Comparison of techniques for extracting viral RNA from isolation-negative serum for dengue diagnosis by the polymerase chain reaction

Dengue virus RNA purification from human plasma: a comparison of two techniques

Dengue virus RNA purification from human plasma is useful for research and clinical purposes. Dengue is endemic in the Espirito Santo State, Brazil, and it is progressively becoming a hard-to-control public health problem. Dengue virus types 1, 2 and 3 are currently found in Brazilian territory, and recently Dengue virus type 4 has been reported to enter Brazilian borders. This virus spreads rapidly during epidemic outbreaks, and thousands of patients are infected annually, with an underestimated number of deaths in consequence of hemorrhagic Dengue. Because this disease affects mainly developing countries, it is imperative that a robust, rapid and low cost method for viral nucleic acid purification is found. In this manuscript we compare two RNA extraction methods from serum/plasma of patients with clinical diagnosis of dengue. The QIAamp(®) UltraSens Virus Kit (Qiagen Inc., Valencia, USA) and the less expensive Chomczynski-Sacchi method were used to analyze a total of 47 samples. After nucleic acid purification, reverse transcription and polymerase chain reaction amplification with dengue virus type 2 specific primers were performed. This subtype is the most prevalent in our geographical location. Thirty-four samples were positive when RNA was extracted by the Chomczynski-Sacchi technique, whereas only 27 of these were positive when the QIAamp(®) UltraSens Virus Kit was used. These results favor the utilization of the more affordable technique for the purification of viral RNA, which is especially important for developing countries.

Evaluation of pre-analytical variables in the quantification of dengue virus by real-time polymerase chain reaction

An accurate molecular diagnosis for viral pathogens is highly dependent on pre-analytical procedures. The efficiencies of two viral RNA extraction methods (liquid phase partition and silica-based adsorption chromatography) and the effects of handling and storage on the stability of RNA isolated from dengue virus (DENV) were studied. Viral RNA extracted from spiked sera or clinical samples characterized with DENV infection were quantified by TaqMan real-time PCR. The presence of high serum proteins severely affected the recovery of DENV RNA by the liquid phase partition, but not the silica-based method. The recovery with Trizol liquid phase partition method was significantly improved by a concomitant addition of a co-precipitant and the reduction of sera proteins, resulting in recoveries similar to that of the silica-based methods. Repeated freeze-thaw cycles did not affect the recovery of viral RNA. While intact DENV was found to be stable in serum for up to 2 hour at 25 degrees C, recovery of viral RNA from sera stored in the lysis/binding buffer was stable for up to 5 days. These data indicate that the choice of viral RNA extraction methods, the conditions for handling, and storing of clinical sera critically affect the quantification of viral nucleic acid from clinical samples. This will impact the accuracy and reproducibility of DENV diagnosis by PCR-based assays.

Characterization of Listeria monocytogenes protein Lmo0327 with murein hydrolase activity

Listeria monocytogenes is an ubiquitous gram-positive, opportunistic food-borne human and animal pathogen. To date, five L. monocytogenes autolysins have been characterized: p60, p45, Ami, MurA and Auto and the preliminary results of our studies show that FlaA, a flagellar protein of L. monocytogenes, also has murein-degrading activity. In this study, a gene coding a 144 kDa protein (Lmo0327) with murein hydrolase activity was identified from a lambda Zap expression library of L. monocytogenes EGD genomic DNA, using a direct screening protocol involving the plating of infected Escherichia coli XL1-blue MRF' cells onto medium containing Bacillus subtilis murein, a substrate for autolytic proteins. Protein Lmo0327 has a signal sequence, a N-terminal LRR domain and a C-terminal wall-anchoring LPXTG motif. In order to examine the roles of this enzyme and the putative transcription regulator coded by gene lmo0326 located upstream of lmo0327, both structural genes were insertionally inactivated by site-specific integration of a temperature-sensitive plasmid. We show that Lmo0327 is a surface protein covalently linked to murein and that the putative transcription regulator Lmo0326 can be assumed to positively regulate the expression of gene lmo0327. The enzyme, which we have shown to have murein-hydrolysing activity, plays a role in cell separation and murein turnover.

Duplex reverse transcription-PCR followed by nested PCR assays for detection and identification of Brazilian alphaviruses and flaviviruses

A new approach was developed for the rapid detection and identification of Brazilian alphaviruses and flaviviruses. The methodology involves the genus-specific detection of Alphavirus and Flavivirus by a duplex reverse transcription-PCR (D-RT-PCR), followed by multiplex nested PCR (M-N-PCR) or nested PCR (N-PCR) assays for species-specific identification. By this protocol, 25 arboviruses were specifically detected and identified. Detection levels between 10(1.3) and 10(3.5) 50% tissue culture infective doses (TCID(50))/ml of Flavivirus and Alphavirus strains were achieved by D-RT-PCR, and levels of <1 TCID(50)/ml were achieved by M-N-PCR assays. To assess the suitability and clinical application of this methodology, a total of 101 human or animal stored samples were analyzed. Results obtained suggest that this technique could be applied as a rapid diagnostic tool in clinical samples in which arbovirus infection is suspected and differential diagnosis is required, avoiding the need to test specimens by separate PCR methods.

Detection of dengue viruses in field-caught Aedes aegypti (Diptera: Culicidae) in Maracay, Aragua state, Venezuela by type-specific polymerase chain reaction

Virological surveillance of dengue viruses in Aedes aegypti populations constitutes a powerful tool for early prediction of dengue outbreaks. We have standardized a protocol for viral RNA extraction from individual and pools of mosquitoes that permits a sensitive detection of dengue virus without RNA degradation or PCR inhibition when we apply a semi-nested RT-PCR. The limit of detection for each dengue serotype was 0.1 PFU. In a prospective field study conducted from November 2000 to December 2001, adult female A. aegypti mosquitoes from several municipalities with high dengue transmission in Maracay, Aragua State, Venezuela were collected and screened for dengue viruses using RT-PCR. We analyzed a total of 296 A. aegypti pools (1,632 mosquitoes); of these, 154 pools (469 mosquitoes) were collected from houses with persons with clinical diagnosis of dengue (dengue houses), and 142 pools (1,163 mosquitoes) from adjacent residences (neighbour houses). From the dengue houses, eight mosquito pools (5.2%) were positive for DENV-1 (0.7%), DENV-3 (3.2%) and DENV-4 (1.3%) viruses. From the neighbour houses, 18 mosquito pools (12.7%) were positive for DENV-3 (12%) and DENV-4 (0.7%) viruses. From these 26 RT-PCR positive mosquito pools (containing 1-25 mosquitoes each), 22 pools (84.6%) were positive for DENV-3. The most prevalent serotype in the 2001 dengue outbreak was also DENV-3. The minimum infection rate in both A. aegypti collections, from dengue houses and neighbour houses was 17 and 15 per 1,000, respectively. The relevance of these results for dengue surveillance is discussed.

One-Step RT-PCR protocols improve the rate of dengue diagnosis compared to Two-Step RT-PCR approaches

Dengue is the most important arboviral disease transmitted to humans. In our laboratory, we have been working on the standardization of the polymerase chain reaction (PCR) diagnosis of this disease. In this work, we compared five commercial kits regularly used on reverse-transcription polymerase chain reaction (RT-PCR) protocols: two Two-Step kits (SuperScript II RT/Super Mix kit and reverse transcription system/Taq DNA polymerase) and three One-Step kits (ready-to-go RT-PCR Beads kit, QIAGEN One-Step RT-PCR kit, and AcessQuick RT-PCR system). Thirty-one serum samples of patients with clinical diagnosis of dengue fever (DF) were analyzed by RT-PCR and serology. RNA extraction was done with the QIAamp Viral RNA kit, and cDNA synthesis and PCR done according to the manufacturer's protocol for the five kits. Out of the 31 serum samples collected from patients suspected of having dengue, 27 were IgM-positive, confirming the dengue diagnosis. Out of those, 24 were positive by the ready-to-go RT-PCR Beads kit, 25 were positive by AcessQuick RT-PCR system and 27 were positive by QIAGEN One-Step RT-PCR kit. On the other hand, only six samples were positive by the SuperScript II RT/Super Mix kits and 10 were positive by reverse transcription system/Taq DNA polymerase kit. The best performance observed with the One-Step kits was confirmed in spiked samples with known quantities of dengue-1 virus since they detected up 1 x 10(2) PFU/ml, while the most sensitive Two-Step kit detected up 1 x 10(4) PFU/ml. These data show that One-Step RT-PCR kits yielded a higher rate of dengue virus detection than the Two-Step kits and correlated well with the serological diagnosis.

Improved detection of dengue-1 virus from IgM-positive serum samples using C6/36 cell cultures in association with RT-PCR

Dengue is the most important arboviral disease in the world, and its diagnosis is primarily made by serology. Virus isolation has been successful mainly in clinical samples obtained during the acute phase of illness, and is carried out through inoculation of clinical samples into C6/36 cell monolayers followed by the detection of infection by indirect immunofluorescence assay (IFA). We compared the efficiency of RT-PCR and IFA in the detection of dengue-1 virus after inoculation of C6/36 cells with samples obtained in the convalescent period of dengue infection. Out of 75 IgM-positive samples inoculated into C6/36 cells, 2 were positive by IFA while 17 were positive by RT-PCR. The 2 IFA-positive samples were collected during the acute phase of the illness; 17 positive samples were found by RT-PCR, including the 2 detected by IFA. For both methods, we also investigated the time necessary for viral detection using a fixed dose of 1 x 10(4) viruses/ml. RT-PCR and IFA detected the dengue virus 1 and 4 days after virus inoculation, respectively. The results obtained here indicate that RT-PCR is the most sensitive method in the detection of dengue viruses using C6/36 cells for viral isolation.

Detecting Rice stripe virus (RSV) in the small brown planthopper (Laodelphax striatellus) with high specificity by RT-PCR

Rice stripe disease, caused by Rice stripe virus (RSV), may lead to severe or even crippling losses in many rice-cultured countries and regions. As the most important vector of RSV, the small brown planthopper (SBPH) (Laodelphax striatellus) is largely responsible for the epidemic phase of the disease. Therefore, a rapid identification of RSV in the SBPH is of a great need for disease forecasting. A reverse transcription polymerase chain reaction (RT-PCR) assay is described to amplify a RSV gene in individual L. striatellus. By using primers matched to the viral RNA dependent RNA polymerase gene in RNA1, a 445 bp product was detected in viruliferous SBPHs. Meanwhile, the PCR products produced by the SBPH actin primers constructed across the boundary of an intron and an exon were used as RNA specific positive control for each stage of the experiment to ensure the validity of the negative results. Duplex RT-PCR conditions were established for the simultaneous detection of RSV and actin. This approach can be used for the early detection of RSV in L. striatellus and the subsequent rice stripe disease forecasting.

Development of a RT-nested PCR test detecting pigeon Paramyxovirus-1 directly from organs of infected animals

A RT-nested PCR that amplifies part of the conserved nucleoprotein gene of avian Paramyxovirus type 1 is described. The technique allowed the detection of pigeon Paramyxovirus type 1 (pPMV-1) virus directly from a wide range of infected chicken and pigeon organs, and should be able to detect typical Newcastle disease viruses too. Compared with the reference method, the developed RT-nested PCR was found more sensitive, as it was able to detect virus genome in infected pigeon organs at late stage of infection, when virus isolation failed. Such a molecular technique represents an alternative method of diagnosis for research purposes on pPMV-1 variants, for example to study pathogenesis aspects of the infection or to assess the efficacy of vaccines.