
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Affiliation(s)
- Zheng Ji
- Key Laboratory of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technolog, Xi'an, Shaanxi 710055, China
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Diverse norovirus genotypes identified in sewage-polluted river water in South Africa. Epidemiol Infect 2012; 141:303-13. [DOI: 10.1017/s0950268812000490] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYThis study aimed to assess norovirus (NoV) contamination and genotype diversity in surface water in Gauteng, South Africa. Between January 2008 and December 2010, three rivers, namely Klip, Suikerbosrant, and Rietspruit were monitored for NoV genogroup (G)I and GII. Viruses were recovered using the glass wool adsorption-elution technique and detected by real-time reverse transcription–polymerase chain reaction. From 2008 to 2010, NoVs were detected in 66% (70/106) of Klip river samples. The Rietspruit and Suikerbosrant rivers were contaminated with NoV in 95% (20/21) and 21% (5/24) of samples, respectively. NoV-positive samples comprised of 33% GI, 29% GII and 38% of both GI and GII strains. Based on partial capsid gene analysis (region C), 16 NoV genotypes (6 GI, 10 GII) were identified. The major genotypes detected were GI.4, GI.5 and GII.4. These rivers could be a potential source of NoV infection for communities using the water for domestic or recreational purposes.
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Yang N, Qi H, Wong MML, Wu RSS, Kong RYC. Prevalence and diversity of norovirus genogroups I and II in Hong Kong marine waters and detection by real-time PCR. MARINE POLLUTION BULLETIN 2012; 64:164-168. [PMID: 22119412 DOI: 10.1016/j.marpolbul.2011.10.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 05/04/2023]
Abstract
Marine waters from six sites around Hong Kong with varying levels of sewage pollution were examined for noroviruses (NoVs) by PCR cloning and sequencing of a highly-variable N-terminal region of the VP1 capsid gene, at the ORF1-ORF2 junction of NoV. Phylogenetic analysis of genogroups GI- and GII-specific PCR clones obtained from different marine sites indicated that human NoV GI.1 and GII.4 strains are the most prevalent genotypes circulating in Hong Kong waters. GI- and GII-specific TaqMan-based real-time PCR assays targeting the ORF1-ORF2 junction of NoVs were used to quantify NoV particles in marine water samples in parallel with total Escherichia coli counts which were enumerated on TBX medium. No correlation of any significance between NoV and E. coli counts was observed which highlighted the inadequacy in using E. coli as a fecal indicator to predict the level of NoVs in marine waters to protect public health.
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Affiliation(s)
- Ning Yang
- Department of Biology and Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Huizhou Qi
- Department of Biology and Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Minnie Man Lai Wong
- Department of Biology and Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Rudolf Shiu Sun Wu
- School of Biological Sciences, University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong Special Administrative Region
| | - Richard Yuen Chong Kong
- Department of Biology and Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region, China.
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Moresco V, Viancelli A, Nascimento MA, Souza DSM, Ramos APD, Garcia LAT, Simões CMO, Barardi CRM. Microbiological and physicochemical analysis of the coastal waters of southern Brazil. MARINE POLLUTION BULLETIN 2012; 64:40-48. [PMID: 22104718 DOI: 10.1016/j.marpolbul.2011.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 10/18/2011] [Accepted: 10/22/2011] [Indexed: 05/04/2023]
Abstract
The aim of this study was to assess the impact of sewage discharge on coastal waters by evaluating the influence of physicochemical parameters on the presence of enteric microorganisms in seawater samples collected from 11 beaches in Florianopolis, Santa Catarina, Brazil, over a one-year period (August 2009 to July 2010). Samples were assessed for the presence of human adenoviruses (HAdV), polyomavirus (JCPyV), hepatitis A virus (HAV), and noroviruses (HuNoV GI and GII). Escherichia coli and physicochemical parameters (salinity, temperature, pH and dissolved oxygen) were also evaluated. From the 132 samples analyzed, 55% were positive for HAdV, 51.5% for HAV, 7.5% for HuNoV GI, 4.5% for HuNoV GII, and 3% for JCPyV. E. coli levels ranged from 8 to 1325 CFU/100mL at all sites. The overall results highlight the problem of sewage discharge into coastal waters and confirm that there is no correlation between viral presence and bacterial contamination.
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Affiliation(s)
- V Moresco
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - A Viancelli
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - M A Nascimento
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - D S M Souza
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - A P D Ramos
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - L A T Garcia
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - C M O Simões
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil
| | - C R M Barardi
- Laboratório de Virologia Aplicada, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina State, CEP 88040-900, Brazil.
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Hartnell R, Lowther J, Avant J, Dancer D, Lees D, Russell J. The development of LENTICULES™ as reference materials for noroviruses. J Appl Microbiol 2011; 112:338-45. [DOI: 10.1111/j.1365-2672.2011.05196.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Romero OC, Straub AP, Kohn T, Nguyen TH. Role of temperature and Suwannee River natural organic matter on inactivation kinetics of rotavirus and bacteriophage MS2 by solar irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:10385-93. [PMID: 22017181 DOI: 10.1021/es202067f] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Although the sunlight-mediated inactivation of viruses has been recognized as an important process that controls surface water quality, the mechanisms of virus inactivation by sunlight are not yet clearly understood. We investigated the synergistic role of temperature and Suwannee River natural organic matter (SRNOM), an exogenous sensitizer, for sunlight-mediated inactivation of porcine rotavirus and MS2 bacteriophage. Upon irradiation by a full spectrum of simulated sunlight in the absence of SRNOM and in the temperature range of 14-42 °C, high inactivation rate constants, k(obs), of MS2 (k(obs) ≤ 3.8 h(-1) or 1-log(10) over 0.6 h) and rotavirus (k(obs) ≤ 11.8 h(-1) or ∼1-log(10) over 0.2 h) were measured. A weak temperature (14-42 °C) dependence of k(obs) values was observed for both viruses irradiated by the full sunlight spectrum. Under the same irradiation condition, the presence of SRNOM reduced the inactivation of both viruses due to attenuation of lower wavelengths of the simulated sunlight. For rotavirus and MS2 solutions irradiated by only UVA and visible light in the absence of SRNOM, inactivation kinetics were slow (k(obs) < 0.3 h(-1) or <1-log(10) unit reduction over 7 h) and temperature-independent for the range considered. Conversely, under UVA and visible light irradiation and in the presence of SRNOM, temperature-dependent inactivation of MS2 was observed. For rotavirus, the SRNOM-mediated exogenous inactivation was only important at temperatures >33 °C, with low rotavirus k(obs) values (k(obs) ≈ 0.2 h(-1); 1-log(10) unit reduction over 12 h) for the temperature range of 14-33 °C. These k(obs) values increased to 0.5 h(-1) at 43 °C and 1.5 h(-1) (1-log(10) reduction over 1.6 h) at 50 °C. While SRNOM-mediated exogenous inactivation of MS2 was triggered by singlet oxygen, the presence of hydrogen peroxide was important for rotavirus inactivation in the 40-50 °C range.
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Affiliation(s)
- Ofelia C Romero
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews, 3230 Newmark Lab, Urbana, Illinois 61801, United States
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Pérez-Sautu U, Sano D, Guix S, Kasimir G, Pintó RM, Bosch A. Human norovirus occurrence and diversity in the Llobregat river catchment, Spain. Environ Microbiol 2011; 14:494-502. [DOI: 10.1111/j.1462-2920.2011.02642.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bucardo F, Lindgren PE, Svensson L, Nordgren J. Low prevalence of rotavirus and high prevalence of norovirus in hospital and community wastewater after introduction of rotavirus vaccine in Nicaragua. PLoS One 2011; 6:e25962. [PMID: 22016794 PMCID: PMC3189239 DOI: 10.1371/journal.pone.0025962] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/14/2011] [Indexed: 11/23/2022] Open
Abstract
Rotavirus (RV) and norovirus (NoV) are major causes of pediatric diarrhea and are altogether associated with approximately 800,000 deaths in young children every year. In Nicaragua, national RV vaccination program using the pentavalent RV5 vaccine from Merck was implemented in October 2006. To determine whether RV vaccination decreased the overall number of RV infections, we investigated the occurrence of RV and NoV in wastewater in the city of León from July 2007 to July 2008 and compared these data with pre-vaccination data. The major finding was the low prevalence of RV compared to NoV in all sampling points (11% vs 44%, p<0.05), and that RV concentration was lower as compared to NoV. RV was observed mainly during the rainy season (July–September), and the majority of all RV detected (6/9) belonged to subgroup (SG) I. The partial VP7-gene obtained from one RV positive sample was similar (99% nt identity) to a G6 VP7-gene of bovine origin and similar to the corresponding gene of the vaccine strain (98%). Furthermore RV G-types 2 and 4 were found in the incoming wastewater. NoV strains were detected throughout the year, of which a majority (20/21) were of genotype GII.4. We conclude that the introduction of RV vaccination reduced the transmission of RV in the community in Nicaragua. However, the burden of diarrhea in the country remains high, and the high prevalence of NoVs in hospital and municipal wastewater is noteworthy. This study highlights the need for further assessment of NoV following RV vaccine introduction.
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Affiliation(s)
- Filemón Bucardo
- Department of Microbiology, University of León, León, Nicaragua
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Per-Eric Lindgren
- Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lennart Svensson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- * E-mail:
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Concentration and diversity of noroviruses detected in Luxembourg wastewaters in 2008-2009. Appl Environ Microbiol 2011; 77:5566-8. [PMID: 21705540 DOI: 10.1128/aem.00632-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Noroviruses (NoV) in 78 wastewater samples from Luxembourg were quantified, cloned, and sequenced in 2008-2009. The concentrations of NoV genogroup II and the relative occurrences of certain genotypes changed significantly during the winter season. NoV genogroup I was frequently detected by real-time reverse transcription-PCR (RT-PCR), albeit at 30-fold lower concentrations than for genogroup II, hampering attempts to assess overall genetic diversity by the cloning/sequencing approach.
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Validation of internal controls for extraction and amplification of nucleic acids from enteric viruses in water samples. Appl Environ Microbiol 2011; 77:4336-43. [PMID: 21602369 DOI: 10.1128/aem.00077-11] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Inhibitors that reduce viral nucleic acid extraction efficiency and interfere with cDNA synthesis and/or polymerase activity affect the molecular detection of viruses in aquatic environments. To overcome these significant problems, we developed a methodology for assessing nucleic acid yields and DNA amplification efficiencies for environmental water samples. This involved adding particles of adenovirus type 5 and murine norovirus and newly developed primer-sharing controls, which are amplified with the same primer pairs and result in the same amplicon sizes as the targets, to these samples. We found that nucleic acid loss during the extraction process, rather than reverse transcription-PCR (RT-PCR) inhibition, more significantly attributed to underestimation of the presence of viral genomes in the environmental water samples tested in this study. Our success rate for satisfactorily amplifying viral RNAs and DNAs by RT-PCR was higher than that for obtaining adequate nucleic acid preparations. We found that inhibitory properties were greatest when we used larger sample volumes. A magnetic silica bead-based RNA extraction method effectively removed inhibitors that interfere with viral nucleic acid extraction and RT-PCR. To our knowledge, this is the first study to assess the inhibitory properties of environmental water samples by using both control virus particles and primer-sharing controls.
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Aw T, Gin KH. Prevalence and genetic diversity of waterborne pathogenic viruses in surface waters of tropical urban catchments. J Appl Microbiol 2011; 110:903-14. [DOI: 10.1111/j.1365-2672.2011.04947.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Iizuka S, Oka T, Tabara K, Omura T, Katayama K, Takeda N, Noda M. Detection of sapoviruses and noroviruses in an outbreak of gastroenteritis linked genetically to shellfish. J Med Virol 2010; 82:1247-54. [DOI: 10.1002/jmv.21791] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yun SI, Kim JK, Song BH, Jeong AY, Jee YM, Lee CH, Paik SY, Koo Y, Jeon I, Byun SJ, Lee YM. Complete genome sequence and phylogenetic analysis of a recombinant Korean norovirus, CBNU1, recovered from a 2006 outbreak. Virus Res 2010; 152:137-52. [PMID: 20599576 DOI: 10.1016/j.virusres.2010.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/19/2022]
Abstract
We have determined the complete nucleotide and deduced amino acid sequences of the RNA genome of CBNU1, a human norovirus (NoV) recovered from a 2006 outbreak in South Korea. The genome of 7547 nucleotides, excluding a 3'-poly(A) tail of 11-105 nucleotides, encodes three overlapping open reading frames (ORFs): ORF1 (nucleotides 5-5104), ORF2 (nucleotides 5085-6731), and ORF3 (nucleotides 6731-7495). In a comparison to 108 other currently available completely sequenced NoVs representing all five genogroups (GI-GV) except GIV, the CBNU1 strain was highly similar to GII.3 NoVs. Multiple sequence alignments of the completely sequenced NoV genomes revealed five hypervariable regions throughout their genomes: two in ORF1, one in ORF2, and two in ORF3. At both the nucleotide and amino acid levels, genome-based phylogenetic analyses invariably showed that the CBNU1 strain was most closely related to three GII.3 NoVs: the American Texas/TCH04-577 and the two Japanese Saitama U18 and Saitama U201 strains; furthermore, these genome-based phylogenetic topologies corresponded most closely to those based on the ORF2 genes, as compared to those based on the ORF1 and ORF3 genes. Subsequent ORF2-based phylogenetic analyses of a selection of 126 other NoVs representing all 19 GII genotypes, in combination with genome-based Simplot analyses, showed that the CBNU1 strain was a recombinant GII.3 NoV with a breakpoint at the ORF1/ORF2 junction between two putative parent-like strains, Guangzhou/NVgz01 and Texas/TCH04-577. Overall, the CBNU1 strain represents the first Korean human NoV whose genome has been completely sequenced and for which its relationship with a large panel of genetically diverse NoVs has been extensively characterized.
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Affiliation(s)
- Sang-Im Yun
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, 12 Gaeshin-Dong, Heungduk-Ku, Cheongju, Chungbuk, South Korea
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Aw TG, Gin KYH. Environmental surveillance and molecular characterization of human enteric viruses in tropical urban wastewaters. J Appl Microbiol 2010; 109:716-730. [PMID: 20233263 DOI: 10.1111/j.1365-2672.2010.04701.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To study the prevalence and genotypes of waterborne pathogenic viruses in urban wastewaters in the tropical region. METHODS AND RESULTS Viruses in wastewaters collected at three water reclamation plants in Singapore were studied by molecular methods. Over a 6-month sampling period, adenoviruses, astroviruses and both norovirus genogroups I (GI) and II (GII) were detected in 100% of the sewage and secondary effluent. Enteroviruses and hepatitis A viruses (HAV) were found in 94 and 78% of sewage, and 89 and 28% of secondary effluent, respectively. By using quantitative real-time PCR, estimated concentrations of astrovirus in the sewage were 1-2 orders of magnitude higher than those for adenovirus, noroviruses GI and GII. Genotyping of environmental isolates revealed multiple genotypes of GI and GII noroviruses. Coxsackieviruses A, astrovirus type 1 and adenovirus type 41 were prevalent. Norovirus GII/4 and coxsackievirus A24 isolates in wastewaters were closely related to respective outbreak strains isolated previously in Singapore. CONCLUSIONS This study showed the widespread occurrence of all tested enteric virus groups in urban wastewaters. Genetic diversity of astroviruses, enteroviruses and noroviruses in the tropical region was observed. SIGNIFICANCE AND IMPACT OF THE STUDY The high prevalence and great genetic diversity of human enteric viruses in urban wastewaters strongly supports the need of further comprehensive studies for evaluating the public health risk associated with viral pathogens in water environments.
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Affiliation(s)
- T G Aw
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - K Y-H Gin
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
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Victoria M, Rigotto C, Moresco V, de Abreu Corrêa A, Kolesnikovas C, Leite JPG, Miagostovich MP, Barardi CRM. Assessment of norovirus contamination in environmental samples from Florianópolis City, Southern Brazil. J Appl Microbiol 2010; 109:231-8. [PMID: 20059621 DOI: 10.1111/j.1365-2672.2009.04646.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS To assess norovirus (NoV) contamination in aquatic ecosystems in the city of Florianópolis, in Southern Brazil, to provide epidemiological data that can support actions for environmental contamination control. METHODS AND RESULTS An adsorption-elution method, followed by ultrafiltration, was performed to concentrate the viruses. NoV were detected using semi-nested PCR and quantified by real-time PCR. From June 2007 to May 2008, NoV were detected in 23% (22/94) of the samples analysed, including seawater, drinking water, superficial water (creek and brackish lagoon) and treated sewage. The mean viral loads for genogroups (G)I and GII in treated sewage samples were 297 and 440 genomic copies (gc) l(-1) , respectively, whereas creek water samples contained 2603 and 1361 gc l(-1) , respectively. Six samples were sequenced: two samples were GII.4, two were GII.2 and two were GI.3. CONCLUSIONS NoV were detected in all water types analysed, demonstrating the widespread contamination of this geographical area with several cocirculating strains belonging to GI and GII. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates the environmental spread of NoV in environmental waters and highlights the potential hazard for human health following the consumption of or contact with these waters, which could result in waterborne or foodborne acute gastroenteritis.
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Affiliation(s)
- M Victoria
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute - FIOCRUZ, Rio de Janeiro, Brazil.
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