1
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Hussain R, Khalid H, Fatmi MQ. HCV genotype-specific drug discovery through structure-based virtual screening. PURE APPL CHEM 2022. [DOI: 10.1515/pac-2021-1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Hepatitis C Virus (HCV) poses great threat worldwide, and is a major cause for liver cancer. HCV genome encodes polyprotein that is subsequently cleaved into independently functioning proteins, which spread viral infection in host. The Non-Structural 3 (NS3) protease is responsible for cleaving the polyprotein, and may serve as a potential drug target. Since HCV has seven genotypes, the available drugs are predominantly designed for genotype 1 (GT1), and others prevalent in Europe. Consequently, these drugs lose efficacy when they are used for different genotypes. The current perspective study aims to find potential drug candidate against genotype 3 (GT3), prevalent in South Asia. The current study employed molecular docking technique and in silico ADME prediction tool to highlight potentially active compounds against HCV NS3 GT3. The study revealed Li_PIO_114 and Li_PIH_191 as potential lead compounds, as suggested by their docking score and ADME properties. These two compounds could be further optimized to improve their drug likeliness for curing HCV GT3.
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Affiliation(s)
- Rashid Hussain
- Department of Chemistry , Forman Christian College University , Lahore 54000 , Pakistan
| | - Hira Khalid
- Department of Chemistry , Forman Christian College University , Lahore 54000 , Pakistan
| | - Muhammad Qaiser Fatmi
- Department of Biosciences , COMSATS University Islamabad , Park Road, Chak Shahzad , Islamabad 45600 , Pakistan
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2
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AlMalki WH, Shahid I, Abdalla AN, Johargy AK, Ahmed M, Hassan S. Virological surveillance, molecular phylogeny, and evolutionary dynamics of hepatitis C virus subtypes 1a and 4a isolates in patients from Saudi Arabia. Saudi J Biol Sci 2021; 28:1664-1677. [PMID: 33732052 PMCID: PMC7938134 DOI: 10.1016/j.sjbs.2020.11.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022] Open
Abstract
Hepatitis C virus (HCV) subtypes are pre-requisite to predict endemicity, epidemiology, clinical pathogenesis, diagnosis, and treatment of chronic hepatitis C infection. HCV genotypes 4 and 1 are the most prevalent in Saudi Arabia, however; less consensus data exist on circulating HCV subtypes in infected individuals. This study was aimed to demonstrate the virological surveillance, phylogenetic analysis, and evolutionary relationship of HCV genotypes 4 and 1 subtypes in the Saudi population with the rest of the world. Fifty-five clinical specimens from different parts of the country were analyzed based on 5′ untranslated region (5′ UTR) amplification, direct sequencing, and for molecular evolutionary genetic analysis. Pair-wise comparison and multiple sequence alignment were performed to determine the nucleotide conservation, nucleotide variation, and positional mutations within the sequenced isolates. The evolutionary relationship of sequenced HCV isolates with referenced HCV strains from the rest of the world was established by computing pairwise genetic distances and generating phylogenetic trees. Twelve new sequences were submitted to GenBank, NCBI database. The results revealed that HCV subtype 4a is more prevalent preceded by 1a in the Saudi population. Molecular phylogeny predicts the descendants’ relationship of subtype 4a isolates very close to Egyptian prototype HCV strains, while 1a isolates were homogeneous and clustering to the European and North American genetic lineages. The implications of this study highlight the importance of HCV subtyping as an indispensable tool to monitor the distribution of viral strains, to determine the risk factors of infection prevalence, and to investigate clinical differences of treatment outcomes among intergenotypic and intragenotypic isolates in the treated population.
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Affiliation(s)
- Waleed H AlMalki
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Imran Shahid
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia.,Department of Pharmacology and Toxicology, Faculty of Medicine, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Ayman K Johargy
- Medical Microbiology Department, Faculty of Medicine, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Muhammad Ahmed
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Sajida Hassan
- Viral Hepatitis Program, Laboratory of Medicine, University of Washington, Seattle, WA, USA
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3
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Huang YC, Huang CF, Liu SF, Liu HY, Yeh ML, Huang CI, Hsieh MH, Dai CY, Chen SC, Yu ML, Chuang WL, Huang JF. The performance of HCV GT plus RUO reagent in determining Hepatitis C virus genotypes in Taiwan. PLoS One 2021; 16:e0246376. [PMID: 33513184 PMCID: PMC7845948 DOI: 10.1371/journal.pone.0246376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/15/2021] [Indexed: 11/18/2022] Open
Abstract
Background and aims Hepatitis C virus (HCV) genotyping is a pivotal tool for epidemiological investigation, guiding management and antiviral treatment. Challenge existed in identifying subtypes of genotype-1 (G-1) and genotype (GT) of indeterminate. Recently, the Abbott HCV RealTime Genotype Plus RUO assay (HCV GT Plus) has been developed aiming to overcome the limitations. We aimed to evaluate the performance of the assay compared with 5’ UTR sequencing in clinical samples. Materials and methods Eligible individuals were treatment chronic hepatitis C patients that were enrolled consecutively in a medical center and two core regional hospitals in southern Taiwan from Oct 2017 through Aug 2018. The patient with genotype 1 without subtype and indeterminate previously genotyped by Abbott RealTime HCV GT II will further determinate by Abbott HCV RealTime HCV GT Plus. All of the genotype results were validated by 5' UTR sequencing as a reference standard. Results A total of 100 viremic CHC patients were recruited, including 63 G-1 patients (male: 28), and 37 patients (male: 15) of indeterminate genotyped by Abbott RealTime HCV GT II assay (HCV GT II), respectively. The detection rate of 63 GT1 samples without subtype were 93.7% (59/63), 37 indeterminate samples without genotype were 62.2 (23/37) by HCV GT Plus. 5' UTR sequencing confirmed HCV GT Plus characterized results for 84.7% (50/59) of type1, with 100% (4/4), 82.8 (24/29) and 84.6% (22/26) for 1a, 1b and type6; 65.2% (15/23) of indeterminate with 100% (3/3) and 60% (12/20) for 1b and type 6 samples, respectively. Conclusions The Abbott RealTime HCV GT Plus RUO assay provides additional performance in GT detection.
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Affiliation(s)
- Ying-Chou Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chung-Feng Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shu-Fen Liu
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hung-Yin Liu
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ming-Lun Yeh
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-I Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Meng-Hsuan Hsieh
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chia-Yen Dai
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shinn-Chern Chen
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ming-Lung Yu
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Jee-Fu Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Centre, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- * E-mail:
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4
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Sallam M, Batarseh R, Natsheh A, Abbadi J, Al-Fraihat E, Yaseen A, Kaddomi D, Khamees N, Mahafzah A, Şahin GÖ. An update on hepatitis C virus genotype distribution in Jordan: a 12-year retrospective study from a tertiary care teaching hospital in Amman. BMC Infect Dis 2019; 20:3. [PMID: 31892307 PMCID: PMC6938611 DOI: 10.1186/s12879-019-4735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
Background Nucleic acid hybridization (NAH) of hepatitis C virus (HCV) is a practical and reliable tool for virus genotyping. Genotype assignment is an important factor in the prediction of treatment success in chronic hepatitis C patients. The aim of this study was to determine the genotype distribution among HCV clinical isolates in Jordan between 2007 and 2018. Methods Electronic and paper-based clinical data registry records from 2007 to 2018 at the Jordan University Hospital (JUH) were retrospectively examined for individuals with HCV genotype, HCV viral load, and alanine aminotransferase (ALT) testing results. Genotype determination was based on NAH technique using the HCV 5′ untranslated region (5′ UTR) with 386 requests available from 342 unique individuals. Results A total of 263 out of 342 unique individuals (76.9%) had genotyping results available for final analysis with 259 individuals each having a single genotyping result. The most common HCV genotypes in the study were: genotype 4 (n = 142, 54.0%), genotype 1 (n = 87, 33.1%), genotype 3 (n = 16, 6.1%), genotype 2 (n = 9, 3.4%), other undetermined genotypes (n = 5, 1.9%) and mixed infections (n = 4, 1.5%). Sub-genotyping results were available for 46 individuals as follows: sub-genotype 4c/d (n = 13, 28.3%), sub-genotype 1a (n = 11, 23.9%), sub-genotype 1b (n = 10, 21.7%), sub-genotype 4a (n = 8, 17.4%), sub-genotype 3a (n = 2, 4.3%), sub-genotypes 2a/c and 4 h (n = 1, 2.2% for both). Individuals infected with genotype 1 showed higher viral load when compared to those infected with genotype 4 (p = 0.048, t-test). Younger HCV-infected individuals (< 52 years) had higher ALT levels compared to older individuals (p = 0.036, t-test). Self-reported risk factors for HCV acquisition included: history of previous surgery, invasive dental procedures, and blood transfusion, delivery at home, circumcision at home and wet cupping therapy (hijama). Conclusions High genetic diversity of HCV was found in Jordan, with genotypes 4 and 1 as the most prevalent genotypes co-circulating in the country. Potential impact of virus genotype on disease markers (viral load, ALT) was detected and needs further assessment. The study can be helpful to plan for future prevention and management of HCV infection in Jordan.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.
| | - Rawan Batarseh
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Anas Natsheh
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Jumana Abbadi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Esraa Al-Fraihat
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Alaa' Yaseen
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Doaa Kaddomi
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Nadia Khamees
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Gülşen Özkaya Şahin
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.,Department of Clinical Microbiology, Laboratory Medicine, Skåne University Hospital, 22100, Lund, Sweden
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5
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Uribe-Noguez LA, Mata-Marín JA, Ocaña-Mondragón A, Pompa-Mera EN, Ribas-Aparicio RM, Arroyo-Anduiza CI, Gomez-Torres ME, Chaparro-Sánchez A, Gaytán-Martínez J, Mauss S. Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico. J Infect Chemother 2019; 26:205-210. [PMID: 31537472 DOI: 10.1016/j.jiac.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.
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Affiliation(s)
- Luis Antonio Uribe-Noguez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico; Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico; Centro de Simulación Médica, Facultad Mexicana de Medicina, Universidad La Salle, Mexico City, Mexico.
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alicia Ocaña-Mondragón
- Laboratorio Central de Epidemiología, División de Laboratorios de Vigilancia e Investigación Epidemiológica, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Ericka Nelly Pompa-Mera
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico
| | - Carla Ileana Arroyo-Anduiza
- Departamento de Patología Clínica, Banco Central de Sangre, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - María Elena Gomez-Torres
- Laboratorio de Urgencias, Hospital de Infectología, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alberto Chaparro-Sánchez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Jesus Gaytán-Martínez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Stefan Mauss
- Center for HIV and Hepatogastroenterology, Duesseldorf, Germany
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6
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Mesbahi Z, Kabbaj H, Malki H, Bouihat N, Qrafli M, Belefquih B, Marcil S, Challine D, Pawlotsky JM, Bouvier M, Seffar M. Indeterminate genotypes of hepatitis C virus by the Abbott RealTime HCV Genotype II assay in Morocco. About eight cases resolved by a sequencing method. J Med Virol 2018; 90:1352-1357. [PMID: 29663433 DOI: 10.1002/jmv.25191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022]
Abstract
The early detection and genotyping of the hepatitis C virus (HCV) are important in the management of this infection. The genotype is the major factor influencing treatment decisions. That's why it is necessary to use fast and accurate methods in its determination. This study reports, over a period of 3 years (from May 2012 to July 2015), the percentage of indeterminate genotypes by the Abbott RealTime HCV Genotype II test and their results using a sequencing technique. Of 309 samples of 309 patients tested, 11 were indeterminate (4.4%). There were three cases of cross-reactivity (1b/4 in one case, 2/5 in two cases) and a possible co-infection 1 + 4. Among those indeterminate genotypes, cross-reactivities and co-infections, ten samples were tested by sequencing. The results were for four of them a 1d subtype, five were a 2i subtype and one was a 2l subtype. These results support the thesis of complementarity between the two methods: genotyping for the detection of mixed reactions and sequencing for resolving indeterminate cases by genotyping.
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Affiliation(s)
- Zineb Mesbahi
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Hakima Kabbaj
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Houcine Malki
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Najat Bouihat
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Mounia Qrafli
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Bouchra Belefquih
- Laboratory of Virology, Cheikh Khalifa Hospital, Casablanca, Morocco
| | - Sarrah Marcil
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Dominique Challine
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Magali Bouvier
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Myriam Seffar
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
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7
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High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping. Clin Microbiol Infect 2017; 23:775.e1-775.e6. [DOI: 10.1016/j.cmi.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 01/17/2023]
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8
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Olmstead AD, Lee TD, Chow R, Gunadasa K, Auk B, Krajden M, Jassem AN. Development and validation of a real-time, reverse transcription PCR assay for rapid and low-cost genotyping of hepatitis C virus genotypes 1a, 1b, 2, and 3a. J Virol Methods 2017; 244:17-22. [PMID: 28219761 DOI: 10.1016/j.jviromet.2017.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
Hepatitis C virus (HCV) infection affects millions of people and leads to liver fibrosis, cirrhosis, and hepatocellular carcinoma. Treatment regimen selection requires HCV genotype (Gt) and Gt 1 subtype determination. Use of a laboratory developed, reverse transcription (RT)-PCR assay was explored as a low-cost, high-throughput screening approach for the major HCV genotypes and subtypes in North America. A commercial line probe assay (LiPA) was used for comparison. Sequencing and/or an alternative PCR assay were used for discordant analyses. Testing of 155 clinical samples revealed that a paired, duplex real-time RT-PCR assay that targets Gts 1a and 3a in one reaction and Gts 1b and 2 in another had 95% overall sensitivity and individual Gt sensitivity and specificity of 98-100% and 85-98%, respectively. The RT-PCR assay detected mixed HCV Gts in clinical and spiked samples and no false-positive reactions occurred with rare Gts 3b, 4, 5, or 6. Implementation of the RT-PCR assay, with some reflex LiPA testing, would cost only a small portion of the cost of using LiPA alone, and can also save 1.5h of hands-on time. The use of a laboratory developed RT-PCR assay for HCV genotyping has the potential to reduce cost and labour burdens in high-volume testing settings.
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Affiliation(s)
- Andrea D Olmstead
- University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Tracy D Lee
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Ron Chow
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Kingsley Gunadasa
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Brian Auk
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha N Jassem
- British Columbia Centre for Disease Control Public Health Laboratory, Provincial Health Services Authority, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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9
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Souii A, Elargoubi A, Fallecker C, Mastouri M, Drouet E. Hepatitis C Genotype Prevalence in Monastir Region, Tunisia: Correlation between 5' Untranslated Region (5'UTR), Non-structural 5B (NS5B), and Core Sequences in HCV Subtyping. Curr Microbiol 2016; 73:324-334. [PMID: 27189386 DOI: 10.1007/s00284-016-1064-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/07/2016] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. It constitutes a major public health around the world. There is no vaccine available against HCV, and current therapies are effective in only small percentage of patients. HCV has wide population-specific genotype variability. Genotype knowledge and viral load assessment are equally important for designing therapeutic strategies. Taking into account that the molecular epidemiology of HCV variants circulating in Tunisia is not yet well elucidated, and that, at present, little is known about the distribution pattern of HCV in Monastir region (Tunisia), we aimed, herein, to evaluate the prevalence of HCV genotypes in Monastir and to identify risk-related factors. For this purpose, 50 anti-HCV antibody-positive cases were diagnosed and subjected to viral RNA extraction, amplification, genotyping, and viral load quantification. Molecular epidemiology was studied by 5' untranslated region (5' UTR) sequencing as compared with the non-structural 5B (NS5B) and core region sequences. Overall concordance between 5' UTR, core, and NS5B sequencing was 100 %. The highest prevalent genotype was 1b (50 %) followed by genotypes 1a (16 %), 4a (12 %), 2a (10 %), 2c (8 %), and 3a (4 %). Interestingly, the subtype 1b had a statistically significant higher viral load than the other genotypes followed by subtype 1a. Based on these data, this study revealed a high prevalence of HCV genotype 1 (subtypes 1b and 1a) compared to other genotypes. A continued monitoring of HCV and knowledge of circulating genotypes could impact on future vaccine formulations.
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Affiliation(s)
- Amira Souii
- Department of Biotechnology, Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, 09 Sreet Zouhair Essafi, 1006, Tunis, Tunisia.
| | - Aida Elargoubi
- Laboratory of Microbiology of the University Hospital Center Fattouma Bourguiba of Monastir, Avenue Farhat HACHED, 5000, Monastir, Tunisia
| | - Catherine Fallecker
- Institute of Structural Biology (Ibs), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, Street of Martyrs, 38042, Grenoble, France
| | - Maha Mastouri
- Laboratory of Microbiology of the University Hospital Center Fattouma Bourguiba of Monastir, Avenue Farhat HACHED, 5000, Monastir, Tunisia.,Laboratory of Contagious Diseases and Biologically Active Substances, LR99 - ES27, Faculty of Pharmacy, University of Monastir, Avicenne Street, 5000, Monastir, Tunisia
| | - Emmanuel Drouet
- Institute of Structural Biology (Ibs), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, Street of Martyrs, 38042, Grenoble, France
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Saludes V, Quer J, Gregori J, Bascuñana E, García-Cehic D, Esteban JI, Ausina V, Martró E. Identification of hepatitis C virus genotype 3 by a commercial assay challenged by natural polymorphisms detected in Spain from patients with diverse origins. J Clin Virol 2016; 78:14-9. [PMID: 26946155 DOI: 10.1016/j.jcv.2016.02.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/14/2015] [Accepted: 02/24/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) genotyping is crucial in clinical practise for determining the type and duration of antiviral therapy. Between 2009 and 2014, 24 (7.95%) of all HCV genotype 3 (HCV-3) cases obtained indeterminate results via the RealTime HCV Genotype II assay (Abbott) at a tertiary care center in Spain. HCV-3 is the second most common genotype worldwide. Moreover, it has been associated with a higher risk of liver disease progression and a lower response to the latest antivirals. OBJECTIVE Given the clinical significance of accurately identifying HCV-3, we aimed to characterize the genetic diversity of the HCV 5' untranslated region (5' UTR), the target of genotyping assays, by ultradeep pyrosequencing (UDPS). STUDY DESIGN For the 24 indeterminate samples, the 5' UTR-core was amplified and subjected to UDPS with the 454/GS-Junior platform (Roche). The genotype/subtype of each identified haplotype was assigned by phylogenetic analysis. For comparison, three additional samples correctly identified as HCV-3 by the real-time assay were also analyzed. RESULTS HCV genotyping based on 5' UTR-core UDPS was in agreement with NS5B Sanger sequencing in all cases, confirming the absence of mixed infections and recombination events. The generated 5' UTR sequences proved the presence of one to three polymorphisms at the probe-binding site of the Abbott assay, thereby differentiating indeterminate from correctly genotyped HCV-3 samples. CONCLUSIONS The observed naturally occurring polymorphisms provide insight into regional differences observed with genotype 3, their impact on genotyping assay performance, and potential improvement and designing options.
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Affiliation(s)
- Verónica Saludes
- Microbiology Service, Germans Trias i Pujol University Hospital, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Spain; Centro de Investigación Biomédica en Red (CIBER) en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Spain
| | - Elisabet Bascuñana
- Microbiology Service, Germans Trias i Pujol University Hospital, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Spain
| | - Damir García-Cehic
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicente Ausina
- Microbiology Service, Germans Trias i Pujol University Hospital, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Elisa Martró
- Microbiology Service, Germans Trias i Pujol University Hospital, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Spain; Centro de Investigación Biomédica en Red (CIBER) en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
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11
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A Pan-HIV Strategy for Complete Genome Sequencing. J Clin Microbiol 2015; 54:868-82. [PMID: 26699702 DOI: 10.1128/jcm.02479-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/16/2015] [Indexed: 01/23/2023] Open
Abstract
Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5' end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance.
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12
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Nyan DC, Swinson KL. A method for rapid detection and genotype identification of hepatitis C virus 1-6 by one-step reverse transcription loop-mediated isothermal amplification. Int J Infect Dis 2015; 43:30-36. [PMID: 26686938 DOI: 10.1016/j.ijid.2015.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/26/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Hepatitis C virus (HCV) is probably the leading cause of liver cirrhosis and hepatocellular carcinoma globally. Diagnostic tools conventionally used for the detection and identification of HCV infection are technically demanding, time-consuming, and costly for resource-limited environments. This study reports the development of the first rapid loop-mediated reverse transcription isothermal amplification assay that rapidly detects and identifies HCV genotypes in blood components. METHODS RNA extracted from donor plasma and serum specimens was applied to a one-step reverse transcription loop-mediated isothermal amplification reaction performed with HCV-specific oligonucleotides. Reactions were conducted at 63.5 °C for 30-60 min. The diagnostic characteristics of the assay were investigated and validated with clinical specimens. RESULTS Electrophoretic analysis of amplification revealed detection and identification of HCV genotypes 1-6. Positive amplification revealed unique ladder-like banding patterns that identified each HCV genotype. The assay demonstrated a sensitivity of 91.5% and specificity of 100%. Rapid naked-eye detection of HCV infection was facilitated by observation of an intense fluorescent glow of amplified targets under UV illumination. CONCLUSION These diagnostic characteristics highlight the potential utility of this assay for the rapid detection and genotype identification of HCV infection in field and point-of-care settings in endemic regions and resource-limited environments.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Kevin L Swinson
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
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Messina JP, Humphreys I, Flaxman A, Brown A, Cooke GS, Pybus OG, Barnes E. Global distribution and prevalence of hepatitis C virus genotypes. Hepatology 2015; 61:77-87. [PMID: 25069599 PMCID: PMC4303918 DOI: 10.1002/hep.27259] [Citation(s) in RCA: 1066] [Impact Index Per Article: 118.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/09/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED Hepatitis C virus (HCV) exhibits high genetic diversity, characterized by regional variations in genotype prevalence. This poses a challenge to the improved development of vaccines and pan-genotypic treatments, which require the consideration of global trends in HCV genotype prevalence. Here we provide the first comprehensive survey of these trends. To approximate national HCV genotype prevalence, studies published between 1989 and 2013 reporting HCV genotypes are reviewed and combined with overall HCV prevalence estimates from the Global Burden of Disease (GBD) project. We also generate regional and global genotype prevalence estimates, inferring data for countries lacking genotype information. We include 1,217 studies in our analysis, representing 117 countries and 90% of the global population. We calculate that HCV genotype 1 is the most prevalent worldwide, comprising 83.4 million cases (46.2% of all HCV cases), approximately one-third of which are in East Asia. Genotype 3 is the next most prevalent globally (54.3 million, 30.1%); genotypes 2, 4, and 6 are responsible for a total 22.8% of all cases; genotype 5 comprises the remaining <1%. While genotypes 1 and 3 dominate in most countries irrespective of economic status, the largest proportions of genotypes 4 and 5 are in lower-income countries. CONCLUSION Although genotype 1 is most common worldwide, nongenotype 1 HCV cases—which are less well served by advances in vaccine and drug development—still comprise over half of all HCV cases. Relative genotype proportions are needed to inform healthcare models, which must be geographically tailored to specific countries or regions in order to improve access to new treatments. Genotype surveillance data are needed from many countries to improve estimates of unmet need.
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Affiliation(s)
- Jane P Messina
- Spatial Epidemiology and Ecology Group, Department of Zoology, University of OxfordOxford, UK
| | - Isla Humphreys
- Peter Medawar Building for Pathogen Research, University of Oxford, and Oxford NHIR BRCOxford, UK
| | | | - Anthony Brown
- Peter Medawar Building for Pathogen Research, University of Oxford, and Oxford NHIR BRCOxford, UK
| | - Graham S Cooke
- Division of Infectious Diseases, St Mary's Campus, Imperial CollegeLondon, UK
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, and Oxford NHIR BRCOxford, UK
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