Viral gastroenteritis outbreaks in deployed British troops during 2002-7

OBJECTIVES

The aim of this study was to see what lessons could be learnt from the suspected viral gastroenteritis outbreaks that have occurred in deployed British troops during 2002-7.

METHOD

Epidemiological and laboratory data from identifiable outbreaks were reviewed, including epidemic curves and the results of PCR testing for enteropathic viruses.

RESULTS

The epidemic curves of outbreaks varied predictably in accordance with the size of the population at risk and whether this population was constant or expanding. Of 11 outbreaks identified, 10 (91%) had a proven viral cause and 10 (91%) occurred in Iraq. Of 84 enteropathic viruses identified, 61 (73%) were noroviruses and these included both unknown strains and those that were common in the UK and Europe. Of the 10 viral outbreaks, 3 (30%) occurred in medical units, 5 (50%) were associated with large-scale relief in place (RiP) deployments and 5 (50%) involved >3 different viruses, which is strongly suggestive of food or water contamination.

CONCLUSION

These findings can help to predict future viral gastroenteritis outbreaks and target improved prevention strategies appropriately. However, more systematic studies are now required.

Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes

Background

Human noroviruses are a highly diverse group of viruses classified into three of the five currently recognised Norovirus genogroups, and contain numerous genotypes or genetic clusters. Noroviruses are the major aetiological agent of endemic gastroenteritis in all age groups, as well as the cause of periodic epidemic gastroenteritis. The noroviruses most commonly associated with outbreaks of gastroenteritis are genogroup II genotype 4 (GII-4) strains. The relationship between genotypes of noroviruses with their phenotypes and antigenic profile remains poorly understood through an inability to culture these viruses and the lack of a suitable animal model.

Methodology/Principal Findings

Here we describe a study of the diversity of amino acid sequences of the highly variable P2 region in the major capsid protein, VP1, of the GII-4 human noroviruses strains using sequence analysis and homology modelling techniques.

Conclusions/Significance

Our data identifies two sites in this region, which show significant amino acid substitutions associated with the appearance of variant strains responsible for epidemics with major public health impact. Homology modelling studies revealed the exposed nature of these sites on the capsid surface, providing supportive structural data that these two sites are likely to be associated with putative variant-specific epitopes. Furthermore, the patterns in the evolution of these viruses at these sites suggests that noroviruses follow a neutral network pattern of evolution.

European multicenter evaluation of commercial enzyme immunoassays for detecting norovirus antigen in fecal samples

A total of 2,254 fecal samples were tested in a European multicenter evaluation of commercially available norovirus antigen detection assays. Two commercial enzyme immunoassays, IDEIA Norovirus (Oxoid; Thermo Fisher Scientific, Ely, United Kingdom) and RIDASCREEN Norovirus (R-Biopharm, Darmstadt, Germany), were included in the evaluation, and their performance was compared with the results of reverse transcription-PCR (RT-PCR). Included in the evaluation were samples collected in sporadic cases of gastroenteritis, samples from outbreaks in which two or more samples were collected, well-characterized samples representing genotypes currently cocirculating within Europe, and samples collected from patients with gastroenteritis caused by a pathogen other than norovirus. The sensitivities and specificities of the IDEIA Norovirus and RIDASCREEN Norovirus assays were 58.93 and 43.81% and 93.91 and 96.37%, respectively, compared with RT-PCR. The sensitivities of both assays for outbreak investigations improved when six or more samples from an outbreak were examined. The IDEIA Norovirus assay exhibited reactivity to a broader range of norovirus genotypes than the RIDASCREEN Norovirus assay, which showed genotype-dependent sensitivities. The results indicate that, if used, these assays should serve as screening assays and the results should be confirmed by RT-PCR.

Inter-seasonal diversity of norovirus genotypes: Emergence and selection of virus variants

This study describes a method used to determine the diversity of NoVs co-circulating in the community that consisted of the analysis of a limited number of strains collected from outbreaks occurring at different times of the NoV season. The diversity of twenty NoV strains collected from outbreaks occurring at the beginning of each NoV season (September) was compared to the diversity found in the middle (December) and at the end of the season (March). The method was validated through the characterisation of greater numbers of strains at times when novel genotypes or variants were detected. A total of 864 strains from outbreaks of gastroenteritis from the 2003/04, 2004/05 and 2005/06 seasons were genotyped, with the majority of outbreaks occurring in the UK. There was a greater diversity of NoV genotypes at the beginning of two of the three seasons, 2003/04 and 2005/06, when compared to strains circulating at the end of the seasons, and GII-4 NoV strains predominated (>90%) at the end of each season. Data from this study also identified the co-circulation and differentiation of three major GII-4 variants (v2, v3, and v4). Detailed analysis of a larger number of strains throughout each season confirmed that variants emerged, became the predominant circulating strain and were ultimately replaced with another variant selected from a pool of variants. By June 2006, GII-4 v4 (Hu/NoV/Rhyl440/2005/UK) emerged as the predominant GII-4 strain, usurping the previous GII-4 v3 strain [Hu/NoV/Hunter284E/040/AU] to become the commonest co-circulating strain, in the UK in 2006.

Characterisation of small double stranded RNA molecule in Cryptosporidium hominis, Cryptosporidium felis and Cryptosporidium meleagridis

Coding regions of double stranded RNA molecules from 3 human faecal samples containing Cryptosporidium hominis, C. felis and C. meleagridis were characterised by sequencing and compared with that previously obtained for C. parvum. Sequences outside the coding regions were also obtained. Overall similarities of between 86% and 92% and between 86% and 93% were observed in the nucleotide and amino acid sequences respectively between these species. These larger sequences will allow further molecular tools for detection, identification and characterisation of Cryptosporidium spp.

Characterization of sapoviruses collected in the United Kingdom from 1989 to 2004

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).

Environmental monitoring for gastroenteric viruses in a pediatric primary immunodeficiency unit

The aim of this study was to determine if gastroenteric viruses were present on surfaces and equipment in a pediatric primary immunodeficiency unit (PPIU) by environmental sampling using swabs and subsequent nucleic acid extraction and reverse transcriptase PCR assays. A PPIU was chosen, and 11 swabs were taken at the same sites every 2 weeks for 6 months. Nested/heminested PCR assays were used to screen for astroviruses (AsV), noroviruses (NoV), and rotaviruses (RV). AsV, NoV, and RV were detected at multiple swab sites during the study period. NoV was the most frequently detected virus on environmental surfaces; however, RV was detected on 79% and NoV on 50% of swabbing dates during the study period. Toilet taps were the most contaminated sites. Fecal samples from selected patients in the unit were also screened during the study period, and patients excreted AsV, NoV, and RV at times during the study. New cleaning schedules and changes in some of the PPIU sanitary furniture have been suggested as a means of reducing environmental contamination.

Gastroenteritis outbreak in British troops, Iraq

Gastroenteritis affected many British military personnel during the war in Iraq. In the first month, 1,340 cases were seen; 73% of patients required hospital admission and 36% were hospital staff. In a survey of 500 hospital staff, 76% reported gastroenteritis, which was more likely in clinical workers. Investigations showed only caliciviruses.

Characterisation of norovirus strains in rural Ghanaian children with acute diarrhoea

The incidence of calicivirus infection in Ghana and many other African countries is not known. Thirteen (15.9%) of the 82 diarrhoeic stool samples tested for caliciviruses were positive for noroviruses (NoVs). NoVs were present in all age groups and were detected only during the diarrhoea peak that coincided with the peak rotavirus season. Ten (76.9%) of the NoV detected were genogroup II (GII) NoVs and the remaining three (23.1%) genogroup I (GI) NoVs. The predominant GII detected was GII-4 (60%, 6/10). Three of the GII NoVs were determined to be recombinants of GII-8/GII-14 as deduced from the sequencing of the region spanning the Orf1/2 junction. The GII genotypes formed four clusters with published GII sequences. The data shown enhances understanding of NoV diversity in Ghanaian children and demonstrate the global spread of distinct common genotypes to African countries.

Use of a heminested reverse transcriptase PCR assay for detection of astrovirus in environmental swabs from an outbreak of gastroenteritis in a pediatric primary immunodeficiency unit

An outbreak of astrovirus gastroenteritis occurred in the Primary Immunodeficiency Unit at Newcastle General Hospital in March 2004. Environmental swabbing of the unit was undertaken after the outbreak, with multiple sites swabbed pre- and postcleaning. Astroviruses were detected in four environmental swabs and from two patient fecal samples using heminested reverse transcriptase PCR. An astrovirus genotype 3 strain was identified in both environmental swabs and fecal specimens and was the strain identified as being responsible for the outbreak. Environmental transmission of the virus was thought to have occurred by contamination of a syringe pump outside the laminar-flow curtain of a patient who was admitted with astrovirus gastroenteritis. This was subsequently transmitted to a cubicle next door and to a television/games console in a parents' room in the ward. Environmental monitoring of surfaces/equipment, using PCR assays for gastroenteric viruses in hospital situations where infection can give rise to serious clinical complications, may have a role in controlling and monitoring cleaning and the subsequent prevention of nosocomial transmission of gastroenteritis.

Multiple norovirus genotypes characterised from an oyster-associated outbreak of gastroenteritis

The diversity of norovirus (NV) genotypes was investigated in persons who were ill with acute gastroenteritis associated with the consumption of oysters. Initial results from a commercial enzyme immunoassay (EIA) indicated a mixed NV genogroup I (GI) and II (GII) outbreak. A reverse-transcriptase (RT)-PCR for NVs was applied to nucleic acid extracted from faecal specimens collected from symptomatic cases. Using primers that amplified contiguous sequences in the ORF1/2 region of the NV genome and a hemi-nested PCR derived from this assay, three different GII and two GI NV genotypes were detected and the strains were characterised by DNA sequencing. Using this approach a recombinant NV genotype, rGII-3a (recombinant Harrow/Mexico) the predominant strain identified in several symptomatic cases from the outbreak, was detected and characterised. No other gastroenteric viruses, including rotavirus, astrovirus, sapovirus and adenovirus 40/41 were detected by RT-PCR and PCR.

Detection of multiple enteric virus strains within a foodborne outbreak of gastroenteritis: an indication of the source of contamination

An outbreak of acute gastroenteritis of suspected viral aetiology occurred in April 2003 in the British Royal Fleet Auxiliary ship (RFA) Argus deployed in the Northern Arabian Gulf. There were 37 cases amongst a crew of 400 personnel. Of 13 samples examined from cases amongst the crew, six enteric viruses were detected by reverse transcriptase polymerase chain reaction (RT-PCR). Five different viruses were identified including, three norovirus genotypes, a sapovirus and a rotavirus. No multiple infections were detected. A common food source was implicated in the outbreak and epidemiological analysis showed a statistically significant association with salad as the source of the outbreak, with a relative risk of 3.41 (95% confidence interval of 1.7-6.81) of eating salad on a particular date prior to the onset of symptoms. Faecal contamination of the salad at source was the most probable explanation for the diversity of viruses detected and characterized.

Diversity of enteric viruses detected in patients with gastroenteritis in a tertiary referral paediatric hospital

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.

Asymptomatic and symptomatic excretion of noroviruses during a hospital outbreak of gastroenteritis

During an investigation of a hospital outbreak of norovirus gastroenteritis identified as being caused by a recombinant genogroup II (rGII-3a) strain, fecal specimens collected from asymptomatic staff and patients were tested by nested PCR. A GII-4 norovirus strain, the predominant strain associated with outbreaks in hospitals over the last few years, was detected in 26 and 33% of asymptomatic staff and patients, respectively. No rGII-3a (Harrow/Mexico) norovirus strains were detected in the samples of asymptomatic staff or patients.

Application of the heteroduplex mobility assay (HMA) for the investigation of the genomic diversity among noroviruses in environmental samples

Recent studies have demonstrated the widespread contamination of river and seawater with noroviruses (NV), often with more than one strain. The heteroduplex mobility assay (HMA) in which amplicons from study samples are hybridised (by denaturing and reannealing) to amplicons from reference strains and resolved by electrophoresis, has the potential to provide a simple and rapid means to identify samples containing multiple NV strains and to establish the diversity of strains within that sample. PCR amplicons from environmental samples that were tested directly in the HMA assay were shown to contain more than one strain. In order to evaluate HMA for investigations of NV diversity in environmental samples, amplicons from three representative samples were cloned and, for each, 20 amplicons derived from individual clones were analysed by HMA. Between two and six different HMA profiles were demonstrated among clones from a single sample indicating the extent of NV diversity in the sample. Sequence analysis confirmed the relationship of HMA profile and NV 'genotype'. Far greater diversity was seen among Genogroup (G) II (Ni/E3) amplicons than Genogroup (G) I (Ando/E3) amplicons (generated from the RNA dependent RNA polymerase region of the ORF1 of noroviruses), which often contained only a single strain, which is reflective of the greater prevalence of GII NVs over GI NVs. Overall, four GII and four GI strains were identified in these environmental water/sewage samples.

Diversity of noroviruses cocirculating in the north of England from 1998 to 2001

A study was undertaken to investigate the diversity of noroviruses (NVs) in fecal samples from patients from 529 outbreaks and 141 sporadic cases of gastroenteritis in the North of England from September 1998 to August 2001. NV strains were detected by electron microscopy and characterized by a combination of the Grimsby virus antigen enzyme-linked immunosorbent assay, reverse transcriptase PCR, the heteroduplex mobility assay, and DNA sequencing. Twenty-one distinct NV strains, including several novel or variant strains not seen previously, were found circulating in the population studied. Genogroup II NVs were responsible for 83% of the outbreaks. Several strains cocirculated at any one time. The Bristol (Grimsby/Lordsdale) and Hawaii (Girlington) genotypes were the most prevalent among the NVs identified, detected in 49 and 20% of the outbreaks, respectively. A limited number of other genogroup II and I strains were cocirculating. The virus populations detected in hospitals and nursing homes were distinct from those found in community-based outbreaks. Outbreaks in hospitals and nursing homes were more likely to be caused by genogroup II strain Grimsby or Girlington (P < 0.0001) than by other genogroup II or I strains.

Quantitation of group A rotavirus by real-time reverse-transcription-polymerase chain reaction: correlation with clinical severity in children in South India

The epidemiology and pathogenesis of rotaviruses are not completely understood, although recent developments in polymerase chain reaction (PCR) techniques now make it possible to quantify the viral load during an infective episode and investigate its relevance to clinical features of the disease. We studied rotavirus-positive stool samples collected from 10 children without symptoms of gastroenteritis and from 81 children with acute gastroenteritis and in whom the clinical severity of disease was recorded. A semi-quantitative real-time reverse-transcription (RT)-PCR was used to estimate the rotavirus load and to assess its correlation with the Vesikari score for severity of diarrhoea. There was a significant negative correlation (r = -0.80, P < 0.001) between severity and the PCR cycle at which the PCR amplicons were detectable (crossing point) on the assay, indicating that children with more severe diarrhoea excrete more virus than children with less severe disease.

Chronic excretion of a norovirus in a child with cartilage hair hypoplasia (CHH)

We have demonstrated the long-term excretion of a stable recombinant norovirus in a patient with cartilage hair hypoplasia (CHH), with a T cell immunodeficiency, following bone marrow transplantation (BMT). The patient excreted an ARG320/1999/US-like recombinant norovirus (rGII-3) for 156 days during a period of immune reconstitution. The child was symptomatic during the period of virus shedding. It is not known if the child acquired the recombinant strain or if recombination occurred in vivo.

Evaluation of a broadly reactive nucleic acid sequence based amplification assay for the detection of noroviruses in faecal material

A recently described nucleic acid sequence based amplification (NASBA) assay for the detection of genogroup I (GI) and genogroup II (GII) norovirus RNA in faecal samples was evaluated against a reverse transcription polymerase chain reaction (RT-PCR). Both assays were used to screen a panel of 38 faecal samples known to contain 17 different norovirus strains and 131 clinical samples collected from 60 gastroenteritis outbreaks of unknown aetiology. The NASBA assay detected 13 out of the 17 strains of norovirus in the characterised panel, failing to detect a single GII strain and three GI strains. There was 90% agreement between the two assays used to detect norovirus in clinical samples from outbreaks. NASBA detected norovirus RNA in all 64 samples positive by RT-PCR and also detected norovirus RNA in additional 13 samples that were negative by RT-PCR. The sensitivity and specificity of NASBA was 100% and 80%, respectively, compared to RT-PCR results. The norovirus NASBA assay was shown to be highly sensitive and specific, and its ease of use and rapid turnaround time makes it a favourable alternative to RT-PCR for the investigation of norovirus outbreaks.

Noroviruses associated with acute gastroenteritis in a children's day care facility in Rio de Janeiro, Brazil

Noroviruses (Norwalk-like viruses) are an important cause of gastroenteritis worldwide. They are the most common cause of outbreaks of gastroenteritis in the adult population and occur in nursing homes for the elderly, geriatric wards, medical wards, and in hotel and restaurant settings. Food-borne outbreaks have also occurred following consumption of contaminated oysters. This study describes the application of a reverse transcription-polymerase chain reaction (RT-PCR) assay using random primers (PdN6) and specific Ni and E3 primers, directed at a small region of the RNA-dependent RNA polymerase-coding region of the norovirus genome, and DNA sequencing for the detection and preliminary characterisation of noroviruses in outbreaks of gastroenteritis in children in Brazil. The outbreak samples were collected from children <5 years of age at the Bertha Lutz children's day care facility at Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, that occurred between 1996 and 1998, where no pathogen had been identified. At the Bertha Lutz day care center facility, only Fiocruz's employee children are provided for, and they come from different social, economic and cultural backgrounds. Three distinct genogroup II strains were detected in three outbreaks in 1997/98 and were most closely related to genotypes GII-3 (Mexico virus) and GII-4 (Grimsby virus), both of which have been detected in paediatric and adult outbreaks of gastroenteritis worldwide.

Methods for the detection and characterisation of noroviruses associated with outbreaks of gastroenteritis: Outbreaks occurring in the north-west of England during two norovirus seasons

This article describes the methods used to investigate 407 outbreaks of acute non-bacterial gastroenteritis occurring in the North-West of England between January 2000 and July 2001 and suspected to be caused by noroviruses (NV) [Mayo (2002) Arch Virol 147:1655-1663]. These included 319 outbreaks in hospitals and nursing homes and 88 other settings. Eight hundred and seventy-one faecal samples from 407 outbreaks were tested using electron microscopy (EM), an enzyme-linked immunosorbent assay (ELISA) specific for Grimsby virus (GRV) capsid antigen and/or by reverse transcriptase-polymerase chain reaction (RT-PCR) for NV, allowing the utility of each assay for routine diagnosis to be assessed. Preliminary genomic characterisation of detected strains was performed using the heteroduplex mobility assay (HMA) and DNA sequencing. The results demonstrate the continuing predominance of GII-4 GRV strain of NV as a cause of outbreaks, particularly in hospital and nursing home settings. Overall, NV were detected in 223/407 (55%) of outbreaks tested. However, a wide range of apparently diverse strains was identified, including several not previously reported. Genomic characterisation revealed clusters of linked outbreaks not recognised previously.

Molecular diversity of noroviruses associated with outbreaks on cruise ships: comparison with strains circulating within the UK

The molecular diversity of norovirus (NV) strains associated with 26 outbreaks of NV gastroenteritis has been determined. The outbreaks occurred on 14 cruise ships from seven cruise lines, during the period from 1998 to 2002. The ships cruised in seas worldwide, including the Mediterranean, the Baltic and the Caribbean. Genogroup I NVs were more common in the cruise ship setting than in hospitals, with 38% of the cruise ship outbreaks associated with genotype I NVs, as compared to < 10% in hospital and other semi-closed institutions in the UK. Outbreaks on cruise ships were more common in the period April to September, than in the winter. Two mixed genogroup I and II outbreaks were detected, which suggested contaminated food or water as the source of the infection.

A rapid method for identifying diversity within PCR amplicons using a heteroduplex mobility assay and synthetic polynucleotides: application to characterisation of dsRNA elements associated with Cryptosporidium

A 173-bp fragment of the small extra-chromosomal double-stranded RNA (dsRNA) element of Cryptosporidium parvum was generated by reverse transcriptase PCR from nucleic acid extracted from whole faeces of 18 epidemiologically unrelated cases of cryptosporidiosis. Eleven different sequences were detected and two selected as reference DNA in a heteroduplex mobility assay (HMA). Although sequence diversity was detected, this was difficult to characterise because of the similarity in electrophoretic mobility of the homo- and heteroduplex bands. A PCR method was devised to generate synthetic polynucleotides of greater sequence diversity for use in the HMA. The presence of the synthetic 173-bp fragments was enriched by using, as template for the PCR, material excised from the area of the heteroduplex bands in stained electrophoresis gels. Nine novel sequences were generated and evaluated as reference sequences in the HMA. One of these with 20 bp different from the original sequence was selected for use in the HMA for improved resolution of heteroduplex and homoduplex bands and number of patterns easily resolved (nine different patterns corresponding to different DNA sequences). This method may be useful for analysis of DNA where there is limited natural variation or little sequence variation is described.

Molecular epidemiological analysis of Cryptosporidium isolates from humans and animals by using a heteroduplex mobility assay and nucleic acid sequencing based on a small double-stranded RNA element

Two extrachromosomal double-stranded RNA (dsRNA) elements occur in Cryptosporidium parvum. A heteroduplex mobility assay (HMA) was developed for the rapid characterization of sequence diversity in a 173-bp fragment of the small dsRNA element of Cryptosporidium with either a natural sequence from Cryptosporidium meleagridis or a synthetic sequence as reference DNA. The 173-bp fragment was generated from 265 samples of whole feces (242 from humans and 18 from livestock with C. parvum genotype 1 or 2, 4 from humans with Cryptosporidium felis, and 1 from a human with C. meleagridis). The HMA method identified 21 patterns in C. parvum (8 in genotype 1, 12 in genotype 2, and a type common to both genotypes), 4 patterns in C. felis, and 1 pattern in C. meleagridis. All patterns were confirmed as distinct by DNA sequencing. For genotype 1, a single HMA type was found in 89% of samples: 64 of 65 cases from three waterborne outbreaks, all 16 cases from eight intrafamilial outbreaks, and 17 of 28 sporadic cases. Among the remaining 11 sporadic cases due to genotype 1, seven other HMA types were detected. For genotype 2, a single HMA type was found in 72% of samples: 36 of 43 cases from three waterborne outbreaks, 11 of 15 cases from seven intrafamilial outbreaks, 44 of 75 sporadic cases, and all 18 samples from livestock. Within the intrafamilial outbreaks, two other HMA types were identified: the same HMA type was detected in samples from cases within the same outbreak. Among the sporadic cases due to genotype 2, 10 additional HMA types were detected.

Evaluation of a commercial ELISA for detecting Norwalk-like virus antigen in faeces

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.

An outbreak of viral gastroenteritis following environmental contamination at a concert hall

In January 1999, an outbreak of viral gastroenteritis affected more than 300 people who attended a metropolitan concert hall over a 5-day period. Norwalk-like virus (NLV) was confirmed in faecal samples by reverse transcription polymerase chain reaction assay. The index case was a concert attendee who vomited in the auditorium and adjacent male toilet. Gastrointestinal illness occurred among members of 8/15 school parties who attended the following day. Children who sat on the same level of the auditorium as the index case were much more likely to be ill than those seated elsewhere (relative risk 7.1, 95% confidence interval 5.4-9.2. P < 0.001). The majority of other reported cases had not been present on the evening of the vomiting incident. Disinfection procedure was poor and the disinfectant used contained no sodium hypochlorite. Transmission most likely occurred through direct contact with contaminated fomites. The outbreak has implications for disinfection procedures following vomiting incidents at public venues.

Distribution of rotavirus G and P types in north and south Indian children with acute diarrhoea in 1998-99

VP7 and VP4 genotypes of 82 rotavirus strains from children with acute diarrhoea during November 1998-January 1999, in 4 Indian towns, were determined by reverse-transcription PCR. Overall, 68/82 (83%) could be VP7- and 52/82 (63%) VP4-typed. Geographical differences in rotavirus circulation have implications for future vaccination strategies.

Rotavirus G and P genotypes in rural Ghana

An epidemiological study of rotavirus infection was conducted on specimens collected from patients with gastroenteritis and domiciled in the rural Upper Eastern Region of Ghana during 1998. Fifty isolates, randomly selected from 165 human group A rotavirus-positive samples, were G and P characterized by a reverse transcription (RT)-PCR assay using a seminested multiplex method. Rotaviruses of the G3 genotype were found to be the predominant strain (78%), followed by G2 (14%) and G1 (2%). Mixed infections, as shown by combinations of G3 and G2 (4%) and G3 and G1 (2%), were also observed. P typing showed P[4] (72.34%) to be the prevalent strain, followed by P[6] (21.3%), P[8] (2.13%), and a combination of P[4] and P[6] (4.3%).

Capsid protein diversity among Norwalk-like viruses

We have determined the complete capsid gene sequence of 20 Norwalk-like viruses (NLVs) collected predominantly from outbreaks in the UK between 1989 and 1996. These comprised nine genogroup I and eleven genogroup II strains. Phylogenetic analysis of these and 15 published sequences suggest seven genomic sub-groups within genogroup I, including three previously described. In genogroup II, eight sub-groups were apparent, of which four were novel. Amino acid identities between strains of distinct genogroups ranged from 37 to 44% while varying between 61 and 100% for strains within a genogroup. Separate phylogenetic analyses of the N-terminus and central variable region of the capsid showed good correlation. Sequence divergence between strains was greatest within the central variable region, with amino acid sequence identities as low as 28% within a genogroup. These 15 genomic sub-groups provide a framework for further investigations of genetic and antigenic relationships within this calicivirus clade.

Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses"

Genomic characterization of Norwalk-like human caliciviruses (NLVs) originating from outbreaks and sporadic cases of acute gastroenteritis has revealed surprisingly high levels of diversity, even in the RNA polymerase gene, which is anticipated to be highly conserved. Since information on antigenic relationship is limited, due to the lack of a tissue culture system for these viruses, strains mostly are described on the basis of their genetic relatedness. However, the lack of uniformly applied criteria has led to a confusing array of strains with different groups employing different names for similar genetic lineages. Our goal was to conduct a structured analysis of genomic relationships among NLV strains in an attempt to provide an interim framework for genotyping. We assembled a panel of 31 potentially distinct genogroup I (GGI) and genogroup II (GGII) NLVs that reflected the diversity seen in strains detected by our laboratories and in published sequences. Phylogenetic analysis of sequences from regions of the open reading frames (ORF) 1, 2 and 3 was performed in order to investigate genomic relationships. The strains sequenced fell into seven phylogenetic groups in GGI and at least five phylogenetic groups in GGII, based on greater than 80% nucleotide identity in the region of ORF2 encoding the N-terminus of the capsid protein, and consistent clustering with high bootstrap values irrespective of the method used. Analysis of the ORF1 and ORF3 regions supported for most strains the clustering as established for those derived from ORF2. In the ORF1 region, used by most laboratories for diagnostic RT-PCR, clustering was consistent when a putative genotype border was set at 15% nucleotide mismatches for viruses in GGI and at 10% for viruses in GGII. Two strains grouped within different clusters based on ORF1 and ORF2 indicating that recombination may have occurred. We discuss the implications of these observations for the classification and typing of NLVs.

Widespread environmental contamination with Norwalk-like viruses (NLV) detected in a prolonged hotel outbreak of gastroenteritis

A protracted outbreak of Norwalk-like virus (NLV)-associated gastroenteritis occurred in a large hotel in North-West England between January and May 1996. We investigated the pattern of environmental contamination with NLV in the hotel during and after the outbreak. In the ninth week, 144 environmental swabs taken from around the hotel were tested for NLV by nested RT-PCR. The sites were categorized according to the likelihood of direct contamination with vomit/faeces. The highest proportion of positive samples were detected in directly contaminated carpets, but amplicons were detected in sites above 1.5 m which are unlikely to have been contaminated directly. The trend in positivity of different sites paralleled the diminishing likelihood of direct contamination. A second environmental investigation of the same sites 5 months after the outbreak had finished were all negative by RT-PCR. This study demonstrates for the first time the extent of environmental contamination that may occur during a large NLV outbreak.

The heteroduplex mobility assay (HMA) as a pre-sequencing screen for Norwalk-like viruses

Molecular epidemiological studies of Norwalk-like viruses (NLVs), previously known as small round structured viruses (SRSVs), are dependant currently on DNA sequencing of PCR amplicons, which is expensive and time consuming. The Heteroduplex Mobility assay (HMA) was evaluated as a method for identification of PCR amplicons from the commonly circulating NLV strains without DNA sequencing. The procedure was developed for use with two reference strains, a Mexico virus-like strain (MXV-like; Hu¿NLV¿RBH¿1993¿UK) and the Grimsby virus strain (Hu¿NLV¿Gimsby¿1995¿UK), and was optimised with regards to the annealing and electrophoresis conditions and the electrophoresis gel matrix. Using the optimised conditions, amplicons of less than 90% sequence identity formed visible heteroduplexes, allowing the strains to be placed into three categories; Mexico-like, Grimsby-like and non-Mexico virus/non-Grimsby virus strains. Outbreak strains 'genotyped' previously by DNA sequencing as Mexico virus or Grimsby virus were identified correctly by the heteroduplex mobility assay. The procedure was applied prospectively to strains from 130 outbreaks occurring in the UK between 1997 and 1998. Heteroduplex mobility assay was successful on 120 (92%) strains of which 68 (57%) were GRV-like strains, three (2.5%) were Mexico virus-like strains and 49 (41%) were categorised as non- Mexico/non-Grimsby virus strains. Amplicons from 50 of the 120 strains were sequenced and there was perfect correlation between the heteroduplex mobility assay categorisation and phylogenetic analysis. HMA offers a rapid, robust and far cheaper alternative to sequencing for the identification of prevalent Norwalk-like virus genotypes for molecular epidemiological studies.

Genomic characterisation of the large segment of a rabbit picobirnavirus and comparison with the atypical picobirnavirus of Cryptosporidium parvum

The 2362 base pair sequence of the larger of the two double stranded RNA genome segments of a rabbit strain of picobirnavirus (PBV) has a major open reading frame (ORF) of 591 amino acids and two smaller ORFs of 55 and 155 amino acids. A clone of the segment did not hybridise with other viral bisegmented ds RNAs from faecal samples. There is no relationship in sequence or organisation between this PBV sequence and the bisegmented dsRNAs found associated with Cryptosporidium parvum. This suggests that there are at least two distinct classes of bisegmented dsRNA viruses or viral-like agents in faeces.

The bovine Newbury agent-2 is genetically more closely related to human SRSVs than to animal caliciviruses

The hypothesis that the enteric bovine calici-like virus Newbury agent (NA-2) belongs to the family Caliciviridae was examined by genome sequence analysis. Use of solid-phase immune electron microscopy allowed samples with good levels of virus to be identified and amplification of the genome was achieved by reverse transcription-polymerase chain reaction. Examination of a 216-amino-acid sequence in the RNA-dependent RNA polymerase gene and a 116-amino-acid sequence in the capsid gene showed that NA-2 had the closest deduced amino acid identity (77 to 80% for the polymerase region and 67 to 73% for the capsid region) to the morphologically indistinguishable human SRSVs (small round structured viruses) of genogroup 1, which are classified as members of the Caliciviridae. It had a weak relationship (<34.5% deduced amino acid identity) in both the polymerase and the capsid regions to animal caliciviruses, all of which have classical morphology. This is the first genomic data from a nonhuman virus with SRSV morphology. It confirms the hypothesis that the bovine enteric calici-like virus NA-2 is a member of the family Caliciviridae and endorses the observation to date that viruses with SRSV morphology are genomically distinct.

The role of environmental contamination with small round structured viruses in a hospital outbreak investigated by reverse-transcriptase polymerase chain reaction assay

In May 1994 an outbreak of vomiting and diarrhoea occurred in a 28-bed long-stay ward for the mentally infirm. The predominant symptoms were vomiting, diarrhoea, malaise and abdominal pain lasting for approximately 12 h in most cases. The attack rate was 62% (13/21) for patients and 46% (16/35) for staff members. Infection control measures were implemented (containment of infectious individuals, hand hygiene among staff and environmental decontamination) and the ward was closed to admissions. Affected staff were excluded from contact with patients and their food until asymptomatic for 72 h. The outbreak lasted for 17 days. Faecal samples from nine symptomatic persons were negative for bacterial enteric pathogens, Giardia, Cryptosporidium and group A rotavirus. Electron microscopy of 12 faecal samples and one sample of vomitus revealed small round structured virus (SRSV) particles in one faecal sample. A further 30 faecal samples and seven vomitus samples were tested by reverse transcription polymerase chain reaction (RT-PCR) for SRSV of which 12 (40%) and 1 (14%) were positive respectively. Twenty-eight throat swabs from symptomatic and asymptomatic patients were collected, three (9.5%) of which were positive for SRSV by RT-PCR. Thirty-six environmental swabs were collected on the affected ward, and 11 (30%) were positive by RT-PCR. Positive swabs were from lockers, curtains and commodes and confined to the immediate environment of symptomatic patients. The distribution of contamination supports the rationale of cohorting sick patients.

A nested reverse transcriptase PCR assay for detection of small round-structured viruses in environmentally contaminated molluscan shellfish

We describe the evaluation of a nested reverse transcriptase PCR (RT-PCR) procedure for the detection of small round-structured viruses (SRSVs) in molluscan shellfish and the application of this assay for the detection of SRSVs in commercially produced shellfish and in shellfish implicated in outbreaks of gastroenteritis. The range of virus strains detected and the sensitivity of detection were evaluated by using a representative panel of 21 well-characterized SRSV strains. The nested RT-PCR detected 15 of 21 SRSVs, demonstrating that the assay detects a broad range of SRSVs including strains from both genogroup I and genogroup II. Seeding experiments showed the nested RT-PCR assay to be 10 to 1,000 times more sensitive than the single-round RT-PCR assay for the detection of SRSV in shellfish. SRSV-contaminated samples were identified by nested RT-PCR for shellfish grown in polluted harvesting areas and for shellfish associated with outbreaks of gastroenteritis which were negative by a previously described single-round RT-PCR. The assay was shown to be effective for investigation of virus elimination during commercial shellfish processing procedures such as depuration and relaying and has potential applications for monitoring at-risk shellfish harvesting areas, for investigation of SRSV contamination in shellfish from producers linked to gastroenteritis outbreaks, and for the direct detection of virus in shellfish implicated in outbreaks.

Detection of small round structured viruses in shellfish by reverse transcription-PCR

We describe the application of a previously developed sample extraction procedure to the detection of small round structured viruses (SRSVs) in shellfish. Initial seeding experiments showed that PCR inhibitor removal and virus recoveries were comparable to those in previous studies with poliovirus. Shellfish from a range of sewage-contaminated sites were then tested for the presence of SRSVs by using broadly reactive PCR primers followed by Southern blotting with internal probe sites. Positive results were obtained from 5 of 31 field samples tested. Four of these positive samples were from highly polluted sites. PCR product sequence analysis confirmed their identity as SRSV and showed sequence diversity compared with virus controls, suggesting that the results were not a consequence of PCR cross-contamination. Finally, shellfish associated with four separate outbreaks of viral gastroenteritis were tested by PCR and Southern blot for the presence of SRSVs. All outbreak samples tested gave positive results. As far as we are aware, this is the first demonstration of the detection in environmentally contaminated shellfish of the SRSVs responsible for human gastroenteritis. This development may help contribute to the further development of public health controls for molluscan shellfish.

Broadly reactive reverse transcriptase polymerase chain reaction for the diagnosis of SRSV-associated gastroenteritis

A limitation to date of reverse transcriptase polymerase chain reactions (RT-PCRs) for the detection of small, round structured viruses (SRSVs) has been that they have detected only a narrow range of SRSVs due to the marked genomic diversity among strains. A total of 331 faecal samples collected from 136 separate incidents of gastroenteritis occurring in the UK between 1992 and 1994 were examined by RT-PCR employing a single primer pair (N1/E3). SRSV RNA was detected in samples from 93 of 101 (91%) incidents shown to be SRSV-associated by electron microscopy (EM) and in 5 of 35 (14%) SRSV-negative incidents. Amplification products were tested by Southern blot hybridisation with a pool of four digoxigenin (DIG)-labelled oligonucleotides derived from genomic sequence data of SRSV SPIEM types UK 1 to 4. Products from approximately 5% of amplified strains did not hybridise. The N1/E3 primer pair were shown to be SRSV-specific by their failure to amplify other faecal viruses including other human caliciviruses with typical calicivirus morphology. Hybridisation of PCR products with the individual oligonucleotides relating to SRSV SPIEM types UK 1-4 was investigated: 1 of 60 (1.7%) reacted with the UK1 probe, 2/60 (3.4%) reacted with the UK2 probe, 51/60 (85%) with the UK3 probe, and 27/60 (45%) reacted with the UK4 probe. All PCR products that hybridised with the UK4 probe hybridised with the UK3 probe; 6 (10%) failed to hybridise. Identification of this primer pair facilitates routine diagnosis of SRSV infection by RT-PCR and offers the potential for direct detection in food and environmental samples.

Detection of a picobirnavirus associated with Cryptosporidium positive stools from humans

A picobirnavirus with an atypical genome profile was detected by polyacrylamide gel electrophoresis (PAGE) in 37% (20/54) of human faecal samples also containing oocysts of Cryptosporidium typical of C. parvum. This virus shares many of the characteristics of the previously described picobirnaviruses, but has a significantly smaller genome (1.75 and 1.55 Kbp).

Detection and characterisation of bisegmented double-stranded RNA viruses (picobirnaviruses) in human faecal specimens

The prevalence of picobirnaviruses (PBVs) in human stools was investigated by polyacrylamide gel electrophoresis (PAGE) analysis of 832 faecal specimens collected between 1982 and 1993 from patients in various clinical groups. Similar prevalences (9-13%) were detected in patients with or without gastroenteritis and throughout the age range of 3 to > 65 years. Two methods for the extraction of nucleic acid, a phenol/chloroform method and a guanidinium thiocynate (GTC)/silica method, were compared. Detection of PBVs by PAGE was three times more sensitive following RNA extraction by the GTC/silica method. Characterisation of three strains was carried out. Segment sizes ranged from 1.625 to 1.95 kilo base pairs (Kbp) and 2.2 to 2.5 Kbp for the fast and slow migrating bands, respectively. The nuclic acid was shown to be double-stranded RNA (dsRNA) by nuclease digestion. PBV-like particles were detected by electron microscopy in two PAGE-positive stools. Virion diameters ranged from 35 to 41 nm and a buoyant density of 1.38-1.4 g/ml in caesium chloride (CsCl) was demonstrated. These findings suggest that PBVs are widespread in humans in the United Kingdom. However, no disease association could be demonstrated.