Identification of Norwalk virus in artificially seeded shellfish and selected foods

Aptamer Based Nanoprobes for Detection of Foodborne Virus in Food and Environment Samples: Recent Progress and Challenges

Accepting the fact that there is a huge number of virus particles in food that lead to several infectious diseases, eliminating of the foodborne virus from food is tangible. In 2020, the appearance of new SARS-CoV-2 variants had remarked the importance of food safety in our lives. Detection virus is a dynamic domain. Recently, many papers have tried to detect several foodborne viruses by using conventional sensing platforms including ELISA (enzyme-linked immunosorbent assay), PCR (polymerase chain reaction-based methods) and NASBA (nucleic acid sequence-based amplification). However, small sizes, low infective doses and discrete distribution of the foodborne virus have converted these microorganisms into the most challengeable pathogen in the food samples matrix. Foodborne virus detection exploiting aptamer-based biosensors has attracted considerable attention toward the numerous benefits of sourcing from aptamers in which a variety of viruses could be detected by conjugation of aptamer-virus. The development of multiple sensing methodologies and platforms in terms of aptasensor application in real food and environment samples has demonstrated promising results. In this review, we present the latest developments in myriad types of aptasensors (including electrochemical, optical and piezoelectric aptasensor) for the quantification of foodborne viruses. Working strategies, benefits and disadvantages of these platforms are argued.

Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics

Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.

Application of a simple method using minute particles of amorphous calcium phosphate for recovery of norovirus from cabbage, lettuce, and ham

In this study, the amorphous calcium phosphate (ACP) method developed previously for calicivirus concentration from water was applied for norovirus detection from food. The viral recovery from cabbage, lettuce, or ham (10g of each) was firstly examined in seeding experiments with feline caliciviruses (FCVs). The viruses were concentrated by viral adsorption to ACP particles (0.3g) in the eluent solution (40ml) from foods, collection of the particles by centrifugation, followed by dissolution of the particles with 3.3M citric acid (3ml). In ham, FCV recovery was improved by addition of ascorbic acids into the eluent solution before ACP-particle adsorption. Quantitative real-time reverse transcription-PCR (qRT-PCR) revealed that FCV recoveries were 32-33%, 50-55%, and 37-46% from cabbage, lettuce, and ham, respectively, when seeded with 10(3)-10(4) viruses, and detection limits were estimated ∼10(3) genomic copies in all 3 foods. Subsequently, the ACP-concentration method was evaluated for norovirus (NoV) detection from these 3 foods. The recoveries and detection limit of NoVs determined by qRT-PCR were 12-41% and 10(3) (genomic copies) from cabbage, 30-57% and 10(3) from lettuce, and 20-26% and 10(4) from ham, when seeded with 10(3)-10(5) viruses. This simple method may be suitable for NoV detection from these foods.

Rapid detection of norovirus in naturally contaminated food: foodborne gastroenteritis outbreak on a cruise ship in Brazil, 2010

Norovirus (NoV) is a prevalent pathogen of foodborne diseases; however, its detection in foods other than shellfish is often time consuming and unsuccessful. In 2010, an outbreak of acute gastroenteritis occurred on a cruise ship in Brazil, and NoV was the etiologic agent suspected. The objectives of this study were to report that a handy in-house methodology was suitable for NoV detection in naturally contaminated food, and perform the molecular characterization of food strains. Food samples (blue cheese, Indian sauce, herbal butter, soup, and white sauce) were analyzed by ELISA, two methods of RNA extraction, TRIzol(®) and QIAamp(®), following conventional RT-PCR. The qPCR was used in order to confirm the NoV genogroups. GI and GII NoV genogroups were identified by conventional RT-PCR after RNA extraction by means of the TRIzol(®) method. Two GII NoV samples were successfully sequenced, classified as GII.4; and they displayed a genetic relationship with strains from the Asian continent also isolated in 2010. GII and GI NoV were identified in distinct food matrices suggesting that it was not a common source of contamination. TRIzol(®) extraction followed by conventional RT-PCR was a suitable methodology in order to identify NoV in naturally contaminated food. Moreover, food samples could be processed within 8 h indicating the value of the method used for NoV detection, and its potential to identify foodborne gastroenteritis outbreaks in food products other than shellfish. This is the first description in Brazil of NoV detection in naturally contaminated food other than shellfish involved in a foodborne outbreak.

An outbreak of norovirus infection in a long-term care facility in Brazil

ABSTRACT Objective: To describe a norovirus outbreak in a Brazilian long-term care facility from July 8 to 29, 2005. Methods: In the first 48 to 72 hours after onset of symptoms in inpatients and employees, the main infection control strategies were staff education, emphasis on hand washing, implementing contact precautions up to 48-72 hours after resolution of symptoms, complete cleaning of the rooms and exclusion of symptomatic employees from work until 48-72 hours after resolution of their symptoms. Epidemiological and clinical characteristics of the norovirus infections were described based on chart review. Results: The incidence among inpatients and employees was 41.3% and 16.25%, respectively. The main symptom was diarrhea, affecting 100% of inpatients and employees. Forty-four percent of specimens were positive by RIDASCREEN® Norovirus analyses, and identified as norovirus genogroup GII. Seventy percent of inpatients were women and their age range was 51-98 years. Inpatients had in average two comorbid conditions – 87.3% with cardiovascular or chronic pulmonary condition and 47.6% with dementia. There was not relapse or death. Conclusions: The early infection-control measures associated to surveillance are required to keep long-term care facilities free of noroviruses and to protect those who are most vulnerable.

Identification and molecular characterization of norovirus in são paulo state, Brazil

Norovirus (NoV), previously called Norwalk-like virus, represents an important group of human pathogens associated with outbreaks of nonbacterial gastroenteritis. Epidemiological surveys of outbreaks have shown that the most important routes of transmission are person-to-person contacts and contaminated food and water, with the virus affecting adults and children. NoV is classified into genogroups, being genogroups GI, GII and GIV found in humans. In view of the high genetic diversity of NoV and the lack of information about this virus in Brazil, the aim of the present study was the molecular characterization of NoV isolated from diarrheic stool samples of patients from São Paulo State. In this study, 204 stool specimens collected during diarrhea outbreaks were analyzed by RT-PCR, and 12 were sequenced for genogroup confirmation. One-step PCR was performed in order to amplify the B region of ORF 1 using the MON 431, 432, 433 and 434 primer pool. From total, 32 (15.7%) stool specimens were positive for NoV genogroup GII. Comparison of the sequences of the PCR products to GenBank sequences showed 88.8% to 98.8% identity, suggesting the presence of genogroup GII in gastroenteritis outbreaks in São Paulo State.

An efficient and rapid method for recovery of norovirus from food associated with outbreaks of gastroenteritis

Noroviruses have emerged as the most common cause of foodborne outbreaks of acute nonbacterial gastroenteritis. In this study, two methods for the extraction of viruses from deli ham were compared. Using both methods, as little as 1 to 10 reverse transcription (RT)-PCR units of inoculated norovirus and enterovirus could be detected by nested RT-PCR assays. The fastest and most efficient extraction method based on TRIzol LS Reagent was chosen to identify viruses in food items associated with three different outbreaks. Norovirus was detected using nested (real time) RT-PCR assays that target the genome region routinely used for diagnosis of human cases, thereby facilitating the comparison of sequences detected in food and clinical specimens. For one outbreak, a norovirus sequence (163/163 nucleotides) identical to those detected in clinical samples was found on salami sliced by a food handler with a recent history of gastroenteritis. For the other two outbreaks, norovirus was detected on leftovers of spareribs and ham, but fecal samples from affected persons were not available. The methods used in this study may be useful in future outbreak investigations because the extraction method is easy to perform and suitable for this particular type of food and the detection method facilitates direct comparison of patient and food data.

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.

Procedure for rapid concentration and detection of enteric viruses from berries and vegetables

Several hepatitis A virus (HAV) and norovirus (NV) outbreaks due to consumption of berries and vegetables have been reported during recent years. To facilitate the detection of enteric viruses that may be present on different fresh and frozen products, we developed a rapid and sensitive detection method for HAV, NV, and rotavirus (RV). Initial experiments focused on optimizing the composition of the elution buffer, improving the viral concentration method, and evaluating the performance of various extraction kits. Viruses were extracted from the food surface by a direct elution method in a glycine-Tris (pH 9.5) buffer containing 1% beef extract and concentrated by ultrafiltration. Occasionally, PCR inhibitors were present in the processed berry samples, which gave relatively poor detection limits. However, this problem was overcome by adding a pectinase treatment in the protocol, which markedly improved the sensitivity of the method. After optimization, this concentration method was applied in combination with real-time reverse transcription-PCR (RT-PCR) using specific primers in various types of berries and vegetables. The average detection limits were 1 50% tissue culture infective dose (TCID(50)), 54 RT-PCR units, and 0.02 TCID(50) per 15 g of food for HAV, NV, and RV, respectively. Based on our results, it is concluded that this procedure is suitable to detect and quantify enteric viruses within 6 h and can be applied for surveillance of enteric viruses in fresh and frozen products.

Health risks of enteric viral infections in children

Children are at a greater risk of infections from serious enteric viral illness than adults for a number of reasons. Most important is the immune system, which is needed to control the infection processes. This difference can lead to more serious infections than in adults, who have fully developed immune systems. There are a number of significant physiological and behavioral differences between adults and children that place children at a greater risk of exposure and a greater risk of serious infection from enteric viruses. Although most enteric viruses cause mild or asymptomatic infections, they can cause a wide range of serious and life-threatening illnesses in children. The peak incidence of most enteric viral illnesses is in children <2yr of age, although all age groups of children are affected. Most of these infections are more serious and result in higher mortality in children than adults. The fetus is also affected by enterovirus and infectious hepatitis resulting in significant risk of fetal death or serious illness. In addition to the poliovirus vaccine, the only vaccine available is for hepatitis A virus (HAV). A vaccine for rotavirus has currently been withdrawn, pending review because of potential adverse effects in infants. No specific treatment is available for the other enteric viruses. Enteric viral infections are very common in childhood. Most children are infected with rotavirus during the first 2yr of life. The incidence of enteroviruses and the viral enteric viruses ranges from 10% to 40% in children and is largely dependent on age. On average, half or more of the infections are asymptomatic. The incidence of hepatitis A virus is much lower than the enteric diarrheal viruses. There is no current evidence for hepatitis E virus (HEV) acquisition in children in the U.S. Enteric viral diseases have a major impact on direct and indirect health care costs (i.e., lost wages) and amount to several billion dollars a year in the U.S. Total direct and indirect costs for nonhospitalized cases may run from $88/case for Norwalk virus to $1,193/case for enterovirus aseptic meningitis. Direct costs of hospitalization ran from $887/case for Norwalk virus to $86,899/case for hepatitis A. These costs are based on 1997-1999 data. Generally, attack rates during drinking water outbreaks are greater for children than adults. The exception appears to be hepatitis E virus where young adults are more affected. However, pregnant women suffer a high mortality, resulting in concurrent fetal death. Also, secondary attack rates are much higher among children, probably because of fewer sanitary habits among this age group. Overall, waterborne outbreaks of viral disease have a greater impact among children than adults. To better quantify the impact on children, the literature hould be further reviewed for case studies of waterborne outbreaks where data are available on the resulting illness by age group. The EPA and/or Centers for Disease Control should attempt to collect these data as future outbreaks are documented.

Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods

Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10(-1) reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 10(0) to 10(2) reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods.

Modified concentration method for the detection of enteric viruses on fruits and vegetables by reverse transcriptase-polymerase chain reaction or cell culture

Fruits and vegetables may act as a vehicle of human enteric virus if they are irrigated with sewage-contaminated water or prepared by infected food handlers. An elution-concentration method was modified to efficiently detect, by reverse transcriptase-polymerase chain reaction (RT-PCR) or by cell culture, contamination by poliovirus, hepatitis A virus (HAV), and Norwalk-like virus (NLV) of various fresh and frozen berries and fresh vegetables. The protocol included washing the fruit or vegetable surface with 100 mM Tris-HCl, 50 mM glycine, and 3% beef extract, pH 9.5 buffer, which favors viral elution from acid-releasing berries, supplemented with 50 mM MgCl2 to reduce the decrease in viral infectivity during the process. The viral concentration method was based on polyethylene glycol precipitation. Copurified RT-PCR inhibitors and cytotoxic compounds were removed from viral concentrates by chloroform-butanol extraction. Viruses from 100 g of vegetal products could be recovered in volumes of 3 to 5 ml. Viral RNAs were isolated by a spin column method before molecular detection or concentrates were filtered (0.22-microm porosity) and inoculated on cell culture for infectious virus detection. About 15% of infectious poliovirus and 20% of infectious HAV were recovered from frozen raspberry surfaces. The percentage of viral RNA recovery was estimated by RT-PCR to be about 13% for NLV, 17% for HAV, and 45 to 100% for poliovirus. By this method, poliovirus and HAV RNA were detected on products inoculated with a titer of about 5 x 10(1) 50% tissue culture infectious dose per 100 g. NLV RNA was detected at an initial inoculum of 1.2 x 10(3) RT-PCR amplifiable units. This method would be useful for the viral analysis of fruits or vegetables during an epidemiological investigation of foodborne diseases.

Foodborne viruses

Foodborne and waterborne viral infections are increasingly recognized as causes of illness in humans. This increase is partly explained by changes in food processing and consumption patterns that lead to the worldwide availability of high-risk food. As a result, vast outbreaks may occur due to contamination of food by a single foodhandler or at a single source. Although there are numerous fecal-orally transmitted viruses, most reports of foodborne transmission describe infections with Norwalk-like caliciviruses (NLV) and hepatitis A virus (HAV), suggesting that these viruses are associated with the greatest risk of foodborne transmission. NLV and HAV can be transmitted from person to person, or indirectly via food, water, or fomites contaminated with virus-containing feces or vomit. People can be infected without showing symptoms. The high frequency of secondary cases of NLV illness and - to a lesser extent - of hepatitis A following a foodborne outbreak results in amplification of the problem. The burden of illness is highest in the elderly, and therefore is likely to increase due to the aging population. For HAV, the burden of illness may increase following hygienic control measures, due to a decreasing population of naturally immune individuals and a concurrent increase in the population at risk. Recent advances in the research of NLV and HAV have led to the development of molecular methods which can be used for molecular tracing of virus strains. These methods can be and have been used for the detection of common source outbreaks. While traditionally certain foods have been implicated in virus outbreaks, it is clear that almost any food item can be involved, provided it has been handled by an infected person. There are no established methods for detection of viruses in foods other than shellfish. Little information is available on disinfection and preventive measures specifically for these viruses. Studies addressing this issue are hampered by the lack of culture systems. As currently available routine monitoring systems exclusively focus on bacterial pathogens, efforts should be made to combine epidemiological and virological information for a combined laboratory-based rapid detection system for foodborne viruses. With better surveillance, including typing information, outbreaks of foodborne infections could be reported faster to prevent further spread.

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

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

Rapid and efficient extraction method for reverse transcription-PCR detection of hepatitis A and Norwalk-like viruses in shellfish

As part of an effort to develop a broadly applicable test for Norwalk-like viruses and hepatitis A virus (HAV) in shellfish, a rapid extraction method that is suitable for use with one-step reverse transcription (RT)-PCR-based detection methods was developed. The method involves virus extraction using a pH 9.5 glycine buffer, polyethylene glycol (PEG) precipitation, Tri-reagent, and purification of viral poly(A) RNA by using magnetic poly(dT) beads. This glycine-PEG-Tri-reagent-poly(dT) method can be performed in less than 8 h on hard-shell clams (Mercenaria mercenaria) and Eastern oysters (Crassostrea virginica) and, when coupled with RT-PCR-based detection, can yield results within 24 h. Observed sensitivities for seeded shellfish extracts are as low as 0.015 PFU of HAV and 22.4 RT-PCR50 units for Norwalk virus. Detection of HAV in live oysters experimentally exposed to contaminated seawater is also demonstrated. An adaptation of this method was used to identify HAV in imported clams (tentatively identified as Ruditapes philippinarum) implicated in an outbreak of food-borne viral illness. All of the required reagents are commercially available. This method should facilitate the implementation of RT-PCR testing of commercial shellfish.

"Norwalk-like viruses" as a cause of foodborne disease outbreaks

While outbreaks of foodborne disease remain an important public health concern, their aetiology is not identified in a majority of instances. In targeted studies, the application of newly developed molecular assays has demonstrated that a large proportion of these outbreaks may be caused by the "Norwalk-like viruses" (NLV), a genus of genetically related viruses belonging to the family Caliciviridae. NLV outbreaks associated with consumption of faecally contaminated oysters are frequently reported and can best be controlled by preventing contamination of oyster-harvesting waters. Infectious foodhandlers are another frequent source of contamination, and such transmission can be minimised by exclusion of ill foodhandlers and the maintenance of strict personal hygiene. Molecular assays have greatly refined the epidemiological investigation of foodborne NLV outbreaks, allowing the linking of outbreaks in different locations and permitting the identification of the virus in the implicated vehicle. The development of simpler and more sensitive assays and their use on a broader scale will assist in defining the true burden of foodborne NLV outbreaks and improve strategies for their prevention and control.

Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses

Gastroenteritis is one of the most common illnesses of humans, and many different viruses have been causally associated with this disease. Of those enteric viruses that have been established as etiologic agents of gastroenteritis, only the human caliciviruses cannot be cultivated in vitro. The cloning of Norwalk virus and subsequently of other human caliciviruses has led to the development of several new diagnostic assays. Antigen detection enzyme immunoassays (EIAs) using polyclonal hyperimmune animal sera and antibody detection EIAs using recombinant virus-like particles have supplanted the use of human-derived reagents, but the use of these assays has been restricted to research laboratories. Reverse transcription-PCR assays for the detection of human caliciviruses are more widely available, and these assays have been used to identify virus in clinical specimens as well as in food, water, and other environmental samples. The application of these newer assays has significantly increased the recognition of the importance of human caliciviruses as causes of sporadic and outbreak-associated gastroenteritis.

Detection methods for human enteric viruses in representative foods

Although viral foodborne disease is a significant problem, foods are rarely tested for viral contamination, and when done, testing is limited to shellfish commodities. In this work, we report a method to extract and detect human enteric viruses from alternative food commodities using an elution-concentration approach followed by detection using reverse transcription-polymerase chain reaction (RT-PCR). Fifty-gram lettuce or hamburger samples were artificially inoculated with poliovirus type 1 (PV1), hepatitis A virus (HAV), or the Norwalk virus and processed by the sequential steps of homogenization, filtration, Freon extraction (hamburger), and polyethylene glycol (PEG) precipitation. To reduce volumes further and remove RT-PCR inhibitors, a secondary PEG precipitation was necessary, resulting in an overall 10- to 20-fold sample size reduction from 50 g to 3 to 5 ml. Virus recoveries in secondary PEG concentrates ranged from 10 to 70% for PV1 and 2 to 4% for HAV as evaluated by mammalian cell culture infectivity assay. Total RNA from PEG concentrates was extracted to a small volume (30 to 40 microl) and subjected to RT-PCR amplification of viral RNA sequences. Detection limit studies indicated that viral RNA was consistently detected by RT-PCR at initial inoculum levels > or =102 PFU/50-g food sample for PV1 and > or =10(3) PFU/50-g food sample for HAV. In similar studies with the Norwalk virus, detection at inoculum levels > or =1.5 X 10(3) PCR-amplifiable units/50-g sample for both food products was possible. All RT-PCR amplicons were confirmed by subsequent Southern hybridization. The procedure reported represents progress toward the development of methods to detect human enteric viral contamination in foods other than shellfish.

Viruses and bivalve shellfish

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

Development of methods to detect "Norwalk-like viruses" (NLVs) and hepatitis A virus in delicatessen foods: application to a food-borne NLV outbreak

"Norwalk-like viruses" (NLVs) and hepatitis A virus (HAV) are the most common causes of virus-mediated food-borne illness. Epidemiological investigations of outbreaks associated with these viruses have been hindered by the lack of available methods for the detection of NLVs and HAV in foodstuffs. Although reverse transcription (RT)-PCR methods have been useful in detecting NLVs and HAV in bivalve mollusks implicated in outbreaks, to date such methods have not been available for other foods. To address this need, we developed a method to detect NLVs and HAV recovered from food samples. The method involves washing of food samples with a guanidinium-phenol-based reagent, extraction with chloroform, and precipitation in isopropanol. Recovered viral RNA is amplified with HAV- or NLV-specific primers in RT-PCRs, using a viral RNA internal standard control to identify potential sample inhibition. By this method, 10 to 100 PCR units (estimated to be equivalent to 10(2) to 10(3) viral genome copies) of HAV and Norwalk virus seeded onto ham, turkey, and roast beef were detected. The method was applied to food samples implicated in an NLV-associated outbreak at a university cafeteria. Sliced deli ham was positive for a genogroup II NLV as determined by using both polymerase- and capsid-specific primers and probes. Sequence analysis of the PCR-amplified capsid region of the genome indicated that the sequence was identical to the sequence from virus detected in the stools of ill students. The developed method is rapid, simple, and efficient.

Identification of hepatitis E virus in clinical specimens: amplification of hydroxyapatite-purified virus RNA and restriction endonuclease analysis

A multi-site nested reverse transcription and polymerase chain reaction (RT-PCR) followed by restriction endonuclease analysis (REA) was developed to identify hepatitis E virus (HEV) in clinical specimens. Four sets of primers were selected to amplify regions in the HEV genome supposed to encode the helicase, polymerase, and parts of the viral capsid protein. Digestion of the nested PCR products with HinfI, HaeII, AvaII, BglI, KpnI, SmaI, or EcoRI generated readily recognizable profiles that confirm the HEV sequences and/or distinguish the unique Mexico genotype (our positive control) from all other isolates (Asian genotype). In addition, the hydroxyapatite (HA) adsorption method was compared to other adsorption and extraction methods widely used to purify viral RNA from clinical specimens for RT-PCR. All methods presented the same sensitivity of recovery of HEV RNA, but only the adsorption methods efficiently removed fecal enzymatic inhibitors. The HA method gave the best results and was the most economic in terms of time, cost, manipulations and reagents. The method was validated by screening a small number of serum and fecal specimens available from patients with acute non-A,B,C hepatitis in Nepal. HEV RNA was identified in half (5/11) of the fecal specimens obtained from patients with evidence of recent HEV infection, but in none of the 14 patients without a serological marker for hepatitis E.

Epidemiology and detection as options for control of viral and parasitic foodborne disease

Human enteric viruses and protozoal parasites are important causes of emerging food and waterborne disease. Epidemiologic investigation and detection of the agents in clinical, food, and water specimens, which are traditionally used to establish the cause of disease outbreaks, are either cumbersome, expensive, and frequently unavailable or unattempted for the important food and waterborne enteric viruses and protozoa. However, the recent introduction of regulatory testing mandates, alternative testing strategies, and increased epidemiologic surveillance for food and waterborne disease should significantly improve the ability to detect and control these agents. We discuss new methods of investigating foodborne viral and parasitic disease and the future of these methods in recognizing, identifying, and controlling disease agents.

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.

Detection of Norwalk virus and hepatitis A virus in shellfish tissues with the PCR

A method for the detection of Norwalk virus and hepatitis A virus from shellfish tissues by PCR was developed. Virus was added to the stomach and hepatopancreatic tissues of oysters or hard-shell clams, and viral nucleic acids were purified by a modification of a previously described method (R.L. Atmar, T.G. Metcalf, F.H. Neill, and M.K. Estes, Appl. Environ. Microbiol. 59:631-635, 1993). The new method had the following advantages compared with the previously described method: (i) more rapid sample processing; (ii) increased test sensitivity; (iii) decreased sample-associated interference with reverse transcription-PCR; and (iv) use of chloroform-butanol in place of the chlorofluorocarbon trichlorotrifluoroethane. In addition, internal standards for both Norwalk virus and hepatitis A virus were made which demonstrated when inhibitors to reverse transcription-PCR were present and allowed quantitation of the viral nucleic acids present in samples. This assay can be used to investigate shellfish-associated gastroenteritis outbreaks and to study factors involved in virus persistence in shellfish.