The electron microscopical and physical characteristics of small round human fecal viruses: an interim scheme for classification

Impact of duck astrovirus on susceptibility to infection across duck ages

An outbreak of duck astrovirus (DAstV) has occurred in duck farming regions of China, causing substantial economic setbacks in the duck industry. This investigation aimed to examine the variations in DAstV pathogenicity among ducks at different age intervals. Infections were induced in ducks at distinct age groups (1, 7, 14, 21, and 28 d) utilizing the DAstv-1-GDB-2022 strain. The results indicate increased pathogenicity of the DAstv-1-GDB-2022 strain in ducklings aged 21 to 28 d, manifesting as liver and kidney enlargement, severe bleeding, and potential fatalities. Conversely, ducklings aged 1 and 14 d displayed milder symptoms postinfection. Notably, viral shedding continued in ducks of diverse age groups even 21 d postinfection (Dpi). Moreover, DAstV replicates in various tissues, predominantly affecting the liver. Immunohistochemical tests using rabbit anti-DAstV antibodies revealed robust positive signals in both the liver and kidneys, which correlated with the clinical symptom severity observed through macroscopic and microscopic examinations. Serum biochemical assays and indirect ELISA demonstrated a consistent response to DAstV infection across different age groups, with older ducklings exhibiting increased sensitivity. In conclusion, this study successfully replicated clinical symptoms similar to those of natural DAstV infection using the DAstv-1-GDB-2022 strain. Importantly, we systematically delineated the differences in susceptibility to DAstV among ducks at various ages, laying the foundation for further research into the pathogenic mechanisms of DAstV and potential vaccine development.

Development of Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of Human Norovirus Major Capsid Protein

Human Norwalk viruses (HuNoVs), the most common etiological agents of acute gastroenteritis, are genetically diverse RNA viruses that frequently cause mass food poisoning internationally. Although nucleic acid detection methods, such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR), are the gold standard for the diagnosis of norovirus infection, alternative methods are needed for the specific and sensitive viral protein detection for rapid diagnosis and surveillance. In this study, we developed a robust and high-throughput targeted proteomic assay workflow to directly detect the VP1 major capsid protein of HuNoVs. A parallel reaction monitoring (PRM) assay using a high-resolution mass spectrometer was used to detect representative peptides derived from VP1 in six different HuNoV genotypes. An optimized protocol using synthesized heavy isotope-labeled peptides as internal standards was also used to simultaneously genotype and quantify the VP1 protein in human stool specimens. This method is expected to become a new tool for studying the molecular epidemiology of HuNoV and to shed new light on targeted proteomics in clinical practice.

An Insight into the Molecular Characteristics and Associated Pathology of Chicken Astroviruses

The chicken astrovirus (CAstV) is a ubiquitous enteric RNA virus that has been associated mainly with conditions, such as the runting-stunting syndrome, severe kidney disease, visceral gout, and white chick syndrome, in broiler-type chickens worldwide. Sequence analysis of the capsid genes’ amino acids of the strains involved in these conditions reveals a genetic relationship and diversity between and within the CAstV genogroups and subgroups based on phylogenetic analysis, genetic distance (p-dist), and pathogenicity. While the two genogroups (A and B) are demarcated phylogenetically, their pairwise amino acid sequence identity is 39% to 42% at a p-dist of 0.59 to 0.62. Group-A consists of three subgroups (Ai, Aii, and Aiii) with an inter- and intra-subgroup amino acid identity of 78% to 82% and 92% to 100%, respectively, and a p-dist of 0.18 to 0.22. On the other hand, the six subgroups (Bi, Bii, Biii, Biv, Bv, and Bvi) in Group-B, with a p-dist of 0.07 to 0.18, have an inter- and intra-subgroup amino acid identity of 82% to 93% and 93% to 100%, respectively. However, these groupings have little to no effect on determining the type of CAstV-associated pathology in chickens.

A Bibliometric Analysis of the Literature on Norovirus Disease from 1991-2021

Norovirus (NoV) is one of the oldest recognized diseases and the leading causal pathogen for acute gastroenteritis (AGE) worldwide. Though numerous studies have been reported on NoV disease, limited research has explored the publication trends in this area. As a result, the objective of this work was to fill the void by conducting a bibliometric study in publication trends on NoV studies as well as discovering the hotspots. The Web of Science central assemblage database was hunted for publications from 1991 to 2021 with “norovirus” in the heading. Microsoft Excel 2016, VOSviewer, R Bibliometrix, and Biblioshiny packages were deployed for the statistical analysis of published research articles. A total of 6021 published documents were identified in the Web of Science database for this thirty-year study period (1991–2021). The analyses disclosed that the Journal of Medical Virology was the leading journal in publications on norovirus studies with a total of 215 published articles, the Journal of Virology was the most cited document with 11,185 total citations. The United States of America (USA) has the most significant productivity in norovirus publications and is the leading country with the highest international collaboration. Analysis of top germane authors discovered that X. Jiang (135) and J. Vinje (119) were the two top relevant authors of norovirus publications. The commonly recognized funders were US and EU-based, with the US emerging as a top funder. This study reveals trends in scientific findings and academic collaborations and serves as a leading-edge model to reveal trends in global research in the field of norovirus research. This study points out the progress status and trends on NoV research. It can help researchers in the medical profession obtain a comprehensive understanding of the state of the art of NoV. It also has reference values for the research and application of the NoV visualization methods. Further, the research map on AGE obtained by our analysis is expected to help researchers efficiently and effectively explore the NoV field.

Characteristics of Norovirus Food Poisoning Outbreaks in Korea in the 2000s

ABSTRACT

Norovirus food poisoning outbreaks in Korea (South) appeared in the 2000s and have been increasing since then. We aimed to investigate the epidemiological features of norovirus food poisoning outbreaks in Korea from 2002 to 2017, on the basis of official food poisoning statistics and publically reliable reports, and to find any associations with climate factors. Norovirus was the most common cause of food poisoning among known causative substances in Korea during the study period. More than one-third of the outbreaks occurred in group meal service facilities, including school lunch programs. A few of these facilities used groundwater contaminated with noroviruses to wash or cook food, which contributed to outbreaks. Norovirus occurrences showed strong seasonality: cold and relatively dry winter air may help norovirus to flourish. Both norovirus genotypes GI and GII that are infectious to humans were detected, with GII becoming more prevalent than GI. According to our correlation analysis in connection with climate factors, average temperatures, the highest and lowest temperatures, precipitation, the number of rain days, and humidity showed a significant negative correlation with a monthly norovirus occurrence (P < 0.05). The lowest temperature and average temperature had higher coefficients of correlation, -0.377 and -0.376, respectively. The norovirus outbreaks in Korea showed complex etiological characteristics, although more prevailed in wintertime, and are now a major public health problem. The use of groundwater in group meal service settings is a public health issue, as well as a norovirus concern; therefore, groundwater used in food service facilities and businesses should be treated for safety.

HIGHLIGHTS

Development of multi-epitope subunit vaccine for protection against the norovirus' infections based on computational vaccinology

Human Norovirus belongs to a family Calciviridae, and was identified in the outbreak of gastroenteritis in Norwalk, due to its seasonal prevalence known as "winter vomiting disease." Treatment of Norovirus infection is still mysterious because there is no effective antiviral drugs or vaccine developed to protect against the infection, to eradicate the infection an effective vaccine should be developed. In this study, capsid protein (A7YK10), small protein (A7YK11), and polyprotein (A7YK09) were utilized. These proteins were subjected to B and T cell epitopes prediction by using reliable immunoinformatics tools. The antigenic and non-allergenic epitopes were selected for the subunit vaccine, which can activate cellular and humoral immune responses. Linkers joined these epitopes together. The vaccine structure was modelled and validated by using Errat, ProSA, and rampage servers. The modelled vaccine was docked with TLR-7. The stability of the docked complex was evaluated by MD simulation. To apply the concept in a wet lab, the reverse translated vaccine sequence was cloned in pET28a (+). The vaccine developed in this study requires experimental validation to ensure its effectiveness against the disease.Communicated by Ramaswamy H. Sarma.

Identification of astroviruses in bovine and buffalo calves with enteritis

Astroviruses (AstVs) have been identified in the stools of calves with enteritis and in the brain tissues of bovines with encephalitis but their pathogenic role has not been clarified. In this study, we report the detection and characterization of bovine and water buffalo AstV strains identified in young bovine and buffalo calves with enteritis in Italy between 2012 and 2015. By negative staining transmission electron microscopy (TEM) observation, AstV-like particles were identified in the stools of the animals and AstV RNA was confirmed molecularly. The sequence (~3.2-kb) at the 3′ end of the genome was determined for two bovine and two buffalo AstVs. Sequence and phylogenetic analysis on the partial ORF1b and full-length ORF2 revealed a marked genetic diversity although the viruses were distantly related to other AstV identified from ruminants. Gathering sequence information on ruminant AstVs is important to understand the extent of inter-species circulation and for the development of reliable, specific diagnostic tools.

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Astroviruses in ruminants are neglected enteric viruses.

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Recently, neurotropic strains have been identified in ruminants.

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Astrovirus was detected in outbreaks of enteritis in cattle and buffalo in Italy.

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Genome sequencing of the viruses unveiled marked genetic diversity.

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Implementing the diagnostics is pivotal to conceive surveillance studies.

Microbial Contamination of Fresh Produce: What, Where, and How?

Promotion of healthier lifestyles has led to an increase in consumption of fresh produce. Such foodstuffs may expose consumers to increased risk of foodborne disease, as often they are not subjected to processing steps to ensure effective removal or inactivation of pathogenic microorganisms before consumption. Consequently, reports of ready-to-eat fruit and vegetable related disease outbreak occurrences have increased substantially in recent years, and information regarding these events is often not readily available. Identifying the nature and source of microbial contamination of these foodstuffs is critical for developing appropriate mitigation measures to be implemented by food producers. This review aimed to identify the foodstuffs most susceptible to microbial contamination and the microorganisms responsible for disease outbreaks from information available in peer-reviewed scientific publications. A total of 571 outbreaks were identified from 1980 to 2016, accounting for 72,855 infections and 173 deaths. Contaminated leafy green vegetables were responsible for 51.7% of reported outbreaks. Contaminated soft fruits caused 27.8% of infections. Pathogenic strains of Escherichia coli and Salmonella, norovirus, and hepatitis A accounted for the majority of cases. Large outbreaks resulted in particular biases such as the observation that contaminated sprouted plants caused 31.8% of deaths. Where known, contamination mainly occurred via contaminated seeds, water, and contaminated food handlers. There is a critical need for standardized datasets regarding all aspects of disease outbreaks, including how foodstuffs are contaminated with pathogenic microorganisms. Providing food business operators with this knowledge will allow them to implement better strategies to improve safety and quality of fresh produce.

White Chick Syndrome Associated with Chicken Astrovirus in Ontario, Canada

Sixty-four cases of white chick syndrome (WCS) in broiler breeders producing affected progeny were reported from seven hatcheries in Ontario, Canada, between 2009 and 2016, with 43 of those originating from two hatcheries owned by a single company. WCS cases were identified by the presence of typical chicks in the hatchery that were generally weak with pale to white down, enlarged abdomens, and occasionally brown wiry fluff on the dorsum of the neck. Affected embryos and chicks had characteristic gross and histologic liver lesions, and livers were positive for chicken astrovirus (CAstV) RNA by real-time reverse transcriptase PCR. Affected broiler breeder flocks experienced egg production drops of 0% to 21% and hatchability drops of 0% to 68.4%. The amino acid sequence of the region encoding the capsid gene of WCS viruses demonstrated all Ontario CAstV to be in Group B, Subgroup Bii.

Discovery of novel astrovirus genotype species in small ruminants

Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the prediction of multiple recombination events in four of five newly discovered full or almost full-length genome sequences suggests a plausible interspecies transmission. The findings point out the occurrence and fecal shedding of previously unknown AstV in sheep and goats and pave the way towards a better understanding of the diversity and transmission of AstV in small ruminants.

Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety

Transmission electron microscopy (TEM) is the only imaging technique allowing the direct visualization of viruses, due to its nanometer‐scale resolution. Between the 1960s and 1990s, TEM contributed to the discovery of many types of viruses and served as a diagnostic tool for identifying viruses directly in biological samples, either in suspension or in sections of tissues or mammalian cells grown in vitro in contact with clinical samples. The diagnosis of viral infections improved considerably during the 1990s, with the advent of highly sensitive techniques, such as enzyme‐linked immunosorbent assay (ELISA) and PCR, rendering TEM obsolete for this purpose. However, the last 20 years have demonstrated the utility of this technique in particular situations, due to its “catch‐all” nature, making diagnosis possible through visualization of the virus, without the need of prior assumptions about the infectious agent sought. Thus, in several major outbreaks in which molecular techniques failed to identify the infectious agent, TEM provided the answer. TEM is also still occasionally used in routine diagnosis to characterize infections not diagnosed by molecular assays. It is also used to check the microbiological safety of biological products. Many biopharmaceuticals are produced in animal cells that might contain little‐known, difficult‐to‐detect viruses. In this context, the “catch‐all” properties of TEM make it possible to document the presence of viruses or virus‐like particles in these products.

Propagation of Astrovirus VA1, a Neurotropic Human Astrovirus, in Cell Culture

Astrovirus VA1/HMO-C (VA1; mamastrovirus 9) is a recently discovered astrovirus genotype that is divergent from the classic human astroviruses (mamastrovirus 1). The gastrointestinal tract is presumed to be the primary site of infection and pathogenicity for astroviruses. However, VA1 has been independently detected in brain tissue of five cases of human encephalitis. Studies of the pathogenicity of VA1 are currently impossible because there are no reported cell culture systems or in vivo models that support VA1 infection. Here, we describe successful propagation of VA1 in multiple human cell lines. The initial inoculum, a filtered clinical stool sample from the index gastroenteritis case cluster that led to the discovery of VA1, was first passaged in Vero cells. Serial blind passage in Caco-2 cells yielded increasing copies of VA1 RNA, and multistep growth curves demonstrated a >100-fold increase in VA1 RNA 72 h after inoculation. The full-length genomic and subgenomic RNA strands were detected by Northern blotting, and crystalline lattices of viral particles of ∼26-nm diameter were observed by electron microscopy in infected Caco-2 cells. Unlike other human astrovirus cell culture systems, which require addition of exogenous trypsin for continued propagation, VA1 could be propagated equally well with or without the addition of trypsin. Furthermore, VA1 was sensitive to the type I interferon (IFN-I) response, as VA1 RNA levels were reduced by pretreatment of Caco-2 cells with IFN-β1a. The ability to propagate VA1 in cell culture will facilitate studies of the neurotropism and neuropathogenesis of VA1.IMPORTANCE Astroviruses are an emerging cause of central nervous system infections in mammals, and astrovirus VA1/HMO-C is the most prevalent astrovirus in cases of human encephalitis. This virus has not been previously propagated, preventing elucidation of the biology of this virus. We describe the first cell culture system for VA1, a key step necessary for the study of its ability to cause disease.

Complete genome sequence analysis of chicken astrovirus isolate from India

Objective

Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens.

Methods

Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein.

Results

The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.

Electronic supplementary material

The online version of this article (doi:10.1007/s11259-016-9673-6) contains supplementary material, which is available to authorized users.

Development and validation of an immunohistochemistry procedure for the detection of a neurotropic bovine astrovirus

Members of the Astroviridae family are best known to cause diarrhea in different mammalian species. Lately, some strains have been associated with encephalitis in humans, minks and cattle. In this study, we developed an immunohistochemistry (IHC) procedure for the detection of a neurotropic bovine astrovirus (BoAstV-CH13/NeuroS1), which is associated with non-suppurative encephalitis in cattle. We expressed five recombinant antigens corresponding to different putative viral proteins of BoAstV-CH13/NeuroS1. Antigens were then used for the production of hyperimmune sera in rabbits. Out of the five hyperimmune sera, the one directed against the conserved N-terminus of the viral capsid protein, termed ORF2-con, clearly surpassed the others in the detection of viral antigens in IHC in terms of strong signal intensity and low background staining. The accuracy of the ORF2-con IHC protocol was then evaluated using different sets of brain tissue samples: 30 samples from 9 animals with confirmed BoAstV-CH13/NeuroS1 infection, 30 samples from 8 animals with non-suppurative encephalitis of another etiology and 30 samples from apparently healthy slaughtered animals. The IHC was positive only with tissue samples from animals with a known positive BoAstV-CH13/NeuroS1 status, but not with those from negative ones, indicating a good diagnostic sensitivity and specificity of the assay. The ORF2-con IHC procedure is therefore an adequate tool for the detection of BoAstV-CH13/NeuroS1 infections in cattle.

Incubation periods of viral gastroenteritis: a systematic review

BACKGROUND

Accurate knowledge of incubation period is important to investigate and to control infectious diseases and their transmission, however statements of incubation period in the literature are often uncited, inconsistent, and/or not evidence based.

METHODS

In a systematic review of the literature on five enteric viruses of public health importance, we found 256 articles with incubation period estimates, including 33 with data for pooled analysis.

RESULTS

We fit a log-normal distribution to pooled data and found the median incubation period to be 4.5 days (95% CI 3.9-5.2 days) for astrovirus, 1.2 days (95% CI 1.1-1.2 days) for norovirus genogroups I and II, 1.7 days (95% CI 1.5-1.8 days) for sapovirus, and 2.0 days (95% CI 1.4-2.4 days) for rotavirus.

CONCLUSIONS

Our estimates combine published data and provide sufficient quantitative detail to allow for these estimates to be used in a wide range of clinical and modeling applications. This can translate into improved prevention and control efforts in settings with transmission or the risk of transmission.

Astroviruses as causative agents of poultry enteritis: genetic characterization and longitudinal studies on field conditions

Astroviruses (AstVs) are nonenveloped RNA small round viruses (SRVs) with a genome of 6.8-7.9 kb. Known avian AstVs are spread worldwide; they have been associated with poult enteritis and mortality syndrome in the United States and reported in Italy in intensive turkey and guinea fowl flocks. Nevertheless, their real prevalence and their pathogenic role in avian enteritis affecting Italian flocks is far from clear. Negative staining electron microscopy (nsEM) is used for the routine diagnosis of avian enteric SRVs, although it cannot distinguish morphologically similar particles. Enzyme-linked immunosorbent assay (ELISA), reverse-transcription PCR (RT-PCR), and genomic sequencing are now used for this specific purpose. We analyzed 329 samples of chicken, turkey, and guinea fowl intestinal contents from Italian poultry flocks. Most samples were from enteritis outbreaks, but we also included samples from three longitudinal studies (one on 11 broiler flocks and the other two on a guinea fowl flock). We first examined the samples with nsEM. SRVs, including AstVs, are often associated with rotaviruses and were the most commonly detected morphotypes in avian enteric diseases. We then analyzed 124 of the samples with an RT-PCR targeting the open reading frame (ORF)-1b of AstV. This gene codes for an RNA-dependent polymerase. We then sequenced and genetically analyzed the RT-PCR positive samples. Phylogenetic analysis distinguished three defined clusters: the first included guinea fowl AstVs and turkey AstVs-2; the second, chicken AstVs; and the third was formed by avian nephritis viruses (ANVs). No strains clustered with turkey AstVs-1. The results indicate that ORF-1b presents certain genetic variability, even among AstVs from the same species. In longitudinal studies, samples retrieved from the same shed were homogeneous, with some exceptions suggesting possible coexistence of different genetic types in the same unit. The finding of ANV-like viruses in commercial guinea fowls underlines the genetic variability of AstVs and strengthens the hypothesis of a varied intraherd situation.

Extraneous agent detection in vaccines--a review of technical aspects

The quality and safety of commercial vaccines have a profound importance. Contrary to all precautions and efforts the use of biological material in vaccine development and production may lead to potential contamination of the vaccines with known and unknown extraneous agents (EAs).

In veterinary field official lists of EAs have been compiled as legal framework to describe the potential agents, which must be tested during manufacture of vaccines. Nevertheless, detection of known and unknown contaminants in vaccines is a common duty for manufacturers and authorities of both veterinary and human field sharing similar needs of special technical approaches. State-of-art molecular methods such as randomly primed PCR combined with massive parallel sequencing (MPS) or microarrays may open new perspectives in extraneous agent testing. The robustness and efficacy of this technical approach in vaccine control was clearly demonstrated on a human vaccine example when porcine circovirus type 1 (PCV1) contamination was revealed in Rotarix, a human rotavirus vaccine. The consequences and implications are reviewed hereby from a veterinary regulatory point of view.

Astrovirus Structure and Assembly

Recent structural studies on the astrovirus virion and viral proteins have yielded exciting new insights into the molecular mechanisms of the astrovirus life cycle. The 25 Å-resolution cryo-electron microscopy (Cryo-EM) reconstructions of the astrovirus virion reveal a solid capsid shell studded with spikes. Proteolytic maturation of the virus particle results in capsid conformational changes, most prominently at the spikes. High-resolution crystal structures of the human and avian astrovirus capsid spike domains have shed light on potential host receptors and species specificity. Together, both the structural studies on the astrovirus virion and capsid spike domains have revealed similarities to hepatitis E virus, suggesting an evolutionary relationship. The only other structural information on astrovirus is from the high-resolution crystal structure of the protease that is involved in nonstructural polyprotein processing. Overall, these structural studies have led a better understanding of the astrovirus life cycle, including astrovirus assembly, virus release, maturation, receptor binding, antibody neutralization, and nonstructural polyprotein processing.

Achievement V - Methods for breaking the transmission of pathogens along the food chain: Detection of viruses in food

Traditionally the focus for control of food-borne disease has been bacteria. During the last decade viruses have emerged as important sources of food borne human disease. Since the traditional bacteriological indicators, are not reliable for viral contamination, new methods are needed. PCR has enhanced the detection of virus in food. A challenge for developing detection reliable methods for viruses in food is that food matrices vary in composition, high sequence variability and inhibitors may be present. Therefore it is necessary to develop assays that have high diagnostic sensitivity, are broad and robust, and combine sample concentration and removal of inhibitors.

Segmentation expression of capsid protein as an antigen for the detection of avian nephritis virus infection in chicken flocks

Subclinical pathological changes in the kidneys of broiler chickens and suppression of growth caused by the avian nephritis virus (ANV) affect poultry flocks worldwide. A test for detection of virus-specific antibodies in serum would be useful for epidemiological investigations, however the poor propagation in cell cultures has restricted the development of serological tests based on the use of ANV particles as antigens. An enzyme-linked immunosorbent assay (ELISA) was developed for detection of ANV-specific antibodies in chicken serum, using a recombinant protein antigen prepared by segmentation expression of the capsid protein antigen epitope of ANV (HM029238) transfected into Escherichia coli. The expressed fusion protein was detected by Western blotting with ANV-positive serum, and the optimal immunoreactive fusion P1 protein was determined. Using the optimized P1-ELISA, ANV-specific antibodies were detected in commercial chicken flocks aged 10-25 days obtained from the Liaoning Province, China. Out of 960 serum samples, 459 (47.8%) were positive for infection with ANV. These results indicate that the P1-ELISA is helpful for preliminary serological diagnosis of ANV infection, and could be used to for screening in ANV infection and for determining antibodies against ANV.

Astrovirus infections in humans and animals - molecular biology, genetic diversity, and interspecies transmissions

Astroviruses are small, non-enveloped, positive sense, single-stranded RNA viruses first identified in 1975 in children suffering from diarrhea and then described in a wide variety of animals. To date, the list of animal species susceptible to astrovirus infection has expanded to 22 animal species or families, including domestic, synantropic and wild animals, avian, and mammalian species in the terrestrial and aquatic environments. Astrovirus infections are considered among the most common cause of gastroenteritis in children, second only to rotavirus infections, but in animals their association with enteric diseases is not well documented, with the exception of turkey and mink astrovirus infection. Genetic variability has been described in almost all astrovirus species sufficiently examined infecting mammals and birds; however, antigenic variability has been demonstrated for human astroviruses but is far less investigated in animal viruses. Interestingly, there is an increasing evidence of recombination events occurring in astroviruses, which contributes to increase the genetic variability of this group of viruses. A wide variety of species infected, the evident virus genetic diversity and the occurrence of recombination events indicate or imply either cross-species transmission and subsequent virus adaptation to new hosts or the co-infection of the same host with different astroviruses. This can also favor the emergence of novel astroviruses infecting animals or with a zoonotic potential. After more than 30 years from their first description in humans, there are many exciting streams of research to be explored and intriguing questions that remain to be answered about the relatively under-studied Astroviridae family. In the present work, we will review the existing knowledge concerning astrovirus infections in humans and animals, with particular focus on the molecular biology, interspecies transmission and zoonotic potential of this group of viruses.

Elevation of serum transaminases with norovirus infection

From November to December in 2006, we experienced 4 pediatric cases with an elevation of the serum transaminase levels accompanied by acute gastroenteritis. All examined stool specimens were norovirus positive according to the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) assay. The clinical courses of these cases were the same as those of common gastroenteritis. Blood examinations showed only a slight elevation of the transaminase levels at the onset of gastroenteritis, while the symptoms were severe. Interestingly, the transaminase levels significantly increased after gastroenteritis disappeared. The average period between the onset of gastroenteritis and the peak of transaminase levels was 13.8 days. In all cases, the patients were treated with the administration of glycyrrhizin, and the transaminase levels returned to normal approximately 4 weeks (average 26.8 days) after the onset of gastroenteritis, thus suggesting that an elevation of the transaminase levels in association with norovirus gastroenteritis may therefore be a self-limited process which may demonstrate a relatively good natural prognosis. Norovirus is one of the important pathogens which cause an elevation in the serum transaminase levels in young children. When an elevation in the transaminase levels in association with gastroenteritis is observed in young children, it is important to continuously follow up such patients even after the gastroenteritis has disappeared and to perform a virus search based on examinations of stool specimens using an RT-PCR assay in order to detect the presence of norovirus infections.

Metagenomics for the discovery of novel human viruses

Modern laboratory techniques for the detection of novel human viruses are greatly needed as physicians and epidemiologists increasingly deal with infectious diseases caused by new or previously unrecognized pathogens. There are many clinical syndromes in which viruses are suspected to play a role, but for which traditional microbiology techniques routinely fail in uncovering the etiologic agent. In addition, new viruses continue to challenge the human population owing to the encroachment of human settlements into animal and livestock habitats, globalization, climate change, growing numbers of immunocompromised people and bioterrorism. Metagenomics-based tools, such as microarrays and high-throughput sequencing are ideal for responding to these challenges. Pan-viral microarrays, containing representative sequences from all known viruses, have been used to detect novel and distantly-related variants of known viruses. Sequencing-based methods have also been successfully employed to detect novel viruses and have the potential to detect the full spectrum of viruses, including those present in low numbers.

Detection and molecular characterization of enteric viruses from poult enteritis syndrome in turkeys

This study was conducted to detect and characterize enteric viruses [rotavirus, turkey astrovirus-2 (TAstV-2), reovirus, and turkey coronavirus] from cases of poult enteritis syndrome (PES) in Minnesota turkeys. Of the intestinal contents collected from 43 PES cases, 25 were positive for rotavirus and 13 for small round viruses by electron microscopy (EM). Of the enteric virus-positive cases by EM (n=27), 16 cases had rotavirus or small round viruses alone and the remaining 11 cases had both viruses. None of the cases were positive for reovirus or coronavirus by EM. However, with reverse transcription-PCR (RT-PCR), 40 cases (93%) were positive for rotavirus, 36 (84%) for TAstV-2, and 17 (40%) for reovirus. None of the cases were positive for turkey coronavirus by RT-PCR. The viruses from all cases were detected either alone or in combination of 2 or 3 by RT-PCR. Thus, 8 (19%) cases were positive for a single virus, whereas a combination of viruses was detected in the remaining 35 (81%) cases. The rota-TAstV-2 combination was the most predominant (n=18 cases). Fifteen cases were positive for all 3 viruses. The rotaviruses had sequence homology of 89.8 to 100% with previously published sequences of turkey rotaviruses at the nucleotide level. The TAstV-2 had sequence homology of 84.6 to 98.7% with previously published TAstV-2, whereas reoviruses had sequence homology of 91.6 to 99.3% with previously published sequences of turkey reoviruses. Phylogenetic analysis revealed that rota- and reoviruses clustered in a single group, whereas TAstV-2 clustered in 2 different groups. In conclusion, a larger number of PES cases was positive for rotavirus, TAstV-2, and reovirus by RT-PCR than with EM. The presence of more than one virus and changes at the genetic level in a virus may affect the severity of PES in turkey flocks.

Experimental reproduction of poult enteritis syndrome: clinical findings, growth response, and microbiology

Poult enteritis syndrome (PES) is an infectious disease of turkey poults characterized by diarrhea, dullness, and depression. Five experiments were conducted to reproduce the disease in turkey poults using intestinal contents of PES-affected birds. In all experiments, poults at 14 d of age were divided into 4 groups and were orally given 2 mL of unfiltered supernatant, filtered supernatant, sediment dissolved in PBS, or PBS alone. Inocula in experiments 1, 3, and 5 consisted of intestinal contents from PES-affected birds of less than 2 wk of age, whereas those in experiments 2 and 4 consisted of intestinal contents from PES-affected birds of 4 to 6 wk of age. Poults in all groups were observed daily for clinical signs. The BW and microbiological criteria in experiments 1, 3, and 5 were evaluated at 5, 10, and 15 d postinoculation, whereas in experiments 2 and 4, these observations were made at 10 and 20 d postinoculation. Rotavirus, astrovirus, and Salmonella were present in all 5 inocula. Diarrhea and depression were the major signs in poults given PES material. Significant retardation of growth was observed in poults given any of the 3 PES materials, but this effect was more pronounced in poults given the sediment inoculum. Rotavirus, astrovirus, and Salmonella were detected in poults given PES material. In some cases, enterovirus was also detected. No major difference was noticed in experimental reproduction of PES when intestinal contents from different age birds were used as the inoculum.

Detection of TT virus by single-primer sequence-independent amplification in multiple samples collected from an outbreak of gastroenteritis

A panel of gastroenteritis outbreak samples was subjected to a virus purification and concentration algorithm followed by a sequence-independent amplification method devised to detect viral enteric pathogens. The application of these methods allowed the identification of torque teno virus (TTV) in one outbreak. The complete genome sequence of 3,260 nt was obtained through "genome walking", and four open reading frames were deduced from the genomic sequence. Phylogenetic analysis grouped this virus in TTV genetic group 3, clustering with genotype 27, with 85% similarity at the nt level with strain SAa-01.

Viral detection by electron microscopy: past, present and future

Viruses are very small and most of them can be seen only by TEM (transmission electron microscopy). TEM has therefore made a major contribution to virology, including the discovery of many viruses, the diagnosis of various viral infections and fundamental investigations of virus-host cell interactions. However, TEM has gradually been replaced by more sensitive methods, such as the PCR. In research, new imaging techniques for fluorescence light microscopy have supplanted TEM, making it possible to study live cells and dynamic interactions between viruses and the cellular machinery. Nevertheless, TEM remains essential for certain aspects of virology. It is very useful for the initial identification of unknown viral agents in particular outbreaks, and is recommended by regulatory agencies for investigation of the viral safety of biological products and/or the cells used to produce them. In research, only TEM has a resolution sufficiently high for discrimination between aggregated viral proteins and structured viral particles. Recent examples of different viral assembly models illustrate the value of TEM for improving our understanding of virus-cell interactions.

Sensitive and rapid detection of norovirus using duplex TaqMan reverse transcription-polymerase chain reaction

Conventional reverse transcription-polymerase chain reaction (RT-PCR) to detect norovirus (NV) is a complex of multi-step procedure that requires gel electrophoresis as well as hybridization or sequencing to confirm the final diagnosis. A duplex TaqMan RT-PCR was developed to detect and classify genogroup (G) I and GII of NV. The primers and TaqMan probes for this assay were selected from the region of open reading frame (ORF) 1-ORF2 junction. A total of 796 stool specimens from 103 outbreaks of gastroenteritis, and a series of 46 stool specimens containing most NV genotypes was used for this study. For these specimens from 103 outbreaks, NV was detected and classified by the duplex TaqMan RT-PCR in 536 of the 541 specimens tested previously to be positive using the conventional RT-PCR. Two hundred fifty-one of the 255 specimens that were negative by the conventional RT-PCR were also negative by the TaqMan RT-PCR. No false positive result was observed for other enteric RNA viruses such as rotavirus and sapovirus. This is the first report on the development of a duplex TaqMan RT-PCR end-point assay for detection and differentiation of GI and GII of NV strains simultaneously followed by genotyping. These results suggest the practical application of this duplex TaqMan RT-PCR is useful for the detection of NV in clinical specimens.

Genomic analysis of closely related astroviruses

To understand astrovirus biology, it is essential to understand factors associated with its evolution. The current study reports the genomic sequences of nine novel turkey astrovirus (TAstV) type 2-like clinical isolates. This represents, to our knowledge, the largest genomic-length data set available for any one astrovirus type. The comparison of these TAstV sequences suggests that the TAstV species contains multiple subtypes and that recombination events have occurred across the astrovirus genome. In addition, the analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection.

Small round viruses: classification and role in food-borne infections

Since the first observation of Norwalk virus in the electron microscope in 1972, many different small virus particles in the size range 20-40 nm have been described world-wide in association with outbreaks of gastroenteritis. Progress characterizing these agents has been hampered by the relatively small numbers of particles present in clinical material and the lack of success in culturing them. Although the relationship between some of these viruses remains confusing, a number of distinct groups has emerged, based on morphological features and limited physical data. Immuno-electron microscopy has proved valuable in detecting viruses but the addition of antibody can mask surface morphological features. Examination of viruses in negatively stained preparations without added antibody has revealed distinct morphological differences and viruses previously thought to be simply antigenic variants within the Norwalk group of viruses clearly belong to other groups. Preliminary evidence suggests that one human virus unrelated to Norwalk has a single-stranded DNA genome and is a parvovirus. Some groups have been implicated in outbreaks of food-borne gastroenteritis, particularly after the consumption of shellfish, and their role in other food-borne and water-borne outbreaks is being increasingly recognized.

In vitro cell culture infectivity assay for human noroviruses

A 3-dimensional organoid human small intestinal epithelium model was used.

Human noroviruses cause severe, self-limiting gastroenteritis that typically lasts 24–48 hours. Because of the lack of suitable tissue culture or animal models, the true nature of norovirus pathogenesis remains unknown. We show that noroviruses can infect and replicate in a 3-dimensional (3-D), organoid model of human small intestinal epithelium. Cells grown on porous collage-coated beads under fluid shear conditions in rotating wall vessel bioreactors differentiate into 3-D architectures resembling both the morphologic and physiologic function of in vivo tissues. Microscopy, PCR, and fluorescent in situ hybridization provided evidence of norovirus infection. Cytopathic effect and norovirus RNA were detected at each of the 5 cell passages for genogroup I and II viruses. Our results demonstrate that the highly differentiated 3-D cell culture model can support the natural growth of human noroviruses, whereas previous attempts that used differentiated monolayer cultures failed.

Gastroenteric Viruses

In recent years, viruses have been recognized increasingly as an important cause of foodborne infections. More than 160 enteric viruses are excreted in the feces of infected individuals, and some may also be present in the vomitus. Food and water are directly contaminated with fecal material, through the use of sewage sludge in agriculture, sewage pollution of shellfish culture beds, or may be contaminated by infected food-handlers.

Applicability of microarray technique for the detection of noro- and astroviruses

Noroviruses and astroviruses are widespread viral agents causing gastroenteritis. Noroviruses are actually a diverse group of viruses. A new microarray-based detection method is presented for both noro- and astroviruses. This method enables simultaneous identification of genogroups and types of noro- and astroviruses. For pre-amplification, the monoplex- and multiplex-RT-PCR assays were applied to test sensitivity. The 202 specimens were used to determine the specificity, precision, and accuracy of the microarray. Stool samples representing 13 of norovirus GI and GII genotypes were assayed. The microarray detected all but one genotype. In a panel of 74 stool samples, 45 tested positive for norovirus by microarray, against 35 by a conventional PCR-method. In addition, microarray detected some double infections. In a panel of archival samples, astroviruses of genotype 4 frequently emerged in Finland from 1977 to 1997. This study demonstrates that microarray is useful for simultaneous monitoring of several viruses and their subtypes. Microarray provides a convenient tool for the detection of RNA viruses for which frequent changes in the panel of detection primers may be required.

Characterization of a cross-reactive linear epitope in human genogroup I and bovine genogroup III norovirus capsid proteins

The Southampton norovirus (SV) capsid protein was expressed as VLPs by recombinant baculoviruses in insect cells and was used to immunize mice for the production of monoclonal antibodies (mAbs). One mAb, CM54, showed broad cross-reactivity to genogroup I (GI) noroviruses, but was not reactive to GII capsid proteins. Interestingly mAb CM54 reacted to a bovine norovirus capsid protein. Immunoblot analysis indicated the binding site for CM54 was located in the shell domain between amino acid residues 102-225 of the SV capsid protein. The epitope was mapped to high resolution using a peptide array and was located to the sequence LEDVRN at amino acid residues 162-167. Alignment of norovirus capsid protein sequences confirmed the epitope sequence was common to particular groups of human and bovine noroviruses. Modeling of the epitope onto the recombinant NV capsid protein revealed it was located to the inner surface of the shell domain.

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).

Experience from the development of a diagnostic single tube real-time PCR for human caliciviruses, Norovirus genogroups I and II

Detection of caliciviruses requires high mutation tolerance and throughput. The development of a rational simple, single tube reverse transcription-real-time quantitative PCR (QPCR) technique for human noroviruses (NV) is reported here. A dual-probe, triple-primer system (NM system) was used for simultaneous detection and preliminary differentiation of NV genogroups in fecal samples. The design was based on a comprehensive analysis of all 1140 NV sequences available in GenBank. A touch-down amplification protocol improved the frequency of detection. The final QPCR was evaluated with 71 fecal samples from outbreak and sporadic cases in Sweden (1997-2004), all calicivirus-positive by electron microscopy. Up to 56 (79 %) were positive. The method is more rational than NV detection methods described previously, and should be a developmental basis for large-scale routine methods for detection of NV.

Application of transmission electron microscopy to the clinical study of viral and bacterial infections: present and future

Transmission electron microscopy has had a profound impact on our knowledge and understanding of viruses and bacteria. The 1000-fold improvement in resolution provided by electron microscopy (EM) has allowed visualization of viruses, the existence of which had previously only been suspected as the causative agents of transmissible infectious disease. Viruses are grouped into families based on their morphology. Viruses from different families look different and these morphological variances are the basis for identification of viruses by EM.

Electron microscopy initially came to prominence in diagnostic microbiology in the late 1960s when it was used in the rapid diagnosis of smallpox, by differentiating, on a morphological basis, poxviruses from the less problematic herpesviruses in skin lesions. Subsequently, the technique was employed in the diagnosis of other viral infections, such as hepatitis B and parvovirus B19. Electron microscopy has led to the discovery of many new viruses, most notably the various viruses associated with gastroenteritis, for which it remained the principal diagnostic method until fairly recent times. Development of molecular techniques, which offer greater sensitivity and often the capacity to easily process large numbers of samples, has replaced EM in many areas of diagnostic virology. Hence the role of EM in clinical virology is evolving with less emphasis on diagnosis and more on research, although this is likely only to be undertaken in specialist centres. However, EM still offers tremendous advantages to the microbiologist, both in the speed of diagnosis and the potential for detecting, by a single test, any viral pathogen or even multiple pathogens present within a sample.

There is continuing use of EM for the investigation of new and emerging agents, such as SARS and human monkeypox virus. Furthermore, EM forms a vital part of the national emergency response programme of many countries and will provide a frontline diagnostic service in the event of a bioterrorism incident, particularly in the scenario of a deliberate release of smallpox virus.

In the field of bacteriology, EM is of little use diagnostically, although some bacterial pathogens can be identified in biopsy material processed for EM examination. Electron microscopy has been used, however, to elucidate the structure and function of many bacterial features, such as flagellae, fimbriae and spores and in the study of bacteriophages. The combined use of EM and gold-labelled antibodies provides a powerful tool for the ultrastructural localisation of bacterial and viral antigens.

Development of antigen-capture enzyme-linked immunosorbent assay and RT-PCR for detection of turkey astroviruses

Turkey astrovirus (TAstV) is an important agent of poult enteritis. The diagnosis of astroviruses has been dependent mainly on electron microscopy (EM) or immune EM (IEM). To develop other simple, rapid, and reliable diagnostic assays, two antigen-capture enzyme-linked immunosorbent assays (AC-ELISAs), polyclonal AC-ELISA and monoclonal AC-ELISA, were developed in this study. Monoplex and multiplex reverse transcription-polymerase chain reactions (RT-PCRs) were also developed using nondegenerate primer sets specific to the capsid region and degenerate primer pairs specific to the polymerase area of two TAstV. EM was included for comparison. Fecal or intestinal contents samples from naturally and experimentally infected poults with enteritis were examined using the developed assays. The polyclonal AC-ELISA had higher sensitivity and wider detection spectrum than the monoclonal AC-ELISA with group-specific monoclonal antibody (MAb), whereas the monoclonal AC-ELISA had very high specificity but lower sensitivity, which was estimated at 0.06 microg of viral proteins. Small round viruses (SRV) that could be astroviruses or other small viruses were detected in 34.4% of the samples examined by EM. The monoplex RT-PCR results amplified with primers SRV-1-3 and SRV-1-5 revealed that the positive rate of astroviruses was 45.3%, which was 10.9% higher than that of EM even if other SRVs were not excluded. Multiplex RT-PCR with SRV-1-3 and SRV-1-5 and AFCP-F1 and AFCP-R1 and the monoplex RT-PCR with degenerate primers verified that the positive rate of astroviruses was 59.4%, which was 25% higher than that of EM. Both RT-PCRs showed good specificity and wider detection spectrum compared with earlier published data.

Deletion analysis of the sapovirus VP1 gene for the assembly of virus-like particles

Human sapovirus (SaV) strains are agents of gastroenteritis. They cannot be grown in cell culture. In this study, constructs containing SaV N- and C-terminal-deleted recombinant capsid proteins (rVP1) were expressed in a baculovirus expression system to allow us to better understand the sequence requirements for the formation of virus-like particles (VLPs). Only proteins derived from N-terminal-deleted rVP1 constructs that began 49 nucleotides downstream assembled into VLPs, which included both small and native-size VLPs. Our results were similar to those reported in a rabbit hemorrhagic disease virus (RHDV) N- and C-terminal-deleted rVP1 expression study but were distinct from those reported in a norovirus N- and C-terminal-deleted rVP1 expression study, suggesting that SaV and RHDV may have similar expression requirements.

Survival of viruses on fresh produce, using MS2 as a surrogate for norovirus

AIMS

To study the survival and removal of viruses from fresh fruit and vegetables using the bacteriophage MS2 as a potential surrogate for noroviruses.

METHOD AND RESULTS

Survival of MS2 in buffer and on fresh produce was studied at 4, 8 and 22 degrees C. At 4 and 8 degrees C a reduction of <1 log10 was observed after 50 days in buffer; however a reduction in excess of 1 log10 occurred within 9 days at 22 degrees C. Similar results were obtained with fresh produce with virus survival times exceeding the shelf life of the produce. In washing experiments, using a chlorine wash (100 ppm), in all but one case <1.5 log10 MS2 bacteriophage was removed from fruit and vegetables. The mean across all produce types was 0.89 log10. With potable water, reduction was lower (0.3 log mean across all produce types).

CONCLUSIONS

MS2 survived for prolonged periods, both in buffer and on fresh produce, at temperatures relevant to chilled foods. It was not removed effectively by chlorine washing.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteriophage MS2 has been evaluated as a potential surrogate for noroviruses on fresh produce. Experimental results together with current knowledge of norovirus resistance and survival indicate that MS2 could be used as an effective surrogate in future evaluations.

Replication and packaging of Norwalk virus RNA in cultured mammalian cells

Human noroviruses, the most common cause of nonbacterial gastroenteritis, are characterized by high infectivity rate, low infectious dose, and unusually high stability outside the host. However, human norovirus research is hindered by the lack of a cell culture system and a small animal model of infection. Norwalk virus (NV) is the prototype strain of human noroviruses. We report here replication of NV viral RNA and its packaging into virus particles in mammalian cells by intracellular expression of native forms of NV viral RNA devoid of extraneous nucleotide sequences derived from the expression vector by the use of replication-deficient vaccinia virus MVA encoding the bacteriophage T7 RNA polymerase (MVA/T7). Expressed genomic RNA was found to replicate; NV subgenomic RNA was transcribed from genomic RNA by use of NV nonstructural proteins expressed from genomic RNA and was subsequently translated into NV capsid protein VP1. Viral genomic RNA was packaged into virus particles generated in mammalian cells. The cesium chloride (CsCl) density gradient profile of virus particles containing genomic RNA was similar to that of NV purified from stool. These observations indicate that the NV cDNA constructed here is a biologically infectious clone, and that mammalian cells have the ability to replicate NV genomic RNA. This work establishes a mammalian cell-based system for analysis of human norovirus replication and, thus, makes it feasible to investigate antiviral agents in mammalian cells.

Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus in Japan

Norovirus (NV) (formerly called Norwalk-like virus) is the most common cause of acute nonbacterial gastroenteritis in humans. Recently, we reported an NV genotyping scheme based on variability in the capsid N-terminal/shell (N/S) domain gene (Katayama et al., Virology 299:225-239, 2002). We found 19 genotypes, including nine of genogroup I and 10 of genogroup II. In the present study, we investigated the molecular epidemiology of NV from 66 outbreaks that occurred in Saitama Prefecture, Japan, from 1997 to 2002. We screened 416 stool specimens by a real-time reverse transcription (RT)-PCR method (Kageyama et al., J. Clin. Microbiol. 41:1548-1557, 2003) and detected 156 NV-positive specimens, from which we amplified the capsid N/S domain gene by RT-PCR and then cloned the PCR products. After sequencing these clones, we obtained 368 sequence variants (strains). By applying our classification scheme to the strains from Saitama and other published strains, we identified a total of 31 genotypes, including an additional five genotypes for genogroup I and seven for genogroup II. Of the 31 genotypes, 26 were present in the Saitama area during that time period. These results provide additional evidence for the great diversity of human NV genotypes. Specimens from all shellfish-related infections contained multiple genotypes, including several new genotypes. On the other hand, single genotypes were observed mostly in outbreaks that originated in semiclosed communities. Thus, the number of NV genotypes in each outbreak depended on the route of transmission.

Clinical manifestation of norovirus gastroenteritis in health care settings

Noroviruses are generally believed to cause relatively mild gastroenteritis of short duration in otherwise healthy adults. However, outbreaks in health care settings are common and affect vulnerable populations. During 2002-2003, a total of 4 major hospitals, 11 community hospitals, and 135 nursing homes in the county of Avon, England, were prospectively monitored for outbreaks of gastroenteritis. For 482 hospital staff, 166 nursing home staff, and 266 nursing home residents, the median duration of norovirus gastroenteritis was 2 days, with 75% achieving complete recovery within 3 days. The median duration of norovirus gastroenteritis for 730 hospital patients was 3 days (75% of the patients achieved complete recovery within 5 days), which was significantly longer than that for all other groups (P<.001). Therefore, infection in hospitalized persons may be more severe than that in other groups in the community at large. This increased duration of acute illness should be considered when implementing measures to prevent transmission in hospital settings.

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.

Antigenic and Genomic Characterization of Turkey Enterovirus-Like Virus (North Carolina, 1988 Isolate): Identification of the Virus as Turkey Astrovirus 2

A small round virus (SRV) was isolated in 1988 from droppings of enteritis-affected turkeys in North Carolina and tentatively identified as an enterovirus on the basis of size (18-24 nm in diameter), intracytoplasmic morphogenesis, and a single-stranded RNA genome of approximately 7.5 kb. Additional characterization studies based on antigenic and genomic analyses were done to determine the relationship of this turkey enterovirus-like virus (TELV) to turkey astrovirus 2 (TAstV2), a recently characterized SRV of turkeys. Cross-immunofluorescence studies with TELV- and TAstV2-specific antisera indicated a close antigenic relationship between these viruses. TELV RNA was amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with oligonucleotide primers specific for TAstV2 polymerase gene (open reading frame [ORF] 1b) and capsid protein gene (ORF 2). Subsequent sequence analyses of these TELV-derived RT-PCR products indicated a high degree of similarity with polymerase gene (98.8%) and capsid gene (96.9%) of TAstV2. These studies definitively identify TELV (North Carolina, 1988 isolate) as TAstV2.

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.