Detection of Grapevine leafroll-associated virus 7 using real time qRT-PCR and conventional RT-PCR

Nine isolates of Grapevine leafroll-associated virus 7 (GLRaV-7) from diverse geographical regions were sequenced to design more sensitive molecular diagnostic tools. The coat protein (CP) and heat shock protein 70 homologue (HSP70h) genes of these nine isolates were sequenced. Sequences were then used to design more sensitive molecular diagnostic tools. Sequence identity among these isolates ranged between 90 to 100% at the nucleotide and amino acid levels. One RT-PCR and two qRT-PCR assays were used to survey 86 different grapevines from the University of California, Davis Grapevine Virus Collection, the Foundation Plant Services collection and the USDA National Clonal Germplasm Repository, Davis, CA with primers designed in conserved regions of the CP and HSP70h genes. Results revealed that qRT-PCR assays designed in the HSP70h gene was more sensitive (29.07% positives) than that designed in the CP gene (22.09% positives) and both qRT-PCR assays proved to be more sensitive than RT-PCR.     

Early diagnosis of SARS coronavirus infection by real time RT-PCR.

BACKGROUND: A novel coronavirus was recently identified as the aetiological agent of Severe Acute Respiratory Syndrome (SARS). Molecular assays currently available for detection of SARS-coronavirus (SARS-CoV) have low sensitivity during the early stage of the illness. OBJECTIVE: To develop and evaluate a sensitive diagnostic test for SARS by optimizing the viral RNA extraction methods and by applying real-time quantitative RT-PCR technology. STUDY DESIGN: 50 nasopharyngeal aspirate (NPA) samples collected from days 1-3 of disease onset from SARS patients in whom SARS CoV infections was subsequently serologically confirmed and 30 negative control samples were studied. Samples were tested by: (1) our first generation conventional RT-PCR assay with a routine RNA extraction method (Lancet 361 (2003) 1319), (2) our first generation conventional RT-PCR assay with a modified RNA extraction method, (3) a real-time quantitative RT-PCR assay with a modified RNA extraction method. RESULTS: Of 50 NPA specimens collected during the first 3 days of illness, 11 (22%) were positive in our first generation RT-PCR assay. With a modification in the RNA extraction protocol, 22 (44%) samples were positive in the conventional RT-PCR assay. By combining the modified RNA extraction method and real-time quantitative PCR technology, 40 (80%) of these samples were positive in the real-time RT-PCR assay. No positive signal was observed in the negative controls. CONCLUSION: By optimizing RNA extraction methods and applying quantitative real time RT-PCR technologies, the sensitivity of tests for early diagnosis of SARS can be greatly enhanced.     

Molecular diagnosis of Papaya meleira virus (PMeV) from leaf samples of Carica papaya L. using conventional and real-time RT-PCR

Papaya meleira virus (PMeV) is the causal agent of papaya sticky disease. This study describes two methods for molecular diagnosis of PMeV using conventional and real-time PCR. These methods were shown to be more efficient than current methods of viral detection using extraction of PMeV dsRNA and observation of symptoms in the field. The methods described here were used to evaluate the effect of inoculation of papaya plants with purified PMeV dsRNA on the progress of PMeV infection. A single inoculation with PMeV dsRNA was observed to delay the progress of the virus infection by several weeks. The possibility of vertical transmission of PMeV was also investigated. No evidence was found for PMeV transmission through seeds collected from diseased fruit. The implications of these results for the epidemiology of PMeV and the management of papaya sticky disease are discussed.     

Optimizing dengue diagnosis by RT-PCR in IgM-positive samples: comparison of whole blood, buffy-coat and serum as clinical samples

Dengue, a major public health problem in tropical and sub-tropical regions, is the most important arboviral disease of humans. Early diagnosis is very important on follow-up of infected patients, especially those at risk of the severe manifestations of this disease. Aiming at the improvement of the molecular diagnosis of these infections and due to the lack of studies that indicated the best sample for dengue virus detection by RT-PCR, viral detection by RT-PCR in blood, serum and buffy-coat of 75 IgM-positive serum samples for dengue was evaluated. Out of the 75 samples, 17 were positive for dengue using RT-PCR and from these samples, three were positive in the blood, 14 positive in the serum and eight positive in the buffy-coat. These results indicate that serum is the best clinical sample for RT-PCR amplification of dengue genomes.     

Development of a real time RT-PCR to detect and type ovine pestiviruses

A real time one-step RT-PCR was designed to detect and type border disease virus (BDV), bovine viral diarrhea virus (BVDV) type 1 and BVDV type 2 in ovine samples. The real time RT-PCR was shown to behave in a linear manner and had limits of detection of 100-1000 copies of viral RNA as judged by in vitro transcribed RNA. The real time RT-PCR was validated on 50 clinical samples from UK flocks and was more sensitive than a virus isolation and a classical nested RT-PCR (nRT-PCR). The results of real time RT-PCR virus typing agreed completely with sequencing. The majority of ovine isolates were BDV; a small proportion were BVDV type 1. BVDV type 2 was not detected in any sample. This test appears reliable and can be used for the typing of ovine pestiviruses in the UK.     

Sensitivity of bhk-21 cells supplemented with diethylaminoethyl-dextran for detection of street rabies virus in saliva samples.

A tissue culture system for detecting rabies virus from saliva samples of suspected animals was developed and compared to suckling mouse inoculation. Swab samples were obtained from the mouth of the animal heads received for rabies diagnosis; these swabs were submerged in maintenance medium. The maintenance medium was inoculated intracerebrally into suckling mice and onto BHK-21 cells with diethylaminoethyl (DEAE)-dextran (BHK/DEAE) and without (BHK). Rabies immunofluorescence was performed on the brain of the mice dying during the observation period and also on both tissue culture systems every day after infection. The BHK-DEAE system detected 28 positive samples obtained from 48 rabid animals and the BHK system detected 18. By suckling mouse inoculation only 11 of the same positive samples were detected. A total of 90 samples was studied by the three methods. Rabies virus was detected by the tissue culture methods earlier than by suckling mouse inoculation. The BHK-DEAE method was an economic and fast method for rabies virus detection in saliva samples, which could be used for ecological and pathogenesis studies, as well for rabies diagnosis before the death of the suspected animal.     

Molecular detection and characterization of human enteroviruses directly from clinical samples using RT-PCR and DNA sequencing

Enteroviruses are common human pathogens associated with a wide spectrum of symptoms ranging from asymptomatic infection to acute flaccid paralysis and neonatal multi-organ failure. Molecular methods that provide rapid diagnosis and increased sensitivity have been developed for the diagnosis of enterovirus infection using oligonucleotide primers complementary to conserved sequences located in the 5' untranslated region (UTR), but data generated from these regions are not sufficiently discriminatory for typing due to the lack of correlation between their nucleic acid sequence and serotype specificity. Sequences derived from the gene encoding the capsid VP1 correlate with serotype, and therefore provide the opportunity for the development of molecular typing methods consistent with present serogical methods. In this study, oligonucleotide primers that amplify a region of the 5'UTR to detect enterovirus RNA, and the region encoding the enterovirus VP1 N-terminus to characterize virus strains were used in nested and semi-nested RT-PCRs, respectively. The ability of the VP1 RT-PCR to amplify diverse viruses within genotypes and genogroups was confirmed by the correct identification of both prototype strains, and strains circulating currently of the same genotypes. The molecular methods proved their utility through the detection of enteroviruses that failed to grow in cell culture, their subsequent characterization and the characterization of strains that failed to serotype in neutralization assays. Molecular methods increased significantly the sensitivity of detection (P < 0.001) and of characterization (P < 0.01) of enteroviruses when compared to classical methods.     

Evaluation of conventional castaneda and lysis centrifugation blood culture techniques for diagnosis of human brucellosis

We investigated the role of the lysis centrifugation blood culture technique over the conventional Castaneda technique for the diagnosis of human brucellosis. The lysis centrifugation technique has been found to be more sensitive in both acute (20% higher sensitivity; P < 0.00001) and chronic (40% higher sensitivity; P = 0.087) forms of brucellosis. The major advantage of lysis centrifugation was in the mean detection time, which was only 2.4 days in acute and 2.7 days in chronic cases, with 103 out of 110 (93.6%) and 17 out of 20 (85%) cultures from acute and chronic brucellosis, respectively, detected before the conventional culture was positive. Our results confirmed the potential usefulness of the lysis technique in diagnosis and institution of appropriate antibiotic therapy.     

Validation of real time RT-PCR applied to cell culture for diagnosis of any known genotype of viral haemorrhagic septicaemia virus

Viral haemorrhagic septicaemia virus (VHSV), a member of the Rhabdoviridae family, is a major viral pathogen of cultured salmonid fish, and also infects a wide range of marine fish species. In the present study, two real time PCR protocols (based on SYBR Green and TaqMan^®) were developed for the detection of strains belonging to all known genotypes of VHSV. Validation of the procedure, in terms of sensitivity, specificity and repeatability/reproducibility (R&R), was also performed. For this purpose, several pairs of primer amplifying regions corresponding to viral G and N genes were assayed. In the SYBR Green-based real time PCR, these primers failed to detect strains from some of the genotypes and/or showed low R&R. In order to improve the detection capacity, a multiplex procedure was designed, which enabled detection of all strains, with high R&R. The sensitivity of the procedure was measured, and a detection limit of 1 fg/μl of viral RNA or 10 copies of cloned plasmid was established. On the other hand, the TaqMan probe-based multiplex real time PCR detected all European strains, with similar levels of sensitivity and R&R, but failed to detect the American types.     

Cytotoxic flow-cytometric crossmatches (flow-tox): a comparison with conventional cytotoxicity crossmatch techniques.

Detection and avoidance of donor-reactive antibodies in the sera of potential organ transplant recipients is key to a successful transplant outcome. Techniques of antibody detection that use flow cytometry are more sensitive than those that rely upon a visual determination of cytotoxicity. However, as conventionally performed, flow-cytometric crossmatches do not distinguish between cytotoxic (complement fixing) and noncytotoxic antibodies because both types of antibodies can bind to a cell and be detected by laser-activated fluorochrome photon emission. In 1989 we described two techniques for detecting cytotoxic antibodies using flow-cytometric techniques [1]. In 1990, we expanded the application of these new techniques that we called flow cytotoxicity assays or "Flow-Tox" [2]. Flow-Tox crossmatches demonstrate an increase in both sensitivity and specificity over conventional cytotoxicity crossmatches.     

Rapid detection of influenza A and B viruses in clinical specimens by Light Cycler real time RT-PCR.

BACKGROUND: the influenza viruses cause morbidity and mortality annually among children and elderly. Surveillance and rapid diagnosis is imperative in the reference laboratory, as clinical symptoms are insufficient for proper diagnosis. OBJECTIVES: this study involved the design of a rapid detection method for influenza A and B viruses using real time RT-PCR from clinical specimens. Methods were specifically designed for use on the Light Cycler. The sensitivity and specificity were also to be determined. STUDY DESIGN: the identification and discrimination of influenza A and B viruses employs two dual probe systems based on fluorescence resonance energy transfer (FRET) technology. Following submission by physicians participating in the Florida sentinel influenza network, 58 specimens were chosen for testing using both tissue culture and Light Cycler methods. RESULTS: of the 35 identified positive for influenza virus via tissue culture isolation, the Light Cycler results matched identification and typing with 100% agreement. However, the Light Cycler recognized 16 additional specimens that were positive for the presence of the virus. RT-PCR and nucleotide sequencing confirmed the presence of influenza A virus in these specimens. Using tenfold serial dilutions, the sensitivity of the Light Cycler method was determined to be 0.01 TCID50. The lower limit of RNA detection was determined as 1.6 x 10(-7) microg for influenza A virus, and 1.2 x 10(-7) microg for influenza B virus. Specificity of the Light Cycler method was determined by testing specimens containing adenovirus, parainfluenza virus and echovirus, all of which yielded negative results with no discernible background. CONCLUSIONS: overall, this newly developed method of simultaneous detection and typing of influenza types A and B using the Light Cycler proves to be more sensitive than tissue culture isolation, with corresponding specificity. This technique may be valuable for surveillance and rapid identification of influenza for early diagnosis.     

A quantification of human cells using an ERV-3 real time PCR assay

A novel approach to quantifying human cells using a real time PCR assay was developed. The target sequence used in the assay is a 135 bp segment within the unique 1.7 kb Hind III / Pst I fragment of the ERV-3 envelope gene. ERV-3 is a full-length human endogenous retrovirus present in known copy number in all human cells. The detection range of ERV-3 by real time PCR is from 10(6) to 10(1). The precision described, sensitivity and specificity of the assay indicate that the ERV-3 sequence is an accurate cell quantitation marker. The quantitative ERV-3 assay enables simple, fast, and reproducible detection and quantitation of the cell number. The assay can be used to determine the sample DNA conditions and also it can be used to adjust the quantitative DNA measurements of other target gene assays relative to the number of cell equivalents.