• Microbiology and Biotechnology Letters
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• v.43 no.1
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• pp.79-83
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• 2015

The Cucurbitaceae are a plant family that consist of over a hundred genera, the most important of which are squash, pumpkin, zucchini, some gourds, cucumber and watermelon. These are among the top imported seeds in Korea. At the time of their import, the Squash mosaic virus (SqMV), the Cucumber green mottle mosaic virus (CGMMV) and the Kyuri green mottle mosaic virus (KGMMV) are designated as regulated viruses for quarantine in Korea. This study was conducted to develop specific primer sets for easy and rapid detection of SqMV, CGMMV and KGMMV. RT-PCR with the nested PCR primer sets and modified positive control plasmids were capable of highly sensitive detection and verification of such viruses. In addition, developed diagnostic PCR systems applied to quarantine sites detected 47 cases of SqMV, 67 cases of CGMMV and 17 cases of KGMMV between 2010 and the first half of 2014.

• Journal of Chest Surgery
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• v.33 no.8
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• pp.669-675
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• 2000

Background: Tuberculous pleurisy is the leading cause of pleural effusion in Korea. And differential diagnosis of tuberculous pleurisy with other cause is clinically very important. Traditional diagnostic methods such as routine analysis of pleural fluid, staining for acid-fast bacilli or pleural biopsy have major inherent limitaion. This study was designed to evaluate the significance of pleural fluid polymerase chain reaction(PCR) and adenosine deaminase (ADA) activity in early diagnosis of tuberculous pleurisy. Material and Method: Between March 1996 and July 1997, 198 patients with pleural effusion reviewed retrospectively. The study group included 112 cases with tuberculous effusion and 86 cases with non-tuberculous effusions, whose diagnoses were confirmed by pleural biopsy, microbiological methods, or cytology. We compared the results of PCR and pleural fluid levels of ADA between tuberculous and non-tuberculous effusions. Result: Mean age was 47.54$\pm$19.52 years(range 2 to 85 years). The positive rate of PCR was significantly higher in tuberculous group than non-tuberculous group(p<0.05). The sensitivty, specificity, positive predictive value(PPV), and negative predictive value(NPV) for PCR were 31.7, 90.9, 83.0, and 48.8%, respectively. Mean ADA activity was significantly higher in tuberculous group than non-tuberculous group(83.2 U/L vs 49.8 U/L)(p<0.05). With diagnostic thresholds of 40 U/L, the sensitivity, specificity, PPV, and NPV of ADA for tuberculosis were 75.9, 70.9, 77.3, and 69.3% respectively. At a level of 70 U/L, the sensitivity, specificity, PPV, and NPV of ADA for tuberculosis were 70.1, 75.9, 82.9, and 60.3% respectively. Conclusion: PCR is very highly specific, but less sensitive methods in diagnosis of tuberculous pleurisy. But ADA level of pleural fluid has acceptable sensitivity and specificity in diagnosis of tuberculous pleurisy. ADA activity is more useful test in the evaluation of pleural effusions.

• Journal of Microbiology and Biotechnology
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• v.31 no.3
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• pp.358-367
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• 2021

The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID-19) as an international health emergency. Current diagnostic tests are based on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method, which is the gold standard test that involves the amplification of viral RNA. However, the RT-qPCR assay has limitations in terms of sensitivity and quantification. In this study, we tested both qPCR and droplet digital PCR (ddPCR) to detect low amounts of viral RNA. The cycle threshold (CT) of the viral RNA by RT-PCR significantly varied according to the sequences of the primer and probe sets with in vitro transcript (IVT) RNA or viral RNA as templates, whereas the copy number of the viral RNA by ddPCR was effectively quantified with IVT RNA, cultured viral RNA, and RNA from clinical samples. Furthermore, the clinical samples were assayed via both methods, and the sensitivity of the ddPCR was determined to be equal to or more than that of the RT-qPCR. However, the ddPCR assay is more suitable for determining the copy number of reference materials. These findings suggest that the qPCR assay with the ddPCR defined reference materials could be used as a highly sensitive and compatible diagnostic method for viral RNA detection.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7345-7349
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• 2013

Background: Because of the high prevalence of hepatocellular carcinoma (HCC) in Egypt, new markers with better diagnostic performance than alpha-feto protein (AFP) are needed to help in early diagnosis. The aim of this work was to compare the clinical utility of both serum and mRNA glypican3 (GPC3) as probable diagnostic markers for HCC among Egyptian patients. Materials and Methods: A total of 60 subjects, including 40 with HCC, 10 with cirrhosis and 10 normal controls were analyzed for serum GPC3 (sGPC3) by ELISA. GPC-3 mRNA from circulating peripheral blood mononuclear cells was amplified by RT-PCR. Both markers were compared to some prognostic factors of HCC, and sensitivity of both techniques was compared. Results: Serum glypican-3 and AFP were significantly higher in the HCC group compared to cirrhotic and normal controls (p<0.001). Sensitivity and specificity were (95% each) for sGlypican-3, (82.5% and 85%) for AFP, and (100% and 90%) for Glypican3 mRNA, and (80% and 95%) for double combination between sGPC3 and AFP respectively. Conclusion: Both serum GPC-3 and GPC-3mRNA are promising diagnostic markers for early detection of HCC in Egyptian patients. RT- PCR proved to be more sensitive (100%) than ELISA (95%) in detecting glypican3.

• Korean Journal of Veterinary Service
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• v.44 no.3
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• pp.163-168
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• 2021

The rapid and reliable detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in isolating infected patients and preventing further viral transmission. In this study, we evaluated the clinical diagnostic performances of a commercial real-time reverse transcription loop-mediated isothermal amplification (RRT-LAMP) assay (Isopollo^® COVID-2 assay, M-monitor, Daegu, Korea) using eighty COVID-19 suspected clinical samples and compared these with the results of a commercial real-time reverse transcription polymerase chain reaction (RT-qPCR) assay (Allplex^TM 2019-nCoV rRT-QPCR Assay, SeeGene, Seoul, Korea). The results of the RRT-LAMP assay targeting the N or RdRp gene of SARS-CoV-2 showed perfect agreement with the RT-qPCR assay results in terms of detection. Furthermore, the RRT-LAMP assay was completed in just within a 20-min reaction time, which is significantly faster than about the 2 h currently required for the RT-qPCR assay, thus enabling prompt decision making regarding the isolation of infected patients. The RRT-LAMP assay will be a valuable tool for rapid, sensitive, and specific detection of SARS-CoV-2 in human or unexpected animal clinical cases.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.5
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• pp.691-697
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• 2021

Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (Vp_AHPND) and Enterocytozoon hepatopenaei (EHP) are the two most important pathogens in shrimp aquaculture and they have caused enormous losses to the shrimp industry worldwide. In ponds, the major target organ for the two pathogens is the hepatopancreas, and infection with EHP is a known potential risk factor for Vp_AHPND infection. This study aimed to develop a PCR (polymerase chain reaction)-based diagnostic method for simultaneously detecting Vp_AHPND and EHP. The newly developed PCR diagnostic method could be used to test various samples, such as seawater, shrimp, and feces. The diagnostic method exhibited high sensitivity and specificity for both pathogens. This will help reduce the potential economic losses that may have been caused by the two major shrimp pathogens, Vp_AHPND and EHP, and will allow for the efforts and time spent combatting them to be dedicated elsewhere.

• Tuberculosis and Respiratory Diseases
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• v.45 no.3
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• pp.519-528
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• 1998

Background: Diagnosis of pulmonary tuberculosis is not easy when the sputum smear for Mycobacterium tuberculosis(M. Tb) is negative. We evaluated the clinical utility of polymerase chain reaction(PCR) for detecting M. Tb in bronchoalveolar lavage(BAL) samples. Methods: We recruited 84 patients whose sputum smear for M. Tb were negative or not available due to no production of sputum. We performed bronchoalveolar lavage for acid-fast stain, culture of mycobacteria, and PCR assay of BAL fluid. We analyzed the results of microbiologic examination. Results: The sensitivity of BAL fluid smear, culture, and PCR were 20%, 38%, and 40%, respectively. The specificity of BAL fluid PCR was 95%. The positive predictive value of PCR was 89%. The smear of BAL fluid was positive in 17%. The PCR of BAL fluid was the only diagnostic test in 17%. Therefore, the BAL fluid analysis including smear and PCR was diagnostic in 34 % within 24 hours. The BAL fluid analysis including smear, PCR, and culture was diagnostic in 55% within 2 month. Conclusion: The BAL fluid PCR was valuable method in the diagnosis of pulmonary tuberculosis in patients whose sputa were not available or reveal negative smear.

• Tuberculosis and Respiratory Diseases
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• v.43 no.2
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• pp.128-137
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• 1996

Background : We can diagnose pulmonary tuberculosis with sputum AFB smear and culture, but sputum AFB smear has low sensitivity and culture needs long period, and they are not available in the patients who can not expectorate effectively. Recently developed, PCR is a fast diagnostic tool in tuberculosis, but false positive and false negative are important problems. So, we studied the diagnostic value of bronchoalveolar lavage fluid AFB smear, culture, PCR through the bronchoscopy. Methods : The 67 pulmonary tuberculosis patients and 43 non-pulmonary tuberculosis patients were analyzed with their sputum specimen AFB smear and culture. Also, bronchoscopy and bronchoalveolar lavage were done, and bronchoalveolar lavage fluid AFB smear, culture and PCR were done. Results: 1) In the cases of pulmonary tuberculosis, the sensitivity of sputum AFB smear and culture were 32.8% and 57.4%, respectively. And the sensitivity of bronchoalveolar lavage fluid AFB smear and culture were 47.8% and 80.6%. respectively. 2) In the cases of pulmonary tuberculosis, the sensitivity and the positive predictive value(for predicting a positive culture) of PCR were 80.6% and 81.5%, respectively. 3) In the cases of sputum AFB smear-negative and culture-negative pulmonary tuberculosis, the sensitivity of bronchoalveolar lavage fluid AFB smear, culture, PCR, and the positive predictive value(for predicting a positive culture) of PCR were 23.1%, 100%, 88.5%, and 82.4%, respectively. 4) The specificity of bronchoalveolar lavage fluid PCR was 77.0%. 5) The median number of days between obtaining a specimen and starting therapy was 5 days for sputum AFB smear, 9 days for bronchoalveolar lavage fluid AFB smear, 26 days for bronchoalveolar lavage fluid PCR, 32 days for sputum culture, 56 days for bronchoalveolar lavage fluid culture. Conclusion : The sensitivity of bronchoalveolar lavage fluid AFB smear and culture are higher than sputum AFB smear and culture. So, the bronchoscopy must be considered for evaluating suspected cases of pulmonary tuberculosis in patients from whom smears of expectorated sputum do not reveal mycobacteria or from whom no sputum can be obtained. Especially, combined with PCR, it is expected that pulmonary tuberculosis can be diagnosed more rapidly and more accurately, so bronchoalveolar lavage fluid APB smear and PCR can be helpful in the early treatment of pulmonary tuberculosis.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.273-273
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• 2013

Recently, Point-of-care (POC) testing microdevices enable to do the patient monitoring, drug screening, pathogen detection in the outside of hospital. Immunochromatographic strip (ICS) is one of the diagnostic technologies which are widely applied to POC detection. Relatively low cost, simplicity to use, easy interpretations of the diagnostic results and high stability under any circumstances are representative advantages of POC diagnosis. It would provide colorimetric results more conveniently, if the genetic analysis microsystem incorporates the ICS as a detector part. In this work, we develop a reverse transcriptase-polymerase chain reaction (RT-PCR) microfluidic device integrated with a ROSGENE strip for colorimetric influenza H1N1 virus detection. The integrated RT-PCR- ROSGENE device is consist of four functional units which are a pneumatic micropump for sample loading, 2 ${\mu}L$ volume RT-PCR chamber for target gene amplification, a resistance temperature detector (RTD) electrode for temperature control, and a ROSGENE strip for target gene detection. The device was fabricated by combining four layers: First wafer is for RTD microfabrication, the second wafer is for PCR chamber at the bottom and micropump channel on the top, the third is the monolithic PDMS, and the fourth is the manifold for micropump operation. The RT-PCR was performed with subtype specific forward and reverse primers which were labeled with Texas-red, serving as a fluorescent hapten. A biotin-dUTP was used to insert biotin moieties in the PCR amplicons, during the RT-PCR. The RT-PCR amplicons were loaded in the sample application area, and they were conjugated with Au NP-labeled hapten-antibody. The test band embedded with streptavidins captures the biotin labeled amplicons and we can see violet colorimetric signals if the target gene was amplified with the control line. The off-chip RT-PCR amplicons of the influenza H1N1 virus were analyzed with a ROSGENE strip in comparison with an agarose gel electrophoresis. The intensities of test line was proportional to the template quantity and the detection sensitivity of the strip was better than that of the agarose gel. The test band of the ROSGENE strip could be observed with only 10 copies of a RNA template by the naked eyes. For the on-chip RT-PCR-ROSGENE experiments, a RT-PCR cocktail was injected into the chamber from the inlet reservoir to the waste outlet by the micro-pump actuation. After filling without bubbles inside the chamber, a RT-PCR thermal cycling was executed for 2 hours with all the microvalves closed to isolate the PCR chamber. After thermal cycling, the RT-PCR product was delivered to the attached ROSGENE strip through the outlet reservoir. After dropping 40 ${\mu}L$ of an eluant buffer at the end of the strip, the violet test line was detected as a H1N1 virus indicator, while the negative experiment only revealed a control line and while the positive experiment a control and a test line was appeared.

• Korean Journal Plant Pathology
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• v.14 no.2
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• pp.130-135
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• 1998

This study was carried out to detect cymbidium mosaic potexvirus (CymMV) and odontoglossum ringspot tobamovirus (ORSV) in cultivated orchid plants in Korea. The standard double antibody sandwich enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR) were carried out for detection of the viruses in the collected orchid samples. ELISA was suitable for massive-scale diagnostic method for virus detection in orchids. RT-PCR was rapid, time-saving and reliable detective method, and detection limit data showed that RT-PCR was 103 times more sensitive than ELISA. Of the 321 individual orchids representing 5 orchids genera tested by the ELISA, CymMV and ORSV were detected in 15.6% and 22.4%, and mixed infection of the both viruses with 4.9%, respectively. Of the Cymbidium plants tested, cultivated plants showed 52.5% virus infection rate with either CymMV or ORSV and both viruses.