• 대한의생명과학회지
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• 제22권3호
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• pp.83-97
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• 2016

The measurement of viral load in HIV-1 infected patients is essential for the establishment of a therapeutic strategy. Several commercial assays have shown shortcomings in quantifying rare genotypes of HIV-1 such as minor groups of N and O. In this study, the HIV-1 RT-qPCR assay was developed. The primers and probe of HIV-1 were designed to target the pol gene and to increase the detection efficiency of various subtypes including group N and O. The HIV-1 quantitative RT-qPCR assay was assessed for its analytical performance and clinical evaluation. The LoD was determined to 33.9 IU/ml. The LoD of several subtypes including A, C, D, CRF_01AE, F, CRF_02AG, G and H, were determined to less than 40 IU/ml. The HIV-1 quantitative RT-qPCR assay was evaluated using the China National Reference Panel of HIV-1 RNA to determine the analytical performance. The results were all within the acceptable range. The clinical evaluation was performed at Hunan CDC in China. The clinical evaluation results were compared with those of the China domestic commercial kit. A significant correlation (fresh samples; $R^2=0.84$, P<0.001, frozen samples; $R^2=0.76$, P<0.001) between the two systems was observed for 64 fresh samples and 76 frozen samples with viral loads, and the Bland-Altman plot showed good agreement (98.4%, 96.1%, respectively). In conclusion, the HIV-1 quantitative RT-qPCR assay had comparable analytical performance with several commercial kits. The study provides basic data for the research of HIV-1 diagnosis and the development of P < HIV-1 molecular diagnostic assay.

• 한국동물위생학회지
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• 제30권4호
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• pp.489-496
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• 2007

An oligonucleotide microarray system was developed for the simultaneous detection of porcine epidemic diarrhea virus, transmissible gastroenteritis virus, porcine enteric calicivirus, porcine group A and C rotavirus. RNAs of the reference viruses and porcine diarrhea samples were extracted and amplified using one-step multiplex RT-PCR in the presence of cyanine 5-dCTP and hybridized on the microarray chip that spotted the virus-specific oligonucleotides. This system were approximately 10-to 100-fold higher in sensitivity than conventional RT-PCR, and the assay time was less than 3 hours. The relative sensitivity and specificity were 92% and 72.2%, respectively, based on 102 porcine diarrhea samples using RT-PCR as gold standard. These results suggested that the oligonucleotide microarray system in this study be probably more reliable and reproducible means for detecting porcine enteric viruses and that it could be of substantial use in routine diagnostic laboratories.

• Journal of Microbiology and Biotechnology
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• 제20권10호
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• pp.1450-1456
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• 2010

Accurate and rapid diagnosis of Pandemic Influenza A/H1N1 2009 virus (H1N1 2009) infection is important for the prevention and control of influenza epidemics and the timely initiation of antiviral treatment. This study was conducted to evaluate the performance of several diagnostic tools for the detection of H1N1 2009. Flocked nasopharyngeal swabs were collected from 254 outpatients of suspected H1N1 2009 during October 2009. This study analyzed the performances of the RealTime Ready Inf A/H1N1 Detection Set (Roche), Influenza A (H1N1) Real-Time Detection Kit (Bionote), Seeplex Influenza A/B OneStep Typing Set [Seeplex Reverse Transcriptase PCR (RT-PCR)], BinaxNow Influenza A & B Test Kit [Binax Rapid Antigen Test (RAT)], and SD BIOLINE Influenza Ag kit (SD RAT). Roche and Bionote real-time RT-PCR showed identical results for the H1N1 2009 hemagglutinin gene. Compared with real-time RT-PCR, the sensitivities and specificities were 83.7% and 100% for Seeplex RT-PCR, 64.5% and 94.7% for Binax RAT, and 69.5% and 100% for SD RAT. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT in patients aged over 21 years were 73.7%, 47.4%, and 57.9%, respectively. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT on the day of initial symptoms were mostly lower (68.8%, 56.3%, and 31.3%, respectively). In conclusion, multiplex RT-PCR and RAT for the detection of H1N1 2009 were significantly less sensitive than real-time RT-PCR. Moreover, a negative RAT may require more sensitive confirmatory assays, because it cannot be ruled out from influenza infection.

• Genomics & Informatics
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• 제21권2호
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• pp.24.1-24.7
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• 2023

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

• 한국동물위생학회지
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• 제27권3호
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• pp.273-280
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• 2004

The studies were performed for the PRRS antigen and antibody detection from breeding farms, artificial insemination(AI) center and growing farms in Jeonbuk province. 1. Specific PRRS primers were successfully amplified ORF6 617bp and ORF7 448 bp on agarose gel. 2. RT-PCR method has been establish by commercial kit and the thermal cycler program consisted of 30 cycles: $95^{\circ}C$ for 30 sec, $45^{\circ}C$ for 30 sec, and $72^{\circ}C$ for 45 sec. 3. The results of PRRS antibody test by ELISA method in AI centers were $6.6\%,\;53.3\%$ and breeding farms $65\%,\;65\%\;and\;38.7\%$, respectively. The serological positive of the antibody in gilt higher than sow. 4. The sero-positive of the PRRS antibody showed average $21\%$ in domestic farms, $56.2\%$ in breeding farms, and $29.9\%$ in AI center.

• 농업과학연구
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• 제49권4호
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• pp.821-831
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• 2022

American plum line pattern virus (APLPV), a member of the genus Ilarvirus in the family Bromoviridae, is one of the plant quarantine pathogens in Korea. In this study, 15 candidate primer sets were designed and examined to develop a reverse transcription polymerase chain reaction (RT-PCR) assay for plant quarantine inspection of APLPV. Using APLPV-infected and healthy samples, the primer sets were assessed for APLPV detection. To confirm the occurrence of nonspecific reactions, six ilarviruses (Apple mosaic virus, Asparagus virus 2, Blueberry shock virus, Prune dwarf virus, Prunus necrotic ringspot virus, and Tobacco streak virus) and 10 target plants (Prunus mume, P. yedoensis, P. persica, P. armeniaca, P. dulcis, P. tomentosa, P. avium, P. glandulosa, P. salicina, and P. cerasifera) were examined. Finally, two primer sets were selected. These primer sets could generate the expected amplicons even with at least 1 ng of the total RNA template in concentration-dependent amplifications. In addition, a positive clone was developed for use as a positive control in the abovementioned RT-PCR assay.

• Journal of Microbiology and Biotechnology
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• 제30권3호
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• pp.459-468
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• 2020

This study established a new polymerase spiral reaction (PSR) that combines with reverse transcription reactions for HCV detection targeting 5'UTR gene. To avoid cross-contamination of aerosols, an isothermal amplification tube (IAT), as a separate containment control, was used to judge the result. After optimizing the RT-PSR reaction system, its effectiveness and specificity were tested against 15 different virus strains which included 8 that were HCV positive and 7 as non-HCV controls. The results showed that the RT-PSR assay effectively detected all 8 HCV strains, and no false positives were found among the 7 non-HCV strains. The detection limit of our RT-PSR assay is comparable to the real-time RT-PCR, but is more sensitive than the RT-LAMP. The established RT-PSR assay was further evaluated for detection of HCV in clinical blood samples, and the resulting 80.25% detection rate demonstrated better or similar effectiveness compared to the RT-LAMP (79.63%) and real-time RT-PCR (80.25%). Overall, the results showed that the RT-PSR assay offers high specificity and sensitivity for HCV detection with great potential for screening HCV in clinical blood samples.

• 식물병연구
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• 제26권3호
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• pp.170-178
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• 2020

바이러스의 정확한 진단법 확립은 바이러스의 피해 및 확산을 예방하는데 매우 중요하게 작용한다. 대부분의 딸기 바이러스는 조직내에 낮은 역가로 분포하여 진단이 어렵고, 특히 딸기 조직은 다당류 및 페놀화합물의 함유가 많아 RNA 추출이 어려운 것으로 알려져 있다. 딸기 우량묘 생산에 필요한 바이러스 검정기술을 확립하기 위해 본 연구에서는 딸기 잎에서 바이러스 진단을 위해 가장 최적의 RNA 추출방법 정립을 위해 다양한 상용 키트와 시약을 이용하여 RNA 추출효율 비교하였다. 바이러스 진단을 통한 RNA 추출효율을 분석하기 위해 SMoV 감염주인 미홍 딸기 품종을 이용하여 다양한 단계에서 잎조직으로부터 RNA를 추출하고 바이러스 진단을 수행하였다. 식물 RNA 추출 방법 가운데 상업용으로 판매되는 RNeasy plant mini kit (Qiagen)를 이용하는 경우 본 연구에서 살펴본 one-step 또는 two-step RT-PCR 방법과 무관하게 SMoV의 검출이 잘 되었다. 또한, 딸기 우량묘의 바이러스 검정에 대한 신뢰있는 진단방법을 구축하기 위해 주요 딸기 바이러스인 strawberry mild yellow edge virus (SMYEV), strawberry mottle virus (SMoV), strawberry latent ringspot virus (SLRSV), strawberry crinkle virus (SCV), strawberry pallidosis associated virus (SPaV), strawberry vein banding virus (SVBV) 및 strawberry necrotic shock virus (SNSV) 7종에 대한 유전자 합성을 통해 진단클론을 제작하였다. 각 클론의 합성유전자를 기반으로 7종의 딸기바이러스 프라이머 세트를 설계하고 편리한 진단법 수행을 위해 동일한 PCR 조건을 설정하였다.

• The Plant Pathology Journal
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• 제39권4호
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• pp.309-318
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• 2023

Huanglongbing (HLB) is one of the most destructive diseases in citrus, which imperils the sustainability of citriculture worldwide. The presumed causal agent of HLB, 'Candidatus Liberibacter asiaticus' (CLas) is a non-culturable phloem-limited α-proteobacterium transmitted by Asian citrus psyllids (ACP, Diaphorina citri Kuwayama). A widely adopted method for HLB diagnosis is based on quantitative real-time polymerase chain reaction (qPCR). Although HLB diagnostic qPCR provides high sensitivity and good reproducibility, it is limited by time-consuming DNA preparation from plant tissue or ACP and the requirement of proper lab instruments including a thermal cycler to conduct qPCR. In an attempt to develop a quick assay that can be deployed in the field for CLas detection, we developed a real-time loop-mediated isothermal amplification (rt-LAMP) assay by targeting the CLas five copy nrdB gene. The rt-LAMP assay using various plant sample types and psyllids successfully detected the nrdB target as low as ~2.6 Log10 copies. Although the rt-LAMP assay was less sensitive than laboratory-based qPCR (detection limit ~10 copies), the data obtained with citrus leaf and bark and ACP showed that the rt-LAMP assay has >96% CLas detection rate, compared to that of laboratory-based qPCR. However, the CLas detection rate in fibrous roots was significantly decreased compared to qPCR due to low CLas titer in some root DNA sample. We also demonstrated that the rt-LAMP assay can be used with a crude leaf DNA extract which is fully deployable in the field for quick and reliable HLB screening.

• 대한수의학회지
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• 제40권1호
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• pp.42-48
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• 2000

Akabane disease is transmitted through mosquitoes in cattle, sheep and goats. It shows congenital abnormalities including encephalomyetitis, hydranencephaly, neurogenic arthrogryposis, and deformed neonatal calves. Akabane viruses, 93FMX and K-9 strain, were isolated from fetal matrix of aborted cow and blood of healthy cow, respectively. S gene sequences of 93FMX and K-9 showed 100% homology with that of OBE-1 strain isolated in Japan. Based upon our sequencing data, we synthesized specific primers for PCR diagnosis. Using these primers, we were able to amplify the S gene of Akabane virus not only from the culture fluid of Vero cells but also from the brain tissue of suckling mouse inoculated with, Akabane virus. These PCR products were confirmed by Southern blot hybridization. Not only the sensitivity of PCR test was high enough to detect the viruses of $10^{1.0}TCID_{50}/ml$, but also the time for diagnosis was significantly shorter than that of the virus isolation by tissue culture method. This method was also effective for the detection of Akabane virus in the cerebrum of fetus. RT-PCR method may be used for a useful diagnostic test of the clinical cases of Akabane disease.