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Riaz S, Bashir MF, Haider S, Rahid N. Association of genotypes with viral load and biochemical markers in HCV-infected Sindhi patients. Braz J Microbiol 2016; 47:980-986. [PMID: 27528079 PMCID: PMC5052380 DOI: 10.1016/j.bjm.2016.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/05/2016] [Indexed: 12/16/2022] Open
Abstract
The presented study had two objectives. The first was to examine distributions of Hepatitis C Virus (HCV) genotypes in Sindh, Pakistan, where HCV is prevalent. The other was to explore clinically relevant relationships between the genotypes, viral load (measured by real-time polymerase chain reaction assays) and biochemical markers. For this, 1471 HCV-infected patients in six cities in Sindh were recruited and sampled. HCV genotype distributions varied among the cities, but genotype 3a was most prevalent, followed by 3b, 1a and 1b (detected in 51.5, 22.7. 9.25 and 3.2% of the cases, respectively). No type-specific sequences were detected in serum samples from 189 (12.8%) of the 1471 patients. Frequencies of low (<200,000IU/mL serum), intermediate (200,000-600,000IU/mL serum) and high (>600,000IU/mL serum) viral loads were respectively 45.4, 16.5 and 38.1% for patients infected with genotype 3, and 16.9, 36.9 and 46.2%, respectively, for patients with other genotypes. Infection with genotype 1a was associated with significantly higher (p<0.005) alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase titers than infection with genotype 3a. The results will help in the formulation of treatment strategies.
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Affiliation(s)
- Saba Riaz
- Citilab and Research Centre, Division of Molecular Pathology, Lahore, Pakistan; University of the Punjab, Department of Microbiology and Molecular Genetics, Lahore, Pakistan.
| | - Muhammad Faisal Bashir
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan; Citilab and Research Centre, Division of Molecular Pathology, Lahore, Pakistan
| | - Saleem Haider
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan; University of the Punjab, Institute of Agricultural Sciences, Lahore, Pakistan.
| | - Naeem Rahid
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan
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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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Athar MA, Xu Y, Xie X, Xu Z, Ahmad V, Hayder Z, Hussain SS, Liao Y, Li Q. Rapid detection of HCV genotyping 1a, 1b, 2a, 3a, 3b and 6a in a single reaction using two-melting temperature codes by a real-time PCR-based assay. J Virol Methods 2015; 222:85-90. [PMID: 26068393 DOI: 10.1016/j.jviromet.2015.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/26/2015] [Accepted: 05/26/2015] [Indexed: 12/18/2022]
Abstract
The genotype of the hepatitis C virus (HCV) is an important indicator for antiviral therapeutic response. We hereby described development of a rapid HCV genotyping approach that enabled the identification of the six most common HCV subtypes of Asia, i.e., 1a, 1b, 2a, 3a, 3b, and 6a, in a single reaction. Using two dual-labeled, self-quenched probes that target the core region of the HCV genome, the exact subtype could be accurately identified by two-melting temperature codes determined from the two respective probes in a real-time PCR assay. Analytical sensitivity studies using armored RNA samples representing each of the six HCV subtypes showed that 5 copies/reaction of HCV RNA could be detected. The assay was evaluated using 244 HCV-positive serum samples and the results were compared with sequencing analysis. Of the 224 samples, subtype 3a (127, 52.3%) was the dominant, followed by 1b (51, 20.9%), 3b (47, 19.3%), 2a (8, 3.3%), 6a (4, 1.6%) and the least was subtype 1a (1, 0.4%). Moreover, 6 (2.5%) mixed infection samples were also detected. These results were fully concordant with sequencing analysis. We concluded that this real-time PCR-based assay could provide a rapid and reliable tool for routine HCV genotyping in most Asian countries.
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Affiliation(s)
- Muhammad Ammar Athar
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China
| | - Ye Xu
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China
| | - Xiaoting Xie
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhenxing Xu
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen 361005, Fujian, China
| | - Vakil Ahmad
- Division of Health Biotechnology, National Institute for Biotechnology & Genetic Engineering, P.O. Box 577, Faisalabad, Punjab, Pakistan
| | - Zulfiqar Hayder
- Department of Pathology, Quid-e-Azam Medical College, Bahawalpur, Punjab, Pakistan
| | - Syed Sajid Hussain
- Department of Pathology, Quid-e-Azam Medical College, Bahawalpur, Punjab, Pakistan
| | - Yiqun Liao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361005, Fujian, China.
| | - Qingge Li
- The State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Engineering Research Center of Molecular Diagnostics, Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China.
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