OBJECTIVETo develop an one-tube multiplex RT-PCR assay for simultaneous detection of six human coronaviruses (HCoVs).

METHODSGenbank sequences of six human coronaviruses, including HCoV-NL63, HCoV-229E, SARS-CoV, HCoV-OC43, MERS-CoV, and HCoV-HKU1, were included as reference sequences. Primers were designed based on multiple alignment of reference sequences, targeting the conserved regions of each species of HcoV. Virus strains and nucleic acid preserved in our lab were used as template in developing this automatic-electrophoresis-based one-tube multiplex RT-PCR assay. Detection limits and reproducibility were also evaluated with these templates. Samples with infection of other respiratory viruses preserved in our lab were used to evaluate specificity of this assay. Finally, we tested this assay with 140 clinical samples that were validated by real-time PCR in parallel.

RESULTSThis automatic-electrophoresis-based multiplex RT-PCR assay was able to detect six human coronaviruses simultaneously. All positive samples in this study were detected with at least one specific fragment of anticipated length (195, 304, 332, 378, 415, 442 bp) . No fragment was detected in negative controls. Detection limits of 1.0×10(1-1.0)×10(2) copies/µl were achieved in tests of single virus. No cross reaction was observed with other respiratory viruses. This multiplex RT-PCR assay showed the same sensitivity and specificity to that of individual real-time RT-PCR validated with clinical samples. Both methods detected 28 positive samples (20%) .

CONCLUSIONSSix HCoVs can be detected in one tube by this novel multiplex RT-PCR assay with high sensitivity and specificity.

An improved method for extracting high quality and quantity RNA from a jelly mushroom and a dimorphic fungus—Tremella fuciformis which is especially rich in polysaccharides, is described. RNA was extracted from T. fuciformis mycelium M1332 and its parental monokaryotic yeast-like cells Y13 and Y32. The A260/280 and A260/230 ratios were both approximately 2, and the RNA integrity number was larger than 8.9. The yields of RNA were between 108 and 213 µg/g fresh wt. Downstream molecular applications including reverse transcriptional PCR and quantitative real-time PCR were also performed. This protocol is reliable and may be widely applicable for total RNA extraction from other jelly mushrooms or filamentous fungi rich in polysaccharides.
Agaricales* ; Fungi ; Humans ; Methods* ; Mycelium ; Parents ; Polymerase Chain Reaction ; Polysaccharides* ; Real-Time Polymerase Chain Reaction ; RNA*

OBJECTIVETo establish a specific TaqMan-based Real-time PCR assay for the detection of hepatitis A virus in serum samples.

METHODSAccording to the references, primers-probe sets which were located in 5'-NCR, the most conservative part of HAV genome were designed and therefore we established a TaqMan real-time RT-PCR assay with great performance of specificity, sensitivity and reproducibility. And then it was used in the detection of HAV RNA in serum from HAV patients.

RESULTSThe HAV Real-time RT-PCR assay established in this study were able to detect HAV RNA and its detection limit ranged from 0.1CCID50/reaction to 0.01CCID50/reaction. When the detection of a same sample was repeated for three times, coefficients of varistion (CV) of intra- and inter-assay were calculated and they were all less than 2.0% and 2.6% respectively. Our data suggested that there were 5.18 x 10(2) - 4.93 x 10(7) RNA copies in 1 ml of the serum from acute HAV patients.

CONCLUSIONThe TaqMan-based Real-time PCR assay established in this study was specific and precise for the rapid detection of HAV RNA. It was applied successfully in the pathogen detection of clinical samples.

OBJECTIVETo validate and supplement the libraries of serial analysis of gene expression (SAGE) by the application of the real-time quantitative polymerase chain reaction PCR).

METHODSThe primers were designed based on the full sequences of the genes. Nine single matched tags, 6 multiple matched tags, 1 non-matched tag due to the update of the National Center for Biotechnology Information (NCBI) database, and 2 non-matched tags were selected to fulfill the validation of real-time PCR.

RESULTSThe genes were all specifically amplified by the primers pairs. The expressions of the single matched tags were identical to those of the SAGE libraries; however, the expressions of only 3 genes of the 6 multi-matched tags were identical to those of the SAGE libraries. The PCR data of the non-matched tag due to the update of the NCBI database were opposite to those of the SAGE libraries. The data did not support the significant difference of the non-matched gene of the SAGE libraries.

CONCLUSIONSReal-time PCR is a reliable tool for the validation of high through-put data such as SAGE. The reliability of data depends on the match of the tags of the SAGE libraries.

PURPOSE: Monitoring pneumococcal carriage rates is important. We developed and evaluated the accuracy of a real-time reverse transcription polymerase chain reaction (RT-PCR) protocol for the detection of Streptococcus pneumoniae. METHODS: In October 2014, 157 nasopharyngeal aspirates were collected from patients aged <18 years admitted to Chung-Ang University Hospital. We developed and evaluated a real-time PCR method for detecting S. pneumoniae by comparing culture findings with the results of the real-time PCR using genomic DNA (gDNA). Of 157 samples, 20 specimens were analyzed in order to compare the results of cultures, realtime PCR, and real-time RT-PCR. RESULTS: The concordance rate between culture findings and the results of real-time PCR was 0.922 (P <0.01, Fisher exact test). The 133 culture-negative samples were confirmed to be negative for S. pneumoniae using real-time PCR. Of the remaining 24 culture-positive samples, 21 were identified as S. pneumonia-positive using real-time PCR. The results of real-time RT-PCR and real-time PCR from 20 specimens were consistent with culture findings for all S. pneumoniae-positive samples except one. Culture and real-time RT-PCR required 26.5 and 4.5 hours to perform, respectively. CONCLUSIONS: This study established a real-time RT-PCR method for the detection of pneumococcal carriage in the nasopharynx. Real-time RT-PCR is an accurate, convenient, and time-saving method; therefore, it may be useful for collecting epidemiologic data regarding pneumococcal carriage in children.
Child* ; DNA ; Humans ; Methods ; Nasopharynx ; Pneumonia ; Polymerase Chain Reaction* ; Real-Time Polymerase Chain Reaction ; Reverse Transcription* ; RNA* ; Streptococcus pneumoniae

PURPOSE: The aim of this study was to evaluate the diagnostic value of a peptide nucleic acid (PNA)-mediated PCR clamping method for the detection of BRAFV600E mutations in fine needle aspiration cytology (FNAC). METHODS: One hundred sixty four patients underwent FNAC to evaluate BRAFV600E mutations between April 2011 and November 2011. Among them, forty-two patients were diagnosed with papillary thyroid carcinoma in a permanent pathologic specimen. A PNA-mediated PCR clamping method and a Dual-Priming Oligonucleotide (DPO)-based Real-time PCR method were used to detect the BRAFV600E mutation. We compared the result of mutation between the two methods. RESULTS: A BRAF mutation was found in 31 samples created by the PNA-mediated PCR clamping method, and in 28 samples in the DPO-based Real-time PCR method. The rate of BRAF mutation was 73.8% in association with the PNA-mediated PCR clamping method, and 66.7% in association with the DPO-based Real-time PCR method. There was no statistical differences between the two methods (P>0.05). CONCLUSION: The PNA-mediated PCR clamping method may be an alternative to the DPO-based Real-Time PCR method for detection of BRAF mutations in thyroid nodules.
Biopsy, Fine-Needle* ; Constriction* ; Humans ; Methods* ; Polymerase Chain Reaction* ; Real-Time Polymerase Chain Reaction ; Thyroid Neoplasms ; Thyroid Nodule

BACKGROUND/AIMS: The incidence and severity of Clostridium difficile infection (CDI) have increased worldwide, resulting in a need for rapid and accurate diagnostic methods. METHODS: A retrospective study was conducted to compare CDI diagnosis methods between January 2014 and December 2014. The stool samples, which were obtained in presumptive CDI patients, were compared for their diagnostic accuracy and rapidity, including real-time polymerase chain reaction (PCR) of toxin genes, C. difficile toxin assay, and culture for C. difficile. RESULTS: A total of 207 cases from 116 patients were enrolled in this study and 117 cases (56.5%) were diagnosed as having CDI. Among the 117 cases, the sensitivities of real-time PCR, C. difficile toxin assay, and culture for C. difficile were 87.2% (102 cases; 95% CI, 80.7%–92.8%), 48.7% (57 cases; 95% CI, 41.0%–59.8%), and 65.0% (76 cases; 95% CI, 60.2%–78.5%), respectively (P < 0.005). Notably, 34 cases (29.0%) were diagnosed with CDI by real-time PCR only. The time required to obtain results was 2.27 hours (136.62±82.51 minutes) for real-time PCR, 83.67 hours (5,020.66±3,816.38 minutes) for toxin assay, and 105.79 hours (6,347.68±3,331.46 minutes) for culture (P < 0.005), respectively. CONCLUSIONS: We confirmed that real-time PCR of toxin genes is the most effective diagnostic method for accurate and early diagnosis of CDI. It also helps to diagnose hypervirulent CDI, such as ribotype 027 infection.
Clostridium difficile ; Clostridium ; Diagnosis ; Early Diagnosis ; Humans ; Incidence ; Methods ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Retrospective Studies ; Ribotyping

The laboratory-based diagnosis of viral infection has been evolving over the years, to increase objectivity, accuracy, and sensitivity via the continuous development of various technologies. Cell culture, which is one of the methods used for the diagnosis of viral infection, is a “gold-standard” approach; however, it is time consuming and is associated with a high risk of contamination. To overcome these shortcomings, molecular biology methods, such as conventional polymerase chain reaction (cPCR), real-time PCR, and sequencing, have been used recently for virus diagnosis. Realtime PCR has higher accuracy and sensitivity compared with cPCR. Moreover, realtime PCR can quantify viral nucleic acids by confirming the amplification using the threshold cycle, which is the initial amplification point. Real-time PCR applications for the detection of various types of viruses in clinical settings should be based on the use of appropriate samples, nucleic acid extraction according to virus characteristics, and selection of diagnostic methods using sensitivity and specificity targets. In addition, the implementation of real-time PCR requires to evaluate the performance of the test protocol by measuring sensitivity, specificity, accuracy, and reproducibility. The verified real-time PCR method is an easy, fast, and accurate method for monitoring the diagnosis and treatment outcomes in a clinical setting. In this review, we summarize the characteristics of the typical diagnostic methods for viral infection, especially of the advanced real-time PCR method, to detect human pathogenic viruses.
Cell Culture Techniques ; Diagnosis* ; Humans ; Methods ; Molecular Biology ; Nucleic Acids ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction* ; Sensitivity and Specificity

Agrobacterium tumefaciens-mediated transformation (ATMT), as a simple and versatile method, achieves successful transformation in the yeast-like cells (YLCs) of Tremella fuciformis with lower efficiency. Establishment of a more efficient transformation system of YLCs is important for functional genomics research and biotechnological application. In this study, an enzymolysis-assisted ATMT method was developed. The degradation degree of YLCs depends on the concentration and digestion time of Lywallzyme. Lower concentration (≤0.1%) of Lywallzyme was capable of formation of limited wounds on the surface of YLCs and has less influence on their growth. In addition, there is no significant difference of YLCs growth among groups treated with 0.1% Lywallzyme for different time. The binary vector pGEH under the control of T. fuciformis glyceraldehyde-3-phosphate dehydrogenase gene (gpd) promoter was utilized to transform the enzymolytic wounded YLCs with different concentrations and digestion time. The results of PCR, Southern blot, quantitative real-time PCR (qRT-PCR) and fluorescence microscopy revealed that the T-DNA was integrated into the YLCs genome, suggesting an efficient enzymolysis-assisted ATMT method of YLCs was established. The highest transformation frequency reached 1200 transformants per 106 YLCs by 0.05% (w/v) Lywallzyme digestion for 15 min, and the transformants were genetically stable. Compared with the mechanical wounding methods, enzymolytic wounding is thought to be a tender, safer and more effective method.
Agrobacterium ; Blotting, Southern ; Digestion ; Genome ; Genomics ; Methods ; Microscopy, Fluorescence ; Oxidoreductases ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Wounds and Injuries

BACKGROUND: Mutations in the gene encoding transforming growth factor-beta induced (TGFBI) are associated with corneal dystrophies. We evaluated the diagnostic performance of the GENEDIA Avellino corneal dystrophy (ACD) mutation detection kit and GENEDIA corneal dystrophy screening master mix (Green Cross Medical Science Co., Korea) by comparing it with an in-house sequencing method. METHODS: The study group consisted of 40 patients with Avellino corneal dystrophy (ACD) and 40 patients suspected to suffer from ACD; 40 healthy individuals were used as the control. All samples used for this study were previously obtained. All results obtained using the kit were evaluated for sensitivity, specificity, and detection limit. RESULTS: The sensitivity of the GENEDIA ACD kit was 100.0% with a positive mean+/-2SD Ct (cycle threshold) value of 25.87+/-1.24 and an excellent coefficient of variation value of 0.02 in ACD group. All normal control samples were negative, indicating a specificity of 100% for the GENEDIA kit. The detection limit was set at a DNA concentration of >0.2 ng/microL. Direct sequencing results obtained using the GENEDIA master mix and the in-house method agreed for all 20 ACD samples. Additional R555W mutation detected in four ACD-suspected samples were suggestive of the diagnosis of granular corneal dystrophy type I. CONCLUSIONS: The GENEDIA ACD detection kit and master mix showed acceptable results, demonstrating high sensitivity and specificity, and may be considered for clinical application. Furthermore, the GENEDIA master mix was useful for the detection of mutations in exons 4 and 12 of the TGFBI gene.
Diagnosis ; DNA ; Exons ; Humans ; Limit of Detection ; Mass Screening* ; Methods ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity