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4 "Real-time polymerase chain reaction"
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Original Articles
Clinical epidemiological applicability of real-time polymerase chain reaction for COVID-19
Geehyuk Kim, Jun-Kyu Kang, Jungho Kim, Jiyoung Lee, Jin Gwack
Osong Public Health Res Perspect. 2022;13(4):252-262.   Published online July 27, 2022
DOI: https://doi.org/10.24171/j.phrp.2022.0135
  • 1,375 View
  • 114 Download
Graphical AbstractGraphical Abstract AbstractAbstract PDF
Objectives
Real-time polymerase chain reaction is currently used as a confirmatory test for coronavirus disease 2019 (COVID-19). The test results are interpreted as positive, negative, or inconclusive, and are used only for a qualitative classification of patients. However, the test results can be quantitated using threshold count (Ct) values to determine the amount of virus present in the sample. Therefore, this study investigated the diagnostic usefulness of Ct results through various quantitative analyzes, along with an analysis of clinical and epidemiological characteristics.
Methods
Clinical and epidemiological data from 4,642 COVID-19 patients in April 2021 were analyzed, including the Ct values of the RNA-dependent RNA polymerase (RdRp), envelope (E), and nucleocapsid (N) genes. Clinical and epidemiological data (sex, age, underlying diseases, and early symptoms) were collected through a structured questionnaire. A correlation analysis was used to examine the relationships between variables.
Results
All 3 genes showed statistically significant relationships with symptoms and severity levels. The Ct values of the RdRp gene decreased as the severity of the patients increased. Moreover, statistical significance was observed for the presence of underlying diseases and dyspnea.
Conclusion
Ct values were found to be related to patients’ clinical and epidemiological characteristics. In particular, since these factors are closely related to symptoms and severity, Ct values can be used as primary data for predicting patients’ disease prognosis despite the limitations of this method. Conducting follow-up studies to validate this approach might enable using the data from this study to establish policies for preventing COVID-19 infection and spread.
Comparison of Three Different Methods for Detection of IL28 rs12979860 Polymorphisms as a Predictor of Treatment Outcome in Patients with Hepatitis C Virus
Abolfazl Fateh, Mohammadreza Aghasadeghi, Seyed D. Siadat, Farzam Vaziri, Farzin Sadeghi, Roohollah Fateh, Hossein Keyvani, Alireza H. Tasbiti, Shamsi Yari, Angila Ataei-Pirkooh, Seyed H. Monavari
Osong Public Health Res Perspect. 2016;7(2):83-89.   Published online April 30, 2016
DOI: https://doi.org/10.1016/j.phrp.2015.11.004
  • 2,197 View
  • 17 Download
  • 17 Citations
AbstractAbstract PDF
Objectives
This study aimed to evaluate the specificity, sensitivity, cost, and turn-around time of three methods of gene polymorphism analysis and to study the relationship between IL28B rs12979860 and SVR rate to pegIFN-α/RVB therapy among patients with chronic hepatitis C.
Methods
A total of 100 samples from chronic hepatitis C patients were analyzed in parallel using the three methods: direct sequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system (ARMS)-PCR.
Results
The different profiles for IL28B rs12979860 alleles (CC, CT, and TT) obtained with PCR-RFLP, ARMS-PCR, and direct sequencing were consistent among the three methods. Prevalence of rs12979860 genotypes CC, CT and TT in HCV genotype 1a was 10(19.6%), 35(68.6%), and six (11.8%), respectively, and in HCV genotype 31, it was 13(26.5%), 31(63.3%), and five (10.2%), respectively. No significant difference was seen between rs12979860 genotype and HCV genotype (p = 0.710).
Conclusion
Screening by ARMS – PCR SNOP detection represents the most efficient and reliable method to determine HCV polymorphisms in routine clinical practice.

Citations

Citations to this article as recorded by  
  • MicroRNAs Profiling in HIV, HCV, and HIV/HCV Co-Infected Patients
    Mohsen Moghoofei, Sohrab Najafipour, Shayan Mostafaei , Ahmad Tavakoli , Farah Bokharaei-Salim , Saied Ghorbani, Davod Javanmard, Hadi Ghaffari , Seyed Hamidreza Monavari
    Current HIV Research.2021; 19(1): 27.     CrossRef
  • Occult hepatitis C virus infection in hemophilia patients and its correlation with interferon lambda 3 and 4 polymorphisms
    Amir Hossein Nafari, Ahmad Ayadi, Zahra Noormohamadi, Fatemeh Sakhaee, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
    Infection, Genetics and Evolution.2020; 79: 104144.     CrossRef
  • Polymerase Chain Reaction Assay Using the Restriction Fragment Length Polymorphism Technique in the Detection of Prosthetic Joint Infections: A Multi-Centered Study
    Ataollah Moshirabadi, Mohammad Razi, Peyman Arasteh, Mohammad Mahdi Sarzaeem, Saman Ghaffari, Saied Aminiafshar, Kami Hosseinian Khosroshahy, Fatemeh Maryam Sheikholeslami
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  • One-Step ARMS-PCR for the Detection of SNPs—Using the Example of the PADI4 Gene
    Ehnert, Linnemann, Braun, Botsch, Leibiger, Hemmann, Nussler
    Methods and Protocols.2019; 2(3): 63.     CrossRef
  • Epstein–Barr virus and risk of breast cancer: a systematic review and meta-analysis
    Mohammad Farahmand, Seyed Hamidreza Monavari, Zabihollah Shoja, Hadi Ghaffari, Mehdi Tavakoli, Ahmad Tavakoli
    Future Oncology.2019; 15(24): 2873.     CrossRef
  • Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography
    Eyal Shteyer, Louis Shekhtman, Tal Zinger, Sheri Harari, Inna Gafanovich, Dana Wolf, Hefziba Ivgi, Rima Barsuk, Ilana Dery, Daniela Armoni, Mila Rivkin, Rahul Pipalia, Michal Cohen Eliav, Yizhak Skorochod, Gabriel S. Breuer, Ran Tur-kaspa, Yonit Weil Wien
    PLOS ONE.2019; 14(1): e0210173.     CrossRef
  • Correlation of CD81 and SCARB1 polymorphisms on virological responses in Iranian patients with chronic hepatitis C virus genotype 1
    Milad Nafari, Shiva Irani, Farzam Vaziri, Safoora Gharibzadeh, Fatemeh Sakhaee, Mohammad Khazeni, Naser Kalhor, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
    Infection, Genetics and Evolution.2018; 62: 296.     CrossRef
  • First detection of human hepegivirus-1 (HHpgV-1) in Iranian patients with hemophilia
    Yazdan Bijvand, Mohammad Reza Aghasadeghi, Fatemeh Sakhaee, Parviz Pakzad, Farzam Vaziri, Alireza Azizi Saraji, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
    Scientific Reports.2018;[Epub]     CrossRef
  • Evaluation of TRIM5 and TRIM22 polymorphisms on treatment responses in Iranian patients with chronic hepatitis C virus infection
    Setareh Mobasheri, Nazanin Irani, Abbas Akhavan Sepahi, Fatemeh Sakhaee, Fatemeh Rahimi Jamnani, Farzam Vaziri, Seyed Davar Siadat, Abolfazl Fateh
    Gene.2018; 676: 95.     CrossRef
  • Data Mining and Machine Learning Algorithms Using IL28B Genotype and Biochemical Markers Best Predicted Advanced Liver Fibrosis in Chronic Hepatitis C
    Hend Ibrahim Shousha, Abubakr Hussein Awad, Dalia Abdelhamid Omran, Mayada Mohamed Elnegouly, Mahasen Mabrouk
    Japanese Journal of Infectious Diseases.2018; 71(1): 51.     CrossRef
  • IL28B rs12980275 and HLA rs4273729 genotypes as a powerful predictor factor for rapid, early, and sustained virologic response in patients with chronic hepatitis C
    Parvaneh Sedighimehr, Shiva Irani, Fatemeh Sakhaee, Farzam Vaziri, Mohammadreza Aghasadeghi, Seyed Mehdi Sadat, Fatemeh Rahimi Jamnani, Abolfazl Fateh, Seyed Davar Siadat
    Archives of Virology.2017; 162(1): 181.     CrossRef
  • Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C)
    Wai-Ying Fong, Chi-Chun Ho, Wing-Tat Poon
    Diagnostics.2017; 7(2): 27.     CrossRef
  • Effect of IL15 rs10833 and SCARB1 rs10846744 on virologic responses in chronic hepatitis C patients treated with pegylated interferon-α and ribavirin
    Sahar Sadeghi, Mehdi Davari, Esmaeil Asli, Safoora Gharibzadeh, Farzam Vaziri, Fatemeh Rahimi Jamnani, Abolfazl Fateh, Seyed Davar Siadat
    Gene.2017; 630: 28.     CrossRef
  • High platelet count and high probability of CALR detection in myeloproliferative neoplasms
    Reza Shirzad, Zari Tahan-nejad, Javad Mohamadi-asl, Mohammad Seghatoleslami, Ahmad Ahmadzadeh, Amal Saki Malehi, Najmaldin Saki
    Comparative Clinical Pathology.2017; 26(1): 25.     CrossRef
  • A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C
    Seyed Hamidreza Monavari, Roohollah Fateh, Farzam Vaziri, Fatemeh Rahimi Jamnani, Enayat Anvari, Farzin Sadeghi, Parviz Afrough, Ava Behrouzi, Fatemeh Sakhaee, Sepideh Meidaninikjeh, Hamidreza Mollaie, Alireza Hadizadeh Tasbiti, Shamsi Yari, Maryam Sadegh
    Scandinavian Journal of Clinical and Laboratory In.2017; 77(4): 247.     CrossRef
  • EGFR rs11506105 and IFNL3 SNPs but not rs8099917 are strongly associated with treatment responses in Iranian patients with chronic hepatitis C
    M Asnavandi, M Zargar, F Vaziri, F R Jamnani, S Gharibzadeh, A Fateh, S D Siadat
    Genes & Immunity.2017; 18(3): 144.     CrossRef
  • Genetic Variation in Interleukin-28B and Response to Peg-IFNα-2a/RBV Combination Therapy in Patients with Hepatitis C Virus Infection
    Farah Bokharaei-Salim, Mostafa Salehi-Vaziri, Farzin Sadeghi, Khadijeh Khanaliha, Maryam Esghaei, Seyed Hamidreza Monavari, Seyed Moayed Alavian, Shahin Fakhim, Hossein Keyvani
    Jundishapur Journal of Microbiology.2016;[Epub]     CrossRef
Evaluation and Comparison of Molecular and Conventional Diagnostic Tests for Detecting Tuberculosis in Korea, 2013
Sang-Hee Park, Chang-Ki Kim, Hye-Ran Jeong, Hyunjin Son, Seong-Han Kim, Mi-Sun Park
Osong Public Health Res Perspect. 2014;5(Suppl):S3-S7.   Published online December 31, 2014
DOI: https://doi.org/10.1016/j.phrp.2014.10.006
  • 1,815 View
  • 16 Download
  • 7 Citations
AbstractAbstract PDF
Objectives
A fast and accurate diagnosis is necessary to control and eliminate tuberculosis (TB). In Korea, TB continues to be a serious public health problem. In this study, diagnostic tests on clinical samples from patients suspected to have TB were performed and the sensitivity and specificity of the various techniques were compared. The main objective of the study was to compare various diagnostic tests and evaluate their sensitivity and specificity for detecting tuberculosis.
Methods
From January 2013 to December 2013, 170,240 clinical samples from patients suspected to have TB were tested with smear microscopy, acid-fast bacilli culture, and real-time polymerase chain reaction (PCR). The test results were compared and data were analyzed.
Results
A total of 8216 cultures tested positive for TB (positive detection rate, 4.8%). The contamination rate in the culture was 0.6% and the isolation rate of nontuberculous mycobacteria was 1.0%. The sensitivity and specificity of smear microscopy were 56.8% and 99.6%, respectively. The concordance rate between the solid and liquid cultures was 92.8%. Mycobacterium isolates were not detected in 0.4% of the cases in the liquid culture, whereas no Mycobacterium isolates were detected in 6.8% of the cases in the solid culture. The sensitivity and specificity of real-time PCR for the solid culture were 97.2% and 72.4%, respectively, whereas the corresponding data for the liquid culture were 93.5% and 97.2%.
Conclusion
The study results can be used to improve existing TB diagnosis procedure as well as for comparing the effectiveness of the assay tests used for detecting Mycobacterium tuberculosis isolates.

Citations

Citations to this article as recorded by  
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    Ana Paula de Oliveira Tomaz, Sonia Mara Raboni, Gislene Maria Botão Kussen, Keite da Silva Nogueira, Clea Elisa Lopes Ribeiro, Libera Maria Dalla Costa, Padmapriya P. Banada
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    Narda Medina, Ana Alastruey-Izquierdo, Danicela Mercado, Oscar Bonilla, Juan C. Pérez, Luis Aguirre, Blanca Samayoa, Eduardo Arathoon, David W. Denning, Juan Luis Rodriguez-Tudela
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Brief Report
Acute Human Cytomegalovirus Infection with Bleeding in Iran
Behzad Pourhossein, Farhad Yaghmaei, Saber Esmaeili, Omid Banafshi, Shahla Afrasiabian, Mohammad Reza Shirzadi, Mark Schleiss, Ehsan Mostafavi
Osong Public Health Res Perspect. 2014;5(6):383-386.   Published online December 31, 2014
DOI: https://doi.org/10.1016/j.phrp.2014.10.003
  • 1,677 View
  • 24 Download
AbstractAbstract PDF
In December 2011, a 42-year-old male farmer was admitted to a hospital in Sanandaj (Western Iran) with fever and anemia in order to check whether he suffered from some infectious diseases. During the first 3 days after admission, the patient gradually developed progressive oliguria, fever, abdominal pain in the right upper quadrant, leukocytosis with toxic granulation, petechiae and ecchymosis, oral bleeding, and vomiting. The sonographic findings revealed splenomegaly and an increase in the thickness of the gall bladder wall. In order to manage the patient and taking into consideration the most probable differential diagnoses, diagnostic tests were performed on two blood samples collected from him, and real-time polymerase chain reaction for human cytomegalovirus was positive.

PHRP : Osong Public Health and Research Perspectives