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Abstract
PURPOSE OF REVIEW Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen. RECENT FINDINGS Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied. SUMMARY Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.
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2
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Bennett S, Gunson RN. The development of a multiplex real-time RT-PCR for the detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. J Virol Methods 2017; 242:30-34. [PMID: 28040514 PMCID: PMC7173313 DOI: 10.1016/j.jviromet.2016.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 11/07/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Abstract
Viral gastroenteritis is a major health problem with significant morbidity and economic consequences. Viral gastroenteritis is caused by a number of viruses, including norovirus, rotavirus, adenovirus, astrovirus, and sapovirus. Conventional diagnosis is based on direct antigen detection and electron microscopy, however enzyme immunoassay's are insensitive and not available for all relevant pathogens, and electron microscope (EM) is no longer routinely carried out in most laboratories. Most laboratories now offer norovirus real-time PCR testing however the availability of other assays is variable. Commercial methods for the detection of inflectional intestinal disease (IID) are available but these can be expensive and are not commonly used. This paper describes the development of a single multiplex assay for the simultaneous detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. The multiplex was evaluated by assessing endpoint sensitivity, specificity, panel of clinical samples, quality control (QC) panel and the robustness and reproducibility of the multiplex.
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Affiliation(s)
- Susan Bennett
- West of Scotland Specialist Virology Centre, United Kingdom.
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, United Kingdom
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3
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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.
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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:
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4
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Yokoyama M, Oka T, Kojima H, Nagano T, Okabe T, Katayama K, Wakita T, Kanda T, Sato H. Structural basis for specific recognition of substrates by sapovirus protease. Front Microbiol 2012; 3:312. [PMID: 22973264 PMCID: PMC3433708 DOI: 10.3389/fmicb.2012.00312] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/08/2012] [Indexed: 01/31/2023] Open
Abstract
Sapovirus (SaV) protease catalyzes cleavage of the peptide bonds at six sites of a viral polyprotein for the viral replication and maturation. However, the mechanisms by which the protease recognizes the distinct sequences of the six cleavage sites remain poorly understood. Here we examined this issue by computational and experimental approaches. A structural modeling and docking study disclosed two small clefts on the SaV protease cavity that allow the stable and functional binding of substrates to the catalytic cavity via aromatic stacking and electrostatic interactions. An information entropy study and a site-directed mutagenesis study consistently suggested variability of the two clefts under functional constraints. Using this information, we identified three chemical compounds that had structural and spatial features resembling those of the substrate amino acid residues bound to the two clefts and that exhibited an inhibitory effect on SaV protease in vitro. These results suggest that the two clefts provide structural base points to realize the functional binding of various substrates.
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Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
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5
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[Survival strategies of human norovirus]. Uirusu 2010; 60:21-32. [PMID: 20848862 DOI: 10.2222/jsv.60.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human norovirus is a mutatable non-enveloped RNA virus capable of causing acute gastroenteritis in humans. Thus far, no experimental systems can propagate this virus in large amounts. Recent progresses in viral genomics and bioinformatics have led to a better understanding of molecular evolution of this virus in human populations. In addition, progresses in studies of the related noroviruses, those are replicable in laboratory systems, have led to a rapid accumulation of information on structural biology of norovirus. Furthermore, progresses in public health and water environment researches have led to a better understanding of viral ecology. In this review, I will first summarize fundamental characteristics of norovirus and its molecules. Then, I will summarize structure and molecular evolution of norovirus GII/4 subtype, which is now responsible for majorities of norovirus outbreaks in the world. Finally I will discuss survival strategies of human norovirus in nature by integrating the information.
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6
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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.
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7
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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.
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Affiliation(s)
- Akira Iwakiri
- Miyazaki Prefectural Institute for Public Health and Environment, Japan
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8
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Identification of a porcine calicivirus related genetically to human sapoviruses. J Clin Microbiol 2008; 46:1907-13. [PMID: 18417656 DOI: 10.1128/jcm.00341-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whether animals may act as reservoirs for human caliciviruses is unclear. By sequence analysis of a short fragment of the RNA-dependent RNA polymerase (RdRp) region, porcine sapovirus (SaV) strains that genetically resemble human SaVs have been detected in piglets, but more-informative sequences (capsid gene) were not available for a precise characterization. In this study, the 3' terminus (the 3' end of open reading frame 1 [ORF1], including the polymerase complex and the complete capsid; ORF2; and the 3' untranslated region) of one such human SaV-like strain, 43/06-18p3/2006/It, was determined, revealing that these viruses are more related genetically to human (47.4 to 54.9% amino acid identity) than to animal (35.2 to 44.7% amino acid identity) SaVs in the capsid gene. In addition, the recombination-prone RdRp-capsid junction region was highly conserved with those of human SaVs of genogroup GI. The presence of porcine viruses similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants.
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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.
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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
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Logan C, O'Leary JJ, O'Sullivan N. Real-time reverse transcription PCR detection of norovirus, sapovirus and astrovirus as causative agents of acute viral gastroenteritis. J Virol Methods 2007; 146:36-44. [PMID: 17644197 DOI: 10.1016/j.jviromet.2007.05.031] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 05/28/2007] [Accepted: 05/31/2007] [Indexed: 10/23/2022]
Abstract
The design and development of highly sensitive real-time reverse transcription PCR assays for the detection of norovirus genogroups I, II and IV, sapovirus genogroups I, II and IV, and human astrovirus from stool samples is described. Examination of 140 stool samples from paediatric patients exhibiting symptoms of diarrhoea and/or vomiting resulted in increased detection levels as compared to examination by electron microscopy. Real-time PCR resulted in a 200% increase in the rate of detection of norovirus as compared to electron microscopy. Only genogroup II noroviruses were detected in the stool specimens and when examined using partial-genotyping primers all were identified as clustering with the genogroup II/4(Bristol/Lordsdale) cluster. Sapovirus was not detected in any of the stool specimens by electron microscopy while 11% (15/140) of specimens were sapovirus positive by real-time RT-PCR, accounting for 36% of calicivirus diarrhoea. Real-time RT-PCR resulted in a tenfold increase in the rate of detection of astrovirus when compared to detection by electron microscopy with both type 1 and type 4 human astroviruses being detected in circulation. The results highlight the importance of the introduction of molecular methods for the routine screening of stool samples for causative agents of viral gastroenteritis.
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Affiliation(s)
- Catriona Logan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland.
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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.
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12
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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.
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Affiliation(s)
- Grant S Hansman
- Department of Virology II, National Institute of Infectious Diseases, Musashi-murayama, Tokyo, Japan.
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Wang QH, Costantini V, Saif LJ. Porcine enteric caliciviruses: genetic and antigenic relatedness to human caliciviruses, diagnosis and epidemiology. Vaccine 2006; 25:5453-66. [PMID: 17234307 PMCID: PMC2735111 DOI: 10.1016/j.vaccine.2006.12.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 11/29/2006] [Accepted: 12/11/2006] [Indexed: 11/17/2022]
Abstract
Porcine enteric caliciviruses include sapoviruses and noroviruses. Porcine sapoviruses infect pigs of all ages and cause diarrhea in young pigs, whereas porcine noroviruses were detected exclusively from adult pigs without clinical signs. Importantly, certain porcine norovirus strains were genetically and antigenically related to human noroviruses. This raises public health concerns that pigs may be reservoirs for emergence of epidemic human norovirus strains. This article reviews the discovery of porcine noroviruses and sapoviruses, their classification, diagnosis, epidemiology and genetic and antigenic relatedness to human caliciviruses.
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Affiliation(s)
- Qiu-Hong Wang
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Veronica Costantini
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691
| | - Linda J. Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691
- *Corresponding author: Dr. Linda J. Saif, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691; Phone: 330-263-3744; Fax: 330-263-3677; E-mail:
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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: 31] [Impact Index Per Article: 1.7] [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.
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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
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15
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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.
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Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan.
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16
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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.
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Affiliation(s)
- M Okada
- Division of Virology, Chiba Prefectural Institute of Public Health, Chuo-ku, Chiba-shi, Chiba, Japan.
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17
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Gallimore CI, Iturriza-Gomara M, Lewis D, Cubitt D, Cotterill H, Gray JJ. Characterization of sapoviruses collected in the United Kingdom from 1989 to 2004. J Med Virol 2006; 78:673-82. [PMID: 16555276 DOI: 10.1002/jmv.20592] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A fecal archive containing 115 sapovirus (SaV) strains detected in samples collected from 15 outbreaks and 98 sporadic cases of gastroenteritis between 1989 and 2004 in the UK were characterized in order to determine the genomic diversity within SaV co-circulating in the human population. Strains were characterized by partial sequencing of the genes encoding the RNA-dependent RNA polymerase (RdRp) region and/or the polymerase/capsid (Pol/Cap) junction of the open reading frame (Orf) 1. Overall, SaV of genogroup I genotype 1 (GI 1) were the predominant strains circulating in the UK in each year between 1989 and 2004. During 2004, GII 1 was the predominant strain. These two SaV types accounted for 89.5% of the sporadic cases and outbreaks in the UK. The remaining cases were caused by six other SaV genotypes. On the basis of partial sequencing of the RdRp and capsid encoding genes of strains, which did not show sufficient homology to any of the currently recognized genotypes, we propose the inclusion of a presumptive fourth genotype within genogroup I (GI 4).
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Affiliation(s)
- Chris I Gallimore
- Enteric Virus Unit, Virus Reference Department, Centre for Infections, Health Protection Agency, Colindale, London, United Kingdom.
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Wang QH, Han MG, Funk JA, Bowman G, Janies DA, Saif LJ. Genetic diversity and recombination of porcine sapoviruses. J Clin Microbiol 2006; 43:5963-72. [PMID: 16333083 PMCID: PMC1317165 DOI: 10.1128/jcm.43.12.5963-5972.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Human SaVs are genetically variable and have been classified into four genogroups (GI, -II, -IV, and -V). To date, only two genetically similar porcine SaV strains have been reported that belong to GIII. To investigate the genetic diversity of porcine SaVs and their genetic relatedness to human strains, we sequenced 286 nucleotides (nt) of the RNA-dependent RNA polymerase (RdRp) region of nine porcine SaVs detected from field pig fecal samples collected in U.S. swine farms during the period from 1999 to 2003. One strain (Po/SaV/MI-QW19/2002/US) was most closely related to human GII SaVs. We also sequenced 3 kb of the viral genome, including the partial RdRp (766 to 790 nt), the complete capsid, the ORF2 and the 3'-untranslated region of four strains representative for the positive farms or for the distinct genetic clusters. From the sequence analysis of the complete capsid, we identified a potential new genogroup of porcine SaVs, with Po/SaV/OH-JJ681/00/US as the representative strain. Furthermore, two potential porcine SaV recombinants were identified. To our knowledge this is the first report of a porcine SaV strain more closely related genetically to human SaVs and the occurrence of porcine SaV recombinants. The presence of porcine SaVs more similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants if intragenogroup human strains exist.
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Affiliation(s)
- Qiu-Hong Wang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA
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Oka T, Hansman GS, Katayama K, Ogawa S, Nagata N, Miyamura T, Takeda N. Expression of sapovirus virus-like particles in mammalian cells. Arch Virol 2005; 151:399-404. [PMID: 16132181 DOI: 10.1007/s00705-005-0613-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Accepted: 07/01/2005] [Indexed: 10/25/2022]
Abstract
Sapovirus (SaV) is an etiological agent of acute gastroenteritis in human and swine. SaV can be divided into five genogroups, GI to GV. Virus-like particles (VLPs) morphologically similar to native SaV have been expressed for GI, GII, GIII and GV strains in insect cells, although only low expression levels were observed for GII strains. In this study, we report the successful expression of SaV GII VLPs using cultured mammalian COS-7 and 293T cells. Our results demonstrated that this mammalian expression system was able to express and form SaV VLPs.
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Affiliation(s)
- T Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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Oka T, Katayama K, Ogawa S, Hansman GS, Kageyama T, Miyamura T, Takeda N. Cleavage activity of the sapovirus 3C-like protease in Escherichia coli. Arch Virol 2005; 150:2539-48. [PMID: 16052286 DOI: 10.1007/s00705-005-0591-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 05/19/2005] [Indexed: 11/30/2022]
Abstract
We recently determined the ORF1 cleavage map of Mc10, a human sapovirus (SaV) strain, as follows: NH2-p11-p28-p35(NTPase)-p32-p14(VPg)-p70(Pro-Pol)-p60(VP1)-COOH. This cleavage was dependent on the viral encoded 3C-like protease. To identify the cleavage site of SaV ORF1, putative p70 (Pro-Pol) and p14-p70 (VPg-Pro-Pol) were expressed as N-terminal GST and C-terminal 6 x His-tag fusion proteins in Escherichia coli, and the expressed products were analyzed by SDS-PAGE and Western blotting. Our results indicated that the efficient proteolytic cleavage occurred between p14 (VPg) and p70 (Pro-Pol), and N-terminal amino acid sequencing revealed that the cleavage site was between E(1055) and A(1056). In contrast, the p70 (Pro-Pol) was not further cleaved. We also found that SaV protease cleaved the Q/G site within the rhinovirus 3C protease recognition site. Site-directed mutagenesis in a conserved GDCG motif of the protease completely abolished these proteolytic activities. This is the first report to identify the cleavage site of the SaV ORF1 polyprotein.
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Affiliation(s)
- T Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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Oka T, Katayama K, Ogawa S, Hansman GS, Kageyama T, Ushijima H, Miyamura T, Takeda N. Proteolytic processing of sapovirus ORF1 polyprotein. J Virol 2005; 79:7283-90. [PMID: 15919882 PMCID: PMC1143638 DOI: 10.1128/jvi.79.12.7283-7290.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 01/25/2005] [Indexed: 11/20/2022] Open
Abstract
The genome of Sapovirus (SaV), a causative agent of gastroenteritis in humans and swine, contains either two or three open reading frames (ORFs). Functional motifs characteristic to the 2C-like NTPase (NTPase), VPg, 3C-like protease (Pro), 3D-like RNA-dependent RNA polymerase (Pol), and capsid protein (VP1) are encoded in the ORF1 polyprotein, which is afterwards cleaved into the nonstructural and structural proteins. We recently determined the complete genome sequence of a novel human SaV strain, Mc10, which has two ORFs. To investigate the proteolytic cleavage of SaV ORF1 and the function of protease on the cleavage, both full-length and truncated forms of the ORF1 polyprotein either with or without mutation in (1171)Cys to Ala of the GDCG motif were expressed in an in vitro coupled transcription-translation system. The translation products were analyzed directly by sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by immunoprecipitation with region-specific antibodies. The ORF1 polyprotein was processed into at least 10 major proteins: p11, p28, p35, p32, p14, p70, p60, p66, p46, and p120. Seven of these products were arranged in the following order: NH(2)-p11-p28-p35(NTPase)-p32-p14(VPg)-p70(Pro-Pol)-p60(VP1)-COOH. p66, p46 and p120 were precursors of p28-p35 (NTPase), p32-p14 (VPg), and p32-p14 (VPg)-p70 (Pro-Pol), respectively. Mutagenesis in the 3C-like protease motif fully abolished the proteolytic activity. The cleavage map of SaV ORF1 is similar to those of other heretofore known members of the family Caliciviridae, especially to rabbit hemorrhagic disease virus, a member of the genus Lagovirus.
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Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan.
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Gallimore CI, Cubitt DW, Richards AF, Gray JJ. Diversity of enteric viruses detected in patients with gastroenteritis in a tertiary referral paediatric hospital. J Med Virol 2004; 73:443-9. [PMID: 15170641 DOI: 10.1002/jmv.20110] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The genetic diversity of enteric viruses co-circulating in a cohort of patients with viral gastroenteritis in a large tertiary paediatric hospital in London, UK, was determined. Multiple strains of noroviruses (NV), sapoviruses (SV) and astroviruses (HAsV) were detected in these patients, indicating the likelihood of multiple introductions from different sources, possible sub-clinical infections and simultaneous infection with different viruses in immunocompromised and other patients. Routine screening of immunocompromised patients and infection control procedures are important to prevent nosocomial infection.
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Affiliation(s)
- Chris I Gallimore
- Enteric Virus Unit, Enteric, Respiratory and Neurological Virus Laboratory, Central Public Health Laboratory, Specialist and Reference Microbiology Division, Health Protection Agency, Colindale, London, United Kingdom. christopher.gallimore@hpa/org.uk
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Vipond IB, Caul EO, Hirst D, Carmen B, Curry A, Lopman BA, Pead P, Pickett MA, Lambden PR, Clarke IN. National epidemic of Lordsdale Norovirus in the UK. J Clin Virol 2004; 30:243-7. [PMID: 15135743 DOI: 10.1016/j.jcv.2003.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2003] [Indexed: 10/26/2022]
Abstract
BACKGROUND In early 2002 reports of outbreaks of gastroenteritis reached unprecedented levels in the UK. Forty five Norovirus outbreaks were reported in January 2002. OBJECTIVES The objective of the study was to determine whether the outbreaks were Noroviral in origin and if so whether they represented a homogeneous or heterogeneous collection of Noroviruses by applying EIA and sequence analysis to representative faecal samples. STUDY DESIGN Faecal specimens were collected during the week of highest incidence from 21 outbreaks in a variety of health care settings including hospitals and nursing homes. The outbreaks occurred in geographically distinct regions of the UK and samples were collected by reference laboratories in Glasgow, Manchester, Bristol and Southampton. RESULTS The samples were all positive for Noroviruses by negative stain electron microscopy (EM) and Lordsdale virus (LV) EIA, therefore reverse transcriptase polymerase chain reaction (RT-PCR) amplification and nucleotide sequencing of the Norovirus RNA polymerase gene was performed on amplicons from samples of each of the 21 outbreaks to investigate the nature and extent of diversity. All samples were very closely related to the reference Lordsdale virus genome sequence. LV was first discovered during an hospital outbreak of gastroenteritis in Southampton General Hospital in March 1993. CONCLUSIONS Noroviruses are a major cause of outbreaks of gastroenteritis in health care settings. LV is the predominant Norovirus in the UK and was detected in outbreaks that occurred during the national peak of gastroenteritis reports in January 2002.
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Affiliation(s)
- I B Vipond
- Bristol Public Health Laboratory, Myrtle Road, Bristol, BS2 8EL, UK
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Abstract
PURPOSE OF REVIEW Caliciviruses are a major cause of human illness, and are listed as category B pathogens according to the National Institute of Allergy and Infectious Diseases classification of pathogens important for biodefense. Caliciviruses are commonly encountered in contaminated food and water, and a large variety has been implicated as sources of infection during outbreak investigations. RECENT FINDINGS New names for two of the four genera of the Caliciviridae were approved in 2002. They are Norovirus, for what were previously called Norwalk-like viruses or small, round-structured viruses, and Sapovirus, for what were previously called Sapporo-like viruses. Caliciviruses are highly diverse genetically and antigenically. This diversity complicates the design of diagnostic assays, yet can be used to discriminate contaminating and infecting strains during outbreak investigations. Of particular interest is the recent finding of naturally occurring recombinant Norovirus strains, all of which have been virulent and are widely dispersed and apparently ecologically indistinguishable from other calicivirus strains. This finding is considered in light of the evidence for recombination between caliciviruses and picornaviruses, and recombination as a more general phenomenon for virus evolution. SUMMARY Continued investigations of calicivirus outbreaks are now focusing on the implicated sources of infection. While many foods and environmental waters have long been implicated as outbreak sources, the methods for detecting caliciviruses are being developed and refined. Recognition is now turning to unexpected sources of contamination, such as presumably clean foods and waters, including bottled water and minimally handled foods. Parallels between Norovirus and Salmonella ecology and epidemiology are noted, as a guide to understanding evolving new information about caliciviruses.
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Affiliation(s)
- David O Matson
- Center for Pediatric Research, Eastern Virginia Medical School and Children's Hospital of The King's Daughters, Norfolk, Virginia 23510, USA.
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Richards AF, Lopman B, Gunn A, Curry A, Ellis D, Cotterill H, Ratcliffe S, Jenkins M, Appleton H, Gallimore CI, Gray JJ, Brown DWG. Evaluation of a commercial ELISA for detecting Norwalk-like virus antigen in faeces. J Clin Virol 2003; 26:109-15. [PMID: 12589841 DOI: 10.1016/s1386-6532(02)00267-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A commercially available enzyme immunoassay, the IDEIA Norwalk-like virus (NLV) enzyme linked immunosorbent assay (ELISA; Dako Cytomation, Ely, UK) for detecting NLV antigen in faecal samples and determining the NLV genogroup was evaluated. The performance of the ELISA was compared with that of electron microscopy and the reverse transcription polymerase chain reaction by testing a panel of faecal samples collected from patients involved in outbreaks of gastroenteritis. When compared with reverse transcription-polymerase chain reaction (RT-PCR), the ELISA had a sensitivity and specificity of 55.5 and 98.3%, respectively. This compares with a sensitivity and specificity for EM of 23.9 and 99.2%, respectively. The sensitivity and specificity of the ELISA for determining the aetiology of a Norwalk virus-like outbreak, based on two or more positive samples within an outbreak, were 52.2 and 100% when two samples were collected from an outbreak and 71.4 and 100% when six or more samples were collected. The ELISA correctly identified the NLV genogroups of viruses previously characterised by partial DNA sequencing. The ELISA is a suitable alternative to the preliminary screening by EM for investigating outbreaks of gastroenteritis. Outbreaks, negative by ELISA should be examined by RT-PCR in order to detect strains non-reactive in the assay and virus strains from representative ELISA positive outbreaks should be characterised fully to allow the genetic diversity of NLVs co-circulating in the population to be described.
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Affiliation(s)
- A F Richards
- Enteric Virus Unit, Enteric, Respiratory and Neurological Virus Laboratory, Central Public Health Laboratory, 61 Colindale Ave., London NW9 5HT, UK
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