1
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Farooq S, Faiz S, Wahab AT, Choudhary MI. Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis. Sci Rep 2024; 14:11159. [PMID: 38750152 PMCID: PMC11096182 DOI: 10.1038/s41598-024-59342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
Hepatitis is a major public health issue, affecting 10-17 million people worldwide, with its prevalence continuously increasing. The Hepatitis C virus (HCV) is responsible for liver related diseases, which include liver cirrhosis, hepatocellular carcinoma, and chronic hepatitis. Pakistan is experiencing a serious rise in HCV cases. This study aimed to assess the prevalence and distribution of HCV genotypes in Sindh, Pakistan. Serum samples from HCV-positive patients were collected from various local hospitals in Sindh. These samples were first screened for HCV antibodies using ELISA. Samples that tested positive for HCV RNA underwent further genotyping through sequencing using the standard Sanger method. The genotypes were identified by comparing the sequences with those available in the National Center for Biotechnology Information (NCBI) database, and a phylogenetic tree was constructed. The phylogenetic analysis showed that all isolates in this study were clustered with genotypes 3a and 3b, except for one sequence that was clustered with genotype 1a. No isolates were found to be clustered with reference genomes of genotypes 2, 4, 5, 6, and 7 suggesting that genotype 3a is endemic in this region. The analyzed sequences demonstrated a 98% similarity with reference and isolated sequences. In summary, sequencing of the HCV 5' UTR essential for identifying the predominant genotype of HCV RNA in the Sindh region Further research on the distribution of HCV genotypes in other regions of Pakistan could aid in improving screening processes, identifying more effective treatment options, and developing suitable prevention strategies.
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Affiliation(s)
- Saba Farooq
- Mediagnost Gesellschaft Für Forschung Und Herstellung Von Diagnostika, Reutlingen, Germany.
- National Institute of Virology, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Sirmast Faiz
- National Institute of Virology, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21412, Jeddah, Saudi Arabia
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Quality Assurance for Hepatitis C Virus Point-of-Care Diagnostics in Sub-Saharan Africa. Diagnostics (Basel) 2023; 13:diagnostics13040684. [PMID: 36832172 PMCID: PMC9955859 DOI: 10.3390/diagnostics13040684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
As part of a multinational study to evaluate the Bioline Hepatitis C virus (HCV) point-of-care (POC) testing in sub-Saharan Africa (SSA), this narrative review summarises regulatory standards and quality indicators for validating and approving HCV clinical diagnostics. In addition, this review also provides a summary of their diagnostic evaluations using the REASSURED criteria as the benchmark and its implications on the WHO HCV elimination goals 2030.
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Sharma S, Thomas E, Caputi M, Asghar W. RT-LAMP-Based Molecular Diagnostic Set-Up for Rapid Hepatitis C Virus Testing. BIOSENSORS 2022; 12:298. [PMID: 35624599 PMCID: PMC9138684 DOI: 10.3390/bios12050298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Hepatitis C virus (HCV) infections occur in approximately 3% of the world population. The development of an enhanced and extensive-scale screening is required to accomplish the World Health Organization's (WHO) goal of eliminating HCV as a public health problem by 2030. However, standard testing methods are time-consuming, expensive, and challenging to deploy in remote and underdeveloped areas. Therefore, a cost-effective, rapid, and accurate point-of-care (POC) diagnostic test is needed to properly manage the disease and reduce the economic burden caused by high case numbers. Herein, we present a fully automated reverse-transcription loop-mediated isothermal amplification (RT-LAMP)-based molecular diagnostic set-up for rapid HCV detection. The set-up consists of an automated disposable microfluidic chip, a small surface heater, and a reusable magnetic actuation platform. The microfluidic chip contains multiple chambers in which the plasma sample is processed. The system utilizes SYBR green dye to detect the amplification product with the naked eye. The efficiency of the microfluidic chip was tested with human plasma samples spiked with HCV virions, and the limit of detection observed was 500 virions/mL within 45 min. The entire virus detection process was executed inside a uniquely designed, inexpensive, disposable, and self-driven microfluidic chip with high sensitivity and specificity.
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Affiliation(s)
- Sandhya Sharma
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA;
- Asghar-Lab: Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Emmanuel Thomas
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL 33136, USA;
| | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA;
- Asghar-Lab: Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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Boushi E, Cheha K, Hedar N, Almokdad R, Alassi MW, Kakaje A. Sofosbuvir/ledipasvir safety and efficacy for HCV patients with haemodialysis and liver cirrhosis: a small retrospective study. EGYPTIAN LIVER JOURNAL 2021. [DOI: 10.1186/s43066-021-00150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Hepatitis C virus (HCV) infection is a high prevalent disease. Sofosbuvir/ledipasvir (SOF/LDV) can successfully treat HCV and it was until recently that SOF/LDV was approved by the FDA in haemodialysis patients, but not in patients with liver cirrhosis. This study reports patients on haemodialysis and compensated liver cirrhosis who used this regiment. This is a retrospective study on patients who were on haemodialysis and used SOF/LDV for HCV treatment in one secondary health care facility (a hospital). Treatment consisted of 400g SOF and of 90g LDV once daily. Patients were assessed for HCV RNA at the end of treatment after 12 weeks and after 24 weeks for patients. New symptoms were also assessed.
Results
Our sample contained 16 males and 5 females with a mean age of 40.9 years. Nineteen patients had no cirrhosis of the liver, and the other two had clinical and radiological cirrhosis and had Child–Turcotte–Pugh (CTP) type B. Full follow-up was for only 20 patients and they all had HCV resolved as one patient had died from a stroke. Other factors were assessed such as HCV genotypes, but treatment had the same results with no difference in symptoms development (p>0.05). Twelve patients had HCV genotype 1, eight patients had HCV genotype 4, and one patient had HCV genotype 5.
Conclusion
Despite the small sample size, SOF/LDV combination is suggested to be effective in patients on haemodialysis and who had compensated cirrhosis and CTP type B without the need of dose adjustment or increase duration of treatment, and there were no major complications overall.
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Rafiq S, Majeed MI, Nawaz H, Rashid N, Yaqoob U, Batool F, Bashir S, Akbar S, Abubakar M, Ahmad S, Ali S, Kashif M, Amin I. Surface-enhanced Raman spectroscopy for analysis of PCR products of viral RNA of hepatitis C patients. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 259:119908. [PMID: 33989976 DOI: 10.1016/j.saa.2021.119908] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
In the current study, for a qualitative and quantitative study of Polymerase Chain Reaction (PCR) products of viral RNA of Hepatitis C virus (HCV) infection, surface-enhanced Raman spectroscopy (SERS) methodology has been developed. SERS was used to identify the spectral features associated with the PCR products of viral RNA of Hepatitis C in various samples of HCV-infected patients with predetermined viral loads. The measurements for SERS were performed on 30 samples of PCR products, which included three PCR products of RNA of healthy individuals, six negative controls, and twenty-one HCV positive samples of varying viral loads (VLs) using Silver nanoparticles (Ag NPs) as a SERS substrates. Additionally, on SERS spectral data, the multivariate data analysis methods including Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR) were also carried out which help to illustrate the diagnostic capabilities of this method. The PLSR model is designed to predict HCV viral loads based on biochemical changes observed as SERS spectral features which can be associated directly with HCV RNA. Several SERS characteristic features are observed in the RNA of HCV which are not detected in the spectra of healthy RNA/controls. PCA is found helpful to differentiate the SERS spectral data sets of HCV RNA samples from healthy and negative controls. The PLSR model is found to be 99% accurate in predicting VLs of HCV RNA samples of unknown samples based on SERS spectral changes associated with the Hepatitis C development.
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Affiliation(s)
- Sidra Rafiq
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Faisalabad Campus, Pakistan
| | - Umer Yaqoob
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Imran Amin
- PCR Laboratory, PINUM Hospital, Faisalabad, Pakistan
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Narayanamurthy V, Jeroish ZE, Bhuvaneshwari KS, Samsuri F. Hepatitis C virus (HCV) diagnosis via microfluidics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:740-763. [PMID: 33511975 DOI: 10.1039/d0ay02045a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Humans are subjected to various diseases; hence, proper diagnosis helps avoid further disease consequences. One such severe issue that could cause significant damage to the human liver is the hepatitis C virus (HCV). Several techniques are available to detect HCV under various categories, such as detection through antibodies, antigens, and RNA. Although immunoassays play a significant role in discovering hepatitis viruses, there is a need for point-of-care tests (POCT). Some developing strategies are required to ensure the appropriate selection of POCT for HCV detection, initiate appropriate antiviral therapy, and define associated risks, which will be critical in achieving optimal outcomes. Though molecular assays are precise, reproducible, sensitive, and specific, alternative strategies are required to enhance HCV diagnosis among the infected population. Herein, we described and assessed the potential of various microfluidic detection techniques and confirmatory approaches used in present communities. In addition, current key market players in HCV chip-based diagnosis and the future perspectives on the basis of which the diagnosis can be made easier are presented in the present review.
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Affiliation(s)
- Vigneswaran Narayanamurthy
- Fakulti Teknologi Kejuruteraan Elektrik dan Elektronik, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100 Durian Tunggal, Melaka, Malaysia.
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Agboghoroma CO, Ukaire BC. Prevalence and Risk Factors of Human Immunodeficiency Virus and Hepatitis C Virus Infection among Pregnant Women Attending Antenatal Care at a Tertiary Hospital in Abuja, Nigeria. Niger Med J 2020; 61:245-251. [PMID: 33487847 PMCID: PMC7808292 DOI: 10.4103/nmj.nmj_241_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/16/2020] [Accepted: 08/26/2020] [Indexed: 01/26/2023] Open
Abstract
CONTEXT Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) co-infection in pregnant women has increased potential for Mother-to-Child Transmission risks of both viruses. The reports on the prevalence and risk factors for HIV and HCV co-infection in pregnancy are limited in Nigeria. AIM The aim of the study is to determine the prevalence and potential risk factors for HIV and HCV infection among pregnant women in Abuja. STUDY DESIGN A cross-sectional seroprevalence study carried out on pregnant women attending antenatal clinic of a tertiary hospital in Abuja from July 1st to October 31st 2016. Patients were recruited consecutively and counselled for HIV and HCV. Structured questionnaire was used to collect socio-demographic data, and information on potential risk factors for HIV and HCV infections. Blood samples were collected for HIV and HCV screening using rapid test kits following the national testing algorithm. Data generated were analyzed with statistical package for social sciences (SPSS) version 20.0. P-value less than 0.05 was considered statistically significant. RESULT 252 pregnant women participated in this study. The mean age of the study population was 31.7 ± 4.9 years. The prevalence of HIV and HCV was 12.3% and 1.2% respectively. The prevalence of HIV/HCV co-infection was 0.8%. The prevalence of HCV among HIV positive cohorts was 6.5%. HIV infection was significantly associated with history of blood transfusion (P = 0.047), presence of tattoo/scarification marks (P = 0.009) and multiple sexual partners (P < 0.0001). HCV infections was not significantly associated with any of the risk factors studied. CONCLUSION HIV prevalence is high among the pregnant women. HCV co-infection is common in women who are HIV infected. HIV infection unlike HCV was significantly associated with history of blood transfusion, presence of tattoo/scarification marks and multiple sexual partners.
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Warkad S, Nimse SB, Song KS, Kim T. Development of a Method for Screening and Genotyping of HCV 1a, 1b, 2, 3, 4, and 6 Genotypes. ACS OMEGA 2020; 5:10794-10799. [PMID: 32455199 PMCID: PMC7240817 DOI: 10.1021/acsomega.0c00386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/24/2020] [Indexed: 05/05/2023]
Abstract
The World Health Organization and the World Health Assembly recommended eradicating hepatitis as a public threat by 2030. The accurate genotyping of hepatitis C virus (HCV) is crucial to achieving this goal because it is vital for the selection of anti-HCV therapy required for complete cure of HCV infection. We report the development of a method for accurate genotyping of HCV 1a, 1b, 2, 3, 4, and 6 genotypes. The merits of the developed method for HCV genotyping include (i) requirement of a single polymerase chain reaction (PCR) primer set, (ii) room-temperature detection in 30 min after the PCR, (iii) no need of highly trained professionals, (iv) highly accurate HCV genotyping results afforded by highly specific DNA-DNA hybridization, and (v) probe sequences that can be used on other platforms.
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Naseer K, Saleem M, Ali S, Mirza B, Qazi J. Identification of new spectral signatures from hepatitis C virus infected human sera. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117181. [PMID: 31202032 DOI: 10.1016/j.saa.2019.117181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/01/2019] [Accepted: 05/26/2019] [Indexed: 05/27/2023]
Abstract
Hepatitis C virus (HCV) infection is one of the leading causes of morbidity and mortality worldwide. Mortality linked with HCV infection can be lowered with effective and prompt diagnosis in early stages of infection. In this study potential of Raman spectroscopy to differentiate between healthy and HCV infected serum samples was investigated. Clear differences were observed in the Raman spectra of HCV infected and healthy sera samples. Using the analysis of variance (ANOVA) and t-test (p < 0.001) on Raman spectra of diseased and healthy samples, we observed eleven unique Raman bands at 676, 825, 853, 936, 1029, 1105, 1155, 1305, 1620, 1654 and 1757 cm-1 associated with only HCV infected sera and have not been reported in earlier studies. In addition, six Raman bands at 556, 585, 716, 815, 1273 and 1142 cm-1were observed in healthy sera only. Three Raman bands at 1330, 1526 and 1572 cm-1 were observed in both type of samples but their intensity was drastically reduced in diseased samples. Various multivariate analysis techniques were employed to demonstrate the robustness of the results. We employed multivariate and unsupervised principal component analysis (PCA) in conjunction with supervised classification linear discriminant analysis (LDA), using ten-fold jackknife cross-validation, in order to develop effective diagnostic algorithm technique (PCA-LDA). Our PCA-LDA model yielded sufficient sensitivity and specificity i.e. correctly identified all infected samples included in this study. Ours results indicate that these unique Raman bands have the potential to be used as biomarkers for optical diagnosis of HCV infection.
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Affiliation(s)
- Khulla Naseer
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Saleem
- Agri. & Biophotonics Division, National Institute of Laser and Optronics (NILOP), Lehtrar Road, Islamabad, Pakistan
| | - Safdar Ali
- Directorate General National Repository, P.O. Box 1175, Islamabad, Pakistan
| | - Bushra Mirza
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan
| | - Javaria Qazi
- Faculty of Biological Sciences, Qauid-i-Azam University, Islamabad, Pakistan.
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Utilization rates and clinical outcomes of hepatitis C positive donor hearts in the contemporary era. J Heart Lung Transplant 2019; 38:907-917. [DOI: 10.1016/j.healun.2019.06.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 12/18/2022] Open
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Basharkhah S, Sabet F, Ghezeldasht SA, Mosavat A, Jahantigh HR, Barati E, Shamsian K, Saleh-Moghaddam M, Sharebyani H, Hassannia T, Shamsian SAA. Prediction of HCV load using genotype, liver biomarkers, and clinical symptoms by a mathematical model in patients with HCV infection. Microbiol Immunol 2019; 63:449-457. [PMID: 31373399 DOI: 10.1111/1348-0421.12735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022]
Abstract
Hepatitis C virus (HCV) infection is a major public health problem with about 1.75 million new HCV cases and 71 million chronic HCV infections worldwide. The study aimed to evaluate clinical, serological, molecular, and liver markers to develop a mathematical predictive model for the quantification of the HCV viral load in chronic HCV infected patients. In this cross-sectional study, blood samples were taken from 249 recently diagnosed HCV-infected subjects and were tested for liver condition, viral genotype, and HCV RNA load. Receiver operating characteristics (ROC) curves and multiple linear regression analysis were used to predict the HCV-RNA load. Genotype 3 followed by genotype 1 were the most prevalent genotypes in Mashhad, Northeastern Iran. The maximum levels of viral load were detected in the mixed genotype group, and the lowest levels in the undetectable genotype group. The log of the HCV viral load was significantly associated with thrombocytopenia and higher serum levels of alanine transaminase (ALT). In addition, the log HCV RNA was significantly higher in patients with arthralgia, fatigue, fever, vomiting, or dizziness. Moreover, genotype 3 was significantly associated with icterus. A ROC curve analysis revealed that the best cut-off points for serum levels of aspartate aminotransferase (AST), ALT, and alkaline phosphatase (ALP) were >31, >34, and ≤246 IU/L, respectively. Sensitivity, specificity, and positive predictive values for AST were 87.7%, 84.36%, and 44.6%, for ALT they were 83.51%, 81.11%, and 36%, and for ALP were 72.06%, 42.81%, and 8.3%, respectively. A mathematical regression model was developed that could estimate the HCV-RNA load. Regression model: log viral load = 7.69 - 1.01 × G3 - 0.7 × G1 + 0.002 × ALT - 0.86 × fatigue.
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Affiliation(s)
- Samira Basharkhah
- Department of Biochemistry, Faculty of Science, Payam-e-Noor University of Mashhad, Mashhad, Iran
| | - Faezeh Sabet
- Immunology Research Center, Inflammation and inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sanaz Ahmadi Ghezeldasht
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Arman Mosavat
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Hamid Reza Jahantigh
- Immunology Research Center, Inflammation and inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Barati
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khosrow Shamsian
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Masoud Saleh-Moghaddam
- Department of Biochemistry, Faculty of Science, Payam-e-Noor University of Mashhad, Mashhad, Iran
| | - Hiva Sharebyani
- Immunology Research Center, Inflammation and inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Hassannia
- Department of Internal Medicine, Tehran University of Medical Sciences, Jalal Highway, Tehran, 1411713137, Iran
| | - Seyed Ali Akbar Shamsian
- Department of Mycology and Parasitology, Mashhad University of Medical Sciences, Azadi-Squre, Medical Campus, Mashhad, 9177948564, Iran
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Kao JH, Lin CY, Chuang WL, Cheng YY, Hu JY, Liang WK, Friebe P, Palmer S, Huang CS. Clinical evaluation of IntelliPlex TM HCV genotyping kit for hepatitis C virus genotyping. Diagn Microbiol Infect Dis 2019; 94:344-348. [PMID: 30975461 DOI: 10.1016/j.diagmicrobio.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/24/2022]
Abstract
Genotyping of the hepatitis C virus (HCV) is crucial for determining the most efficient anti-viral therapy. The clinical sensitivity and specificity of the IntelliPlexTM HCV Genotyping Kit was determined by comparing the assay results of 307 specimens with the results obtained by Sanger sequencing. Out of 202 HCV-positive specimens tested, 8 samples yielded discrepant results between the IntelliPlex HCV Genotyping Kit and Sanger sequencing. For 5 of these discrepant samples, the IntelliPlex HCV Genotyping Kit classified the correct genotype but failed to show the same single or dual infected status as determined by Sanger sequencing. A total of 105 samples which tested negative for HCV by In-Vitro-Diagnostics (IVD)-approved viral load assay tested negative for HCV by the IntelliPlex HCV Genotyping Kit. The IntelliPlex HCV Genotyping Kit has a clinical specificity of 100% and a clinical sensitivity of 96.9% and is suited to be used in clinical laboratories to genotype HCV.
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Affiliation(s)
- Jia-Horng Kao
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Gastroenterology and Hepatology, the National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Yen Lin
- School of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University, Kaohsiung. Taiwan; Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | - Jui-Yu Hu
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan
| | | | - Peter Friebe
- PlexBio Co., Ltd., Neihu District, Taipei, Taiwan.
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Warkad SD, Nimse SB, Song KS, Kim T. HCV Detection, Discrimination, and Genotyping Technologies. SENSORS (BASEL, SWITZERLAND) 2018; 18:E3423. [PMID: 30322029 PMCID: PMC6210034 DOI: 10.3390/s18103423] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.
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Affiliation(s)
- Shrikant Dashrath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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Guimarães VDS, Melo TGD, Ferreira RDCD, Almeida SFD, Martins LC. Prevalence of hepatitis C virus genotypes in the State of Pará, Brazil. Rev Soc Bras Med Trop 2018; 51:508-512. [DOI: 10.1590/0037-8682-0457-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/28/2018] [Indexed: 12/11/2022] Open
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15
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Warkad SD, Nimse SB, Song KS, Chantratita W, Pongthanapisith V, Nawale LU, Kim T. Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples. Virol J 2018; 15:107. [PMID: 29996859 PMCID: PMC6042330 DOI: 10.1186/s12985-018-1017-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Background A treatment of HCV infection depends on the genotype and sub-genotype. Therefore, accurate HCV genotyping is critical for selecting the appropriate treatment regimen. Method This study included 280 plasma samples to evaluate the performance of 6 HCV Genotyping 9G test. The performance of 6 HCV Genotyping 9G test for accurate detection of HCV 1a, 1b, 2, 3, 4, and 6 genotypes was evaluated by comparing it with LiPA 2.0 assay and sequencing. Results 6 HCV Genotyping 9G test and LiPA 2.0 assay demonstrated 83.9% (n = 235) agreement. 39/45 samples that showed discrepant results between the two tests were analyzed by sequencing. Sequencing genotyped 39 discrepant samples as 0 (HCV 1a), 24 (HCV 1b), 1 (HCV 6f), 12 (HCV 6i), and 2 (HCV-negative). Results of 6 HCV Genotyping 9G test were very similar to the sequencing as it detected 1, 23, 1, 12, and 2 samples as HCV 1a, 1b, 3 & 6a or 6f, 6i or 6n, and negative, respectively. However, LiPA 2.0 assay showed complete disagreement with sequencing, as it did not detect any of these 39 samples correctly. These results indicate that LiPA 2.0 assay has limitations in identifying HCV genotypes 1b, and 6. The sensitivity, specificity, PPV, and NPV of 6 HCV Genotyping 9G test were 99.5, 98.8, 99.5, and 98.8%, respectively. It is important to note that HCV Genotyping 9G test showed 98.3 and 100% sensitivity for HCV 1b and 6 genotyping, respectively. However, LiPA 2.0 assay demonstrated 57.9 and 71.7% sensitivity for these genotypes. Conclusions 6 HCV Genotyping 9G test identifies HCV 1a, 1b, 2, 3, and 6 with good agreement with sequencing. Hence, 6 HCV Genotyping 9G test has a high clinical value because it can provide critical information to physicians and assist them to use the correct drug for efficient hepatitis C treatment. Electronic supplementary material The online version of this article (10.1186/s12985-018-1017-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shrikant Dasharath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Wasun Chantratita
- Department of Pathology, Faculty of Medicine, Virology Laboratory, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Viroj Pongthanapisith
- Department of Pathology, Faculty of Medicine, Virology Laboratory, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Laxman Uddhav Nawale
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, 1 Okcheon-dong, Chuncheon, 200-702, South Korea.
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16
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Ellipilli S, Phillips JD, Heemstra JM. Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite. Org Biomol Chem 2018; 16:4659-4664. [PMID: 29881861 DOI: 10.1039/c8ob00626a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available δ-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.
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Affiliation(s)
- Satheesh Ellipilli
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
| | - John D Phillips
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
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17
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Sohail A, Khan S, Ullah R, Qureshi SA, Bilal M, Khan A. Analysis of hepatitis C infection using Raman spectroscopy and proximity based classification in the transformed domain. BIOMEDICAL OPTICS EXPRESS 2018; 9:2041-2055. [PMID: 29760968 PMCID: PMC5946769 DOI: 10.1364/boe.9.002041] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 05/25/2023]
Abstract
This work presents a diagnostic system for the hepatitis C infection using Raman spectroscopy and proximity based classification. The proposed method exploits transformed Raman spectra using the proximity based machine learning technique and is denoted as RS-PCA-Prox. First, Raman spectral data is baseline corrected by subtracting noise and low intensity background. After this, a feature transformation of Raman spectra is adopted, not only to reduce the feature's dimensionality but also to learn different deviations in Raman shifts. The proposed RS-PCA-Prox shows significant diagnostic power in terms of accuracy, sensitivity, and specificity as 95%, 0.97 and 0.94 in PCA based transformed domain. The comparison of the RS-PCA-Prox with linear and ensemble based classifiers shows that proximity based classification performs better for the discrimination of HCV infected individuals and is able to differentiate the infected individuals from normal ones on the basis of molecular spectral information. Furthermore, it is observed that characteristic spectral changes are due to variation in the intensity of lectin, chitin, lipids, ammonia and viral protein as a consequence of the HCV infection.
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Affiliation(s)
- Anabia Sohail
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Saranjam Khan
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
| | - Rahat Ullah
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
| | - Shahzad Ahmad Qureshi
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Bilal
- Agri-biophotonics Laboratory, National Institute for Lasers & Optronics, Islamabad, Pakistan
- Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Asifullah Khan
- Pattern Recognition Lab, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
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18
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Dittrich S, Boutthasavong L, Keokhamhoung D, Phuklia W, Craig SB, Tulsiani SM, Burns MA, Weier SL, Dance DAB, Davong V, Vongsouvath M, Mayxay M, Phetsouvanh R, Newton PN, Woods K. A Prospective Hospital Study to Evaluate the Diagnostic Accuracy of Rapid Diagnostic Tests for the Early Detection of Leptospirosis in Laos. Am J Trop Med Hyg 2018; 98:1056-1060. [PMID: 29488460 PMCID: PMC5928825 DOI: 10.4269/ajtmh.17-0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Leptospirosis is a globally important cause of acute febrile illness, and a common cause of non-malarial fever in Asia, Africa, and Latin America. Simple rapid diagnostic tests (RDTs) are needed to enable health-care workers, particularly in low resource settings, to diagnose leptospirosis early and give timely targeted treatment. This study compared four commercially available RDTs to detect human IgM against Leptospira spp. in a head-to-head prospective evaluation in Mahosot Hospital, Lao PDR. Patients with an acute febrile illness consistent with leptospirosis (N = 695) were included in the study during the 2014 rainy season. Samples were tested with four RDTs: (“Test-it” [Life Assay, Cape Town, South Africa; N = 418]; “Leptorapide” [Linnodee, Ballyclare, Northern Ireland; N = 492]; “Dual Path Platform” [DPP] [Chembio, Medford, NY; N = 530]; and “SD-IgM” [Standard Diagnostics, Yongin, South Korea; N = 481]). Diagnostic performance characteristics were calculated and compared with a composite reference standard combining polymerase chain reaction (PCR) (rrs), microscopic agglutination tests (MATs), and culture. Of all patients investigated, 39/695 (5.6%) were positive by culture, PCR, or MAT. The sensitivity and specificity of the RDTs ranged greatly from 17.9% to 63.6% and 62.1% to 96.8%, respectively. None of the investigated RDTs reached a sensitivity or specificity of > 90% for detecting Leptospira infections on admission. In conclusion, our investigation highlights the challenges associated with Leptospira diagnostics, particularly in populations with multiple exposures. These findings emphasize the need for extensive prospective evaluations in multiple endemic settings to establish the value of rapid tools for diagnosing fevers to allow targeting of antibiotics.
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Affiliation(s)
- Sabine Dittrich
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Latsaniphone Boutthasavong
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Dala Keokhamhoung
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Weerawat Phuklia
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Scott B Craig
- Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Australia.,Faculty of Science Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Suhella M Tulsiani
- Section for Global Health, Department of Public Health, Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark.,Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Australia
| | - Mary-Anne Burns
- Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Australia
| | - Steven L Weier
- Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - David A B Dance
- Faculty of Tropical and Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Viengmon Davong
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Rattanaphone Phetsouvanh
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Paul N Newton
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
| | - Kate Woods
- National Infection Service (NIS), Public Health England (PHE), London, United Kingdom.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
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19
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Costi C, Grandi T, Halon ML, Silva MSN, Silva CMDD, Gregianini TS, Possuelo LG, Jarczewski CA, Niel C, Rossetti MLR. Prevalence of hepatitis C virus and human immunodeficiency virus in a group of patients newly diagnosed with active tuberculosis in Porto Alegre, Southern Brazil. Mem Inst Oswaldo Cruz 2017; 112:255-259. [PMID: 28327789 PMCID: PMC5354612 DOI: 10.1590/0074-02760160352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Porto Alegre is the Brazilian state capital with second highest incidence of tuberculosis (TB) and the highest proportion of people infected with human immunodeficiency virus (HIV) among patients with TB. Hepatitis C virus (HCV) infection increases the risk of anti-TB drug-induced hepatotoxicity, which may result in discontinuation of the therapy. OBJECTIVES The aim of this study was (i) to estimate prevalence of HCV and HIV in a group of patients newly diagnosed with active TB in a public reference hospital in Porto Alegre and (ii) to compare demographic, behavioural, and clinical characteristics of patients in relation to their HCV infection status. METHODS One hundred and thirty-eight patients with TB were tested for anti-HCV antibody, HCV RNA, and anti-HIV1/2 antibody markers. HCV RNA from real-time polymerase chain reaction (PCR)-positive samples was submitted to reverse transcription and PCR amplification. The 5′ non-coding region of the HCV genome was sequenced, and genotypes of HCV isolates were determined. FINDINGS Anti-HCV antibody, HCV RNA, and anti-HIV antibodies were detected in 27 [20%; 95% confidence interval (CI), 13-26%], 17 (12%; 95% CI, 7-18%), and 34 (25%; 95% CI, 17-32%) patients, respectively. HCV isolates belonged to genotypes 1 (n = 12) and 3 (n = 4). Some characteristics were significantly more frequent in patients infected with HCV. Among them, non-white individuals, alcoholics, users of illicit drugs, imprisoned individuals, and those with history of previous TB episode were more commonly infected with HCV (p < 0.05). MAIN CONCLUSIONS HCV screening, including detection of anti-HCV antibody and HCV RNA, will be important to improving the management of co-infected patients, given their increased risk of developing TB treatment-related hepatotoxicity.
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Affiliation(s)
- Cintia Costi
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Tarciana Grandi
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Maria Laura Halon
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | | | - Cláudia Maria Dornelles da Silva
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Tatiana Schäffer Gregianini
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Instituto de Pesquisas Biológicas, Laboratório Central do Estado, Porto Alegre, RS, Brasil
| | - Lia Gonçalves Possuelo
- Universidade de Santa Cruz do Sul, Programa de Pós-Graduação em Promoção da Saúde, Santa Cruz do Sul, RS, Brasil
| | - Carla Adriane Jarczewski
- Secretaria Estadual da Saúde do Rio Grande do Sul, Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| | - Christian Niel
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Maria Lucia Rosa Rossetti
- Secretaria Estadual da Saúde do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Luterana do Brasil, Canoas, RS, Brasil
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20
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Neto MF, Butzler MA, Reed JL, Rui X, Fisher MJ, Kelso DM, McFall SM. Immiscible phase filter extraction and equivalent amplification of genotypes 1-6 of hepatitis C RNA: The building blocks for point-of-care diagnosis. J Virol Methods 2017; 248:107-115. [PMID: 28673855 DOI: 10.1016/j.jviromet.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/11/2022]
Abstract
The lack of hepatitis C virus (HCV) diagnostic tests designed for use in decentralized settings is a major obstacle for providing access to treatment and prevention services particularly in low and middle income countries. Here we describe the development and validation of two building blocks of the HCV Quant Assay, a test in development for point-of-care use: 1) an RT-qPCR assay with noncompetitive internal control that equivalently detects the 6 major HCV genotypes and 2) an automated sample prep method using immiscible phase filter technology. This novel assay has wide dynamic range of HCV quantification and a limit of detection of 30IU/ml with 200μl specimen volume. In a preliminary study of 61 clinical specimens, the HCV Quant Assay demonstrated 100% sensitivity and specificity and gave comparable viral load results across 4 logs of IU/ml when compared to the Abbott RealTime HCV Assay.
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Affiliation(s)
- Mário F Neto
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA; University of Illinois Incubator Lab Facility, Chicago, IL 60612, USA
| | - Matthew A Butzler
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Jennifer L Reed
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Xiang Rui
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Mark J Fisher
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - David M Kelso
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Sally M McFall
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA.
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21
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6 HCV Genotyping 9G test for HCV 1a, 1b, 2, 3, 4 and 6 (6a, 6f, 6i and 6n) with high accuracy. J Virol Methods 2017; 246:95-99. [PMID: 28456667 DOI: 10.1016/j.jviromet.2017.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022]
Abstract
According to EASL guidelines and WHO recommendations, the accurate detection of HCV genotypes such as HCV 1a, HCV1b, HCV 2, HCV 3, HCV 4, and HCV 6 (6a, 6f, 6i, 6n) is crucial for the efficient treatment of hepatitis C. HCV Genotyping 9G test allows simultaneous genotyping of HCV 1a, 1b, 2, 3, 4, and 6 (6a, 6f, 6i, and 6n) in clinical samples in 30min. The performance of the test was evaluated by comparison with sequence analysis. Serum samples (n=152) from HCV-infected patients (n=110) and healthy individuals (n=42) were processed under blinded codes. The k coefficient (kappa) values indicated high agreement between the HCV Genotyping 9G test and sequencing. The sensitivity and specificity of the test were 99.1% and 99.7%, respectively. The results indicate that HCV Genotyping 9G test is rapid, reliable, sensitive, and accurate for screening and genotyping of HCV in the clinical specimens.
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22
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Taskova M, Uhd J, Miotke L, Kubit M, Bell J, Ji HP, Astakhova K. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. Anal Chem 2017; 89:4363-4366. [PMID: 28382823 DOI: 10.1021/acs.analchem.7b00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New approaches for genomic DNA/RNA detection are in high demand in order to provide controls for existing enzymatic technologies and to create alternatives for emerging applications. In particular, there is an unmet need in rapid, reliable detection of short RNA regions which could open up new opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA followed by click assembly and analysis of the read sequence by various techniques. As we demonstrate in this paper, using our new approach, a viral RNA sequence can be detected in less than 2 h without the need for cDNA synthesis or any other enzymatic reactions and with a sensitivity of <10 pM target RNA.
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Affiliation(s)
- Maria Taskova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Uhd
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - Matthew Kubit
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - John Bell
- Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States.,Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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23
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Yin HQ, Ji CF, Yang XQ, Wang R, Yang S, Zhang HQ, Zhang JG. An improved gold nanoparticle probe-based assay for HCV core antigen ultrasensitive detection. J Virol Methods 2017; 243:142-145. [PMID: 28189584 DOI: 10.1016/j.jviromet.2017.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 12/22/2022]
Abstract
A gold nanoparticle probe-based assay (GNPA) was developed for ultrasensitive detection of Hepatitis C virus (HCV) core antigen. In the GNPA, after anti-HCV core antigen polyclonal antibodies and single-stranded barcode signal DNA were labeled on gold nanoparticle probe (NP), DNA enzyme was used to degrade the unbound barcode DNAs. The anti-HCV core antigen monoclonal antibodies were coated on magnetic microparticles probe (MMP). Then the NP-HCV core antigen-MMP sandwich immuno-complex was formed when the target antigen protein was added and captured. Magnetically separated, the immuno-complex containing the single-stranded barcode signal DNA was characterized by TaqMan probe based real-time fluorescence PCR. A detection limit of 1 fg/ml was determined for the HCV core antigen which is magnitude greater than that of ELISA (2ng/ml). The coefficients of variation (CV) of intra-assay and inter-assay respectively ranged from 0.22-2.62% and 1.92-3.01%. The improved GNPA decreased the interference of unbound barcode DNAs and may be an new way for HCV core antigen detection.
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Affiliation(s)
- Hui-Qiong Yin
- Beijing Institute of Transfusion Medicine, Beijing 100850, China
| | - Chang-Fu Ji
- Beijing Institute of Transfusion Medicine, Beijing 100850, China
| | - Xi-Qin Yang
- Beijing Institute of Basic Medical Science, Beijing 100850, China
| | - Rui Wang
- Beijing Institute of Transfusion Medicine, Beijing 100850, China
| | - Shu Yang
- Beijing Institute of Transfusion Medicine, Beijing 100850, China
| | - He-Qiu Zhang
- Beijing Institute of Basic Medical Science, Beijing 100850, China
| | - Jin-Gang Zhang
- Beijing Institute of Transfusion Medicine, Beijing 100850, China.
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24
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Chantratita W, Song KS, GunHo C, Pongthanapisith V, Thongbaiphet N, Wongtabtim G, Pasomsub E, Angkanavin K, Nimse SB, Sonawane MD, Warkad SD, Kim T. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping. J Virol Methods 2016; 239:1-8. [PMID: 27793646 DOI: 10.1016/j.jviromet.2016.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 01/05/2023]
Abstract
In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.
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Affiliation(s)
- Wasun Chantratita
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Korea.
| | - Choi GunHo
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon, 24232, Korea.
| | - Viroj Pongthanapisith
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Nipa Thongbaiphet
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Garanyuta Wongtabtim
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Ekawat Pasomsub
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Kanokwan Angkanavin
- Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Korea.
| | - Mukesh Digambar Sonawane
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Korea.
| | - Shrikant Dasharath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 24252, Korea.
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25
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Ashraf A, Chakravarti A, Roy P, Kar P, Siddiqui O. Frequency of nucleotide sequence variations in the internal ribosome entry site region of hepatitis C virus RNA isolated from responding and non-responding patients with hepatitis C virus genotype 3 infection. Virusdisease 2016; 27:251-259. [PMID: 28466036 PMCID: PMC5394696 DOI: 10.1007/s13337-016-0335-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/27/2016] [Indexed: 01/18/2023] Open
Abstract
Located within 5' untranslated region of HCV RNA is internal ribosome entry site (IRES) which directs cap-independent translation of viral polyprotein. Mutations in IRES sequence have been shown to cause changes in efficiency of protein translation in vitro in few instances. No study has been done to investigate association between frequency of nucleotide sequence variations in IRES region of HCV-3 RNA and response to pegylated interferon-α plus ribavirin therapy. Hence, this study was planned to analyze relationship between frequency of nucleotide sequence variations of HCV-3 IRES region and response to therapy. Twenty-seven HCV-3 patients were studied, of whom 19 responded to therapy and 8 did not. Alanine aminotransferase and aspartate aminotransferase levels were significantly lower in responders compared to non-responders. HCV RNA detection and genotyping was performed by nested-PCR and RFLP respectively. Viral load quantification in pre and post therapy samples was done by real time PCR. The viral load was significantly lower in the patients after treatment as compared to before treatment. HCV IRES region from pre-treatment sera of 27 HCV-3 infected patients was amplified by nested PCR and sequenced. Secondary structure of IRES region of HCV-3 was predicted using the M fold Web Server. Mutational analysis revealed hot spot of mutations in HCV-3 IRES region from 40-80 and 210-280 nucleotides. Though more mutations were found in non-responders as compared to responders, this difference was statistically insignificant. Therefore, in addition to IRES region of HCV-3, some other host and viral factors may contribute to therapy outcome.
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Affiliation(s)
- Anzar Ashraf
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Anita Chakravarti
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
- 79, South Park Apartment, Kalkaji, New Delhi, Delhi 110019 India
| | - Priyamvada Roy
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Premashish Kar
- Department of Medicine, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, Delhi 110002 India
| | - Oves Siddiqui
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
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26
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Liu T, Wan Z, Liu J, Zhang L, Zhou Y, Lan K, Hu Y, Zhang C. A novel real-time reverse transcription-polymerase chain reaction assay with partially double-stranded linear DNA probe for sensitive detection of hepatitis C viral RNA. J Virol Methods 2016; 236:132-138. [PMID: 27451264 DOI: 10.1016/j.jviromet.2016.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/11/2016] [Accepted: 07/16/2016] [Indexed: 12/25/2022]
Abstract
The detection and quantification of HCV RNA is very helpful for the management and treatment of HCV related diseases. Detection of low HCV viral load is a great challenge in HCV RNA detection. Here, we developed a novel real-time RT-PCR assay with partially double-stranded linear DNA probe which can detect all HCV genotypes and improve the detection performance. The novel assay has a wide linear dynamic range of HCV RNA quantification (1×10(2)-1×10(11)IU/ml) and a limit of detection of 78IU/ml. The assay exhibits an excellent reproducibility with 2.52% and 1.33% coefficients of variations, for inter- and intra-assays, respectively. To evaluate the viability of the assay, a comparison with a commercial HCV RNA detection kit was performed using 106 serum samples. The lineared correlation coefficient between the novel assay and the commercial HCV RNA detection kit was 0.940. Meanwhile, the deviation between the two methods was tolerable. Therefore, the novel real-time RT-PCR assay was applicable for laboratory diagnosis and monitoring of HCV infection.
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Affiliation(s)
- Tianfu Liu
- Department of Hepatology, Lanzhou University Second Hospital, Lanzhou, Gansu, China; Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, Jiangsu, China
| | - Jia Liu
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Lingyi Zhang
- Department of Hepatology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Yanheng Zhou
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Ke Lan
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Yihong Hu
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China.
| | - Chiyu Zhang
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China.
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27
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Wu X, Wang J, Song J, Li J, Yang Y. An accurate assay for HCV based on real-time fluorescence detection of isothermal RNA amplification. J Virol Methods 2016; 235:152-157. [PMID: 27283884 DOI: 10.1016/j.jviromet.2016.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is one of the common reasons of liver fibrosis and hepatocellular carcinoma (HCC). Early, rapid and accurate HCV RNA detection is important to prevent and control liver disease. A simultaneous amplification and testing (SAT) assay, which is based on isothermal amplification of RNA and real-time fluorescence detection, was designed to optimize routine HCV RNA detection. In this study, HCV RNA and an internal control (IC) were amplified and analyzed simultaneously by SAT assay and detection of fluorescence using routine real-time PCR equipment. The assay detected as few as 10 copies of HCV RNA transcripts. We tested 705 serum samples with SAT, among which 96.4% (680/705) showed consistent results compared with routine real-time PCR. About 92% (23/25) discordant samples were confirmed to be same results as SAT-HCV by using a second real-time PCR. The sensitivity and specificity of SAT-HCV assay were 99.6% (461/463) and 100% (242/242), respectively. In conclusion, the SAT assay is an accurate test with a high specificity and sensitivity which may increase the detection rate of HCV. It is therefore a promising tool to diagnose HCV infection.
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Affiliation(s)
- Xuping Wu
- The Second Hospital of Nanjing, Affiliated to Medical School of Southeast University, Nanjing, China
| | - Jianfang Wang
- The Second Hospital of Nanjing, Affiliated to Medical School of Southeast University, Nanjing, China
| | - Jinyun Song
- The Second Hospital of Nanjing, Affiliated to Medical School of Southeast University, Nanjing, China
| | - Jiayan Li
- The Second Hospital of Nanjing, Affiliated to Medical School of Southeast University, Nanjing, China
| | - Yongfeng Yang
- The Second Hospital of Nanjing, Affiliated to Medical School of Southeast University, Nanjing, China.
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28
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Villar LM, Cruz HM, Barbosa JR, Bezerra CS, Portilho MM, Scalioni LDP. Update on hepatitis B and C virus diagnosis. World J Virol 2015; 4:323-42. [PMID: 26568915 PMCID: PMC4641225 DOI: 10.5501/wjv.v4.i4.323] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/25/2015] [Accepted: 10/23/2015] [Indexed: 02/05/2023] Open
Abstract
Viral hepatitis B and C virus (HBV and HCV) are responsible for the most of chronic liver disease worldwide and are transmitted by parenteral route, sexual and vertical transmission. One important measure to reduce the burden of these infections is the diagnosis of acute and chronic cases of HBV and HCV. In order to provide an effective diagnosis and monitoring of antiviral treatment, it is important to choose sensitive, rapid, inexpensive, and robust analytical methods. Primary diagnosis of HBV and HCV infection is made by using serological tests for detecting antigens and antibodies against these viruses. In order to confirm primary diagnosis, to quantify viral load, to determine genotypes and resistance mutants for antiviral treatment, qualitative and quantitative molecular tests are used. In this manuscript, we review the current serological and molecular methods for the diagnosis of hepatitis B and C.
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