Assessment of different commercial RNA-extraction and RT-PCR kits for detection of hepatitis A virus in mussel tissues

Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes

To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r²=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.

Prevalence of human noroviruses in frozen marketed shellfish, red fruits and fresh vegetables

Noroviruses (NoVs), currently recognised as the most common human food-borne pathogens, are ubiquitous in the environment and can be transmitted to humans through multiple foodstuffs. In this study, we evaluated the prevalence of human NoV genogroups I (GI) and II (GII) in 493 food samples including soft red fruits (n = 200), salad vegetables (n = 210) and bivalve mollusc shellfish (n = 83), using the Bovine Enterovirus type 1 as process extraction control for the first time. Viral extractions were performed by elution concentration and genome detection by TaqMan Real-Time RT-PCR (RT-qPCR). Experimental contamination using hepatitis A virus (HAV) was used to determine the limit of detection (LOD) of the extraction methods. Positive detections were obtained from 2 g of digestive tissues of oysters or mussels kept for 16 h in seawater containing 2.0-2.7 log10 plaque-forming units (PFU)/L of HAV. For lettuces and raspberries, the LOD was, respectively, estimated at 2.2 and 2.9 log10 PFU per 25 g. Of the molluscs tested, 8.4 and 14.4% were, respectively, positive for the presence of GI NoV and GII NoV RNA. Prevalence in GI NoVs varied from 11.9% for the salad vegetables samples to 15.5% for the red soft fruits. Only 0.5% of the salad and red soft fruits samples were positive for GII NoVs. These results highlight the high occurrence of human NoVs in foodstuffs that can be eaten raw or after a moderate technological processing or treatment. The determination of the risk of infection associated with an RT-qPCR positive sample remains an important challenge for the future.

Rotavirus Occurrence in Shellfish with Low Levels of E. coli

The purpose of this study was to evaluate "in field" the accumulation of virus in shellfish and compare it with the concentration of bacterial indicators. Individuals of Mytilus galloprovincialis were placed in two sampling station located in a contaminated coastal bay and in one control station located one kilometer offshore. The presence of Rotavirus and E. coli was assessed weekly both in seawater and in shellfish samples. The Rotavirus genome was detected in water, preliminarily concentrated by tangential flow ultrafiltration method, and in hepatopancreas of mussels by Real-Time PCR. E. coli was enumerated in water matrices by a filtering method and in mussels by the MPN method. Rotaviruses were not recorded in seawater, while in mussels they were detected since third week after placement. E. coli in mussels were always below the limits set in the Regulation (EC) 854/2004. This study suggests the need for a viral indicator to insure the safety for consumption of shellfish.

PCR inhibitors - occurrence, properties and removal

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.

RNA extracted from blood samples with a rapid automated procedure is fit for molecular diagnosis or minimal residual disease monitoring in patients with a variety of malignant blood disorders

Scientific studies in oncology, cancer diagnosis, and monitoring tumor response to therapeutics currently rely on a growing number of clinico-pathological information. These often include molecular analyses. The quality of these analyses depends on both pre-analytical and analytical information and often includes the extraction of DNA and/or RNA from human tissues and cells. The quality and quantity of obtained nucleic acids are of utmost importance. The use of automated techniques presents several advantages over manual techniques, such as reducing technical time and thus cost, and facilitating standardization. The purpose of this study was to validate an automated technique for RNA extraction from cells of patients treated for various malignant blood diseases. A well-established manual technique was compared to an automated technique, in order to extract RNA from blood samples drawn for the molecular diagnosis of a variety of leukemic diseases or monitoring of minimal residual disease. The quality of the RNA was evaluated by real-time quantitative RT-PCR (RQ-PCR) analyses of the Abelson gene transcript. The results show that both techniques produce RNA with comparable quality and quantity, thus suggesting that an automated technique can be substituted for the reference and manual technique used in the daily routine of a molecular pathology laboratory involved in minimal residual disease monitoring. Increased costs of reagents and disposables used for automated techniques can be compensated by a decrease in human resource.

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.

Green onions: potential mechanism for hepatitis A contamination

The largest documented foodborne hepatitis A outbreak in U.S. history occurred in November 2003. The source of that outbreak was green onions from a farm in Mexico. Two biomarkers were used to determine ways in which hepatitis A virus (HAV) can contaminate onions. Fluorescent microspheres (1.0 to 10 microm) and HAV vaccine were placed on the soil and the surfaces of pot-grown onions and in the liquid medium of hydroponically cultivated onions. Reverse transcription PCR (RT-PCR) was used to identify HAV RNA. Microspheres were found on the outside and inside of the pot-grown onions for up to 60 days. RT-PCR revealed HAV RNA from the vaccine in well-washed green onions. In the hydroponically grown onions, microspheres were found throughout the onion after only 1 day. RT-PCR also revealed HAV RNA inside the hydroponically grown onions. Both biomarkers support the hypothesis that HAV can contaminate the inside of the growing onion and can be taken up intracellularly through the roots. Once inside, the particles are impossible to remove by cleaning.

Detection of hepatitis A virus (HAV) in oysters (Crassostrea gigas)

Because shellfish (oysters, clams, and mussels) are filter-feeders, pathogens become concentrated within them, and human consumption of raw, or under-cooked shellfish can result in disease outbreaks. Identification of hepatitis A virus (HAV) in shellfish has been difficult for several reasons: the concentration of virions in shellfish tissues are very low, detection methods based on in vitro propagation are unreliable, recovery of virions from shellfish tissues is inefficient, and PCR inhibitors in shellfish tissues limit the success of RT-PCR. These facts underlie difficulties in determining cause and effect relationships between hepatitis A outbreaks and detection of HAV contamination in shellfish samples. We have developed a reliable and highly sensitive method for detection of HAV in oyster tissues at low levels (0.001 FFU/ml-fluorescent focus units per milliliter). Our method combines dissection of the gastrointestinal oyster tract, organic extraction before PEG precipitation, and RNA extraction with Trizol LS, followed by RT-PCR and hybridization using a digoxigenin-labeled HAV cDNA probe. Our results will benefit both public health officials concerned about hepatitis A infections caused by consumption of HAV-contaminated oysters and shellfish producers who require reliable methods for quality control of commercial oyster production.

Use of armored RNA as a standard to construct a calibration curve for real-time RT-PCR

Armored Enterovirus RNA was used to standardize a real-time reverse transcription (RT)-PCR for environmental testing. Armored technology is a system to produce a robust and stable RNA standard, trapped into phage proteins, to be used as internal control. The Armored Enterovirus RNA protected sequence includes 263 bp of highly conserved sequences in 5' UTR region. During these tests, Armored RNA has been used to produce a calibration curve, comparing three different fluorogenic chemistry: TaqMan system, Syber Green I and Lux-primers. The effective evaluation of three amplifying commercial reagent kits, in use to carry out real-time RT-PCR, and several extraction procedures of protected viral RNA have been carried out. The highest Armored RNA recovery was obtained by heat treatment while chemical extraction may decrease the quantity of RNA. The best sensitivity and specificity was obtained using the Syber Green I technique since it is a reproducible test, easy to use and the cheapest one. TaqMan and Lux-primer assays provide good RT-PCR efficiency in relationship to the several extraction methods used, since labelled probe or primer request in these chemistry strategies, increases the cost of testing.