Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity

Genotype diversity and molecular evolution of noroviruses: A 30-year (1982-2011) comprehensive study with children from Northern Brazil

A chronologically comprehensive 30-year study was conducted that involved children living in Belém, in the Amazon region of Northern Brazil, who participated in eight different studies from October 1982 to April 2011. The children were followed either in the community or in health units and hospitals in order to identify the norovirus genotypes involved in infections during this time. A total of 2,520 fecal specimens were obtained and subjected to RT-PCR and nucleotide sequencing for regions A, B, C, D and P2 of the viral genome. An overall positivity of 16.9% (n = 426) was observed, and 49% of the positive samples were genotyped (208/426), evidencing the presence of several genotypes as follows: Polymerase gene (GI.P4, GII.Pa, GII.Pc, GII.Pe, GII.Pg, GII.Pj, GII.P3, GII.P4, GII.P6, GII.P7, GII.P8, GII.P12, GII.P13, GII.P14, GII.P21, GII.P22), and VP1 gene (GI.3, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.8, GII.10, GII.12, GII.14, GII.17, GII.23). The GII.P4/GII.4 genotype determined by both open reading frames (ORFs) (partial polymerase and VP1 genes) was found for 83 samples, and analyses of the subdomain P2 region showed 10 different variants: CHDC (1970s), Tokyo (1980s), Bristol_1993, US_95/96, Kaiso_2003, Asia_2003, Hunter_2004, Yerseke_2006a, Den Haag_2006b (subcluster “O”) and New Orleans_2009. Recombination events were confirmed in 47.6% (n = 20) of the 42 samples with divergent genotyping by ORF1 and ORF2 and with probable different breakpoints within the viral genome. The evolutionary analyses estimated a rate of evolution of 1.02 x 10⁻² and 9.05 x 10⁻³ subs./site/year using regions C and D from the VP1 gene, respectively. The present research shows the broad genetic diversity of the norovirus that infected children for 30 years in Belém. These findings contribute to our understanding of noroviruses molecular epidemiology and viral evolution and provide a baseline for vaccine design.

Titanium Dioxide Nanoparticles Evoke Proinflammatory Response during Murine Norovirus Infection Despite Having Minimal Effects on Virus Replication

Noroviruses (NoV) have enhanced tropism for the gastrointestinal (GI) tract and are the major cause of nonbacterial gastroenteritis in humans. Titanium dioxide (TiO2) nanoparticles (NPs) used as food additives, dietary supplements, and cosmetics accumulate in the GI tract. We investigated the effect anatase TiO2 NPs on NoV replication and host response during virus infection, using murine norovirus (MNV-1) infection of RAW 264.7 macrophages. Pretreatment with 20 μg/ml anatase NPs significantly reduced the viability of macrophages alone or during virus infection, but did not alter virus replication. In contrast, pre-incubation with 2 μg/ml anatase NPs reduced virus replication fivefold at 48 h. The presence of anatase NPs during MNV-1 infection evoked a pro-inflammatory response, as measured by a significant increase in expression of cytokines, including IL-6, IFN-γ, TNFα and the TGFβ1. No genotoxic insults due to anatase TiO2 NPs alone or to their presence during MNV-1 infection were detected. This study highlights important safety considerations related to NP exposure of the GI tract in individuals infected with noroviruses or other foodborne viruses.

Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses

Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.

Infection of Murine Macrophages by Salmonella enterica Serovar Heidelberg Blocks Murine Norovirus Infectivity and Virus-induced Apoptosis

Gastroenteritis caused by bacterial and viral pathogens constitutes a major public health threat in the United States accounting for 35% of hospitalizations. In particular, Salmonella enterica and noroviruses cause the majority of gastroenteritis infections, with emergence of sporadic outbreaks and incidence of increased infections. Although mechanisms underlying infections by these pathogens have been individually studied, little is known about the mechanisms regulating co-infection by these pathogens. In this study, we utilized RAW 264.7 murine macrophage cells to investigate the mechanisms governing co-infection with S. enterica serovar Heidelberg and murine norovirus (MNV). We demonstrate that infection of RAW 264.7 cells with S. enterica reduces the replication of MNV, in part by blocking virus entry early in the virus life cycle, and inducing antiviral cytokines later in the infection cycle. In particular, bacterial infection prior to, or during MNV infection affected virus entry, whereas MNV entry remained unaltered when the virus infection preceded bacterial invasion. This block in virus entry resulted in reduced virus replication, with the highest impact on replication observed during conditions of co-infection. In contrast, bacterial replication showed a threefold increase in MNV-infected cells, despite the presence of antibiotic in the medium. Most importantly, we present evidence that the infection of MNV-infected macrophages by S. enterica blocked MNV-induced apoptosis, despite allowing efficient virus replication. This apoptosis blockade was evidenced by reduction in DNA fragmentation and absence of poly-ADP ribose polymerase (PARP), caspase 3 and caspase 9 cleavage events. Our study suggests a novel mechanism of pathogenesis whereby initial co-infection with these pathogens could result in prolonged infection by either of these pathogens or both together.

Acute gastroenteritis outbreak caused by a GII.6 norovirus

AIM: To report an acute gastroenteritis outbreak caused by a genogroup 2 genotype 6 (GII.6) strain norovirus in Shanghai, China.

METHODS: Noroviruses are responsible for approximately half of all reported gastroenteritis outbreaks in many countries. Genogroup 2 genotype 4 strains are the most prevalent. Rare outbreaks caused by GII.6 strains have been reported. An acute gastroenteritis outbreak occurred in an elementary school in Shanghai in December of 2013. Field and molecular epidemiologic investigations were conducted.

RESULTS: The outbreak was limited to one class in an elementary school located in southwest Shanghai. The age of the students ranged from 9 to 10 years. The first case emerged on December 10, 2013, and the last case emerged on December 14, 2013. The cases peaked on December 11, 2013, with 21 new cases. Of 45 students in the class, 32 were affected. The main symptom was gastroenteritis, and 15.6% (5/32) of the cases exhibited a fever. A field epidemiologic investigation showed the pathogen may have been transmitted to the elementary school from employees in a delicatessen via the first case student, who had eaten food from the delicatessen one day before the gastroenteritis episodes began. A molecular epidemiologic investigation identified the cause of the gastroenteritis as norovirus strain GII.6; the viral sequence of the student cases showed 100% homology with that of the shop employees. Genetic relatedness analyses showed that the new viral strain is closely related to previously reported GII.6 sequences, especially to a strain reported in Japan.

CONCLUSION: This is the first report to show that norovirus strain GII.6 can cause a gastroenteritis outbreak. Thus, the prevalence of GII.6 noroviruses requires attention.

Role of norovirus in acute gastroenteritis in the Northwest of Spain during 2010-2011

A total of 2,643 samples from patients with gastroenteritis in Galicia (NW Spain) were tested for the presence of Norovirus (NoV). NoV genogroup GI was detected in 416 (15.7%) samples, while NoV genogroup GII was detected in 278 (10.5%) samples. Mixed infections of NoV GI and GII were observed in 53 (2%) samples. Total prevalence of NoV in the analyzed samples was 28.3%. Besides NoV diagnosis assay, all the specimens were also submitted to routine clinical bacteriology tests. Cryptosporidium spp. as well as adenovirus (AdV) and rotavirus (RV) were determined on some samples after specific request by hospital units. The results obtained allowed to determine the disease etiology in 14.4% of the patients. Taking into account all the microorganisms studied, the etiological agent was determined for 39.5% of the cases. The results indicated that NoVs are the leading cause of acute gastroenteritis in all age-groups in Northwestern Spain, and that the lack of routine NoV diagnosis contributes to the underestimation of the importance of this virus, not only in outbreaks, but also in sporadic cases of acute gastroenteritis.

Molecular epidemiology of noroviruses associated with acute sporadic gastroenteritis in children: global distribution of genogroups, genotypes and GII.4 variants

Noroviruses are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. The development of sensitive molecular diagnostic techniques has revolutionized our understanding of norovirus epidemiology over the past two decades, but norovirus strain types associated with sporadic gastroenteritis remain poorly described. Therefore, we conducted a systematic review of studies performed after 2000 to clarify the genotypic distribution of noroviruses in children (≤18 years of age) with sporadic acute gastroenteritis. Genogroup GII norovirus was the most prevalent, accounting for 96% of all sporadic infections. GII.4 was the most prevalent genotype, accounting for 70% of the capsid genotypes and 60% of the polymerase genotypes, followed by the capsid genotype GII.3 (16%) and the polymerase genotype GII.b (14%). The most common ORF1/ORF2 inter-genotype recombinants were GII.b, GII.12, and GII.4 polymerase genotypes combined with the capsid genotype GII.3, accounting for 19% of all genotyped strains. The distribution of GII.4 variants over the last decade was dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008 with GII.4/2006b continuing to date. Genotypes GII.4 and GII.3 have predominated in children during the past decade; this is most notable in the global emergence of GII.4 variant noroviruses. As the burden of rotavirus disease decreases following the introduction of childhood immunization programs, the relative importance of norovirus in the etiology of acute childhood gastroenteritis will likely increase. In order for a successful norovirus vaccine to be developed, it should provide immunity against strains with capsid genotypes GII.4 and GII.3.

Norovirus: an overview

Although noroviruses (NoVs) were the first viral agents linked to gastrointestinal disease, for a long time they have been considered secondary cause of gastroenteritis, second to rotaviruses as etiologic agents. The development of molecular techniques in diagnosing NoV provided a clearer insight into the epidemiological impact of these viruses, which are currently recognized not only as the leading cause of non-bacterial gastroenteritis outbreaks, but also as a major cause of sporadic gastroenteritis in both children and adults. This review focuses on the required knowledge to understand their morphology, genetics, transmission, pathogenesis, and control. Since no vaccine is available, prevention of NoV infection relies mainly on strict community and personal hygiene measures.

Optimization of a real-time RT-PCR assay reveals an increase of genogroup I norovirus in the clinical setting

Although norovirus has been identified as the most common cause of gastroenteritis, the majority of cases have no etiologic agent identified. In this study, we describe the optimization of a real-time RT-PCR assay for the improved detection of genogroup I norovirus in patient specimens based upon sequence data from a collection of representative clinical norovirus sequences. The redesigned assay demonstrated a 64 fold increase in sensitivity, a 2 log decrease in the limit of detection, and an 18% increase in amplification efficiency, when compared to the standard assay. The optimized test also detected GI norovirus in clinical specimens that were initially negative by the standard assay. Use of the optimized assay increased the annual positivity of GI norovirus in Iowa from 1.2% to 4.5%, indicating the prevalence of GI norovirus may be higher than previously identified. Laboratory confirmation of the etiologic agent involved in gasteroenteritis cases is essential for better understanding of the prevalence and transmission of noroviruses.

Molecular epidemiology of genogroup II-genotype 4 noroviruses in the United States between 1994 and 2006

Human noroviruses (NoVs) of genogroup II, genotype 4 (GII.4) are the most common strains detected in outbreaks of acute gastroenteritis worldwide. To gain insight into the epidemiology and genetic variation of GII.4 strains, we analyzed 773 NoV outbreaks reported to the CDC from 1994 to 2006. Of these NoV outbreaks, 629 (81.4%) were caused by GII viruses and 342 (44.2%) were caused by GII.4 strains. The proportion of GII.4 outbreaks increased from 5% in 1994 to 85% in 2006, but distinct annual differences were noted, including sharp increases in 1996, 2003, and 2006 each associated with newly emerging GII.4 strains. Sequence analysis of the full-length VP1 gene of GII.4 strains identified in this study and from GenBank segregated these viruses into at least 9 distinct subclusters which had 1.3 to 3.2% amino acid variation between strains in different subclusters. We propose that GII.4 subclusters be defined as having >5% sequence variation between strains. Our data confirm other studies on the rapid emergence and displacement of highly virulent GII.4 strains.

Identification of monomorphic and divergent haplotypes in the 2006-2007 norovirus GII/4 epidemic population by genomewide tracing of evolutionary history

Our norovirus (NoV) surveillance group reported a >4-fold increase in NoV infection in Japan during the winter of 2006-2007 compared to the previous winter. Because the increase was not linked to changes in the surveillance system, we suspected the emergence of new NoV GII/4 epidemic variants. To obtain information on viral changes, we conducted full-length genomic analysis. Stool specimens from 55 acute gastroenteritis patients of various ages were collected at 11 sites in Japan between May 2006 and January 2007. Direct sequencing of long PCR products revealed 37 GII/4 genome sequences. Phylogenetic study of viral genome and partial sequences showed that the two new GII/4 variants in Europe, termed 2006a and 2006b, initially coexisted as minorities in early 2006 in Japan and that 2006b alone had dominated over the resident GII/4 variants during 2006. A combination of phylogenetic and entropy analyses revealed for the first time the unique amino acid substitutions in all eight proteins of the new epidemic strains. These data and computer-assisted structural study of the NoV capsid protein are compatible with a model of antigenic drift with tuning of the structure and functions of multiple proteins for the global outgrowth of new GII/4 variants. The availability of comprehensive information on genome sequences and unique protein changes of the recent global epidemic variants will allow studies of diagnostic assays, molecular epidemiology, molecular biology, and adaptive changes of NoV in nature.

Genetic analysis of the capsid gene of genotype GII.2 noroviruses

Noroviruses (NoVs) are considered to be a major cause of acute nonbacterial gastroenteritis in humans. The NoV genus is genetically diverse, and genotype GII.4 has been most commonly identified worldwide in recent years. In this study we analyzed the complete capsid gene of NoV strains belonging to the less prevalent genotype GII.2. We compared a total of 36 complete capsid sequences of GII.2 sequences obtained from the GenBank (n = 5) and from outbreaks or sporadic cases that occurred in The Netherlands (n = 10) and in Osaka City, Japan (n = 21), between 1976 and 2005. Alignment of all capsid sequences did not show fixation of amino acid substitutions over time as an indication for genetic drift. In contrast, when strains previously recognized as recombinants were excluded from the alignment, genetic drift was observed. Substitutions were found at five informative sites (two in the P1 subdomain and three in the P2 subdomain), segregating strains into five genetic groups (1994 to 1997, 1999 to 2000, 2001 to 2003, 2004, and 2005). Only one amino acid position changed consistently between each group (position 345). Homology modeling of the GII.2 capsid protein showed that the five amino acids were located on the surface of the capsid and close to each other at the interface of two monomers. The data suggest that these changes were induced by selective pressure, driving virus evolution. Remarkably, this was observed only for nonrecombinant genomes, suggesting differences in behavior with recombinant strains.

Humoral immune responses against norovirus infections of children

In 2 infants with gastroenteritis associated with Norovirus (NoV), serum immunoglobulin (Ig) G, IgM, IgA, and fecal IgA antibody responses against NoV were examined by enzyme-linked immunosorbent assay using 11 different antigenic and genetic types of NoV virus-like particles expressed in insect cells. These two cases were putative primary single NoV infections, because antibodies against NoVs were not detected in acute-phase serums. In one of two cases, long-term excretion of virus RNA for 33 days was observed. Serum IgG responses demonstrated strong seroresponse to the homologous type, and weak seroresponse to the heterologous types within the genogroup. After more than 2 years, the IgG antibody titer remained high to the homologous type and low to the heterologous type within the genogroup. IgM and IgA were specific to the homologous type. IgM was short lived and the serum IgA antibody titer remained low to the homologous type for a long period. These results improve our understanding of the humoral immune response to NoV infection.

Rapid detection of Norovirus based on an automated extraction protocol and a real-time multiplexed single-step RT-PCR

BACKGROUND

Molecular diagnosis of Norovirus infection can be a complex multistep process, which requires significant user intervention and expertise, and is not amenable to automation without extensive validation and optimization.

OBJECTIVES

To develop a real-time multiplexed RT-PCR assay with automated sample preparation that requires only a single-step and a single-tube for reverse transcription, amplification, and detection while exceeding the sensitivity of conventional PCR for broad-spectrum Norovirus detection.

STUDY DESIGN

Limit of detection was assessed against dilutions of clinical specimens. Fifty archived extractions were used to compare TaqMan sensitivity with either a separate RT using random primers or a single-step RT-PCR. The sensitivity of the novel assay was compared with conventional RT-PCR using 100 specimens from gastroenteritis cases.

RESULTS

Automated extraction reduced RNA recovery by 0.5 logs compared to manual extraction but was more effective at removing PCR inhibitors from stool specimens. The optimized single-step real-time RT-PCR demonstrated no reduction in sensitivity. Together, the sensitivity of the novel assay was 19% higher than manual extraction with conventional RT-PCR.

CONCLUSIONS

A semi-automated and simplified molecular diagnostic protocol for the rapid detection of Norovirus has been achieved. PCR inhibitors are present in human fecal specimens and cause a significant problem for Norovirus detection by RT-PCR.

Virological, serological, and clinical features of an outbreak of acute gastroenteritis due to recombinant genogroup II norovirus in an infant home

Norovirus (NV) is an important cause of acute nonbacterial gastroenteritis worldwide. Recently, several sporadic cases due to naturally occurring recombinant NVs have been reported. In January 2000, there was an outbreak of gastroenteritis in an infant home in Sapporo, Japan. Of 34 residents of the home that were less than 2 years old, 23 developed gastrointestinal symptoms and NV infection was confirmed by conventional reverse transcription-PCR to detect the RNA polymerase region of genogroup II NV. In this virus, the RNA polymerase region shared 86% nucleotide identity with Hawaii virus but only 77% with Mexico virus; however, its capsid region shared only 70% identity with Hawaii virus but 90% with Mexico virus. On the other hand, both regions shared a higher 96% nucleotide identity with Arg320 virus, which was found in Mendoza, Argentina, in 1995 and considered to be a recombinant of Hawaii and Mexico viruses. The findings indicate that the virus involved in the outbreak was similar and may have evolved from the Arg320 virus. Clinically the cases were more severe than those of previously reported sporadic or outbreak cases of NV infection.

High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus

Viruses of the Norovirus genus (Caliciviridae family) are a major cause of human gastroenteritis. In some viruses, recombination is an important evolutionary process and therefore we should try to discover the quantity and characteristics of such events in Noroviruses. In order to identify recombination events, multiple sequence alignments were assembled from publicly available strains, and were tested using RAT, a recently developed software tool. Strains identified by RAT as putative recombinants were tested further, using a phylogenetic approach, the LARD software, and a Monte Carlo method, to gain additional support for their status. The identification of two previously described recombinants, WUG1 and Snow Mountain, was made. Furthermore, three instances of hitherto unreported recombination implicating Norovirus strains MD 145-12, Gifu'96 and Saitama U4 were found, with good statistical support for the latter two of these cases. Lordsdale-like viruses were highlighted as major contributors to recombination events during Norovirus evolution. Finally, the relevance of recombinants to the worldwide transmission of Norovirus is discussed.

Self-assembly of the recombinant capsid protein of a bovine norovirus (BoNV) into virus-like particles and evaluation of cross-reactivity of BoNV with human noroviruses

None of the enteric caliciviruses except Po/Sapo/GIII/Cowden/80/US replicates in cell culture, which complicates efforts to develop control strategies or to study viral replication. To develop serological assays for bovine noroviruses (BoNVs) and to determine the cross-reactivity of BoNV with human noroviruses, we generated two recombinant baculoviruses, rCV186-OH and rJNCV, to express the capsid genes of Bo/CV186-OH/00/US (Norovirus genogroup III [GIII], genotype 2 [GIII/2]). rCV186-OH expressed the expected 57-kDa capsid protein, but rJNCV expressed a truncated capsid protein of 35 kDa. Sequence analysis of rJNCV identified a single nucleotide deletion in the P domain of the capsid gene, which introduced a stop codon at amino acid 323. The recombinant capsid protein produced by rCV186-OH but not that produced by rJNCV self-assembled into virus-like particles (VLPs) similar to native BoNV. An antibody-capture enzyme-linked immunosorbent assay (ELISA) and antigen-capture ELISA (Ag-ELISA) detected serum antibody and antigen, respectively, from calves infected with Bo/CV186-OH/00/US but not antibodies or antigens to other enteric viruses. In other tests of the GIII/2 BoNV Ag-ELISA, no cross-reactivity was observed with VLPs from one GI and four GII human noroviruses and porcine sapovirus Cowden strain. Because, like human noroviruses, BoNVs do not grow in cell culture, the BoNV VLPs will be useful in the serological assays described for the detection of BoNV antibody and antigen. Consistent with the phylogenetic analysis of the capsid genes of bovine and human noroviruses (M. G. Han, J. R. Smiley, C. Thomas, and L. J. Saif, J. Clin. Microbiol. 42:5214-5224, 2004), the results suggest that GIII/2 BoNV does not share significant antigenic relationships with the five characterized human noroviruses tested.

Genetic recombination between two genotypes of genogroup III bovine noroviruses (BoNVs) and capsid sequence diversity among BoNVs and Nebraska-like bovine enteric caliciviruses

To determine the genogroups and genotypes of bovine enteric caliciviruses (BECVs) circulating in calves, we determined the complete capsid gene sequences of 21 BECVs. The nucleotide and predicted amino acid sequences were compared phylogenetically with those of known human and animal enteric caliciviruses. Based on these analyses, 15 BECVs belonged to Norovirus genogroup III and genotype 2 (GIII/2) and were genetically distinct from human Norovirus GI and GII. Six BECVs had capsid gene sequences similar to that of the unclassified Nebraska (NB)-like BECV. The 15 bovine noroviruses (BoNVs) were more closely related to Bo/NLV/Newbury-2/76/UK (GIII/2) and other known genotype 2 BoNVs than to genotype 1 Bo/NLV/Jena/80/DE. The BoNV Bo/CV521-OH/02/US showed high nucleotide and amino acid identities (84 and 94%, respectively) with the capsid gene of Bo/NLV/Newbury-2/76/UK, whereas the nucleotide and amino acid sequences of the RNA polymerase gene were more closely related to those of Bo/NLV/Jena/80/DE (77 and 87% identities, respectively) than to those of Bo/NLV/Newbury-2/76/UK (69 and 69% identities, respectively), suggesting that Bo/CV521-OH/02/US is a genotype 1-2 recombinant. Gene conversion analysis by the recombinant identification program and SimPlot also predicted that Bo/CV521-OH/02/US was a recombinant. Six NB-like BECVs shared 88 to 92% nucleotide and 94 to 99.5% amino acid identities with the NB BECV in the capsid gene. The results of this study demonstrate genetic diversity in the capsid genes of BECVs circulating in Ohio veal calves, provide new data for coinfections with distinct BECV genotypes or genogroups, and describe the first natural BoNV genotype 1-2 recombinant, analogous to the previously reported human norovirus recombinants.

Norovirus contamination found in oysters worldwide

Noroviruses (Norwalk-like viruses) are recognized as major causes of acute gastroenteritis worldwide. Outbreaks of norovirus gastroenteritis are often associated with consumption of oysters. In this study, oysters imported into Hong Kong from 11 countries over a 3-year period were screened by RT-PCR. Overall, 53 out of 507 (10.5%) samples were positive for norovirus-RNA, and a wide variety of strains were found. Two novel genetic clusters were detected, which could indicate novel human or animal norovirus strains. However, whether these two new clusters are of human or animal origin is not known. Thirteen outbreaks, in which oysters were implicated as the source of infection were investigated: Norovirus RNA sequences could be detected in oysters from six outbreaks, but only in one outbreak the strains isolated from patients and oysters matched (>98% homology). Therefore, RT-PCR was of use in detecting norovirus contamination of oysters implicated in an outbreak, but was less useful in demonstrating an actual molecular epidemiological link with human cases. It was shown that contamination by noroviruses could be demonstrated in oysters worldwide, and therefore oysters may serve as an important vehicle for introducing novel norovirus strains.

Mutation in a Lordsdale norovirus epidemic strain as a potential indicator of transmission routes

An increase in norovirus outbreaks was reported internationally during 2002 and 2003 and was also observed in Oxfordshire (United Kingdom) hospitals. To understand their epidemiological relationships, viruses from 22 outbreaks (15 from one hospital) were subjected to nucleotide sequencing. The 3'-terminal 3,255 nt or complete genomes were determined for 49 viruses. All outbreaks were caused by a genogroup II norovirus related to the Lordsdale virus (GII 4), common in healthcare settings. The norovirus mutation rate was sufficiently high that the 3,255-nucleotide sequences allowed separate and potentially connected outbreaks to be identified, since all outbreaks with identical sequences were temporally or geographically linked. The high mutation rate was further indicated by four mutations and three microheterogeneities in 3,255 nucleotides during 17 days of norovirus shedding by an immunocompromised patient. The data suggested that multiple virus introductions from the community, occasional transmission among wards, and one instance of ongoing environmental contamination had occurred. The accumulation, or lack, of mutations within an outbreak was also used to indicate the predominant transmission route. In an outbreak where person-to-person spread was thought to predominate, six mutations were detected throughout the genome, whereas one mutation was detected when point source infection was suspected. This norovirus epidemic strain differed from its closest previously described relative by 11.4 to 13.6% in the outer P2 domain of the capsid, which also had a single-amino-acid insertion. Alterations to the capsid structure compared to previous noroviruses may explain the increased number of outbreaks during 2002 and 2003.

Reverse transcription-booster PCR for detection of noroviruses in shellfish

The methods commonly used for norovirus (NV) detection are based on reverse transcription-PCR (RT-PCR) followed by confirmation of the amplified sequence. To increase sensitivity, an RT-booster PCR was developed. The proposed method showed an increase in sensitivity at least 2 log units for all the NV strains tested compared with the standard RT-PCR method. Higher sensitivity was confirmed in tests on experimentally and naturally contaminated shellfish.

Detection of noroviruses in tap water in Japan by means of a new method for concentrating enteric viruses in large volumes of freshwater

A virus concentration method using a cation-coated filter was developed for large-volume freshwater applications. Poliovirus type 1 (LSc 2ab Sabin strain) inoculated into 40 ml of MilliQ (ultrapure) water was adsorbed effectively to a negatively charged filter (Millipore HA, 0.45- micro m pore size) coated with aluminum ions, 99% (range, 81 to 114%) of which were recovered by elution with 1.0 mM NaOH (pH 10.8) following an acid rinse with 0.5 mM H(2)SO(4) (pH 3.0). More than 80% poliovirus recovery yields were obtained from 500-ml, 1,000-ml, and 10-liter MilliQ water samples and from tap water samples. This method, followed by TaqMan PCR detection, was applied to determine the presence of noroviruses in tap water in Tokyo, Japan. In a 14-month survey, 4 (4.1%) and 7 (7.1%) of 98 tap water samples (100 to 532 liters) contained a detectable amount of noroviruses of genotype 1 and genotype 2, respectively. This method was proved to be useful for surveying the occurrence of enteric viruses, including noroviruses, in large volumes of freshwater.

National epidemic of Lordsdale Norovirus in the UK

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.

Molecular characterization of noroviruses detected in diarrheic stools of Michigan and Wisconsin dairy calves: circulation of two distinct subgroups

Noroviruses have emerged as the leading worldwide cause of acute non-bacterial gastroenteritis in humans. The presence of noroviruses in diarrheic stool samples from calves on Michigan and Wisconsin dairy farms was investigated by RT-PCR. Norovirus-positive samples were found on all eight farms studied in Michigan and on 2 out of 14 farms in Wisconsin. Phylogenetic analyses of partial polymerase and capsid sequences, derived for a subset of these bovine noroviruses, showed that these strains formed a group which is genetically distinct from the human noroviruses, but more closely related to genogroup I than to genogroup II human noroviruses. Examination of 2 full and 10 additional partial capsid (ORF2) sequences of these bovine strains revealed the presence of two genetic subgroups or clusters of bovine noroviruses circulating on Michigan and Wisconsin farms. One subgroup is "Jena-like", the other "Newbury agent-2-like".

Detection, quantitation, and phylogenetic analysis of noroviruses in Japanese oysters

Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 10(2) copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.

High rate and changing molecular epidemiology pattern of norovirus infections in sporadic cases and outbreaks of gastroenteritis in Hong Kong

Noroviruses (Norwalk-like viruses (NLV)) are recognised as major causes of acute gastroenteritis worldwide. Numerous studies had been carried out on the molecular epidemiology of norovirus in outbreaks but relatively few on sporadic cases. In this study, the molecular epidemiology of noroviruses in sporadic and outbreak cases of acute gastroenteritis in Hong Kong was examined over a 12-month period from July 2001 to June 2002. Specimens from three groups of patients were used in this study. Nine hundred ninety-five specimens from patients enrolled in the Acute Diarrhoeal Diseases Surveillance Programme of the Department of Health, Hong Kong Government; 735 clinical specimens from hospital patients with acute gastroenteritis, and 122 specimens from 44 norovirus outbreaks. Ninety-two (9.2%) surveillance specimens were positive for norovirus RNA by reverse transcription-polymerase chain reaction (RT-PCR), compared to 123 (16.7%) clinical and 101 (82.8%) outbreak specimens. For the first 6 months of the study period, the predominant strain was the Bristol strain that belongs to genogroup II (GII). In the latter 6 months of the study, genogroup I (GI) and strains belonging to other clusters of GII were seen more commonly. The vast majority of strains belonging to the Bristol virus cluster were closely related to the 95/96-US subset that was associated with pandemic infection from 1995 onwards. This study clearly establishes the importance of norovirus as a cause of sporadic cases of acute gastroenteritis in all age groups in Hong Kong.

Molecular surveillance of enterovirus and norwalk-like virus in oysters relocated to a municipal-sewage-impacted gulf estuary

An 18-month survey was conducted to examine the prevalence of enteric viruses and their relationship to indicators in environmentally polluted shellfish. Groups of oysters, one group per 4 weeks, were relocated to a coastal water area in the Gulf of Mexico that is impacted by municipal sewage and were analyzed for enteroviruses, Norwalk-like viruses (NLV), and indicator microorganisms (fecal coliform, Escherichia coli, and male-specific coliphages). The levels of indicator microorganisms were consistent with the expected continuous pollution of the area. Fourteen of the 18 oyster samples were found by reverse transcription (RT)-PCR to harbor NLV and/or enterovirus sequences. Of the four virus-negative oysters, three had exposure to water temperatures of >29 degrees C. Concomitant with these findings, two of these four oysters also accumulated the lowest levels of coliphages. PCR primers targeting pan-enteroviruses and the NLV 95/96-US common subset were utilized; NLV sequences were detected more frequently than those of enteroviruses. Within the 12-month sampling period, NLV and enterovirus sequences were detected in 58 and 42%, respectively, of the oysters (67% of the oysters tested were positive for at least one virus) from a prohibited shellfish-growing area approximately 30 m away from a sewage discharge site. Eight (4.6%) of the 175 NLV capsid nucleotide sequences were heterogeneous among the clones derived from naturally polluted oysters. Overall, enteric viral sequences were found in the contaminated oysters throughout all seasons except hot summer, with a higher prevalence of NLV than enterovirus. Although a high percentage of the oysters harbored enteric viruses, the virus levels were usually less than or equal to 2 logs of RT-PCR-detectable units per gram of oyster meat.

Identification of a calicivirus isolate of unknown origin

Chinese hamster ovary (CHO) cells manifesting striking cytopathogenic changes in culture were investigated to determine the causative agent. Electron microscopic analyses revealed viral particles of about 40 nm in diameter, displaying typical calicivirus morphology. To date, this virus, designated isolate 2117, exclusively replicates in CHO cells, achieving only moderate titres. After cloning, the coding region of 7928 nucleotides, the 3' non-coding region and the poly(A) tail were sequenced. The genome consists of three open reading frames (ORFs), with the first and second ORF having the same reading frame. The overall genomic organization as well as the nucleotide sequence of isolate 2117 is most similar to that of a recently described canine calicivirus, but also shows significant similarity to the sequences of mink calicivirus and other caliciviruses within the genus Vesivirus: In Western blots, using antibodies against the viral protease, a stable, unprocessed 3CD protein of 68 kDa was identified in homogenates of 2117-infected CHO cells. Furthermore, antibodies raised against ORF 3 reacted with the respective protein in 2117-virions, demonstrating that this predicted 9 kDa protein is a minor structural component of the virion. In addition, an RT-PCR assay was established to detect 2117 viral RNA in biological products such as foetal bovine serum, which will aid the discovery of the origin and host of the virus.

Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR

We have developed an assay for the detection of Norwalk-like viruses (NLVs) based on reverse transcription-PCR (RT-PCR) that is highly sensitive to a broad range of NLVs. We isolated virus from 71 NLV-positive stool specimens from 37 outbreaks of nonbacterial acute gastroenteritis and sequenced the open reading frame 1 (ORF1)-ORF2 junction region, the most conserved region of the NLV genome. The data were subjected to multiple-sequence alignment analysis and similarity plot analysis. We used the most conserved sequences that react with diverse NLVs to design primers and TaqMan probes for the respective genogroups of NLV, GI and GII, for use in a real-time quantitative RT-PCR assay. Our method detected NLV in 99% (80 of 81) of the stool specimens that were positive by electron microscopy, a better detection rate than with the two available RT-PCR methods. Furthermore, our new method also detected NLV in 20 of 28 stool specimens from the same NLV-related outbreaks that were negative for virus by electron microscopy. Our new assay is free from carryover DNA contamination and detects low copy numbers of NLV RNA. It can be used as a routine assay for diagnosis as well as for elucidation of the epidemiology of NLV infections.

An application of microplate hybridization assay for the confirmation and probe typing of "Norwalk-like viruses"

"Norwalk-like virus" (NLV) genomes are generally detected by using reverse transcription-PCR and confirmed by blot hybridization and nucleotide sequencing because of their fastidious nature. In the present study, the confirmation and typing of NLV genomes were carried out using a streptavidin-biotin binding technique and microplate hybridization assay with digoxigenin labeled probes. Eight probe typing sets (G1A, G1B, G2A, G2B, G2C, G2D, G2E, and G2F) formatted from 6 newly designed probes and 8 probes reported elsewhere were used for hybridization. The correlation between probe typing and nucleotide sequencing was found and our 8 probe sets were useful for the typing of NLVs.

Norwalk-like virus 95/96-US strain is a major cause of gastroenteritis outbreaks in Australia

Norwalk-like viruses (NLVs) were detected using a nested reverse transcriptase-polymerase chain reaction (RT-PCR) with primers directed to the RNA polymerase region. Samples were examined from 11 separate outbreaks of gastroenteritis and five sporadic cases of childhood gastroenteritis between 1997 and 2000. Phylogenetic analysis of the 298 bp sequences showed that all strains belong to NLV genogroup II and the majority of the sequenced isolates (30/36) were members of the 95/96-US subset of strains associated with outbreaks recorded worldwide between 1995 and 1996. This was confirmed by analysis of the full length capsid region of a representative Australian isolate. This study demonstrates the usefulness of targeting primers for NLVs to the predominant circulating genotype(s) and confirms the spread of this subtype globally, including the Southern Hemisphere.

Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses

"Norwalk-like viruses" (NLV), a member of the family Caliciviridae, are the major causative agents of acute gastroenteritis and are genetically divided into two groups, genogroup I (GI) and genogroup II (GII). We have determined the complete nucleotide sequences of 10 new NLV strains. Using this information together with eight known NLV sequences, the criteria to further classify genotypes of NLV were investigated. Validation of the topological error based on the bootstrap value and the branch length (distance) allowed us to identify two potential subgenomic regions suitable for the genotyping. They were the putative 3D-like RNA-dependent RNA polymerase (polymerase) and the capsid N-terminal/Shell domains (capsid N/S domain). When the distance distribution analysis was performed, the polymerase-based classification did not separate the strains into internal clusters within the genogroup. Furthermore, a diversity plot analysis of the complete nucleotide sequences of WUG1, a NLV GI strain, and Saitama U1, a NLV GII strain, indicated that the genotype was different between the polymerase and capsid N/S domain, suggesting that these strains are the genetic recombinants. Therefore, polymerase is not suitable for genotyping. On the other hand, the clustering based on the capsid N/S domain successfully distinguished the NLV as well as the grouping based on the antigenicity, as determined by both antigen and antibody ELISAs with recombinant virus-like particles. As the nucleotide sequences of the primers for the capsid N/S domain are highly conserved among the NLV, the amplification of the unknown genotype can be easily performed. This method will facilitate global surveying as well as epidemiologic study on NLV.

Sequence diversity of human caliciviruses recovered from children with diarrhea in Mendoza, Argentina, 1995-1998

Human caliciviruses were detected by EIA and/or RT-PCR in stool specimens from children with diarrhea treated at out- or in-patient facilities between 1995 and 1998 in Mendoza, Argentina. Mexico virus-like strains detected by primers NV36/51 were transiently prevalent in 1995/1996. Significantly more human caliciviruses were detected when primers were designed from contemporaneously circulating strains. Nucleotide sequences of a highly conserved region in the RNA polymerase gene of 10 selected human caliciviruses were determined. Eight strains were Norwalk-like viruses and two strains were Sapporo-like viruses. Seven of the eight Norwalk-like viruses also were positive by the recombinant Mexico virus antigen EIA. The seven Mexico virus EIA-positive strains revealed two patterns in the RNA polymerase sequences: two strains were closest to Mexico virus and the other five strains were closest to Lordsdale virus. One of the five "Lordsdale" viruses was found to be a naturally occurring recombinant between the Mexico virus and Lordsdale human calicivirus genetic clusters [Jiang et al., (1999b) Archives of Virology 144:2377-2387]. The Mexico virus EIA-negative strain had 73-77% nucleotide identity with the closest related Norwalk-like viruses, indicating it might belong to a new genetic cluster of the Norwalk-like virus genus. The two Sapporo-like viruses were distinct genetically; one belonged to the Houston/90 or Parkville cluster and the other to a new cluster. Some strains appeared to have short periods of prevalence and locally adapted primer pairs significantly increased detection rates. The finding of high diversity of circulating strains, including recombinant strains and strains with previously unrecognized genetic identities, highlights a need for studies of human caliciviruses in these children and other populations.

Food-borne outbreak of gastroenteritis associated with genogroup I calicivirus

An outbreak of gastroenteritis affecting 158 of 219 (72%) guests and employees at a hotel is described. Food served at the hotel restaurant is believed to have been the source of the outbreak and to have been contaminated by sick employees working in the restaurant. A secondary attack rate of 22% was seen involving 43 persons in all. In stool specimens from seven of eight patients, Norwalk-like viruses (NLVs) were detected by electron microscopy. While NLV-specific PCR using primers JV12 and JV13 were negative, all specimens examined with primers NVp69 and NVp110 were positive. The failure of primers JV12 and JV13 was attributed to several mismatches in the JV12 primer. Genotyping and sequence analysis revealed that all samples had identical sequences and clustered with genogroup I, and the most closely related well-characterized genotype is Desert Shield. This is the first described food-borne outbreak associated with genogroup I virus in Sweden.

Improved detection of human enteric viruses in foods by RT-PCR

Human enteric viruses (including hepatitis A virus (HAV) and Norwalk-like viruses (NLVs)) are now recognized as common causes of foodborne disease. While methods to detect these agents in clinical specimens have improved significantly over the last 10 years, applications to food samples have progressed more slowly. In an effort to improve the sensitivity and speed of virus detection from non-shellfish food commodities by reverse transcription-polymerase chain reaction (RT-PCR), we (i) evaluated multiple RNA extraction methods; (ii) compared alternative NLV primer sets; and (iii) developed a one-step RT-PCR method. Hamburger and lettuce samples, processed for virus concentration using a previously reported filtration-extraction-precipitation procedure, were inoculated with HAV or NV. Several RNA extraction methods (guanidinium isothiocyanate, microspin column, QIAshredder Homogenizer, and TRIzol) and primer pairs were compared for overall RNA yield (microg/ml), purity (A(260)/A(280)), and RT-PCR limits of detection. The use of TRIzol with the QIAshredder Homogenizer (TRIzol/Shred) yielded the best RT-PCR detection limits (<1 RT-PCR amplifiable units/reaction for NV), and the NVp110/NVp36 primer set was the most efficient for detecting NV from seeded food samples. A one-step RT-PCR protocol using the TRIzol/Shred extraction method and the NVp110/NVp36 or HAV3/HAV5 primer sets demonstrated improved sensitivity (>10-fold) over the routinely used two-step method. HAV RNA was detected by RT-PCR at initial inoculum levels corresponding to <10 and <100 PFU per 300 microl sample concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. NV RNA was detected by RT-PCR at initial inoculum levels <5 and <50 RT-PCR amplifiable units per 300 microl concentrate (corresponding to 6 g food sample) for hamburger and lettuce, respectively. Residual RT-PCR inhibitors were effectively removed as evidenced by the ability to detect viral RNA in food concentrates without prior dilution. The methods reported here show promise for rapid, sensitive detection of human enteric viruses in foods.

Genogroup-specific PCR primers for detection of Norwalk-like viruses

Norwalk-like viruses (NLV) are a major causative agent of nonbacterial gastroenteritis. There are still many NLV strains that are refractory to gene amplification by ordinary reverse transcription-polymerase chain reaction. This is due mainly to the genetic diversity among NLV, especially mismatches in the primer sequences, which limits this technique in clinical utility. In this study, improved primer sets based on the capsid region, to detect both genogroup I and II NLV by genogroup-specific manner, were developed. When stool specimens from gastroenteritis patients, that were positive for NLV by electron microscopy, were tested by this new primer set, all specimens were positive by RT-PCR. Primers described previously for RdRp and capsid protein were capable of amplifying the specimens by 31 and 77%, respectively. Therefore, new primer sets are extremely useful for the amplification and rapid diagnosis of nonbacterial gastroenteritis due to NLV as well as for epidemiological studies.

Molecular epidemiology of calicivirus infections in Norway

The national reference laboratory for calicivirus diagnostics monitors the epidemiology of calicivirus infections in Norway. During winter 1998-1999, 406 fecal samples were received from patients with suspected calicivirus infection. Of these, 76 (19%) were calicivirus positive by a nested reverse transcription-polymerase chain reaction. A number of alternative PCR designs were employed to disclose false negatives, but none were found. One half of the PCR positive samples were sequenced in order to investigate whether various cases represented the same outbreak, and to what extent a single or multiple subtypes were responsible for the morbidity during this season. The sequence data revealed that the majority of cases represented a genotype related to the Lordsdale strain, whereas the remaining cases seemed more sporadic. Most often, samples from particular outbreaks were highly homogeneous. However, in a few cases, samples connected with the same outbreak proved to contain epidemiologically independent strains.

Molecular detection and sequencing of "Norwalk-like viruses" in outbreaks and sporadic cases of gastroenteritis in Ireland

Norwalk-like viruses (NLVs) are now established as the most important causative agents of epidemic gastroenteritis worldwide. The overall objective of this study was to determine the molecular epidemiology of Irish NLV isolates for the first time by obtaining sequence data from specimens originating from outbreaks and sporadic cases of gastroenteritis. Eight samples from sporadic cases of gastroenteritis and nine isolates from separate NLV outbreaks were examined. Of the sporadic isolates, six were shown to be genogroup 2 (G2) by RT-PCR, while two were G1. All of the outbreak isolates were G2. All isolates were partially sequenced within a highly conserved region of ORF1 (RNA-dependent RNA polymerase gene). Sequence data were aligned and a dendogram was constructed. The results indicated that the majority of G2 isolates were seen to cluster with Bristol and Lordsdale virus, while the two G1 specimens were related most closely to Southampton virus. Further downstream sequence analysis of a number of the isolates confirmed this result. It is concluded that the majority of NLV isolates circulating in Ireland belong to the Bristol/Lordsdale clade.

Nucleotide sequence analysis and development of consensus primers of RT-PCR for detection of Norwalk-like viruses prevailing in Japan

A total of 177 different nucleotide sequences of the RNA polymerase region of Norwalk-like viruses (NLVs) genomes, collected via a nation-wide survey project in Japan between 1989 and 1998, were examined by reverse transcription-polymerase chain reaction (RT-PCR) employing various primer pairs. The nucleotide sequences of different strains showed great diversity, with a range of 57 to 100% identities among strains. The strains could be classified into five clusters: Norwalk (NV), Snow Mountain agent/Bristol virus (SMA/BV), Toronto virus/Mexico virus (TV/MX), and Japan specific cluster 1 and 2 (JP-1 and JP-2). Within each cluster there is greater than 85% identity of amino acid sequence (more than 75% identity of nucleotide sequences), based on sequence homology analysis. We believe that two of the five clusters, JP-1and JP-2, define new specific clusters found in Japan according to phylogenetic and pair-wise comparison studies. An RT-PCR procedure was designed using new consensus primer pairs, P1/P2, P1/P3, and Y1/Y2 based on multiple alignment of collected nucleotide sequences, that are expected to detect nearly all NLVs prevailing in Japan. The usefulness of the primers was tested by ten different laboratories in Japan using a panel of ten fecal samples containing different virus strains. The identification of these primer pairs will facilitate routine diagnosis of NLV infection by RT-PCR and offers the potential for their direct detection in food and environmental samples.

Evaluation of nine sets of PCR primers in the RNA dependent RNA polymerase region for detection and differentiation of members of the family Caliciviridae, Norwalk virus and Sapporo virus

Norwalk virus and Sapporo virus were approved as type species of the genus "Norwalk-like viruses" and the genus "Sapporo-like viruses," respectively, in the family Caliciviridae. A total of 116 stool specimens containing Norwalk virus (NV) or Sapporo virus (SV) were tested by RT-PCR and Southern hybridization to evaluate nine sets of PCR primers and seven internal oligonucleotide probes in the RNA dependent RNA polymerase region of NV and SV for detection and differentiation of viruses in the NV and SV. Fifty-five stool samples were collected from 11 outbreaks of NV and/or SV gastroenteritis in an infant home, where residents were infants under 2 years of age, in Sapporo, Japan. Sixty specimens were obtained in Sapporo from sporadic cases in children, mainly under 6 years of age, of acute gastroenteritis due to small round structured viruses detected by EM. There is no single primer pair to detect all NV and SV, and at least three primer pairs, G1 set, G2 set and Sapp35/Sapp36, are required to detect viruses in the NV and SV clades. Many NV and SV strains were successfully classified into one of the NV/genogroup I, NV/genogroup II and SV by single-round RT-PCR and Southern hybridization. The new detection method for SV reported in this study combined with those for NV previously reported may elucidate the importance of Norwalk virus and Sapporo virus as a cause of viral gastroenteritis in all age groups in the world.

Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase

Southampton virus (SHV) is a member of the Norwalk-like viruses (NLVs), one of four genera of the family Caliciviridae. The genome of SHV contains three open reading frames (ORFs). ORF 1 encodes a polyprotein that is autocatalytically processed into six proteins, one of which is p41. p41 shares sequence motifs with protein 2C of picornaviruses and superfamily 3 helicases. We have expressed p41 of SHV in bacteria. Purified p41 exhibited nucleoside triphosphate (NTP)-binding and NTP hydrolysis activities. The NTPase activity was not stimulated by single-stranded nucleic acids. SHV p41 had no detectable helicase activity. Protein sequence comparison between the consensus sequences of NLV p41 and enterovirus protein 2C revealed regions of high similarity. According to secondary structure prediction, the conserved regions were located within a putative central domain of alpha helices and beta strands. This study reveals for the first time an NTPase activity associated with a calicivirus-encoded protein. Based on enzymatic properties and sequence information, a functional relationship between NLV p41 and enterovirus 2C is discussed in regard to the role of 2C-like proteins in virus replication.

Complete nucleotide sequence of the chiba virus genome and functional expression of the 3C-like protease in Escherichia coli

We cloned the genome RNA of the Chiba virus (ChV; Hu/NLV/Chiba 407/1987/JP) and determined its complete nucleotide sequence. The genome is predicted to be a positive-sense, single-stranded RNA of 7697 bases, excluding a poly(A) tract. Comparison of the nucleotide and amino acid sequences with those of other members of the species Norwalk virus (NV) revealed that ChV belongs to genogroup I NV. The ChV genome contains three open reading frames (ORFs). A large 5'-terminal ORF (ORF1) encodes a polyprotein with 1785 amino acids that are likely processed into functional proteins, including RNA helicase, VPg, protease, and RNA-dependent RNA polymerase. ORF2 encodes the capsid protein with 544 amino acids, and a small 3'-terminal ORF (ORF3) encodes a basic protein with 208 amino acids. The amino acid sequences of five cleavage sites in ORF1 are highly conserved compared with those of other members of NV. When expressed in Escherichia coli, the glutathione-S-transferase (GST) fusion protein of the ChV protease connected via a short peptide containing a human rhinovirus 3C protease cleavage site was cleaved into GST and the protease; however, this cleavage did not occur when the Cys mutation was introduced into the putative active site of the protease. Moreover, the ChV protease recognized and cleaved the predicted proteolytic sites between VPg and protease and between protease and RNA polymerase. Therefore, the ChV protease expressed in E. coli retained an enzymatic activity and a substrate specificity similar to that of the human rhinovirus 3C protease.

RT-PCR identification and typing of astroviruses and Norwalk-like viruses in hospitalized patients with gastroenteritis: evidence of nosocomial infections

BACKGROUND

Astroviruses (HAstVs) and 'Norwalk-like viruses' (NLV) are frequent causes of gastroenteritis worldwide, though no data on the strains in circulation or their prevalence is available for France.

OBJECTIVES

We applied molecular methods to detect HAstVs and NLVs by reverse transcription-polymerase chain reaction (RT-PCR) in fecal samples collected during a 2-year period from children and adults hospitalized with gastroenteritis.

STUDY DESIGN

All samples negative for rotavirus and adenovirus by latex agglutination which contained small (25-40 nm) viral particles observed by electron microscopy (EM) were examined by RT-PCR. RT-PCR products were sequenced to characterize the HAstV and NLV strains present.

RESULTS

A total of 75 samples were analyzed by RT-PCR, of which 15 were positive for HAstV and 24 for NLV. Several distinct strains of serotype 1 HAstV, the predominant serotype, circulated during the period. Nineteen of the 24 NLVs were of the G2 genogroup including Mexico-like (n=10), Bristol-like (n=8), and Hawaii-like viruses (n=1); two were genogroup 1. Overall, seven (47%) of the 15 HAstV infections and nine (37.5%) of the 24 NLV infections appeared to be nosocomially acquired based on the date of admission in hospital and the date of illness.

CONCLUSION

This study provides additional evidence of the importance of nosocomial infections caused by NLV and HAstV.

Viruses and bivalve shellfish

The epidemiological data clearly demonstrates that filter feeding bivalve shellfish can, and do, act as efficient vehicles for the transmission of enteric viruses transmitted by the faecal-oral route. This identified hazard has been documented as a cause for concern by various international agencies and has a long history. Disease outbreaks can occur on an epidemic scale as graphically illustrated by an outbreak of Hepatitis A in Shanghai, China in 1988 involving about 300,000 cases. Improvement of harvesting area water quality offers the most sustainable route to improvement in the virological quality of bivalve shellfish sold live. However there is growing awareness, and concern, that current regulatory standards based on faecal coliform monitoring do not fully protect the shellfish consumer from viral infection. New viral test methods based on PCR, and the development of alternative more reliable faecal pollution indicators, offer new approaches for the further development of public health controls. However, further work is required to build a scientific consensus and to understand the implications of their introduction into legislation.

Simultaneous detection and genotyping of "Norwalk-like viruses" by oligonucleotide array in a reverse line blot hybridization format

"Norwalk-like viruses" (NLVs) are the most common cause of outbreaks of nonbacterial gastroenteritis worldwide. To date, the method most widely used for typing of NLV strains is sequencing and subsequent phylogenetic analysis of reverse transcription (RT)-PCR products, which has revealed the existence of stable distinct lineages (genotypes). This typing method is rather costly, not routinely used in clinical laboratories, and not very suitable for the analysis of large numbers of samples. Therefore, we have developed a rapid and simple method for genotyping of NLVs. The method, designated reverse line blot hybridization, is based on the nucleotide divergence of a region of the gene for RNA polymerase which can be used to classify NLVs into genotypes. NLV RNA was amplified by RT-PCR and then hybridized to 18 different membrane-bound oligonucleotides that were able to discriminate among 13 NLV genotypes. Application of the method to a panel of 132 positive stool samples from 34 outbreaks and 20 sporadic cases of gastroenteritis collected in a 6-year period (1994 to 1999) resulted in successful genotyping of 124 samples (94%), as confirmed by phylogenetic analysis. The nucleotide sequences of the remaning eight strains (6%) from three outbreaks did not cluster with the known NLV genotypes. Phylogenetic analysis of the complete and partial open reading frame 2 (capsid gene) sequences of these strains revealed the existence of one novel genotype (Alphatron) and one potentially novel genotype (Amsterdam). This novel method, which allows simultaneous detection and genotyping of NLVs, is useful in the diagnosis and typing of NLVs obtained from outbreaks and in large-scale epidemiological studies.

A diagnostic EIA for detection of the prevalent SRSV strain in United Kingdom outbreaks of gastroenteritis

Small round structured viruses (SRSVs) are the major cause of outbreaks of gastroenteritis in the UK. Diagnosis is problematic due to insensitive electron microscopy (EM) or technically demanding reverse transcription polymerase chain reaction (RT-PCR) techniques. We have studied outbreaks of non-bacterial gastroenteritis using an EIA based upon recombinant capsid protein from the currently prevalent circulating strain of SRSV (Lordsdale Genotype II) and compared its performance against EM and RT-PCR assays. Faecal specimens sent to the Bristol Public Health Laboratory for outbreak investigation from December 1996 to December 1997 were applied retrospectively to the SRSV EIA and results compared with the routine EM and RT-PCR that had been carried out prospectively. Overall, the three tests identified SRSVs in specimens from 70% of the outbreaks (213/305) investigated. Of the 213 total positive outbreaks, the EIA identified 71%, that compared favourably with EM (63%) and RT-PCR (84%). The Lordsdale Genotype II SRSV EIA provides a simple cost-effective assay that will for the first time make detection of currently circulating SRSV strains associated with UK outbreaks available to all routine laboratories. The EIA format makes the assay widely applicable to non-specialist laboratories, unlike the RT-PCR assay, and the improved sensitivity over EM will allow successful screening of UK outbreaks alongside commercial EIAs currently available for adenovirus, astrovirus and rotavirus. Furthermore, the assay will allow rapid identification of emerging SRSV strains.