No abstract available.
Real-Time Polymerase Chain Reaction*

No abstract available.
Real-Time Polymerase Chain Reaction*

To identify herpesviral virions secreted by viral replication, we have established the nuclease-resistance assay (NRA) as a comparative analysis to other conventional assays, including electron microscopy (EM). For this study, we used an efficient experimental in vitro infection model for Alcelaphine herpesvirus 1 (AlHV-1), a gamma herpesvirus, to propagate the virus. The NRA could identify extracellular, cell-free, enveloped virions in the supernatants after 24 hours post inoculation (h.p.i.) of AlHV-1. The results of EM observation were correlated with those of NRA. Mature virions were observed in the clarified, concentrated supernatants from 24 h.p.i. by EM. These results show that sensitivity of the NRA is comparable with that of EM for the identification of mature enveloped virions, which directly presents evidence of herpesviral lytic replication. NRA allows us to differentiate the virus from other member of Herpesviridae, and has extended the possibility of analysis for quantification of shedding viruses when used in conjunction with real-time polymerase chain reaction (PCR).
Herpesviridae ; Microscopy, Electron* ; Real-Time Polymerase Chain Reaction ; Virion*

BACKGROUND: We comparatively evaluated the performance of the conventional COBAS Amplicor HCV test v2.0 (CAM; Roche Molecular Systems, USA) and the newly developed COBAS AmpliPrep/COBAS TaqMan HCV test v2.0 (CAP/CTM; Roche Molecular Systems) for qualitative detection of hepatitis C virus (HCV) RNA in clinical samples. METHODS: Six hundred serum samples (100 HCV-positive, 500 HCV-negative, as determined by CAM) were selected and analysed using the new qualitative HCV RNA test, CAP/CTM qualitative test. Results were compared by confirmatory CAP/CTM quantitative test, which is a quantitative HCV RNA real-time polymerase chain reaction by Roche Molecular Systems, and anti-HCV test (Roche Diagnostics GmbH, Germany). Twenty-two additional serum samples, which gave a gray zone result by CAM, were selected for comparison. RESULTS: The two qualitative HCV RNA assays yielded concordant results for 586 of 600 tested samples (concordance rate, 97.7%; kappa coefficient, 0.92; 95% confidence interval [CI], 0.87 to 0.96; P<0.001). Upon re-testing by CAM, we found that the concordance rate increased to 98.2% (kappa coefficient, 0.93; 95% CI, 0.89 to 0.97; P<0.001). The additional 22 samples showing gray zone results for CAM were retested and were also tested by CAP/CTM. The results for 13 of these samples changed to negative and were now concordant with the CAP/CTM and confirmatory CAP/CTM quantitative results. For the remaining samples, the results were variable. For all the 22 samples, the results of the new CAP/CTM were in agreement with those obtained by confirmatory CAP/CTM quantitative test. CONCLUSIONS: The results of the two assays were in good agreement, with 97.7% concordance rate. However, CAP/CTM is more sensitive than CAM and showed no gray zone results. Therefore, it can be a more efficient and useful test for the qualitative detection of HCV RNA in clinical samples.
Hepacivirus* ; Hepatitis C* ; Hepatitis* ; Real-Time Polymerase Chain Reaction ; RNA

No abstract available.
Diagnosis* ; Real-Time Polymerase Chain Reaction* ; Tuberculosis, Pulmonary*

For our survey of the infection frequency and mixed infection of the viruses causing acute respiratory syndromes, we analyzed those viruses from acute respiratory patients in Seoul. Total 1,038 specimens of oropharyngeal swab were tested by the real-time polymerase chain reaction (PCR) kit (Kogenebiotech, Korea) from Jan. to Dec. in 2013. Virus detection rate causing acute respiratory infection was 46% (476/1,038). The most frequently isolated virus was only hRV (21.6%, 103/476), followed by only ADV (8.96%, 93/476), only IFV A (H3N2) (18.1%, 86/476), and only hCoV (7.8%, 37/476) etc. Most of acute respiratory viruses had severe fever. Infection frequency information and mixed infection status on respiratory viruses circulating in Seoul will be helpful for the management of acute respiratory infection and for epidemiological continuous studies.
Coinfection* ; Fever ; Humans ; Real-Time Polymerase Chain Reaction ; Seoul

BACKGROUND: Broth cultures are increasingly used to detect acid-fast bacilli (AFB). Rapid, simple and accurate methods for differentiation of Mycobacterium tuberculosis complex (MTBC) and nontuberculosis mycobacteria from broth cultures are needed. Immunochromatographic assays (ICTs) for identification of MTBC have been developed. METHODS: The abilities of the BD MGIT TBc Identification Test (Becton Dickinson, USA) and the SD Bioline TB Ag MPT64 (Standard Diagnostics, Korea) to detect MTBC were evaluated in 44 AFB-positive broth cultures. The results of 2 ICTs were compared to those of real-time PCR. RESULTS: The BD MGIT TBc Identification Test and the SD Bioline TB Ag MPT64 showed concordant results with real-time PCR by 100% and 97.7%, respectively. The sensitivity of the BD MGIT TBc Identification and the SD Bioline TB Ag MPT64 was 100% for both, and the specificities of those were 100% and 95.2%, respectively. CONCLUSIONS: Both ICTs are rapid methods for identification of MTBC from broth cultures, and the results of ICTs are in accord with those of real-time PCR.
Immunochromatography ; Mycobacterium ; Mycobacterium tuberculosis ; Real-Time Polymerase Chain Reaction

BACKGROUND: This study was conducted to clarify the frequency of the BRAF mutation in primary melanomas and its correlation with clinicopathologic parameters. METHODS: We analyzed the frequency of BRAF mutation in patients with primary cutaneous melanoma (n=58) or non-cutaneous one (n=27) by performing dual priming oligonucleotide-based multiplex real-time polymerase chain reaction to isolate and to purify the DNA from the formalin-fixed and paraffin-embedded tumors. RESULTS: The BRAF mutation was found in 17.2% (10/58) of patients with primary cutaneous melanoma and 11.1% (3/27) of those with non-cutaneous melanoma. The frequency of BRAF mutation was not correlated with any clinicopathologic parameters with the exception of the patient age. The frequency of the BRAF mutation was significantly higher in patients younger than 60 years as compared with those older than 60 years (p=0.005). CONCLUSIONS: Compared with previous reports, our results showed that the frequency of the BRAF mutation was relatively lower in patients with primary cutaneous melanoma. Besides, our results also showed that the frequency of the BRAF mutation had an inverse correlation with the age. Further studies are warranted to exclude methodological bias, to elucidate the difference in the frequency of the BRAF mutation from the previous reports from a Caucasian population and to provide an improved understanding of the molecular pathogenesis of malignant melanoma.
Bias (Epidemiology) ; DNA ; Humans ; Melanoma ; Real-Time Polymerase Chain Reaction

BACKGROUND: Polymerase chain reaction (PCR) methods from direct specimen are widely used for the rapid and accurate detection of mycobacteria infection. In this study, we evaluated two domestically developed detection kits for Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) using real-time PCR. METHODS: A total of 348 samples from patients with suspected tuberculosis were tested with real-time PCR over seven months. We performed real-time PCR using the recently developed Anyplex plus MTB/NTM Detection kit (Seegene) with the CFX 96TM Realtime PCR System (Bio-Rad Laboratories) and the conventional AdvanSure TB/NTM real-time PCR kit (LG Life Sciences) with the SLAN Real-time PCR detection system (LG Life Sciences) to evaluate their performance for detecting MTB and NTM. RESULTS: The two real-time PCR systems showed 96.8% concordance rate for MTB-positive, NTM-positive, and negative results. Based on culture results, the sensitivity and specificity for the detection of MTB using PCR were 71.0% and 94.9% for Anyplex plus, and 78.1% and 93.9% for AdvanSure, respectively. For the detection of NTM, the sensitivity and specificity were 33.3% and 98.4% for Anyplex plus, and 51.7% and 97.9% for AdvanSure. Both PCR systems showed high MTB positive results in bronchial washing and sputum samples. CONCLUSION: In detecting MTB and NTM, Anyplex plus MTB/NTM (Seegene) and AdvanSure TB/NTM real-time PCR (LG Life Sciences) showed high concordance rate with each other in all samples. Therefore both detection kits can be used as rapid and reliable detection tool for MTB.
Humans ; Mycobacterium tuberculosis* ; Nontuberculous Mycobacteria* ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Sputum ; Tuberculosis

All xenografts from pigs impose infection risk by porcine endogenous retrovirus (PERV). The purpose of this study was to investigate the env constructs with the comparison of the ratio of the competent form to the defective one of env in subtypes, PERV-A, PERV-B and PERV-C in different pig breeds. The results of PCR amplification of env represented that all env subtypes had more than two defective forms which cannot bind to host cells due to the absence of binding regions of env in miniature pigs, SNU and PWG, and farm pig breeds, Duroc, Yorkshire and Landrace. In addition, comparing the full sequences with the defective ones in three subtypes demonstrated that the present percentages of env sequences in defective PERV-A, PERV-B and PERV-C were approximately 50%, 38~45% and 4~11%, respectively, in SNU and PWG pigs whereas PERV-A and PERV-B occupied around 40 to 60% but PERV-C was not detected in farm pigs. Quantitative real-time PCR assays with primers and probes targeted to proline-rich region (PRR) of each env subtype were done to measure the copy numbers of each env subtype. When the reference was set with copy number of PERV-A, the ratio of those of PERV-B and PERV-C to the reference were 1.5 to 6.0 folds high in SNU and PWG pigs while 1.0 or less in farm pigs. These contradictory results of PERV-C constructs and copy numbers in SNU pigs suggests that many truncated or short defective sequences of PERV-C might be present in them.
Endogenous Retroviruses* ; Heterografts ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Swine* ; Transplantation, Heterologous