Pg Of Viral RNA Research Articles

Optimization of a direct real-time quantitative reverse transcription polymerase reaction (DRT-qPCR) assay for the detection of grapevine rupestris stem-pitting associated viruses (GRSPaV) in grapevine

A single step Direct real-time quantitative reverse transcription quantitative polymerase chain reaction (DRT-qPCR) was applied and optimized for the detection of Grapevine rupestris stem-pitting associated virus (GRSPaV) in grapevine. A probe and primer set were designed from conserved genomic regions from eight GRSPaV accessions from GenBank and used with the Direct Plant Extraction Buffer (DiPEB) system in place of total nucleic acid extraction using commercial kits to identify 14 grapevine accessions and field grapevine isolates for the presence of GRSPaV. Optimal detection of GRSPaV was obtained using foliar tissue macerated first in ELISA extraction buffer that was further diluted in DiPEB buffer (1:9 v/v). Middle-aged grape leaves on young canes gave acceptably low Cq (quantification cycle) values, with no significant differences detected between bisected half leaves, refrigerated and frozen leaves, and frozen leaf macerates made in ELISA buffer. Cq values of macerates derived from cambial tissue were comparable to those of leaf tissue macerates. The DRT-qPCR was shown to be a reproducible, specific test capable of detection of as little as 4.59 pg of viral RNA. This is the first study to use this simplified method for the detection of viruses that infect grapevine. Because this system does not require the use of a commercial nucleic acid extraction kit, it provides savings in cost and time allowing higher throughput testing.

Development and Application of a RT-NestPCR Assay for Differential Detection of C-Strain and Wild-Type Viruses of Classical Swine Fever Virus

<p>Due to the urgent need of differentiation of infected from vaccinated animals in control and eradication of classical swine fever (CSF) and the shortcomings of current differential diagnostic tools, this study is aiming to establish a RT-nestPCR assay for differential detection of wild-type viruses and lapinized Chinese vaccine strain (C-strain) of classical swine fever virus (CSFV) of high sensitivity. Two pairs of CSFV-specific primers were designed in the conservative regions of NS5B (a non-structural protein encoded by the CSFV genome, which performs the RNA dependent RNA polymerase activity) and 3? un-translated regions (3?-UTR) to encompass the T-rich insertion uniquely existing in the 3?-UTR of C-strain genome. Thus the amplification fragment of C-strain is longer than that of the wild-type viruses for it contains the T-rich insertion region. Two pairs of primers were used in combination and the wild-type viruses and C-strain of CSFV could be detected and accurately distinguished with a high sensitivity through super fine resolution (SFR) argarose gel electrophoresis that displays the different lengths of the amplicons. The detection limit of the C-strain and Shimen strain were respectively 4.5×10<sup>-2 </sup>pg and 3.2×10<sup>-2 </sup>pg of viral RNA. The results of the specificity test showed that this method can detect different strains of CSFV without amplifying other non-CSFV pathogens. The results of the detection of 400 clinical samples indicated that 16 samples were CSFV positive in total; in which 4 samples were C-Strain positive and 12 were wild-type CSFV positive. The total CSFV positive rate was 4%. The detection results of the 14 batches of C-Strain vaccines showed that all samples displayed bands of C-Strain amplicons in the SFR argarose gel electrophoresis and all vaccines were free of wild-type virus contamination. In conclusion, the RT-nestPCR assay established in the present study could supply a sensitive and specific test method for distinguishing wild-type CSFV infected animals from those vaccinated with C-strain vaccines in the field.</p>

Genome-based detection methods of Macrobrachium rosenbergii nodavirus, a pathogen of the giant freshwater prawn, Macrobrachium rosenbergii dot-blot, in situ hybridization and RT-PCR.

The availability of specific and rapid detection methods is essential for monitoring the health status of farmed species, particularly in viral diseases as in this case early diagnosis is a critical factor in containing disease outbreaks. Three complementary genome-based methods were developed for the detection of Macrobrachium rosenbergii nodavirus (MrNV), i.e. dot-blot hybridization, in situ hybridization and reverse transcriptase-polymerase chain reaction (RT-PCR). Detection limits were established for dot-blot hybridization and RT-PCR and are c. 7 fg and 8 pg of viral RNA, respectively. In situ hybridization indicated that infection was confined to the striated muscle tissue. As a result of its sensitivity, RT-PCR can be used for in-depth investigations to examine the extent of the viral infection and establish the onset of infection in hatcheries. The application of RT-PCR on samples collected from prawn farms in China showed the possible use of this method in routine health monitoring.

One-step RT-PCR for the detection of infectious bursal disease virus in clinical samples.

A single-tube, non-interrupted, one-step RT-PCR has been standardized to amplify the hypervariable region of the VP2 gene sequence of infectious bursal disease virus (IBDV). The technique standardized on purified viral RNA was successfully applied to the detection of the virus directly in clinical samples. The amplified products were confirmed to be IBDV specific by their size in ethidium bromide-stained agarose gel, nested PCR and restriction enzyme digestion. Digestion of the amplicons with StyI restriction enzyme also differentiated classical virus from six very virulent field isolates. The sensitivity of the one-step RT-PCR was found to be 0.2 pg of viral RNA.

A rapid method for detection and identification of flaviviruses by polymerase chain reaction and nucleic acid hybridization.

A polymerase chain reaction (PCR) technique was developed and evaluated for the detection of flaviviruses. A set of sense and antisense oligomeric DNA primers were constructed from nucleotide sequences of the conserved region of the genome of several different flaviviruses. Virus specific complementary DNA (cDNA) was prepared by reverse transcription of total RNA extracted from infected cell cultures. Amplified cDNA was identified by nucleic acid hybridization with specific oligomeric internal probes. Various conditions, such as number of cycles and annealing temperature were examined to optimize the detection of viral RNAs from infected cell cultures. Slot blot hybridization with a radioactive probe was used to evaluate the sensitivity of PCR amplification. The PCR amplified RNA sequences of dengue 2 (DEN-2), West Nile (WN), St. Louis encephalitis (SLE) and Kunjin (KUN) virus and detected 0.1 to 1 pg of viral RNA. Japanese encephalitis (JE), Yellow Fever virus (YF), DEN-1, 3, and 4 viruses were not amplified. The more frequent occurrence of mismatches in the 3' primer binding site may explain the failure to amplify cDNA of these viruses.

Detection of West Nile Virus by the Polymerase Chain Reaction and Analysis of Nucleotide Sequence Variation

A polymerase chain reaction (PCR) assay was developed to rapidly detect and identify West Nile (WN) virus. The RNA from seven isolates of WN virus from six countries and four other flaviviruses (Kunjin, Japanese encephalitis, St. Louis encephalitis, and yellow fever viruses) was reverse-transcribed (RT) and amplified by PCR. The nucleotide sequences of the amplified products were determined by a rapid, automated DNA sequencing method. The WN virus RT/PCR assay detected the target gene segment of sequencing method. The WN virus RT/PCR assay detected the target gene segment of isolates from both the African-Middle Eastern group and the Indian group with a sensitivity of approximately 0.05 pg of viral RNA. Kunjin virus was the only other flavivirus tested that produced a band of the appropriate size. Five of seven WN virus isolates showed 92-98% homology in the nucleotide sequence of their PCR products. The sequence of one isolate was virtually identical to the published sequence of the Nigerian isolate (99.5% homology). No correlation was established between the degree of nucleotide homology, geographic location, time of isolation, or source of the isolates.

Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization.

SummaryGenomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned inE. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes, were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabelling with32P and enzymatic labelling through covalent linkage to peroxidase and chemiluminescence detection. The radioactive probe 174 detected as little as 1 to 3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the familyCoronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in faecal samples using enzymatic probe was compared with conventional diagnostic methods.

A DOT HYBRIDISATION ASSAY FOR DETECTION OF ROTAVIRUS

A "dot" hybridisation technique for the detection of rotavirus in stools and other biological materials is described. The assay is based on the in-situ hybridisation of labelled single-stranded RNA probes, obtained by in-vitro transcription of rotavirus particles, to heat-denatured rotavirus RNA immobilised on nitrocellulose membranes. The method is highly specific and allows for the detection of as little as 8 pg of viral RNA. Its use for the detection of rotavirus in stool suspensions and rectal swabs obtained from children with diarrhoea may facilitate epidemiological studies of rotavirus gastroenteritis.