Detection of hepatitis A virus in environmental samples by antigen-capture PCR

Critical issues in application of molecular methods to environmental virology

Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.

Spatial-Temporal Patterns of Viral Amplification and Interference Initiated by a Single Infected Cell

When viruses infect their host cells, they can make defective virus-like particles along with intact virus. Cells coinfected with virus and defective particles often exhibit interference with virus growth caused by the competition for resources by defective genomes. Recent reports of the coexistence and cotransmission of such defective interfering particles (DIPs) in vivo, across epidemiological length and time scales, suggest a role in viral pathogenesis, but it is not known how DIPs impact infection spread, even under controlled culture conditions. Using fluorescence microscopy, we quantified coinfections of vesicular stomatitis virus (VSV) expressing a fluorescent reporter protein and its DIPs on BHK-21 host cell monolayers. We found that viral gene expression was more delayed, infections spread more slowly, and patterns of spread became more “patchy” with higher DIP inputs to the initial cell. To examine how infection spread might depend on the behavior of the initial coinfected cell, we built a computational model, adapting a cellular automaton (CA) approach to incorporate kinetic data on virus growth for the first time. Specifically, changes in observed patterns of infection spread could be directly linked to previous high-throughput single-cell measures of virus-DIP coinfection. The CA model also provided testable hypotheses on the spatial-temporal distribution of the DIPs, which remain governed by their predator-prey interaction. More generally, this work offers a data-driven computational modeling approach for better understanding of how single infected cells impact the multiround spread of virus infections across cell populations.

IMPORTANCE Defective interfering particles (DIPs) compete with intact virus, depleting host cell resources that are essential for virus growth and infection spread. However, it is not known how such competition, strong or weak, ultimately affects the way in which infections spread and cause disease. In this study, we address this unmet need by developing an integrated experimental-computational approach, which sheds new light on how infections spread. We anticipate that our approach will also be useful in the development of DIPs as therapeutic agents to manage the spread of viral infections.

Development of a quantitative immunocapture real-time PCR assay for detecting structurally intact adenoviral particles in water

Development of rapid, sensitive and specific methods for detection of infectious enteric viruses in water is challenging but crucial for gaining reliable information for risk assessment. An immunocapture real-time PCR (IC-qPCR) was designed to detect jointly the two major viral particle components, i.e. the capsid protein and the viral genome. Targeting both constituents helps circumventing the technical limits of cell culture approaches and the inability of PCR based methods to predict the infectious status. Two waterborne pathogenic virus models, human adenovirus types 2 and 41, were chosen for this study. IC-qPCR showed a detection limit of 10MPNCU/reaction with a dynamic range from 10(2) to 10(6)MPNCU/reaction. Sensitivity was thus 100-fold higher compared to ELISA-based capture employing the same anti-hexon antibodies. After optimisation, application on environmental water samples was validated, and specificity towards the targeted virus types was obtained through the qPCR step. Heat-treated pure samples as well as surface water samples brought evidence that this method achieves detection of encapsidated viral genomes while excluding free viral genome amplification. As a consequence, adenovirus concentrations estimated by IC-qPCR were below those calculated by direct qPCR. The results demonstrate that the IC-qPCR method is a sensitive and rapid tool for detecting, in a single-tube assay, structurally intact and thus potentially infectious viral particles in environmental samples.

Major human Hepatitis A virus genotype in Hong Kong marine waters and detection by real-time PCR

Marine waters from seven sites around Hong Kong with varying levels of sewage pollution were analyzed for Hepatitis A virus (HAV) by PCR cloning and DNA sequencing of the highly variable VP1/2A junction of the HAV genome. Phylogenetic analysis of 10 PCR clones from each of the HAV-positive marine sites indicated that human HAV genotype IB is the most widely distributed type in Hong Kong waters. A sensitive and quantitative TaqMan-based PCR method targeting the 5'-noncoding region (5'-NCR) of HAV was used to quantify HAV particles in marine water samples along with the total Escherichia coli counts being enumerated on TBX medium for comparison. Our results showed that no correlation of any significance between HAV and E. coli counts was observed which underscores the inadequacy in using E. coli as a sanitary standard to predict the levels of HAV in marine waters.

Efficient cellular release of Rift Valley fever virus requires genomic RNA

The Rift Valley fever virus is responsible for periodic, explosive epizootics throughout sub-Saharan Africa. The development of therapeutics targeting this virus is difficult due to a limited understanding of the viral replicative cycle. Utilizing a virus-like particle system, we have established roles for each of the viral structural components in assembly, release, and virus infectivity. The envelope glycoprotein, Gn, was discovered to be necessary and sufficient for packaging of the genome, nucleocapsid protein and the RNA-dependent RNA polymerase into virus particles. Additionally, packaging of the genome was found to be necessary for the efficient release of particles, revealing a novel mechanism for the efficient generation of infectious virus. Our results identify possible conserved targets for development of anti-phlebovirus therapies.

Development and application of a broadly reactive real-time reverse transcription-PCR assay for detection of murine noroviruses

Murine norovirus (MNV) is a viral agent newly identified in laboratory mice and a large number of genetically diverse MNV strains have been reported to date. A broadly reactive TaqMan-based real-time reverse transcription (RT)-polymerase chain reaction (PCR) assay was developed for MNVs. Novel primers and a TaqMan MGB probe were designed targeting highly conserved sequences among MNV strains, which are located in the open reading frames 1 (ORF1)-ORF2 junction region. The quantitative range of this assay was determined as 1.0 × 10(2)-1.0 × 10(8)copies/PCR tube based on a 10-fold serial dilution of plasmid DNA containing the target sequences. Viral RNA in eight murine stool specimens positive by nested RT-PCR assay was measured, and the highest viral RNA load was calculated at 4.7 × 10(6)copies/g-stool. MNV was inoculated into RAW 264.7 cells, and the viral RNA was monitored to validate assay sensitivity. MNV-RNA in the supernatant was detected during in vitro replication, which increased substantially from 5 to 30 h post-infection (hpi) and reached more than 1.0 × 10(10)copies/mL at 96 hpi. This real-time RT-PCR assay is a useful tool to detect and quantify MNV-RNA in in vivo and in vitro studies.

Early Days of Food and Environmental Virology

In July 1962, the author joined the Food Research Institute (FRI), then at the University of Chicago, to become its food virologist. There was a limited record of waterborne viral disease outbreaks at the time; recorded data on foodborne outbreaks were fewer still. Laboratory environmental (water and wastewater) virology was in its infancy, and food virology was in gestation. Detection of viruses was most often attempted by inoculation of primary primate cell cultures, with observation for plaque formation or cytopathic effects. Focus was initially on enteroviruses and reoviruses. Environmental and food samples had to be liquefied if not already in liquid form; clarified to remove solids, bacteria, and fungi; and concentrated to a volume that could be tested in cell culture. Cytotoxicity was also a concern. Studies at the FRI and some other laboratories addressed all of these challenges. The FRI group was the World Health Organization's Collaborating Center for Food Virology for many years. Other topics studied were virus inactivation as functions of temperature, time, matrix, disinfectants, and microbial action; peroral and ex-vivo infectivity; and the suitability of various virus surrogates for environmental monitoring and inactivation experiments. Detection of noroviruses and hepatitis A virus required molecular methods, most often RT-PCR. When it was found that inactivated virus often gave the same RT-PCR signal as that of infectious virus, sample treatments were sought, which would prevent false-positive test results. Many laboratories around the world have taken up food and environmental virology since 1962, with the result that a dedicated journal has been launched.

Risk assessment in shellfish-borne outbreaks of hepatitis A

In the present work, we aimed at determining the relationship between the hepatitis A virus (HAV) numbers in imported frozen coquina clams involved in two hepatitis outbreaks, as well as the risk for human health. Due to HAV unculturability, a standardized TaqMan real-time reverse transcription-PCR controlling the virus/nucleic acid extraction and enzyme efficiencies was employed to figure the exposure dose for clams responsible for hepatitis cases. HAV numbers were then employed to figure the risk of infection based on a dose-response model for echovirus 12. The estimated risk of infection after consumption of lightly cooked clams matched actual attack rates. Our data show that prospective monitoring of bivalve samples may fail to prevent the occurrence of outbreaks, since HAV was detected in 44% of samples directly associated with cases but was undetectable in samples that were randomly collected from the importers and belonged to the same batches. A correlation was nevertheless observed between the prevalence of hepatitis A cases in the harvesting areas and positive HAV isolation in clams, which points to the need to identify and prevent hazards rather than relying on random sampling of finished products to ensure safety. However, when evidence shows that a critical limit of viral contamination has been exceeded in the potential sources of contamination discharging into the shellfish-growing beds, quantitative virological analysis addressing quality assurance and quality control requirements should be performed with the bivalves. This work provides the first evidence of accurate HAV levels in shellfish involved in outbreaks that could be of use for risk assessment purposes.

Indicadores infecciosos e inflamatórios entre trabalhadores da limpeza urbana em São Paulo

O objetivo deste trabalho foi comparar agravos à saúde entre grupos funcionais de trabalhadores da limpeza urbana (TLU) decorrentes de exposição biológica do contato com os Resíduos Sólidos (RS) em São Paulo, 2007. Para tal, amostras dos grupos de TLU e um grupo Controle de servidores ferroviários realizaram entrevistas, contagens sanguíneas, provas de atividade inflamatória, marcadores sorológicos de infecção e exame protoparasitológico de fezes.Ao término, foram avaliados 217 indivíduos. O grupo Controle relatou menor cobertura vacinal para o tétano, enquanto os Varredores tiveram a menor proporção de cobertura para a hepatite B. Os Motoristas usaram mais antibióticos e apresentaram o número de leucócitos mais elevado quando comparados aos Controles. Os Motoristas apresentaram também maiores médias de neutrófilos e monócitos quando comparados aos Varredores. A presença de parasitas nas fezes foi mais frequente entre os Varredores e os Coletores quando comparados aos Controles. Os grupos de Coleta, Transbordo e Aterro apresentaram indicadores de infecções respiratórias e de atividade inflamatória sistêmica similares aos Controles. Não foram observadas diferenças entre episódios de sinusites, pneumonias, marcadores séricos de atividade inflamatória, contato com o vírus da hepatite B ou com a estreptolisina O entre os grupos estudados.

Viral contaminants of molluscan shellfish: detection and characterisation

Environmental virology started with the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. Most shellfish-borne viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets for bivalve virological analysis. The inclusion of virus analysis in regulatory standards for viruses in molluscan bivalve samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. Nowadays methods are available to detect, quantify and characterise viral pathogens in molluscan shellfish to reduce the risks of shellfish-borne virus diseases.

A sensitive and reliable reverse transcriptase PCR-enzyme-linked immunosorbent assay for the detection of human pathogenic viruses in bivalve molluscs

A colorimetric method, reverse transcriptase PCR with an enzyme-linked immunosorbent assay (RT-PCR-ELISA) was evaluated for ease of use, reliability, and sensitivity when detecting known human pathogenic virus present in shellfish, using a traditional polyethylene precipitation or immunocapture virus concentration method. The newly developed ELISA method could successfully detect enteroviruses and noroviruses in artificially and naturally contaminated shellfish. Overall, ELISA was shown to be a robust and sensitive method, which had a detection limit of 10 to 100 50% tissue culture infective dose enterovirus per gram of Crassostrea gigas (Pacific oyster) digestive gland and whole Mytilus edulis (common blue mussel). The technique was easily established in a new laboratory and required no specialized equipment. The method had a high sample throughput capable of screening 96 samples per run, making the technique extremely time efficient. RT-PCR-ELISA is a safe, quick, reliable technique, which has the potential for use as a standard virus detection method.

Comparative evaluation of new TaqMan real-time assays for the detection of hepatitis A virus

Three novel real-time TaqMan RT-PCR assays targeting the 5'-UTR, the viral protease and the viral polymerase regions of the hepatitis A virus (HAV) were developed, evaluated and compared against a new published 5'-UTR TaqMan assay (JN) and a widely used conventional RT-PCR assay (HAVc). All conventional RT-PCR (HAV, SH-Prot and SH-Poly systems) and TaqMan (SH-Prot, SH-Poly, JN and SH-5U systems) assays evaluated were consistent for the detection of the three different HAV strains (HM-175, HAS-15 and LSH/S) used and reproducible for both RNA duplicates with the exception of two reproducibility discrepancies observed with both 5'-UTR real-time systems (JN and SH-5U). Limits of detection for conventional HAV, SH-Prot and SH-Poly RT-PCR systems were found to be equivalent when tested with serially diluted suspensions of the HM-175 strain. Although the four real-time RT-PCR TaqMan assays evaluated herein produced similar and consistent quantification data down to the level of one genomic equivalent copy with their respectively cloned amplicons, significant and important differences were observed for the detection of HAV genomic RNA. Results showed that the new real-time TaqMan SH-Poly and SH-Prot primer and probe systems were more consistent and sensitive by 5 logs as compared to both 5'-UTR designs (JN and SH-5U) used for the detection of HAV genomic RNA as well as for the detection in cell culture by cytopathic effect. Considering their higher analytical sensitivity, the proposed SH-Poly and SH-Prot amplification systems could therefore represent valuable tools for the detection of HAV in clinical, environmental and food samples.

Detection and characterization of hepatitis A virus in water samples in Thailand

AIMS

Outbreaks of hepatitis A in Thailand have been reported continuely and associated with water supply. However, the genetic analysis of hepatitis A virus (HAV) in water is limited. This study described the application of virus concentration method and reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) to detect HAV RNA and analyse the genetic sequence of the virus in environmental water samples.

METHODS AND RESULTS

The HAV from water samples was concentrated by using a developed virus concentration method (adsorption-elution and subsequent speedVac reconcentration) and the viral RNA was detected by RT-nested PCR followed by sequencing of the amplified DNA products. Detection limit of HAV determined by the RT-nested PCR was 1.29 radioimmunofocus assay (RIFA) units ml(-1). The DNA band appeared at 183 basepairs. No cross-reactivity was observed in the presence of other enteric viruses (poliovirus and rotavirus). A total of 180 water samples were collected, concentrated, and detected for HAV. The HAV was found in 6/40 (15%) of water samples collected from a swamp and 3/30 (10%) collected from a canal. Ten river samples and 100 tap water samples stored in containers for drinking and domestic uses were negative for HAV. In sequence analysis of the DNA products and alignment with the HAV sequence deposited in the GenBank, six water samples showed the nucleotide sequence associated with HAV. The 120 nucleotides in the N-terminal VP1 region obtained from two swamp samples showed 95 and 96.7% identity to HAV genotype IA. In nearly all water samples where HAV was present bacterial indicators (faecal coliforms and Escherichia coli) were found for faecal contamination.

CONCLUSIONS

A coupled virus concentration method and RT-nested PCR was successfully applied to examine HAV in water samples collected from various sources. DNA sequencing of nested PCR products showed the genotype IA associated with HAV that is predominate in Thailand.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research is the first study of genetic sequence of HAV in water samples in Thailand. The presence of naturally occurring HAV might pose a potential health risk for people.

Development, evaluation, and standardization of a real-time TaqMan reverse transcription-PCR assay for quantification of hepatitis A virus in clinical and shellfish samples

A standardized real-time reverse transcription-PCR (RT-PCR) assay has been developed for an accurate estimation of the number of genome copies of hepatitis A virus (HAV) in clinical and shellfish samples. Real-time procedures were based on the amplification of a fragment of the highly conserved 5' noncoding region and detection through an internal fluorescent probe, including TaqMan and beacon chemistries, in one- and two-step RT-PCR formats. The best performance in terms of sensitivity and reproducibility was achieved by a one-step TaqMan RT-PCR, with a sensitivity enabling the detection of 0.05 infectious unit and 10 copies of a single-stranded RNA (ssRNA) synthetic transcript. Standard reagents, such as a mengovirus strain and an ssRNA transcript, were employed as controls of nucleic acid extraction and RT-PCR, respectively. The test proved to be highly specific after a broad panel of enteric viruses was tested. Sequence alignment of target regions of the primers and probe proved them to be adequate for the quantification of all HAV genotypes. In addition, a quasispecies analysis of the mutant spectrum indicated that these regions are not prone to variability, thus confirming their robustness.

Diagnosis of hepatitis a virus infection: a molecular approach

Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.

A reliable RT-PCR–ELISA method for the detection of infectious pancreatic necrosis virus (IPNV) in farmed rainbow trout

A new method, termed RT-PCR-ELISA, was evaluated for ease of use, reliability and sensitivity when detecting infectious pancreatic necrosis virus (IPNV) present in trout kidney tissue. The method had comparable sensitivity to existing PCR assays and could successfully detect 1.5 x 10(4) pfu IPNV in artificially contaminated trout kidney samples. The technique was easily established in a new laboratory and required no specialised equipment. The method had a high sample throughput capable of screening 96 samples per run, making the technique extremely time efficient. The RT-PCR-ELISA is a safe, quick, reliable technique, which has the potential for use as a standard virus detection method.

Diagnosis of hepatitis a virus infection: a molecular approach

Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.

Rapid and quantitative detection of hepatitis A virus from green onion and strawberry rinses by use of real-time reverse transcription-PCR

In this study, an immunomagnetic capture method and a real-time reverse transcription-PCR assay were used to quantify hepatitis A virus (HAV) in green onion and strawberry rinses. This combined protocol detected as low as 0.5 PFU HAV in produce rinses and concentrated HAV levels up to 20-fold.

Development and evaluation of a broadly reactive TaqMan assay for rapid detection of hepatitis A virus

Primers and a TaqMan probe for the 5'-untranslated region (UTR) of the hepatitis A virus (HAV) genome were designed and evaluated. The assay detected 0.5 infectious units of HAV and 40 copies of a synthetic transcript and provides an important screening tool for rapid quantitative HAV detection in clinical or environmental samples.

Hepatitis A virus attachment to agri-food surfaces using immunological, virological and thermodynamic assays

AIMS

This study was designed to investigate the ability of hepatitis A virus (HAV) to attach to various food contact surfaces.

METHODS AND RESULTS

HAV attachment was demonstrated after elution of attached viruses from solid surfaces by an immunofluorescent method using anti-HAV-specific antibodies and confocal microscopy. Attachment and survival of HAV on stainless steel, copper, polythene and polyvinyl chloride (PVC) at 20 and 4 degrees C after 2 and 4 h were quantified by plaque assay. HAV was shown to attach almost instantaneously to all four surfaces tested. Attachment of HAV depended on initial viral concentration and was slightly greater at 4 degrees C. The total surface energy (gammaTOT), nonpolar Lifshitz-Van der Waals (gammaLW) and polar short range (gammaSR) hydrogen-bonding components for HAV and each surface as well as total free energy of the system were determined by contact angle measurements using an extended Young equation [Young (1805) Philosophical Transactions of The Royal Society (London) 95, 65-87). The calculation of these parameters predicted the favourable conditions for attachment of HAV to all four surfaces tested.

CONCLUSION

HAV particles attach to stainless steel, copper, polythene and PVC at 20 and 4 degrees C and the total free energy of the interaction is optimal for this attachment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Comprehension of viral attachment to the solid surfaces will permit to successfully disinfect these surfaces and to establish a better surveillance programme for control of viral food-borne illnesses.

Detection of infectious hepatitis A virus by integrated cell culture/strand-specific reverse transcriptase-polymerase chain reaction

AIMS

A novel integrated cell culture/strand-specific reverse transcriptase-polymerase chain reaction (RT-PCR) assay was established for detection of infectious hepatitis A virus (HAV).

METHODS AND RESULTS

The specificity of tagged RT-PCR was assessed using HAV genomic positive-strand RNA extracted from HAV virions as reference. Water samples artificially contaminated with infectious or formalin-inactivated HAV were subjected to integrated cell culture (ICC)/RT-PCR and ICC/strand-specific RT-PCR assays respectively. The tagged RT-PCR had high specificity for HAV negative-strand RNA. By demonstrating the formation of negative-strand RNA replicative intermediate, ICC/strand-specific RT-PCR can distinguish between infectious and non-infectious HAV. The described method detected infectious HAV at inoculation level of 10(0) TCID50 per flask within 4 days.

CONCLUSIONS

The ICC/strand-specific RT-PCR is a novel, rapid, sensitive and reliable method for detection of infectious HAV.

SIGNIFICANCE AND IMPACT OF THE STUDY

Coupled with a suitable virus concentration and purification system, ICC/strand-specific RT-PCR will provide a novel and rapid method for detection of infectious HAV in clinical, environmental and food samples. This assay may be used as an alternative method to test the effective inactivation of inactivated virus vaccines. It may also be adapted to assess the efficacy of disinfection of HAV and enteric viruses in foods and water.

Combined immunomagnetic separation-molecular beacon-reverse transcription-PCR assay for detection of hepatitis A virus from environmental samples

In this study, a molecular-beacon-based real-time reverse transcription (RT)-PCR assay was developed to detect the presence of hepatitis A virus (HAV) in environmental samples. A 125-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time RT-PCR assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, and only HAV was positively identified. When combined with immunomagnetic separation, the real-time RT-PCR assay successfully detected as few as 20 PFU in seeded groundwater samples. Because of its simplicity and specificity, this assay has broad applications for the rapid detection of HAV in contaminated foods or water.

Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus

Hepatitis A virus (HAV) is a major cause of infectious hepatitis worldwide. Detection of HAV in contaminated food or water is a priority research area in laboratories worldwide. Our laboratory has reported previously the development of reverse transcription-polymerase chain reaction (RT-PCR) based detection and typing methods for HAV in contaminated shellfish and produce. It is commonly held that RT-PCR can detect viral genome, but cannot distinguish between infectious and inactivated virus. Therefore, signals obtained after PCR should be considered as false positives unless it can be shown that the sample contains virus capable of infecting a suitable host cell line in culture. We present data to show that this general assumption is not valid. Evidence is provided that demonstrate that signals generated after RT-PCR amplification of viral genome correlated well with the presence of infectious virus in the sample. Viral samples inactivated by heat or UV treatment produced significantly lower signal strength that paralleled infectivity of the sample in cultured cells. The loss of signal strength is most likely the result of damage to the viral RNA that renders it unsuitable for RT-PCR. The correlation between PCR signal and infectivity was better following UV inactivation than heat treatment. The procedure may be adapted to other viruses and inactivating agents.

Detection of hepatitis A virus in shellfish (Mytilus galloprovincialis) with RT-PCR

A PCR assay for the detection of hepatitis A virus (HAV) in shellfish is described. The procedure involves the concentration of viral particles with the use of polyethylene glycol (PEG), followed by viral RNA extraction and purification with oligo(dT) cellulose. Reverse transcriptase-PCR detection was accomplished in a single step with the use of primers specific for the VP3-VP1 region of the genome. The procedure detected one 50% tissue culture infective dose (0.6 PFU) per 25 g of shellfish homogenate. Heminested PCR was then carried out to verify the specificity of the PCR products. The method was used to detect HAV in shellfish samples from EU categories B and C and to evaluate the quality of shellfish in routine monitoring for HAV in view of the relevant public health implications of this foodborne disease.

Capsid functions of inactivated human picornaviruses and feline calicivirus

The exceptional stability of enteric viruses probably resides in their capsids. The capsid functions of inactivated human picornaviruses and feline calicivirus (FCV) were determined. Viruses were inactivated by UV, hypochlorite, high temperature (72 degrees C), and physiological temperature (37 degrees C), all of which are pertinent to transmission via food and water. Poliovirus (PV) and hepatitis A virus (HAV) are transmissible via water and food, and FCV is the best available surrogate for the Norwalk-like viruses, which are leading causes of food-borne and waterborne disease in the United States. The capsids of all 37 degrees C-inactivated viruses still protected the viral RNA against RNase, even in the presence of proteinase K, which contrasted with findings with viruses inactivated at 72 degrees C. The loss of ability of the virus to attach to homologous cell receptors was universal, regardless of virus type and inactivation method, except for UV-inactivated HAV, and so virus inactivation was almost always accompanied by the loss of virus attachment. Inactivated HAV and FCV were captured by homologous antibodies. However, inactivated PV type 1 (PV-1) was not captured by homologous antibody and 37 degrees C-inactivated PV-1 was only partially captured. The epitopes on the capsids of HAV and FCV are evidently discrete from the receptor attachment sites, unlike those of PV-1. These findings indicate that the primary target of UV, hypochlorite, and 72 degrees C inactivation is the capsid and that the target of thermal inactivation (37 degrees C versus 72 degrees C) is temperature dependent.

Emerging waterborne infections: contributing factors, agents, and detection tools

Because microorganisms are easily dispersed, display physiological diversity, and tolerate extreme conditions, they are ubiquitous and may contaminate and grow in water. The presence of waterborne enteric pathogens (bacteria, viruses, and protozoa) in domestic water supplies represents a potentially significant human health risk. Even though major outbreaks of waterborne disease are comparatively rare, there is substantial evidence that human enteric pathogens that are frequently present in domestic water supplies are responsible for low-level incidence of waterborne microbial disease. Although these diseases are rarely debilitating to healthy adults for more than a few hours to a few days, enteric pathogens can cause severe illness, even death, for young children, the elderly, or those with compromised immune systems. As the epidemiology of waterborne diseases is changing, there is a growing global public health concern about new and reemerging infectious diseases that are occurring through a complex interaction of social, economic, evolutionary, and ecological factors. New microbial pathogens have emerged, and some have spread worldwide. Alternative testing strategies for waterborne diseases should significantly improve the ability to detect and control the causative pathogenic agents. In this article, we provide an overview of the current state of knowledge of waterborne microbial pathogens, their detection, and the future of new methods in controlling these infectious agents.

Microbial quality of wastewater: detection of hepatitis A virus by reverse transcriptase-polymerase chain reaction

AIMS

The persistent circulation of hepatitis A virus (HAV) in the Mediterranean area suggests the need for monitoring its presence in the environment. A reverse transcriptase-polymerase chain reaction (RT-PCR) was used to detect the presence of HAV in several consecutive raw sewage and final effluent samples, collected over an 8-month period from an activated sludge treatment plant in southern Italy.

METHODS AND RESULTS

Two distinct purification protocols, either based on antigen-capture with monoclonal antibody (AC) or RNA extraction, were compared. The possible influence of the antibody used in the AC phase was evaluated in preliminary experiments on HAV-spiked samples, using two different monoclonal antibodies. Hepatitis A virus RNA was detected in all but one sewage environmental sample examined. The contemporary presence of enteroviruses, reoviruses and phages was observed, while HAV growth in cell culture was hampered.

CONCLUSIONS

The RT-PCR technique was confirmed to be a valuable tool for the rapid monitoring of HAV in sewage samples. In addition, this study demonstrated that application of different sample purification methods can result in different levels of sensitivity of the assay and that, in the antigen-capture method, the choice of antibody can have a crucial role.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work underlines the need for technical uniformity in environmental studies from different laboratories for a correct and useful comparison of the results.

Pretreatment to avoid positive RT-PCR results with inactivated viruses

Enteric viruses that are important causes of human disease must often be detected by reverse transcription-polymerase chain reaction (RT-PCR), a method that commonly yields positive results with samples that contain only inactivated virus. This study was intended to develop a pretreatment for samples, so that inactivated viruses would not be detected by the RT-PCR procedure. Model viruses were human hepatitis A virus, vaccine poliovirus 1 and feline calicivirus as a surrogate for the Norwalk-like viruses. Each virus was inactivated (from an initial titer of approximately 10(3) PFU/ml) by ultraviolet light, hypochlorite or heating at 72 degrees C. Inactivated viruses, that were treated with proteinase K and ribonuclease for 30 min at 37 degrees C before RT-PCR, gave a negative result, which is to say that no amplicon was detected after the reaction was completed. This antecedent to the RT-PCR method may be applicable to other types of viruses, to viruses inactivated in other ways and to other molecular methods of virus detection.

Detection of hepatitis A virus by the nucleic acid sequence-based amplification technique and comparison with reverse transcription-PCR

A nucleic acid sequence-based amplification (NASBA) technique for the detection of hepatitis A virus (HAV) in foods was developed and compared to the traditional reverse transcription (RT)-PCR technique. Oligonucleotide primers targeting the VP1 and VP2 genes encoding the major HAV capsid proteins were used for the amplification of viral RNA in an isothermal process resulting in the accumulation of RNA amplicons. Amplicons were detected by hybridization with a digoxigenin-labeled oligonucleotide probe in a dot blot assay format. Using the NASBA, as little as 0.4 ng of target RNA/ml was detected per comparison to 4 ng/ml for RT-PCR. When crude HAV viral lysate was used, a detection limit of 2 PFU (4 x 10(2) PFU/ml) was obtained with NASBA, compared to 50 PFU (1 x 10(4) PFU/ml) obtained with RT-PCR. No interference was encountered in the amplification of HAV RNA in the presence of excess nontarget RNA or DNA. The NASBA system successfully detected HAV recovered from experimentally inoculated samples of waste water, lettuce, and blueberries. Compared to RT-PCR and other amplification techniques, the NASBA system offers several advantages in terms of sensitivity, rapidity, and simplicity. This technique should be readily adaptable for detection of other RNA viruses in both foods and clinical samples.

The occurrence of hepatitis A and astroviruses in selected river and dam waters in South Africa

Over a period of one year (June 1997-May 1998) samples of surface waters, used for domestic and recreational purposes, were collected weekly from the same sites on the Klip River and Vaal Dam, Gauteng, South Africa. Sensitive and specific reverse transcriptase-polymerase chain reaction-oligonucleotide probe assays were used to detect HAV and HAstV RNA in concentrates of the water and infectious virus in cell cultures infected with the water concentrates. HAV was detected in 18 (35.3%) of the river and 19 (37.3%) of the dam water samples, often in association with the RNA from other enteric viruses. HAstV was detected less frequently and was present in 11 (21.6%) of the river and 3 (5.9%) of the dam water samples. A seasonal pattern was noted for HAV but not for HAstV. Cell culture amplification in a variety of carefully selected cell culture systems enhanced the detection of both viruses. Infectious viruses were detected in dam water samples where microbiological indicators of faecal pollution were absent or within acceptable limits. The presence of these viruses in the dam and river water could pose a potential health risk for people using these waters for domestic or recreational purposes.

Improved method for the recovery of hepatitis A virus from oysters

Hepatitis A is one of the major infectious diseases epidemiologically associated with worldwide shellfish consumption. Molecular detection using polymerase chain reaction (PCR) to detect hepatitis A virus (HAV) in contaminated shellfish can be hindered by low virus recoveries during the concentration process and by natural PCR inhibitors in shellfish. This study evaluated and modified two major steps of a processing procedure for virus concentration from oysters: acid adsorption-elution and solvent extraction. With the addition of second and third elutions, the acid adsorption-elution step doubled the recovery to 46% of HAV seeded initially. Extraction with chloroform or chloroform-butanol resulted in lower HAV detection limits by reverse transcription-PCR (RT-PCR)-oligoprobing than extraction with the fluorocarbon, Freon. These results led to the following modified procedure: HAV was acid adsorbed at pH 4.8, eluted first with 0.05 M glycine, second with 0.5 M threonine, PEG-precipitated twice, chloroform-extracted twice, RNA-extracted, and RT-PCR (single round) amplified. Using the modified procedure, HAV was detected by RT-PCR in all trials with a seeding density of > or = 1 plaque forming unit (PFU)/g of oyster, and in which the equivalent detection limit was 0.33 PFU of HAV seeded per RT-PCR reaction (corresponding to 111 PCR units). The method developed is capable of detecting low levels of HAV in oysters environmentally contaminated.

Detection of enterovirus and hepatitis A virus RNA in mussels (Mytilus spp.) by reverse transcriptase-polymerase chain reaction

AIMS

A simple and effective method of concentrating and purifying enteric viruses from mussel samples to be detected by nucleic acid extraction reverse transcriptase-polymerase chain reaction (RT-PCR) has been evaluated.

METHODS AND RESULTS

Seeded mussels were processed by alkaline elution, polyethylene glycol (PEG) precipitation, solvent extraction and PEG precipitation. Final concentrates were assayed by infectivity and RT-PCR after nucleic acid extraction. Two RNA extraction methods were comparatively evaluated for removing inhibitory substances: guanidinium thiocyanate extraction and Purescripttrade mark RNA isolation. Both procedures removed most inhibitors allowing the detection of viral RNA at inoculum levels as low as 4 pfu g(-1) for poliovirus type 1 and 1.8-18 most probable number of cytopathogenic units g(-1) for HAV. When inhibitors remained, they were efficiently removed by Sephadex column chromatography before RNA extraction.

CONCLUSION

The described method is effective for the detection of enteric viruses in mussels by RT-PCR. The use of Purescripttrade mark RNA isolation makes the method faster, safer and very easy to perform.

Immunomagnetic separation of a Norwalk-like virus (genogroup I) in artificially contaminated environmental water samples

Rabbit polyclonal antibodies were raised against a recombinant capsid protein from a genogroup I Norwalk-like virus (NLV). Magnetic beads coated with these antibodies were used in immunomagnetic separation (IMS) of the NLV. After capture of the NLV and washing of the beads, viral RNA was heat released and detected by RT-PCR. This IMS procedure was shown to have high sensitivity for detection of homologous NLV, while capture of a genogroup II NLV was less efficient. Antigen capture was not influenced by the content of humic acids in the samples. The combination of IMS and heat release was found to be more efficient than organic extraction of RNA from water contaminated with humic acids. The efficacy and simplicity of IMS/heat release render this combination a feasible tool for the preparation of NLV RNA from environmental samples, although the antigenic diversity of NLV may be a complicating factor.

Concentration and detection of caliciviruses in water samples by reverse transcription-PCR

Human caliciviruses (HuCVs) cause waterborne outbreaks of gastroenteritis. Standard indicators of a safe water supply do not adequately predict contamination of water by viruses, including HuCVs. We developed a method to concentrate and detect HuCVs in water samples by using a cultivable primate calicivirus (Pan-1) as a model. Viable Pan-1 was seeded in different types of water and then filtered with a 1MDS filter, eluted with beef extract (BE), and reconcentrated by polyethylene glycol (PEG) precipitation. The viruses in the final samples were tested by plaque assay or by reverse transcription (RT)-PCR following extraction of the RNA with Trizol. Pan-1 was more sensitive to high-pH treatment than poliovirus was; a pH 9.0 BE solution was found to recover 35% more viable Pan-1 than a pH 9.5 BE solution recovered. Pan-1 was recovered from small volumes of deionized, finished, ground, and surface waters at efficiencies of 94, 73, 67, and 64%, respectively, when samples were assayed after elution without further concentration. When larger volumes of water (up to 40 liters) were tested after elution and concentration with PEG, 38, 19, and 14% of the seeded Pan-1 were recovered from finished, ground, and surface waters, respectively. The limit of detection of Pan-1 by RT-PCR was estimated to be 0.75 to 1.5 PFU in 40 liters of finished water. This method may be adapted for monitoring HuCVs in drinking water and other types of water for public health safety.

Rapid concentration and detection of hepatitis A virus from lettuce and strawberries

Immunomagnetic beads-PCR (IM-PCR), positively-charged virosorb filters (F), or a combination of both methods (F-IM-PCR) were used to capture, concentrate and rapidly detect hepatitis A virus (HAV) in samples of lettuce and strawberries experimentally contaminated. Direct reverse transcriptase-polymerase chain reaction (RT-PCR) amplification of the collected HAV-beads complex showed a detection limit of 0.5 plaque forming units (PFU) of the virus present in 1-ml of wash solution from the produce, which was several hundred-fold more sensitive than that demonstrated by RT-PCR. In separate trials, virus-containing wash solutions from the produce were passed through the filters and the captured virus was eluted with 10 ml volumes of 1% beef extract. Of the 62% filter-captured HAV, an average of 34.8% was eluted by the 1% beef extract. PCR amplification of 2 microl from this eluate failed to produce a clear positive band signal. As little as 10 PFU, present on each piece of the lettuce or strawberry, was detectable by the F-IM-PCR, which was almost 20 times less sensitive than the detection limit of 0.5 PFU by the IM-PCR. However, considering the large volumes (< or =50 ml) used in the F-IM-PCR, the sensitivity of detection could be much greater than that of the IM-PCR, which was restricted to < or =20 ml volumes. These data indicate that the F-IM-PCR method provides the potential for a greater sensitivity of detection than the IM-PCR, since low levels of virus could be detected from large volumes of sample than possible by the IM-PCR method. Although positively-charged filters captured a greater amount of virus than both the IM-PCR and F-IM-PCR methods, direct PCR amplification from beef extract eluates was not successful in detecting HAV from produce.

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.

Contamination of foods by food handlers: experiments on hepatitis A virus transfer to food and its interruption

Hepatitis A virus (HAV) is an important pathogen which has been responsible for many food-borne outbreaks. HAV-excreting food handlers, especially those with poor hygienic practices, can contaminate the foods which they handle. Consumption of such foods without further processing has been known to result in cases of infectious hepatitis. Since quantitative data on virus transfer during contact of hands with foods is not available, we investigated the transfer of HAV from artificially contaminated fingerpads of adult volunteers to pieces of fresh lettuce. Touching the lettuce with artificially contaminated fingerpads for 10 s at a pressure of 0.2 to 0.4 kg/cm(2) resulted in transfer of 9.2% +/- 0.9% of the infectious virus. The pretreatments tested to interrupt virus transfer from contaminated fingerpads included (i) hard-water rinsing and towel drying, (ii) application of a domestic or commercial topical agent followed by water rinsing and towel drying, and (iii) exposure to a hand gel containing 62% ethanol or 75% liquid ethanol without water rinsing or towel drying. When the fingerpads were treated with the topical agents or alcohol before the lettuce was touched, the amount of infectious virus transferred to lettuce was reduced from 9.2% to between 0.3 and 0.6% (depending on the topical agent used), which was a reduction in virus transfer of up to 30-fold. Surprisingly, no virus transfer to lettuce was detected when the fingerpads were rinsed with water alone before the lettuce was touched. However, additional experiments with water rinsing in which smaller volumes of water were used (1 ml instead of 15 ml) showed that the rate of virus transfer to lettuce was 0.3% +/- 0.1%. The variability in virus transfer rates following water rinsing may indicate that the volume of water at least in part influences virus removal from the fingerpads differently, a possibility which should be investigated further. This study provided novel information concerning the rate of virus transfer to foods and a model for investigating the transfer of viral and other food-borne pathogens from contaminated hands to foods, as well as techniques for interrupting such transfer to improve food safety.

Detection of norwalk-like virus in shellfish implicated in illness

In the 1990s, Norwalk-like viruses (NLVs) were identified in patient specimens as the primary pathogen associated with shellfish-borne gastroenteritis in the United States. Identification of these viruses from implicated shellfish has been difficult due to inefficient recovery of viruses, natural polymerase chain reaction (PCR) inhibitors in shellfish, and low virus contamination. Recent improvements to the method of detecting NLVs in shellfish include enhanced processing of virus and shellfish samples, application of nested PCR and nucleotide sequencing, and increased knowledge of NLV genetic diversity. Using a newly developed and sensitive method, an NLV G2 strain was identified in 2 oyster samples implicated in a 1998 California outbreak involving 171 cases. NLV capsid primers demonstrated a greater specificity of PCR detection than did polymerase primers. The 175-base viral capsid nucleotide sequences derived from oysters were 100% identical to those derived from a patient stool sample. This finding supports the epidemiologic associations indicating that contaminated shellfish serve as the vehicle for NLV transmission.

Recovery and detection of enterovirus, hepatitis A virus and Norwalk virus in hardshell clams (Mercenaria mercenaria) by RT-PCR methods

A method for recovery of enteric viruses from hardshell clams (Mercenaria mercenaria) has been developed and evaluated. Seeded 50-g samples of clam tissue homogenates were processed by adsorption elution precipitation, two fluorocarbon extractions and PEG precipitation. Clam concentrates were assayed by infectivity and by RT-PCR after guanidinium isothiocyanate (GIT) extraction and/or an indirect immunomagnetic capture (IC) of the virus using paramagnetic beads. GIT extraction removed PCR inhibitors and allowed a reliable RT-PCR detection of viral RNA. The detection sensitivity of GIT extraction-RT-PCR was < 1 PFU of poliovirus 1, < 10 PFU of HAV and 1-11 PCRU of Norwalk virus. IC was very effective for additional concentration and purification of enteric viruses from clam concentrates removing most RT-PCR inhibitors. The sensitivity of this method was comparable to the GIT extraction and the sample volume tolerance for PCR was increased about 10-fold. Both methods gave similar efficiency for virus detection in samples seeded with low virus levels. The procedure developed in this study is effective for enteric viruses detection in hardshell clams by RT-PCR.

Evaluation of immunomagnetic separation for recovery of infectious Cryptosporidium parvum oocysts from environmental samples

Two commercial immunomagnetic separation (IMS) kits for Cryptosporidium were compared for recovery of oocysts from environmental samples. Oocyst recovery efficiencies with the Dynal and Crypto-Scan kits ranged from 62 to 100% and 34 to 74%, respectively, for seeded environmental water concentrates (turbidity of 210 to 11,480 nephelometric turbidity units). Recovery efficiencies were dependent on the mechanism of agitation during the magnetic capture procedure. An assay combining in vitro cell culture and reverse transcriptase PCR demonstrated that oocysts recovered by IMS retained their infectivity.

Comparison of seven RNA extraction methods on stool and shellfish samples prior to hepatitis A virus amplification

When choosing an extraction method, two parameters have to be considered: recovery of the viral material and elimination or inactivation of inhibitory substances. Seven techniques for extracting hepatitis A virus (HAV) from stool and shellfish samples were compared, in order to identify the protocol most suited to both types of sample and with the best extraction yield. The protocols tested were either techniques for the recovery and purification of total RNA, such as RNAzol, PEG-CETAB, GTC-silica and Chelex, or techniques for isolating specifically HAV using a nucleotide probe or a monoclonal antibody. For stool samples, RNAzol, PEG-CETAB, and magnetic beads with antibody allowed detection of the virus in 11/12 and 12/12 of samples. For shellfish samples, three protocols allowed RNA to be extracted in 90% of cases, RNAzol, PEG-CETAB, and GTC-silica. Their rapidity and low cost make RNAzol and GTC-silica the most suitable for routine diagnostic testing. reserved.

Immunomagnetic capture PCR for rapid concentration and detection of hepatitis A virus from environmental samples

We studied the concentration of hepatitis A virus (HAV) from environmental samples by membrane filter-based urea-arginine phosphate buffer and its detection by using immunomagnetic capture (IC) reverse transcription (RT)-PCR (IC PCR). Magnetic beads coated with anti-HAV rabbit antibodies were used for enrichment and concentration of HAV from environmental samples. IC PCR is sensitive enough to detect as few as 0.04 PFU of cell culture-adapted HAV in inoculated water and sewage samples. IC PCR is specific and does not yield positive reactions with poliovirus 1, HAV RNA, or selected bacteriophages. IC concentrates viruses suspended in small volumes to microliter volumes that can be used directly in RT-PCR. IC concentration of viruses from sewage samples without concentration of inhibitory substances is important for successful RT-PCR detection. In a field trial, 2 of 18 raw sewage samples tested by IC PCR were positive for HAV.