1
|
Matamoros DJP, Worsfold CS, Campos RC, Acuña HMB, Chacón EC, Sánchez CFJ. Molecular characterization of norovirus and sapovirus detected in animals and humans in Costa Rica: Zoo-anthropozoonotic potential of human norovirus GII.4. Open Vet J 2023; 13:74-89. [PMID: 36777439 PMCID: PMC9897497 DOI: 10.5455/ovj.2023.v13.i1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Background Noroviruses (NoV) and sapoviruses (SaV) are major causes of acute viral gastroenteritis in humans worldwide, as well as gastrointestinal infections in animals. However, it has not been determined whether these viruses are zoonotic pathogens. Aim In this study, we investigated the presence of NoV and SaV in stool samples from dogs, pigs, cows, and humans to determine some aspects of the molecular epidemiology and the genetic relationship of several strains present in these species. Methods Polymerase chain reaction and sequencing of NoV and SaV strains present in stool samples from humans and dogs with diarrhea, pigs, and cattle with and without diarrhea were carried out during fragmented periods from 2002 to 2012. Results Of all samples analyzed, 11.6% (123/1,061) of the samples were positive for NoV and 0.88% (9/1,023) were positive for SaV. The phylogenetic analysis confirmed 16 human strains of NoV (HuNoV) belonging to HuNoV G?/GII.P2 (1), GII.4/GII.P4 (5), G?/GII.P4 (9), and GII.6/GII.P6 (1) and allowed us to verify and assign three strains of human SaV to genotypes GI.2 (1) and GII.5 (2). In dogs, eight strains of NoV [HuNoV G?/GII.P4 (4) and canine G?/GVI.P1 (4)] and two strains of canine SaV were determined. In pigs, six strains were assigned to HuNoV G?/GII.P4 and four strains to porcine SaV were assigned to genogroup GIII (2), GVIII (1), and GXI (1). In bovines, five strains were characterized as HuNoV G?/GII.P4. Conclusions This study showed that NoV and SaV prototype strains have been present in humans and dogs in Costa Rica. Additionally, it revealed that the zoonotic potential of SaV is very limited, while the zoonotic implications for HuNoV GII.4 are stronger due to the simultaneous circulation of strains related to HuNoV GII.4 in four species, which suggests a zoo-anthropozoonosis.
Collapse
Affiliation(s)
- Derling José Pichardo Matamoros
- Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica,Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Corresponding Author: Derling José Pichardo Matamoros. Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica.
| | | | - Rocío Cortés Campos
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
| | - Hilda María Bolaños Acuña
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Elena Campos Chacón
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Carlos Francisco Jiménez Sánchez
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
| |
Collapse
|
2
|
Adriaenssens EM, Farkas K, McDonald JE, Jones DL, Allison HE, McCarthy AJ. Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity. WATER RESEARCH 2021; 203:117568. [PMID: 34450465 DOI: 10.1016/j.watres.2021.117568] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed >40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and (+)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment.
Collapse
Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK; Quadram Institute Bioscience, Norwich, NR4 7UQ, UK.
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK; School of Ocean Sciences, Bangor University, Bangor, LL59 5AB, UK
| | - James E McDonald
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Heather E Allison
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Alan J McCarthy
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| |
Collapse
|
3
|
Nagai M, Wang Q, Oka T, Saif LJ. Porcine sapoviruses: Pathogenesis, epidemiology, genetic diversity, and diagnosis. Virus Res 2020; 286:198025. [PMID: 32470356 PMCID: PMC7255249 DOI: 10.1016/j.virusres.2020.198025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022]
Abstract
The first porcine Sapovirus (SaV) Cowden strain was discovered in 1980. To date, eight genogroups (GIII, V-IX) and three genogroups (GIII, GV, and GVI) of porcine SaVs have been detected from domestic pigs worldwide and wild boars in Japan, respectively based on the capsid sequences. Although GIII Cowden strain replicated in the villous epithelial cells and caused intestinal lesions in the proximal small intestines (mainly in duodenal and less in jejunum), leading to mild to severe diarrhea, in the orally inoculated neonatal gnotobiotic pigs, the significance of porcine SaVs in different ages of pigs with diarrhea in the field is still undetermined. This is due to two reasons: 1) similar prevalence of porcine SaVs was detected in diarrheic and non-diarrheic pigs; and 2) co-infection of porcine SaVs with other enteric pathogens is common in pigs. Diagnosis of porcine SaV infection is mainly based on the detection of viral nucleic acids using reverse transcription (RT)-PCR and sequencing. Much is unknown about these genetically diverse viruses to understand their role in pig health and to evaluate whether vaccines are needed to prevent SaV infection.
Collapse
Affiliation(s)
- Makoto Nagai
- Laboratory of Infectious Disease, School of Veterinary Medicine, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5201, Japan
| | - Qiuhong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA.
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
| |
Collapse
|
4
|
Romalde JL, Rivadulla E, Varela MF, Barja JL. An overview of 20 years of studies on the prevalence of human enteric viruses in shellfish from Galicia, Spain. J Appl Microbiol 2017; 124:943-957. [PMID: 29094428 DOI: 10.1111/jam.13614] [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: 06/20/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022]
Abstract
Galicia (NW Spain) has 1490 km of coastline, and its particular topography, characterized by the presence of fiord-like inlets, called rías, with an important primary production, makes this region very favourable for shellfish growth and culture. In fact, Galicia is one of the most important mussel producers in the world. Due to its proximity to cities and villages and the anthropogenic activities in these estuaries, and despite the routine official controls on the bivalve harvesting areas, contamination with material of faecal origin is sometimes possible but, current regulation based on Escherichia coli as an indicator micro-organism has been revealed as useful for bacterial contaminants, this is not the case for enteric viruses. The aim of this review is to offer a picture on the situation of different harvesting areas in Galicia, from a virological standpoint. A recompilation of results obtained in the last 20 years is presented, including not only the data for the well-known agents norovirus (NoV) and hepatitis A virus (HAV) but also data on emerging viral hazards, including sapovirus (SaV), hepatitis E virus (HEV) and aichivirus (AiV). Epidemiological differences related to diverse characteristics of the harvesting areas, viral genotype distribution or epidemiological links between environmental and clinical strains will also be presented and discussed. The presentation of these historical data all together could be useful for future decisions by competent authorities for a better management of shellfish growing areas.
Collapse
Affiliation(s)
- J L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - E Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J L Barja
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
5
|
Gupta S, Singh KP, Jain A, Srivastava S, Kumar V, Singh M. Aetiology of childhood viral gastroenteritis in Lucknow, north India. Indian J Med Res 2016; 141:469-72. [PMID: 26112849 PMCID: PMC4510728 DOI: 10.4103/0971-5916.159298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES Due to limited availability of data on viral aetiology of acute gastroenteritis in north India, the present study was planned to detect rotavirus, norovirus, sapovirus and astrovirus in stool samples of both in hospitalized and non-hospitalized children less than five years of age presenting with acute gastroenteritis. METHODS A total of 278 stool samples from equal number of children were tested for rotavirus antigen using ELISA and for norovirus, sapovirus and astroviruses by reverse transcription (RT)-PCR. RESULTS Of the 169 samples from hospitalized patients, rotavirus, norovirus, sapovirus and astrovirus were detected in 19.5, 2.3, 3.5 and 2.9 per cent samples, respectively. Of the 109 samples collected from the non-hospitalized patients, frequency of rotavirus and sapovirus detection was 9.1 and 1.8 per cent, respectively while norovirus and astrovirus were not detected. INTERPRETATION & CONCLUSIONS Rotavirus was the most frequent cause of viral gastroenteritis in both hospitalized and non-hospitalized children. Maximum positivity of the viruses was seen in children less than two years of age.
Collapse
Affiliation(s)
| | | | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, India
| | | | | | | |
Collapse
|
6
|
Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
7
|
Prevalence and Genetic Diversity of Human Sapoviruses in Shellfish from Commercial Production Areas in Galicia, Spain. Appl Environ Microbiol 2015; 82:1167-1172. [PMID: 26655761 DOI: 10.1128/aem.02578-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 11/21/2015] [Indexed: 11/20/2022] Open
Abstract
The prevalence of human forms of Sapovirus, an emerging pathogen of human gastroenteritis, was investigated in an 18-month survey from class B mollusc-harvesting areas in two Galician rias (northwest Spain). The detection and quantification of Sapovirus was performed by reverse transcription-real-time PCR, according to the recently developed standard method ISO/TS 15216-1:2013, and genotyping by reverse transcription-nested PCR. The bivalve species studied were wild and cultured mussels (Mytilus galloprovincialis), clams (Venerupis philippinarum and Venerupis decussata), and cockles (Cerastoderma edule). Sapovirus was detected in 30 out of 168 samples (17.9%), with cockles being the species with the highest prevalence of positives (28.1%), followed by clams (22.6%), wild mussels (14.3%), and cultured mussels (12.9%). The estuary in the south of the region demonstrated a higher percentage of positive samples (21.8%) than the one in the north (14.4%). Viral contamination levels for the positive samples ranged between 1.9 × 10(3) and 1.4 × 10(5) RNA copies/g of digestive tissue. Thirteen Sapovirus sequences could be obtained based on partial capsid gene sequence and were classified into four genotypes: GI.1 (2 samples), GI.2 (8 samples), GIV.1 (2 samples), and GV.1 (1 sample).
Collapse
|
8
|
Choi HL, Suh CI, Park SW, Jin JY, Cho HG, Paik SY. Whole-Genome Sequencing Analysis of Sapovirus Detected in South Korea. PLoS One 2015; 10:e0132328. [PMID: 26161646 PMCID: PMC4498750 DOI: 10.1371/journal.pone.0132328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/14/2015] [Indexed: 11/18/2022] Open
Abstract
Sapovirus (SaV), a virus residing in the intestines, is one of the important causes of gastroenteritis in human beings. Human SaV genomes are classified into various genogroups and genotypes. Whole-genome analysis and phylogenetic analysis of ROK62, the SaV isolated in South Korea, were carried out. The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF). The genotype of ROK62 is SaV GI-1, and 94% of its nucleotide sequence is identical with other SaVs, namely Manchester and Mc114. Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally. As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.
Collapse
Affiliation(s)
- Hye Lim Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137–701, Republic of Korea
| | - Chang-Il Suh
- Department of Medical Consilience, 152, Dankook University, Jukjeon-ro, Suji-gu, Yongin-si, Gyeonggi-do, 448–701, Republic of Korea
| | - Seung-Won Park
- Division of Biotechnology, Catholic University of Daegu, Daegu, 712–702, Republic of Korea
| | - Ji-Young Jin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137–701, Republic of Korea
| | - Han-Gil Cho
- Division of Public Health Research, Gyeonggi Province Institute of Health and Environment, Suwon, Republic of Korea
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137–701, Republic of Korea
- * E-mail:
| |
Collapse
|
9
|
Stadler J, Zoels S, Fux R, Hanke D, Pohlmann A, Blome S, Weissenböck H, Weissenbacher-Lang C, Ritzmann M, Ladinig A. Emergence of porcine epidemic diarrhea virus in southern Germany. BMC Vet Res 2015; 11:142. [PMID: 26135732 PMCID: PMC4487554 DOI: 10.1186/s12917-015-0454-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the last years, porcine epidemic diarrhea virus (PEDV) has caused devastating enteric diseases in the US and several countries in Asia, while outbreaks in Europe have only been reported sporadically since the 1980s. At present, only insufficient information is available on currently circulating PEDV strains in Europe and their impact on the European swine industry. In this case report, we present epidemic outbreaks of porcine epidemic diarrhea in three farms in South-Western Germany. CASE PRESENTATION Epidemic outbreaks of diarrhea affecting pigs of all age groups were reported in three farms, one fattening farm and two piglet producing farms, in South-Western Germany between May and November 2014. In the fattening farm yellowish, watery diarrhea without evidence of mucus or blood was associated with a massive reduction of feed consumption. Severity of clinical signs and mortality in young suckling pigs varied significantly between the two affected sow farms. While mortality in suckling piglets reached almost 70 % in one sow herd, no increase in suckling piglet mortality was observed in the second sow farm. In all three cases, PEDV was confirmed in feces and small intestines by RT-qPCR. Phylogenetic analyses based on full-length PEDV genomes revealed high identity among strains from all three herds. Moreover, the German strains showed very high nucleotide identity (99.4 %) with a variant of PEDV (OH851) that was isolated in the United States in January 2014. This strain with insertions and deletions in the S-gene (so called INDEL strains) was reported to show lower virulence. Slightly lower identities were found with other strains from the US and Asia. CONCLUSION Phylogenetic information on the distribution of PEDV strains in Europe is severely lacking. In this case report we demonstrate that acute outbreaks of PEDV occurred in southern Germany in 2014. Current strains were clearly different from isolates found in the 1980s and were closely related to a PEDV variant found in the US in 2014. Moreover, the present case report indicates that variant strains of PEDV, containing insertions and deletions in the S gene, which were reported to be of lower virulence, might be able to cause high mortality in suckling piglets.
Collapse
Affiliation(s)
- Julia Stadler
- Clinic for Swine at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians University, Oberschleissheim, Germany.
| | - Susanne Zoels
- Clinic for Swine at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians University, Oberschleissheim, Germany.
| | - Robert Fux
- Institute for Infectious Diseases and Zoonosis at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians University, Munich, Germany.
| | - Dennis Hanke
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
| | - Herbert Weissenböck
- Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine Vienna, Vienna, Austria.
| | | | - Mathias Ritzmann
- Clinic for Swine at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians University, Oberschleissheim, Germany.
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine Vienna, Vienna, Austria.
| |
Collapse
|
10
|
Abstract
Sapoviruses cause acute gastroenteritis in humans and animals. They belong to the genus Sapovirus within the family Caliciviridae. They infect and cause disease in humans of all ages, in both sporadic cases and outbreaks. The clinical symptoms of sapovirus gastroenteritis are indistinguishable from those caused by noroviruses, so laboratory diagnosis is essential to identify the pathogen. Sapoviruses are highly diverse genetically and antigenically. Currently, reverse transcription-PCR (RT-PCR) assays are widely used for sapovirus detection from clinical specimens due to their high sensitivity and broad reactivity as well as the lack of sensitive assays for antigen detection or cell culture systems for the detection of infectious viruses. Sapoviruses were first discovered in 1976 by electron microscopy in diarrheic samples of humans. To date, sapoviruses have also been detected from several animals: pigs, mink, dogs, sea lions, and bats. In this review, we focus on genomic and antigenic features, molecular typing/classification, detection methods, and clinical and epidemiological profiles of human sapoviruses.
Collapse
|
11
|
Mladenova Z, Steyer A, Steyer AF, Ganesh B, Petrov P, Tchervenjakova T, Iturriza-Gomara M. Aetiology of acute paediatric gastroenteritis in Bulgaria during summer months: prevalence of viral infections. J Med Microbiol 2015; 64:272-282. [PMID: 25596126 DOI: 10.1099/jmm.0.000018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Paediatric acute gastroenteritis is a global public health problem. Comprehensive laboratory investigation for viral, bacterial and parasitic agents is helpful for improving management of acute gastroenteritis in health care settings and for monitoring and controlling the spread of these infections. Our study aimed to investigate the role of various pathogens in infantile diarrhoea in Bulgaria outside the classical winter epidemics of rotavirus and norovirus. Stool samples from 115 hospitalized children aged 0-3 years collected during summer months were tested for presence of 14 infectious agents - group A rotavirus, astrovirus, Giardia, Cryptosporidium and Entamoeba using ELISAs; norovirus by real-time RT-PCR; picobirnavirus and sapovirus by RT-PCR; adenovirus using PCR, and Salmonella, Shigella, Escherichia coli, Yersinia and Campylobacter using standard bacterial cultures. Infectious origin was established in a total of 92 cases and 23 samples remained negative. A single pathogen was found in 67 stools, of which rotaviruses were the most prevalent (56.7 %), followed by noroviruses (19.4 %), enteric adenoviruses (7.5 %), astroviruses (6.0 %), bacteria and parasites (4.5 % each) and sapoviruses (1.4 %). Rotavirus predominant genotypes were G4P[8] (46.3 %) and G2P[4] (21.4 %); for astroviruses, type 1a was the most common, while the GII.4/2006b variant was the most prevalent among noroviruses. Bacteria were observed in five cases, with Salmonella sp. as the most prevalent, while parasites were found in ten stool samples, with Giardia intestinalis in five cases. The results demonstrated high morbidity associated with viral infections and that rotavirus and norovirus remain the most common pathogens associated with severe gastroenteritis during summer months in Bulgaria, a country with a temperate climate, and significant molecular diversity among circulating virus strains.
Collapse
Affiliation(s)
- Zornitsa Mladenova
- (former) Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Andrej Steyer
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | | | - Balasubramanian Ganesh
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Petar Petrov
- Infectious Ward, University Hospital 'St Anna', Sofia, Bulgaria
| | - Tanja Tchervenjakova
- Infectious Wards 1 and 2, Specialized Hospital for Infectious and Parasitic Diseases 'Prof. Ivan Kirov', Sofia, Bulgaria
| | | |
Collapse
|
12
|
Kou X, Fan H, Wu Q, Xue L, Zhang J. Development and application of a loop-mediated isothermal amplification assay on rapid and sensitive detection of rotavirus in fecal samples and artificially seeded oysters. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
13
|
Bucardo F, Reyes Y, Svensson L, Nordgren J. Predominance of norovirus and sapovirus in Nicaragua after implementation of universal rotavirus vaccination. PLoS One 2014; 9:e98201. [PMID: 24849288 PMCID: PMC4029982 DOI: 10.1371/journal.pone.0098201] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/29/2014] [Indexed: 11/18/2022] Open
Abstract
Background Despite significant reduction of rotavirus (RV) infections following implementation of RotaTeq vaccination in Nicaragua, a large burden of patients with diarrhea persists. Methods We conducted a community- and hospital-based study of the burden of RV, norovirus (NV) and sapovirus (SV) infections as cause of sporadic acute gastroenteritis (GE) among 330 children ≤ 5 years of age between September 2009 and October 2010 in two major cities of Nicaragua with a RotaTeq coverage rate of 95%. Results We found that NV, SV and RV infections altogether accounted for 45% of cases of GE. Notably, NV was found in 24% (79/330) of the children, followed by SV (17%, 57/330) and RV (8%, 25/330). The detection rate in the hospital setting was 27%, 15% and 14% for NV, SV and RV respectively, whereas in the community setting the detection rate of RV was < 1%. Among each of the investigated viruses one particular genogroup or genotype was dominant; GII.4 (82%) for NV, GI (46%) for SV and G1P[8] (64%) in RV. These variants were also found in higher proportions in the hospital setting compared to the community setting. The GII.4.2006 Minerva strain circulating globally since 2006 was the most common among genotyped NV in this study, with the GII.4-2010 New Orleans emerging in 2010. Conclusions This study shows that NV has become the leading viral cause of gastroenteritis at hospital and community settings in Nicaragua after implementation of RV vaccination.
Collapse
Affiliation(s)
- Filemón Bucardo
- Department of Microbiology, University of León (UNAN-León), León, Nicaragua
| | - Yaoska Reyes
- Department of Microbiology, University of León (UNAN-León), León, Nicaragua
| | - 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:
| |
Collapse
|
14
|
Ottaviani D, Leoni F, Serra R, Serracca L, Decastelli L, Rocchegiani E, Masini L, Canonico C, Talevi G, Carraturo A. Nontoxigenic Vibrio parahaemolyticus strains causing acute gastroenteritis. J Clin Microbiol 2012; 50:4141-3. [PMID: 23052317 PMCID: PMC3502970 DOI: 10.1128/jcm.01993-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/03/2012] [Indexed: 11/20/2022] Open
Abstract
We investigated the virulence properties of four Vibrio parahaemolyticus strains causing acute gastroenteritis following consumption of indigenous mussels in Italy. The isolated strains were cytotoxic and adhesive but, surprisingly, lacked tdh, trh, and type three secretion system 2 (T3SS2) genes. We emphasize that nontoxigenic V. parahaemolyticus can induce acute gastroenteritis, highlighting the need for more investigation of the pathogenicity of this microorganism.
Collapse
Affiliation(s)
- Donatella Ottaviani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento Contaminazioni Batteriologiche dei Molluschi Bivalvi, Ancona, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Bucardo F, Carlsson B, Nordgren J, Larson G, Blandon P, Vilchez S, Svensson L. Susceptibility of children to sapovirus infections, Nicaragua, 2005-2006. Emerg Infect Dis 2012; 18:1875-8. [PMID: 23092588 PMCID: PMC3559137 DOI: 10.3201/eid1811.111581] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe the genetic diversity of sapovirus (SaV) in children in Nicaragua and investigate the role of host genetic factors and susceptibility to SaV infections. Our results indicate that neither ABO blood group, Lewis phenotype, nor secretor status affects susceptibility to SaV infection in Nicaragua.
Collapse
Affiliation(s)
- Filemón Bucardo
- University of León, León, Linköping University, Linköping, Sweden
| | | | | | | | | | | | | |
Collapse
|
16
|
Mauroy A, Van der Poel WHM, der Honing RHV, Thys C, Thiry E. Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection. BMC Vet Res 2012; 8:193. [PMID: 23072668 PMCID: PMC3528410 DOI: 10.1186/1746-6148-8-193] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine. RESULTS The method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences). CONCLUSIONS A rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.
Collapse
Affiliation(s)
- Axel Mauroy
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | | | | | | | | |
Collapse
|
17
|
Nearly constant shedding of diverse enteric viruses by two healthy infants. J Clin Microbiol 2012; 50:3427-34. [PMID: 22875894 DOI: 10.1128/jcm.01589-12] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Stool samples from two healthy infant siblings collected at about weekly intervals during their first year of life were analyzed by PCR for 15 different enteric viral genera. Adenovirus, Aichi virus, Anellovirus, Astrovirus, Bocavirus, Enterovirus, Parechovirus, Picobirnavirus, and Rotavirus were detected. Not detected were Coronavirus, Cardiovirus, Cosavirus, Salivirus, Sapovirus, and Norovirus. Long-term virus shedding, lasting from one to 12 months, was observed for adenoviruses, anelloviruses, bocaviruses, enteroviruses, parechoviruses, and picobirnaviruses. Repeated administration of oral poliovirus vaccine resulted in progressively shorter periods of poliovirus detection. Four nonpolio enterovirus genotypes were also detected. An average of 1.8 distinct human viruses were found per time point. Ninety-two percent (66/72) of the fecal samples tested contained one to five different human viruses. Two British siblings in the mid-1980s showed nearly constant fecal viral shedding. Our results demonstrate that frequent enteric infections with diverse viruses occur during early childhood in the absence of severe clinical symptoms.
Collapse
|
18
|
Human sapovirus classification based on complete capsid nucleotide sequences. Arch Virol 2011; 157:349-52. [PMID: 22075918 DOI: 10.1007/s00705-011-1161-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/07/2011] [Indexed: 10/15/2022]
Abstract
The genetically diverse sapoviruses (SaVs) are a significant cause of acute human gastroenteritis. Human SaV surveillance is becoming more critical, and a better understanding of the diversity and distribution of the viral genotypes is needed. In this study, we analyzed 106 complete human SaV capsid nucleotide sequences to provide a better understanding of their diversity. Based on those results, we propose a novel standardized classification scheme that meets the requirements of the International Calicivirus Scientific Committee. We believe the classification scheme and strains described here will be of value for the molecular characterization and classification of newly detected SaV genotypes and for comparing data worldwide.
Collapse
|
19
|
Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Lee SG, Lee SH, Park SW, Suh CI, Jheong WH, Oh S, Paik SY. Standardized positive controls for detection of norovirus by reverse transcription PCR. Virol J 2011; 8:260. [PMID: 21612660 PMCID: PMC3127839 DOI: 10.1186/1743-422x-8-260] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 05/26/2011] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Norovirus is one of the most common causes of nonbacterial gastroenteritis in humans. Rapid spread by contaminated food and person-to-person transmission through the fecal-oral route are characteristics of norovirus epidemiology and result in high morbidity in vulnerable patient populations. Therefore, detection of norovirus is a major public health concern. Currently, the most common method for detecting and differentiating among norovirus strains in clinical and environmental samples is reverse transcription PCR (RT-PCR). Standardized positive controls used in RT-PCR assays to detect norovirus are designed to overcome the problem of false-negative results due to PCR inhibitors and suboptimal reaction conditions. RESULTS In the current study, four types of RNA transcripts were produced from plasmids: norovirus GI-5 and GII-4 capsid regions with human rotavirus (VP7 gene derived) fragment insertions, and norovirus GI-6 and GII-4 capsid regions with hepatitis A virus (VP1/P2A gene derived) fragment insertions. These size-distinguishable products were used as positive controls under the RT-PCR assay conditions used to detect NoV in stool and groundwater samples. Their reliability and reproducibility was confirmed by multiple sets of experiments. CONCLUSIONS These standardized products may contribute to the reliable and accurate diagnosis by RT-PCR of norovirus outbreaks, when conducted by laboratories located in different regions.
Collapse
Affiliation(s)
- Sung-Geun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Soe-Hyun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Seung-Won Park
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Association, Suwon, 441-707, Republic of Korea
| | - Chang-Il Suh
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Weon-Hwa Jheong
- Environmental Infrastructure Research Department, National Institute of Environmental Research, Incheon 404-170, Republic of Korea
| | - SeHwan Oh
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Soon-Young Paik
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| |
Collapse
|
21
|
Epidemiology and genotype analysis of emerging sapovirus-associated infections across Europe. J Clin Microbiol 2010; 48:2191-8. [PMID: 20392905 DOI: 10.1128/jcm.02427-09] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sapoviruses (SaVs) belong to the Caliciviridae family and can cause gastroenteritis in humans and swine. Despite extensive testing, human sapoviruses have been found only in sporadic cases and in one mixed outbreak in children between 1994 and 2007 in the Netherlands. Here we describe a change in sapovirus epidemiology in the Netherlands resulting in sapovirus outbreaks and infections in adults. From November 2007 to January 2009, 478 outbreaks of acute gastroenteritis were reported to the National Institute for Public Health and the Environment in the Netherlands as a part of ongoing surveillance. Sapoviruses were found to be the most likely cause of 19 outbreaks (4%). During the same 2-year period, sapovirus infections were reported in Sweden, Slovenia, and Hungary. In the Netherlands, further characterization of outbreak strains showed that 12 (63%) sapovirus outbreaks were caused by genotype I.2 viruses. Most patients were adults older than 60 years (range, 1 to 100 years). Phylogenetic analysis using all presently available SaV sequences showed high homology between genotype I.2 strains detected in different geographical regions (Sweden, Slovenia, Taiwan, Japan, and Russia) since 2007. These first reported outbreaks of sapovirus infections in adults in the Netherlands were remarkable. Detection of identical genotypes in many samples might suggest that these viruses have the same origin, and since the infection is spreading fast, the prevalence of sapovirus infection may be increasing. The incidence of sapovirus infections in these countries suggests that a substantial part of Europe is affected by this virus.
Collapse
|
22
|
Detection and genetic analysis of human sapoviruses in river water in Japan. Appl Environ Microbiol 2010; 76:2461-7. [PMID: 20190080 DOI: 10.1128/aem.02739-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples, and a total of 30 SaV strains were identified using six RT-PCR assays followed by cloning and sequence analysis. A newly developed nested RT-PCR assay utilizing a broadly reactive forward primer showed the highest detection efficiency and amplified more diverse SaV genomes in the samples. SaV sequences were frequently detected from November to March, whereas none were obtained in April, July, September, or October. No SaV sequences were detected in the upstream portion of the river, whereas the midstream portion showed high positive rates. Based on phylogenetic analysis, SaV strains identified in the river water samples were classified into nine genotypes, namely, GI/1, GI/2, GI/3, GI/5, GI/untyped, GII/1, GII/2, GII/3, and GV/1. To our knowledge, this is the first study describing seasonal and spatial distributions and genetic diversity of SaVs in river water. A combination of real-time RT-PCR assay and newly developed nested RT-PCR assay is useful for identifying and characterizing SaV strains in a water environment.
Collapse
|
23
|
Dai YC, Xia M, Zhan HC, Liu Y, Li JD, Chen Q, Yu SY, Nie J, Farkas T, Jiang X. Surveillance and risk factors of norovirus gastroenteritis among children in a southern city of China in the fall-winter seasons of 2003-2006. J Paediatr Child Health 2010; 46:45-50. [PMID: 19943862 DOI: 10.1111/j.1440-1754.2009.01616.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM Noroviruses (NoVs) are an important cause of acute gastroenteritis but knowledge on the disease burden and epidemiology in children in the developing countries remains limited. In this study, we performed a surveillance of NoV gastroenteritis in children of China to address some of the questions. METHODS Faecal specimens from children (<5 years of age) at outpatient clinics of the Nan Fang Hospital in Guangzhou, China during the fall-winter seasons in 2003-2006 were tested for rotaviruses (RVs) and NoVs. A questionnaire on clinical records and hygiene habits was collected from each patient. RESULTS Among 957 stool specimens tested, 488 (51%) specimens were positive for RVs. NoVs were detected in 112 (24%) of the 469 RV negative specimens. The Genogroup II (GII), particularly GII-4, viruses were predominant. No significant difference of clinical symptoms, hospitalisation and patient care expenses were found between children infected with NoVs and RVs. Consumption of uncooked food is a risk for NoV infection. Contact with diarrhoea patients is a suspected risk factor. Cutting nails frequently is a protective factor against NoV infection. CONCLUSIONS NoVs are an important cause of acute gastroenteritis in children which need special attention of patient care at the clinics in addition to RVs. The awareness of those risk factors may help future disease control and prevention.
Collapse
Affiliation(s)
- Ying-Chun Dai
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Incidence, diversity, and molecular epidemiology of sapoviruses in swine across Europe. J Clin Microbiol 2009; 48:363-8. [PMID: 19940055 DOI: 10.1128/jcm.01279-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Porcine sapovirus is an enteric calicivirus in domestic pigs that belongs to the family Caliciviridae. Some porcine sapoviruses are genetically related to human caliciviruses, which has raised public health concerns over animal reservoirs and the potential cross-species transmission of sapoviruses. We report on the incidence, genetic diversity, and molecular epidemiology of sapoviruses detected in domestic pigs in a comprehensive study conducted in six European countries (Denmark, Finland, Hungary, Italy, Slovenia, and Spain) between 2004 and 2007. A total of 1,050 swine fecal samples from 88 pig farms were collected and tested by reverse transcription-PCR for sapoviruses, and positive findings were confirmed by sequencing. Sapoviruses were detected in 80 (7.6%) samples collected on 39 (44.3%) farms and in every country. The highest prevalence was seen among piglets aged 2 to 8 weeks, and there was no significant difference in the proportion of sapovirus-positive findings for healthy animals and animals with diarrhea in Spain and Denmark (the only countries where both healthy animals and animals with diarrhea were tested). On the basis of the sequence of the RNA polymerase region, highly heterogeneous populations of viruses representing six different genogroups (genogroups III, VI, VII, and VIII, including potential new genogroups IX and X) were identified, with a predominance of genogroup GIII (50.6%). Genogroup VIII, found in five of the six countries, had the highest degree of homology (up to 66% at the amino acid level) to human sapovirus strains. Sapoviruses are commonly circulating and endemic agents in swine herds throughout Europe. Highly heterogeneous and potential new genogroups of sapoviruses were found in pigs; however, no "human-like" sapoviruses were detected.
Collapse
|
25
|
Genetic diversity of sapovirus infections in Danish children 2005–2007. J Clin Virol 2009; 46:265-9. [DOI: 10.1016/j.jcv.2009.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 06/29/2009] [Accepted: 07/07/2009] [Indexed: 11/20/2022]
|
26
|
A new variant of Norovirus GII.4/2007 and inter-genotype recombinant strains of NVGII causing acute watery diarrhoea among children in Kolkata, India. J Clin Virol 2009; 45:223-9. [DOI: 10.1016/j.jcv.2009.04.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 04/18/2009] [Accepted: 04/26/2009] [Indexed: 01/19/2023]
|
27
|
Harada S, Okada M, Yahiro S, Nishimura K, Matsuo S, Miyasaka J, Nakashima R, Shimada Y, Ueno T, Ikezawa S, Shinozaki K, Katayama K, Wakita T, Takeda N, Oka T. Surveillance of pathogens in outpatients with gastroenteritis and characterization of sapovirus strains between 2002 and 2007 in Kumamoto Prefecture, Japan. J Med Virol 2009; 81:1117-27. [PMID: 19382269 DOI: 10.1002/jmv.21454] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Infectious acute gastroenteritis is an important public health problem worldwide. A total of 639 stool specimens were tested for the presence of diarrhea pathogens. The specimens were from outpatients with acute gastroenteritis who consulted the pediatric clinic in Kumamoto Prefecture, Japan, from June 2002 to December 2007. Of these, 421 (65.9%) were positive for diarrhea pathogens. Among them were norovirus (NoV) in 260 (61.8%), sapovirus (SaV) in 81 (19.2%), rotavirus in 49 (11.6%), adenovirus in 19 (4.5%), enterovirus in 13 (3.1%), astrovirus in 9 (2.1%), kobuvirus in 1 (0.2%), and bacterial pathogens in 11 (2.6%). Mixed infection (co-infection of viruses) was found in 22 (5.2%) of the 421 pathogen-positive stool samples. NoV was the most prevalent pathogen throughout the study period; however, the SaV detection rate was unexpectedly high and was found to be the secondary pathogen from 2005 to 2007. Genetic analysis of SaV with 81 strains demonstrated that SaV strains belonging to genogroup IV emerged in 2007, and dynamic genogroup changes occurred in a restricted geographic area. This study showed that SaV infection is not as rare as thought previously.
Collapse
Affiliation(s)
- Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Science, Kumamoto, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Yoshida T, Kasuo S, Azegami Y, Uchiyama Y, Satsumabayashi K, Shiraishi T, Katayama K, Wakita T, Takeda N, Oka T. Characterization of sapoviruses detected in gastroenteritis outbreaks and identification of asymptomatic adults with high viral load. J Clin Virol 2009; 45:67-71. [DOI: 10.1016/j.jcv.2009.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/19/2009] [Accepted: 03/06/2009] [Indexed: 11/27/2022]
|
29
|
Novel approach for detection of enteric viruses to enable syndrome surveillance of acute viral gastroenteritis. J Clin Microbiol 2009; 47:1674-9. [PMID: 19339472 DOI: 10.1128/jcm.00307-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute gastroenteritis is one of the most common diseases worldwide, with viruses, particularly noroviruses, being the leading cause in developed countries. In The Netherlands, systematic surveillance of gastroenteritis outbreaks of suspected viral etiology was established by the National Institute for Public Health and the Environment in 1994. Since 2002, the total number of outbreaks reported has been increasing, and with that comes the need for sensitive assays that can be performed quickly. In addition, the diagnostic demand changed so that now the proportion of samples from hospitals is higher and there is a need for patient-based test results. In order to target the diagnosis of acute gastroenteritis, we reviewed our data on outbreaks of gastroenteritis and the prevalence of individual viruses to provide a priority list of viruses for which samples should be evaluated. Random primers were used to replace the separate specific primers for each virus used in the reverse transcription steps. The individual PCR assays were replaced by multiplex PCR assays. We employed a two-step method in which in the first step we screened for the most common causes of viral gastroenteritis, noroviruses of genogroup II and rotaviruses of group A, with equine arteritis virus used as the internal control. Subsequently, in the second step, two parallel PCR assays were developed for the detection of noroviruses of genogroup I and equine arteritis virus in one run and adenoviruses, sapoviruses, and astroviruses in the other run. The specificities of the assays were calculated to be 92.5% for the assay for noroviruses of genogroup I and 100% for the assays for all other viruses, the detection limits were equal for all viruses, and the turnaround time was reduced to 1 day compared to the at least 3 days required for the methods used previously. This approach allows the targeted, rapid, and cost-effective elucidation of the causes of acute gastroenteritis outbreaks.
Collapse
|
30
|
Iwakiri A, Ganmyo H, Yamamoto S, Otao K, Mikasa M, Kizoe S, Katayama K, Wakita T, Takeda N, Oka T. Quantitative analysis of fecal sapovirus shedding: identification of nucleotide substitutions in the capsid protein during prolonged excretion. Arch Virol 2009; 154:689-93. [PMID: 19301092 DOI: 10.1007/s00705-009-0358-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 03/05/2009] [Indexed: 11/29/2022]
Abstract
Sapovirus (SaV) is an important pathogen causing gastroenteritis in humans. Quantitative analysis of the viral loads in feces collected from two SaV outbreaks was performed. Our results showed that SaV excretion generally decreased to an undetectable level in 2 weeks; however, some individuals excrete SaV in feces at high concentrations for 2-4 weeks after the onset of illness. In addition, we identified for the first time nucleotide changes in the capsid region during prolonged excretion.
Collapse
Affiliation(s)
- Akira Iwakiri
- Miyazaki Prefectural Institute for Public Health and Environment, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Pang X, Lee B, Tyrrell G, Preiksaitis J. Epidemiology and Genotype Analysis of Sapovirus Associated with Gastroenteritis Outbreaks in Alberta, Canada: 2004–2007. J Infect Dis 2009; 199:547-551. [DOI: 10.1086/596210] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
|
32
|
Lyman WH, Walsh JF, Kotch JB, Weber DJ, Gunn E, Vinjé J. Prospective study of etiologic agents of acute gastroenteritis outbreaks in child care centers. J Pediatr 2009; 154:253-7. [PMID: 18783794 DOI: 10.1016/j.jpeds.2008.07.057] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 06/11/2008] [Accepted: 07/30/2008] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To investigate the etiology of outbreaks of acute gastroenteritis (AGE) in children attending childcare centers (CCCs) in North Carolina between October 2005 and March 2007. STUDY DESIGN In this prospective study of outbreaks of AGE in CCCs, stool specimens from symptomatic children and environmental surface swabs were tested for adenovirus group F, astrovirus, norovirus (NoV), rotavirus group A, and sapovirus using real-time and conventional reverse transcription-polymerase chain reaction assays, and viruses were genotyped by sequencing. RESULTS A total of 29 AGE outbreaks were evaluated, of which 13 (45%) were caused by a single virus, including rotavirus group A (17%), NoV (10%), astrovirus (10%), and sapovirus (7%). Multiple viruses were detected in 3 outbreaks (10%). Environmental swabs from 13 of 22 outbreaks (59%) tested positive for at least 1 virus and confirmed the findings of the same virus in the fecal specimens for 10 of the outbreaks (45%). CONCLUSIONS This study confirms that viruses are major causes of AGE outbreak in CCCs. Our finding of widespread environmental contamination during such outbreaks suggests the need to study the effectiveness of current surface disinfectants against multiple gastroenteritis viruses in CCCs.
Collapse
Affiliation(s)
- Whitney H Lyman
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | |
Collapse
|
33
|
Siebenga J, Beersma M, Vennema H, van Biezen P, Hartwig N, Koopmans M. High Prevalence of Prolonged Norovirus Shedding and Illness among Hospitalized Patients: A Model for In Vivo Molecular Evolution. J Infect Dis 2008; 198:994-1001. [DOI: 10.1086/591627] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
34
|
Ike AC, Hartelt K, Oehme RM, Brockmann SO. Detection and characterization of sapoviruses in outbreaks of gastroenteritis in southwest Germany. J Clin Virol 2008; 43:37-41. [PMID: 18486539 DOI: 10.1016/j.jcv.2008.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 04/04/2008] [Accepted: 04/04/2008] [Indexed: 11/25/2022]
Abstract
BACKGROUND Sapovirus (SV) has been reported from many countries as one of the major causes of gastroenteritis in infants, but its importance for a broader age range is not well appreciated. While previous studies in our regional laboratory and other parts of Germany have identified Norovirus (NV) as a major cause of gastroenteritis in Germany, the prevalence of SV has not been recorded. OBJECTIVES To investigate the prevalence of SV in outbreaks of gastroenteritis in Baden-Württemberg, Germany. STUDY DESIGN Stool specimens from 34 outbreaks of gastroenteritis collected in Baden-Württemberg, Germany in 2002 and 2003, which tested negative for other enteric pathogens were tested for SV by RT-PCR. Positive samples were sequenced and typed using phylogenetic analysis. RESULTS SV was identified in two of 157 (1.3%) specimens. These two viruses belonged to different genotypes of SV and had a nucleotide similarity of only 57%. CONCLUSIONS SV circulates within the study area, but is not an important cause of gastroenteritis in the area.
Collapse
Affiliation(s)
- Anthony C Ike
- Baden-Württemberg State Health Office, District Government Stuttgart, Nordbahnhofstrasse 135, 70191 Stuttgart, Germany.
| | | | | | | |
Collapse
|
35
|
Logan C, O’Sullivan N. Detection of viral agents of gastroenteritis: Norovirus, Sapovirus and Astrovirus. Future Virol 2008. [DOI: 10.2217/17460794.3.1.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Norovirus, Sapovirus and Astrovirus are causative agents of viral gastroenteritis affecting all age groups, but most frequently the young, the elderly and persons in semi-closed communities such as hospitals, nursing homes, military bases and cruise ships. The sensitive and rapid detection of causative agents of viral gastroenteritis is key to the effective implementation of infection control systems. Traditional detection methods such as electron microscopy and antigen detection assays lack sensitivity. The detection of gastrointestinal viruses by molecular methods has resulted in increased levels of detection, and enables the epidemiological investigation of viral strains. The significant diversity of gastrointestinal viruses, in particular Norovirus and Sapovirus, are compounded by increasing reports of virus recombination, and pose an ongoing challenge to the development of sensitive and specific molecular detection assays.
Collapse
Affiliation(s)
- Catriona Logan
- Our Lady’s Children’s Hospital, Department of Microbiology, Crumlin, Dublin 12, Ireland
| | - Niamh O’Sullivan
- Our Lady’s Children’s Hospital, Department of Microbiology, Crumlin, Dublin 12, Ireland, and, Department of Pathology, Coombe Women’s Hospital, Dolphins Barn, Dublin 8, Ireland
| |
Collapse
|
36
|
Zhu D, Fox GE, Chakravarty S. RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses. BMC Bioinformatics 2007; 8:379. [PMID: 17927830 PMCID: PMC2174958 DOI: 10.1186/1471-2105-8-379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 10/10/2007] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available.
Results
We present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses.
Conclusion
This study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using a uniform method. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families.
Collapse
|
37
|
Novel light-upon-extension real-time PCR assays for detection and quantification of genogroup I and II noroviruses in clinical specimens. J Clin Microbiol 2007; 46:164-70. [PMID: 17959761 DOI: 10.1128/jcm.01316-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Norovirus is now recognized as the leading cause of nonbacterial acute gastroenteritis in adults, causing numerous outbreaks worldwide. We have developed two novel light-upon-extension (LUX) real-time PCR assays for detection and quantification of norovirus genogroups I and II. The LUX system uses a fluorophore attached to one primer having a self-quenching hairpin structure, making it cost-effective and specific. The assays were evaluated against clinical stool specimens (n = 103) from Sweden and Nicaragua and compared to established methods. The norovirus assay detected more positive stool specimens (47/103) than conventional PCR (39/103) and corresponded to a TaqMan real-time PCR, with the exception of one specimen. Furthermore, the assays correctly identified all (n = 11) coded control specimens in a reference panel containing various genogroups and genotypes. Both LUX real-time PCR assays had a wide dynamic range, detecting from < or = 10(1) to 10(7) genes per reaction, resulting in a theoretical lower limit of < or = approximately 20,000 viruses per gram of stool. No cross-reactivity was noticed with specimens containing other enteric viruses, and by using melting curve analysis we could differentiate between norovirus genogroups I and II.
Collapse
|
38
|
Amar CFL, East CL, Gray J, Iturriza-Gomara M, Maclure EA, McLauchlin J. Detection by PCR of eight groups of enteric pathogens in 4,627 faecal samples: re-examination of the English case-control Infectious Intestinal Disease Study (1993-1996). Eur J Clin Microbiol Infect Dis 2007; 26:311-23. [PMID: 17447091 DOI: 10.1007/s10096-007-0290-8] [Citation(s) in RCA: 214] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The English case-control Infectious Intestinal Disease Study (1993-1996) failed to detect an enteric pathogen or toxin in 49% of cases of gastroenteritis. In the present study, polymerase chain reaction (PCR) assays were applied to DNA and cDNA generated from 4,627 faecal samples from cases and controls archived during the original study for the detection of norovirus, rotavirus, sapovirus, Campylobacter spp., Salmonella spp., enteroaggregative Escherichia coli, Cryptosporidium spp., and Giardia spp. The percentage of archived samples from cases and from controls in which at least one agent (or toxin) was detected increased from 53% in the original study to 75% and from 19 to 42%, respectively, after the application of PCR assays. Among cases, the following percentages of enteric pathogens were detected: norovirus 36%, rotavirus A 31%, sapovirus 4%, Salmonella spp. 6%, Campylobacter jejuni 13%, Campylobacter coli 2%, other Campylobacter spp. 8%, enteroaggregative E. coli 6%, Giardia spp. 2%, and Cryptosporidium spp. 2%. The present study provides additional insight into the aetiology of infectious intestinal disease in England and highlights the occurrence of viral infections in cases as well as in asymptomatic individuals. Other notable findings include the frequent presence of Campylobacter spp. other than C. jejuni or C. coli, the high frequency of multiple agents in 41% of cases and in 13% of controls, and the variation in the aetiology and rate of infection found for different age groups. The results demonstrate the greater sensitivity of PCR-based methods compared to current conventional methods.
Collapse
Affiliation(s)
- C F L Amar
- Health Protection Agency Centre for Infections, 61 Colindale Avenue, NW9 5EQ, London, UK.
| | | | | | | | | | | |
Collapse
|
39
|
Hansman GS, Oka T, Katayama K, Takeda N. Human sapoviruses: genetic diversity, recombination, and classification. Rev Med Virol 2007; 17:133-41. [PMID: 17340567 DOI: 10.1002/rmv.533] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The family Caliciviridae contains four genera Sapovirus, Norovirus, Lagovirus and Vesivirus, which include Sapporo virus (SaV), Norwalk virus (NoV), Rabbit hemorrhagic disease virus (RHDV) and Feline calicivirus (FCV), respectively. SaV is a causative agent of gastroenteritis in children and adults. SaV can be divided into five genogroups (GI-GV), among which GI, GII, GIV and GV are known to infect humans, whereas SaV GIII infects porcine species. Detection methods include ELISA, RT-PCR and real-time RT-PCR. Since few SaV studies have been conducted, it is difficult to draw correlations between or conclusions about rates of incidence, detection and overall prevalence. Nevertheless, most studies agree that SaV infection is more frequent in young children than adults and that infection in children almost always occurs by 5 years of age. In addition, children at day-care centres and institutions are at greatest risk of SaV-associated infection and transmission. Recently, a number of important findings concerning human SaV were discovered. SaV strains were detected in water samples, which included untreated wastewater specimens, treated wastewater samples and river samples. SaV strains were also detected in shellfish samples destined for human consumption, and recombinant SaV strains were identified in a number of different countries. The purpose of this review was to highlight the current knowledge of human SaV, which appears to be an increasingly important virus causing gastroenteritis in humans.
Collapse
Affiliation(s)
- Grant S Hansman
- Department of Virology II, National Institute of Infectious Diseases, Musashi-murayama, Tokyo, Japan.
| | | | | | | |
Collapse
|
40
|
Svraka S, Duizer E, Vennema H, de Bruin E, van der Veer B, Dorresteijn B, Koopmans M. Etiological role of viruses in outbreaks of acute gastroenteritis in The Netherlands from 1994 through 2005. J Clin Microbiol 2007; 45:1389-94. [PMID: 17360839 PMCID: PMC1865895 DOI: 10.1128/jcm.02305-06] [Citation(s) in RCA: 244] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute gastroenteritis is one of the most common diseases worldwide. In developed countries, viruses, particularly noroviruses, are recognized as the leading cause. In The Netherlands, the surveillance of gastroenteritis outbreaks with suspected viral etiologies (as determined by Kaplan criteria) was established by the National Institute for Public Health and the Environment in 1994. This paper presents an overview of viral gastroenteritis outbreaks reported from 1994 through 2005. A minimum epidemiological data set consisting of the associated setting(s), the probable transmission mode, the date of the first illness and the date of sampling, the number of persons affected, and the number of hospitalizations was requested for each reported outbreak. Stool samples were tested for the presence of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, and Aichi virus by electron microscopy, enzyme-linked immunosorbent assay, and/or reverse transcription-PCR. A total of 6,707 stool samples from 941 gastroenteritis outbreaks were investigated. Noroviruses were detected as the causative agent in 735 (78.1%) of the outbreaks, and rotaviruses, adenoviruses, and astroviruses were found to be responsible for 46 (4.9%), 9 (1.0%), and 5 (0.5%) outbreaks, respectively. Among the gastroenteritis outbreaks in which a mode of transmission was identified, most outbreaks (38.1%) were associated with person-to-person transmission, and the majority (54.9%) of the outbreaks investigated were reported by residential institutions. Since 2002, the total number of outbreaks reported and the number of unexplained outbreaks have increased. Furthermore, the number of rotavirus-associated outbreaks has increased, especially in nursing homes. Despite thorough testing, 115 (12.2%) outbreaks suspected of having viral etiologies remain unexplained. Increases in numbers of reported outbreaks may indicate undefined changes in the criteria for reporting or the emergence of new pathogens.
Collapse
Affiliation(s)
- Sanela Svraka
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
41
|
Okada M, Yamashita Y, Oseto M, Ogawa T, Kaiho I, Shinozaki K. Genetic variability in the sapovirus capsid protein. Virus Genes 2006; 33:157-61. [PMID: 16972029 DOI: 10.1007/s11262-005-0051-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 11/15/2005] [Accepted: 11/21/2005] [Indexed: 11/30/2022]
Abstract
Sapovirus (SV), which causes gastroenteritis in humans, is composed of genetically divergent viruses classified into 5 genogroups. In this study, 2.2-kb nucleotide sequences of the 3' terminus of the genome of 15 SV strains detected in Japan were determined. The 15 SV strains could be classified into four genogroups (GI, GII, GIV and GV), and in two of these, GI and GII, 10 genotypes were identified. The amino acid sequences of the central variable region of the capsid protein showed less than 81% identity when strains belonging to different genotypes were compared. It was therefore supposed that antigenic variety exists between different genotypes. These results will be useful for further genetic and antigenic analyses of SV.
Collapse
Affiliation(s)
- Mineyuki Okada
- Division of Virology, Chiba Prefectural Institute of Public Health, Chiba-shi, Chiba 260-8715, Japan.
| | | | | | | | | | | |
Collapse
|
42
|
Fukuda S, Takao S, Kuwayama M, Shimazu Y, Miyazaki K. Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol 2006; 44:1376-81. [PMID: 16597865 PMCID: PMC1448634 DOI: 10.1128/jcm.44.4.1376-1381.2006] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we developed a one-step, single-tube genogroup-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of norovirus (NoV) genomes targeting from the C terminus of the RNA-dependent RNA polymerase gene to the capsid N-terminal/shell domain region. This is the first report on the development of an RT-LAMP assay for the detection of NoV genomes. Because of the diversity of NoV genotypes, we used 9 and 13 specially designed primers containing mixed bases for genogroup I (GI) and II (GII), respectively. The RT-LAMP assay had the advantages of rapidity, simplicity, specificity, and selectively and could obtain results within 90 min, generally even within 60 min, under isothermal conditions at 62 degrees C. The detection limits for NoV genomes were between 10(2) and 10(3) copies/tube for GI and GII with differentiation by genotype, and no cross-reactions among NoV GI and GII and other gastroenteritis viruses, such as sapovirus, human astrovirus, adenovirus type 40 and 41, and group A and C rotavirus, were found. In the evaluation tests with fecal specimens obtained from gastroenteritis outbreaks, the sensitivity and specificity of the RT-LAMP assay with regard to RT-PCR were 100 and 94% for GI and 100 and 100% for GII, respectively. These findings establish that the RT-LAMP assay is potentially useful for the rapid detection of NoV genomes from fecal specimens in outbreaks of food-borne and person-to-person-transmitted gastroenteritis.
Collapse
Affiliation(s)
- Shinji Fukuda
- Department of Microbiology II, Hiroshima Prefectural Institute of Public Health and Environment, Minami-machi 1-6-29, Minami-ku, Hiroshima 734-0007, Japan.
| | | | | | | | | |
Collapse
|
43
|
Oka T, Yamamoto M, Katayama K, Hansman GS, Ogawa S, Miyamura T, Takeda N. Identification of the cleavage sites of sapovirus open reading frame 1 polyprotein. J Gen Virol 2006; 87:3329-3338. [PMID: 17030867 DOI: 10.1099/vir.0.81799-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sapovirus (SaV), a member of the family Caliciviridae, is a causative agent of acute gastroenteritis in humans and swine and is currently divided into five genogroups, GI–GV. The proteolytic processing of the SaV open reading frame 1 (ORF1) polyprotein with a human GII SaV Mc10 strain has recently been determined and the products are arranged in the following order: NH2–p11–p28–p35 (NTPase)–p32–p14 (VPg)–p70 (Pro–Pol)–p60 (VP1)–COOH. The cleavage site between p14 (VPg) and p70 (Pro–Pol) was identified as E1055/A1056 by N-terminal amino acid sequencing. To identify other cleavage sites, a series of GII SaV Mc10 full-length clones containing disrupted potential cleavage sites in the ORF1 polyprotein were constructed and used to generate linear DNA templates for in vitro coupled transcription–translation. The translation products were analysed by SDS-PAGE or by immunoprecipitation with region-specific antibodies. N-terminal amino acid sequencing with Escherichia coli-expressed recombinant proteins was also used to identify the cleavage site between p32 and p14. These approaches enabled identification of the six cleavage sites of the Mc10 ORF1 polyprotein as E69/G70, Q325/G326, Q666/G667, E940/A941, E1055/A1056 and E1722/G1723. The alignment of the SaV full-length ORF1 amino acid sequences indicated that the dipeptides used for the cleavage sites were either E or Q at the P1 position and A, G or S at the P1′ position, which were conserved in the GI, GII, GIII, GIV and GV SaV ORF1 polyprotein.
Collapse
Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Mami Yamamoto
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Grant S Hansman
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Satoko Ogawa
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Tatsuo Miyamura
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Naokazu Takeda
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| |
Collapse
|
44
|
Oka T, Katayama K, Hansman GS, Kageyama T, Ogawa S, Wu FT, White PA, Takeda N. Detection of human sapovirus by real-time reverse transcription-polymerase chain reaction. J Med Virol 2006; 78:1347-53. [PMID: 16927293 DOI: 10.1002/jmv.20699] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Sapovirus (SaV) is an agent of gastroenteritis for humans and swine, and is divided into five distinct genogroups (GI-GV) based on its capsid gene sequences. Typical methods of SaV detection include electron microscopy (EM), enzyme-linked immunosorbent assay (ELISA), and reverse transcription-polymerase chain reaction (RT-PCR). A novel TaqMan-based real-time RT-PCR assay was developed that is sensitive and has the ability to detect the broad range of genetically diverse human SaV strains. A nucleotide alignment of 10 full-length SaV genome sequences was subjected to similarity plot analysis, which indicated that the most conserved site was the polymerase-capsid junction in open reading frame 1 (ORF1). Based on multiple alignments of the 27 available sequences encoding this junction, we designed sets of primers and TaqMan MGB probes that detect human SaV GI, GII, GIV, and GV sequences in a single tube. The reactivity was confirmed with SaV GI, GII, GIV, and GV control plasmids, and the efficiency ranged from 2.5 x 10(7) to 2.5 x 10(1) copies per tube. Analysis using clinical stool specimens revealed that the present system was capable of detecting SaV GI, GII, GIV, and GV sequences, and no cross-reactivity was observed against other enteric viruses, including norovirus (NoV), rotavirus, astrovirus, and adenovirus. This is the first real-time RT-PCR system that could detect all genogroups of human sapoviruses.
Collapse
Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Okada M, Yamashita Y, Oseto M, Shinozaki K. The detection of human sapoviruses with universal and genogroup-specific primers. Arch Virol 2006; 151:2503-9. [PMID: 16847552 DOI: 10.1007/s00705-006-0820-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 06/08/2006] [Indexed: 11/28/2022]
Abstract
Sapovirus (SV) causes gastroenteritis in humans and comprises genetically divergent viruses. A nested reverse transcription-polymerase chain reaction (RT-PCR) targeting the capsid-protein-coding region was developed using universal and genogroup-specific primer sets. The universal primers were capable of detecting human SV genogroups I, II, IV and V. Genetic analysis of the amplified products enabled us to phylogenetically determine the genotypes of the viruses. In addition, genogroup-specific primers that amplified different lengths of the amplicon depending on the genogroup were developed. These genogroup-specific primers were also used as inner primers for the nested PCR. These two simple RT-PCR methods are powerful tools for both detection and epidemiological studies of human SV.
Collapse
Affiliation(s)
- M Okada
- Division of Virology, Chiba Prefectural Institute of Public Health, Chuo-ku, Chiba-shi, Chiba, Japan.
| | | | | | | |
Collapse
|
46
|
Busani L, Boccia D, Caprioli A, M Ruggeri F, Morabito S, Minelli F, Lana S, Rizzoni G, Giofrè F, Mazzeo M, Tozzi AE. Public health implications of a case of haemolytic-uraemic syndrome associated with a concomitant outbreak of mild gastroenteritis in a small rural community. Epidemiol Infect 2006; 134:407-13. [PMID: 16490147 PMCID: PMC2870377 DOI: 10.1017/s0950268805004735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2005] [Indexed: 11/07/2022] Open
Abstract
The concomitant occurrence of a case of haemolytic-uraemic syndrome (HUS) and 62 cases of mild gastroenteritis in schools of a small rural community in southern Italy induced the health authorities to suspect a foodborne outbreak of shiga-toxin-producing Escherichia coli (STEC) infection. The schools were closed and the catering service involved was investigated. However, STEC were not isolated from the HUS case or from the 56 cases of gastroenteritis examined, and the HUS case and the outbreak of gastroenteritis were probably just coincidental. A retrospective cohort study failed to show any correlation with consumption of school meals and suggested that the outbreak probably started outside the school setting and then spread within the schools by person-to-person transmission. All the cases examined were negative for common enteric pathogens and the responsible agent for the cases of gastroenteritis was not identified. The concern raised in the small community by the occurrence of a severe case of HUS and the lack of a rapid epidemiological assessment excluding the occurrence of a STEC outbreak, turned an epidemic episode of mild gastroenteritis into a public health emergency with relevant socioeconomic consequences. Prompt intervention in outbreaks following timely and effective risk communication are crucial for taking the most appropriate control measures and avoiding the spread of fear and panic in the community.
Collapse
Affiliation(s)
- L Busani
- Istituto Superiore di Sanità, Rome, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Chan MCW, Sung JJY, Lam RKY, Chan PKS, Lai RWM, Leung WK. Sapovirus detection by quantitative real-time RT-PCR in clinical stool specimens. J Virol Methods 2006; 134:146-53. [PMID: 16427707 DOI: 10.1016/j.jviromet.2005.12.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 12/09/2005] [Accepted: 12/19/2005] [Indexed: 11/18/2022]
Abstract
Sapovirus (SV) is one of the major causative agents of viral gastroenteritis affecting all age groups worldwide. A new method for the quantitative detection of SV from clinical stool specimens by real-time reverse transcription-polymerase chain reaction (RT-PCR) based on TaqMan MGB technology was described. Primers and probe were designed to target the RNA-dependent RNA polymerase/capsid genes junction. Performance of the newly developed assay was validated against a panel of 244 clinical stool specimens collected for patients with gastroenteritis. SV was detected in eight (3.3%) specimens. Phylogenetic analysis of the positive isolates suggested that the assay could detect at least SV genogroups I, II and IV. In addition, the assay had an increased detection rate compared with a widely used conventional RT-PCR assay. Quantitative analysis showed that the assay could detect as low as 10 copies of viral cDNA per reaction. No cross-reactivity with norovirus and rotavirus was observed. In conclusion, the assay is a sensitive and specific method for the detection of SV from clinical stool specimens.
Collapse
Affiliation(s)
- Martin C W Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
| | | | | | | | | | | |
Collapse
|
48
|
Affiliation(s)
- R N Gunson
- West of Scotland Specialist Virology Centre, Gartnavel General Hospital, Great Western Road, Glasgow G12 OYN, United Kingdom.
| | | | | |
Collapse
|
49
|
Armah GE, Gallimore CI, Binka FN, Asmah RH, Green J, Ugoji U, Anto F, Brown DWG, Gray JJ. Characterisation of norovirus strains in rural Ghanaian children with acute diarrhoea. J Med Virol 2006; 78:1480-5. [PMID: 16998875 DOI: 10.1002/jmv.20722] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The incidence of calicivirus infection in Ghana and many other African countries is not known. Thirteen (15.9%) of the 82 diarrhoeic stool samples tested for caliciviruses were positive for noroviruses (NoVs). NoVs were present in all age groups and were detected only during the diarrhoea peak that coincided with the peak rotavirus season. Ten (76.9%) of the NoV detected were genogroup II (GII) NoVs and the remaining three (23.1%) genogroup I (GI) NoVs. The predominant GII detected was GII-4 (60%, 6/10). Three of the GII NoVs were determined to be recombinants of GII-8/GII-14 as deduced from the sequencing of the region spanning the Orf1/2 junction. The GII genotypes formed four clusters with published GII sequences. The data shown enhances understanding of NoV diversity in Ghanaian children and demonstrate the global spread of distinct common genotypes to African countries.
Collapse
Affiliation(s)
- George E Armah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Yan H, Abe T, Phan TG, Nguyen TA, Iso T, Ikezawa Y, Ishii K, Okitsu S, Ushijima H. Outbreak of acute gastroenteritis associated with group A rotavirus and genogroup I sapovirus among adults in a mental health care facility in Japan. J Med Virol 2005; 75:475-81. [PMID: 15648058 DOI: 10.1002/jmv.20292] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An outbreak of acute gastroenteritis consisting of 57 cases occurred in a mental health care facility in Takasaki city, Japan during 6th February and 27th March 2002. A total of 18 fecal specimens collected from 17 residents and one member of the medical staff during this outbreak were tested for the presence of viral enteropathogens by RT-PCR and latex agglutination. Group A rotavirus and sapovirus were detected in 5 out of 18 fecal specimens (55.6%). To our knowledge, this is the first finding of an outbreak of gastroenteritis associated with co-circulation of different kinds of viruses such as group A rotavirus and sapovirus. All of group A rotaviruses were typed further as P[4]G2 strains. Both rotavirus and sapovirus were subjected to molecular analysis by sequencing. It was noteworthy that all rotaviruses and sapoviruses had high homologies, respectively, to each other and sapoviruses presented a potential novel sapovirus genogroup I (GI) genotype, which was obviously different from any GI genotypes (GI-a, b, c, and d). The outbreak associated with these viruses spread gradually from dormitory to dormitory, suggesting a spread by person-to-person contact, although investigation on the route of transmission of the outbreak is lacking. The findings confirm the presence of group A rotavirus and sapovirus are important in acute gastroenteritis among adults in Japan.
Collapse
Affiliation(s)
- Hainian Yan
- Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|