Green I-based Real-time PCR Assay Research Articles

Establishment of Duplex SYBR Green I-based Real-time PCR Assay for Simultaneous Detection of Duck Hepatitis A Virus-1 and Duck Astrovirus-3.

Duck viral hepatitis (DVH) mainly affects ducklings under 1 month of age, causes liver necrosis, enlargement, and hemorrhage, and is highly lethal, seriously jeopardizing the duck industry. The prevalence of duck hepatitis A virus (DHAV-1) and duck astrovirus type 3 (DAstV-3) is increasing, and coinfection is common. Moreover, the similar clinical characteristics of the DHAV-1 and DAstV-3 infections and the high frequency of coinfection make diagnosis difficult. In this study, to establish a method for the rapid, simultaneous detection of DHAV-1 and DAstV-3, two pairs of specific primers were designed according to their conserved gene regions. An SYBR® Green I-based qPCR assay was successfully established that can quickly and differentially detect the two viruses. Moreover, the assay is highly specific and does not show cross-reaction with other common viruses. The detection limit of the method is 7.34 × 101 copies/µl and 3.78 × 101 copies/µl for DHAV-1 and DAstV-3, respectively, indicating high sensitivity. A total of 34 clinical samples were tested using the established method; the positive rates for DHAV-1 and DAstV-3 were 14.71% and 8.82%, respectively, and that for coinfection was 2.94% (1/34), which was better than that obtained with conventional PCR. In summary, the SYBR Green I-based qPCR assay established in this study has high specificity, good sensitivity and accuracy, high feasibility, and is rapid. Thus, it can be a powerful tool for the coinfection detection of DHAV-1 and DAstV-3 and for future epidemiologic studies.

Duplex SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus and canine astrovirus

A duplex SYBR Green I-based real-time PCR assay was established for the simultaneous detection of canine kobuvirus (CaKoV) and canine astrovirus (CaAstV). This assay can easily distinguish the two viruses according to their different melting temperatures (Tm) of 80 °C for CaKoV and 86.5 °C for CaAstV; other canine enteroviruses used as controls showed no specific melting peaks. The detection limit of this assay was determined to be 101 copies/μL for both viruses. This method exhibited high repeatability and reproducibility, with a coefficient of variation less than 1.5 %. A total of 48 fecal samples were collected for clinical testing by real-time PCR and confirmed by sequencing. Real-time PCR assay showed a 10.4 % CaKoV-positive rate and a 4.2 % CaAstV-positive rate, and the positive rate of co-infection of the two viruses was 2.1 %, which was consistent with the sequencing results. This assay has many advantages over conventional PCR: it is rapid, sensitive, specific, and reliable for detecting these two viruses in one sample, and it can be used as a tool to detect CaKoV and CaAstV infection or co-infection in clinical settings.

Development of an SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus

Canine kobuvirus (CaKoV) is a causative agent of gastroenteritis in dogs. Rapid detection of CaKoV is important for preventing and controlling this condition. In this study, an SYBR Green I-based quantitative real-time PCR assay was established for CaKoV detection. Specific primers targeting a highly conserved region of the CaKoV 3D gene were developed. After optimization, the method detected a minimum of 1 × 101 copies/μL with high specificity, stability, and repeatability. Moreover, the entire process only required approximately 1.5 h for completion. Our results were supported by those obtained for clinical samples, in which our developed method was successfully applied. The newly established real-time PCR is a rapid, sensitive, specific, and repeatable method for the quantitative detection of CaKoV and can, therefore, be used in epidemiological studies.

Development of a SYBR Green I real-time PCR for detection and quantitation of orthopoxvirus by using Ectromelia virus

Ectromelia virus (ECTV) is the causative agent of mousepox, which has devastating effects in laboratory-mouse colonies and causes economic loss in biomedical research. More importantly, ECTV has been extensively used as an excellent model for studies of the pathogenesis and immunobiology of human smallpox. A rapid and sensitive SYBR Green I-based real-time PCR assay was developed and used for the detection and quantitation of orthopoxvirus by using ECTV in this study. Primers targeted to the highly conserved region of major core protein P4b gene of orthopoxvirus were designed and the standard plasmid was constructed. This assay was able to detect a minimum of 10 copies of standard DNA and 5 TCID50 units of ECTV. In addition, no cross-reactions were observed with two DNA viruses, such as herpes simplex virus and swine pseudorabies virus, and one RNA virus, vesicular stomatitis virus. Furthermore, intra- and inter-assay variability data showed that this method had a highly reproducibility and reliability. Moreover, the current assay was faster and had a higher sensitivity for detection of ECTV genomic DNA in cell cultured and clinical test samples. Therefore, the high sensitivity and reproducibility of this SYBR Green real-time PCR approach is a more effective method than the conventional PCR for ECTV diagnosis and quantitation.

A real-time PCR approach based on SPF10 primers and the INNO-LiPA HPV genotyping extra assay for the detection and typing of human papillomavirus.

A highly sensitive SPF10 real-time PCR was developed to achieve simultaneous amplification and detection of the human papillomavirus (HPV) target. That way, LiPA analysis of the HPV-negative samples can be avoided, reducing workload and cost. Here, we describe in detail a SYBR Green I-based real-time PCR assay based on SPF10 primers using the LightCycler(®) 480 system to generate and detect HPV amplicons, which are compatible with the LiPA assay.

Detection of intestinal bifidobacteria and lactobacilli in patients with Hirschsprung’s disease associated enterocolitis

The etiology of Hirschsprung's disease associated enterocolitis (HAEC) is unknown. Previous investigations have suggested that several factors such as dilation of proximal bowel, changes in colonic mucosal defence, and overgrowth of toxigenic bacteria may be related with it. This study was to quantify bifidobacteria and lactobacilli in the feces of Hirschsprung's disease (HD) patients with or without enterocolitis and those of normal children. Fresh stool specimens were collected at the first three days of the admission from 30 HD patients (aged 2 weeks to 2 years) and 15 healthy age-matched non-HD patients in the morning once a day for at least three days. All of them have not been given probiotics or antibiotics at least 7 days before stool collection. Hematoxylin-eosin and acetylcholinesterase histochemical staining on rectal biopsies of patients with HD confirmed the diagnosis of HD in all 30 patients. The 30 HD patients were divided into two groups based on the clinical history of enterocolitis: the HAEC group (n=10) and HD group (n=20). Fecal bifidobacteria and lactobacilli were consecutively quantified by SYBR Green I-based real-time PCR assay. Data were analyzed using SAS v. 12.6 for Windows. All tests were two-tailed, and P values <0.05 were considered statistically significant. The mean levels of bifidobacteria were 7.35+/-0.59, 8.16+/-1.17, and 8.35+/-0.74 in the HAEC, HD and control groups, respectively. The bifidobacteria colonization levels were lower in the HAEC group than in the HD and control groups (P<0.05, P<0.001 respectively). The mean level of lactobacilli in the HAEC (5.51+/-0.65) and HD groups (5.87+/-0.78) was significantly lower than that in the control group (6.39+/-0.56) (P<0.05). But there was no difference in log numbers of lactobacilli between HAEC and HD groups (P>0.05). The scarcity of bifidobacteria and lactobacilli in HAEC patients may result in a decrease in epithelial barrier function and be a predisposing factor in the development of HAEC. This decline suggests that treatment with probiotics or prebiotics may be beneficial in these individuals. Further research will focus on whether probiotics can decrease the incidence of HAEC.

Application of the rpoS Gene for Species-Specific Detection of Vibrio vulnificus by Real-Time PCR

Vibrio vulnificus is a causative agent of serious diseases in humans, resulting from the contact of wound with seawater or consumption of raw seafood. Several studies aimed at detecting V. vulnificus have targeted vvh as a representative virulence toxin gene belonging to the bacterium. In this study, we targeted the rpoS gene, a general stress regulator, to detect V. vulnificus. PCR specificity was identified by amplification of 8 V. vulnificus templates and by the loss of a PCR product with 36 non-V. vulnificus strains. The PCR assay had the 273-bp fragment and the sensitivity of 10 pg DNA from V. vulnificus. SYBR Green I-based real-time PCR assay targeting the rpoS gene showed a melting temperature of approximately 84 degrees for the V. vulnificus strains. The minimum level of detection by real-time PCR was 2 pg of purified genomic DNA, or 103 V. vulnificus cells from pure cultured broth and 103 cells in 1 g of oyster tissue homogenates. These data indicate that real-time PCR is a sensitive, species-specific, and rapid method for detecting this bacterium, using the rpoS gene in pure cultures and in infected oyster tissues.

Development of SYBR Green I-based real-time PCR assay for detection of drug resistance mutations in cytomegalovirus

Ganciclovir (GCV) is an antiviral drug that is used to treat cytomegalovirus (CMV) infection. However, long-term monotherapy does not commonly result in complete suppression of viral replication and is associated with the emergence of resistant mutants. In this study, a method for detecting CMV resistance mutations was carried out by real-time amplification refractory mutation system PCR (real-time ARMS PCR) using SYBR Green I fluorescent dye. Three recombinant plasmids were constructed by overlapping extension PCR to be used as standard mutation or wild-type models. Four pairs of primers were used to amplify the approximately 150 bp of the UL97 gene spanning codon 460, where mutations associated with resistance to GCV invariably occur. As little as 20% mutants DNA in 10 7 copies/ml mixture DNA were detected. Though this approach was not more sensitive than PCR-restriction fragment length polymorphism (RFLP) for the detection of the presence of mixtures, it was a high-throughput and automation method, and the specific mutation type can be deduced by the real-time ARMS PCR data. Overall, this study has demonstrated an approach that could be a sensitive and rapid method for the detection of GCV resistance-associated mutation in CMV.

Development of intestinal bifidobacteria and lactobacilli in breast-fed neonates

Neonates are subject to numerous factors that affect normal intestinal colonization. This study was to quantify bifidobacteria and lactobacilli in the faeces of breast-fed neonates using quantitative real-time PCR assay, and to investigate the effects of different delivery on the development of bifidobacteria or lactobacilli. The faecal bifidobacteria and lactobacilli of 40 healthy breast-fed neonates were studied prospectively. Twenty infants were vaginally delivered (VD), and 20 by caesarean delivery (CD) with prophylactically 4 g intravenous cefradine administered to their mothers three times. The faecal bifidobacteria and lactobacilli of neonates were consecutively quantified by SYBR Green I-based real-time PCR assay in the first 7 days after birth. The mean levels of bifidobacteria increased from 5.1 to 9.3 in the VD group vs from less than 4.6 to 8.7 in the CD group. The bifidobacteria colonization levels in six samples in the CD group were lower than the limit of detection on day 2. The mean levels of bifidobacteria in the VD group were significantly higher than in the CD group (p<0.05). The mean levels of lactobacilli increased from 4.9 to 7.2 in the VD group vs from 4.9 to 6.9 in the CD group. There was no statistical difference between two groups during the first week (p>0.05). The development of bifidobacteria and lactobacilli showed significant interindividual differences in all infants studied. Primary intestinal bifidobacteria in neonates by caesarean may be disturbed more significantly than lactobacilli.

Rapid diagnosis of human brucellosis by SYBR Green I-based real-time PCR assay and melting curve analysis in serum samples

The aim of this study was to develop a LightCycler-based real-time PCR (LC-PCR) assay and to evaluate its diagnostic use for the detection of Brucella DNA in serum samples. Following amplification of a 223-bp gene sequence encoding an immunogenetic membrane protein (BCSP31) specific for the Brucella genus, melting curve and DNA sequencing analysis was performed to verify the specificity of the PCR products. The intra- and inter-assay variation coefficients were 1.3% and 6.4%, respectively, and the detection limit was 5 fg of Brucella DNA (one genome equivalent). After optimisation of the PCR assay conditions, a standard curve was obtained with a linear range (correlation coefficient=0.99) over seven orders of magnitude from 10(7) to 10 fg of Brucella DNA. The LC-PCR assay was found to be 91.9% sensitive and 95.4% specific when tested with 65 negative control samples and 62 serum samples from 60 consecutive patients with active brucellosis. The assay is reproducible, easily standardised, minimises the risk of infection in laboratory workers, and has a total processing time of <2 h. It could therefore form a promising and practical approach for the rapid diagnosis of human brucellosis.