All Title Author
Keywords Abstract

Genotyping of HCV RNA Reveals That 3a Is the Most Prevalent Genotype in Mardan, Pakistan

DOI: 10.1155/2014/606201

Full-Text   Cite this paper   Add to My Lib


The clinical outcomes of patients infected with hepatitis C virus (HCV) range from acute resolving hepatitis to chronic liver diseases such as liver cirrhosis or hepatocellular carcinoma. Identification of the infecting virus genotype is indispensable for the exploration of many aspects of HCV infection, including epidemiology, pathogenesis, and response to antiviral therapy. 1419 individuals were screened for anti-HCV in this study, of which 166 (11.7%) were found reactive by ICT (Immunochromatographic test). These 166 anti-HCV positive and 26 normal individuals were further analyzed. RNA was extracted from serum and reverse-transcribed to cDNA and the core region of HCV genome was targeted and amplified by multiplex PCR. HCV RNA was detected in 121 individuals, of which 87 were male and 34 were female. Genotype 3a was the most prevalent among all the genotypes observed followed by 3b. Genotypes 1a, 2a, and 2b were found in 10.89%, 13.22%, and 6.61% patients, respectively. 25.41% of the HCV RNA positive samples were not typed. 6.05% of patients were found having mixed genotypes. These findings will not only help the physicians to prescribe more appropriate treatment for the HCV infection but will also draw the attention of health-related policy makers to devise strategies to curb the disease more effectively. 1. Introduction Hepatitis C virus (HCV) is the most frequent cause of chronic viral hepatitis worldwide. In the recent years, infection with HCV has emerged as one of the most common causes of acute and chronic liver diseases all over the world [1]. HCV is a member of the Flaviviridae family that bears approximately 10?kb long positive sense single-stranded RNA (ssRNA) genome. Since anti-HCV testing alone cannot differentiate between acute, chronic, or resolved infection, a supplementary test must also be carried out, involving measurement of anti-HCV immunoglobulin G activity index [2] or antibody reactivities to specific HCV structural and nonstructural proteins [3], to confirm a positive anti-HCV result [1]. HCV is known to have high rate of genetic heterogeneity [4]. This has allowed HCV strains to be classified into a number of genetically distinct groups, known as genotypes, subtypes, isolates, and quasispecies [5]. The genetic variability among HCV strains is 65.8%–68.7% nucleotide sequence identities of full-length sequences for types, 76.9%–80.1% nucleotide sequence identities of full-length sequences for subtypes, and 90.8%–99% nucleotide sequence identities of full-length sequences for isolates and quasispecies [6]. Six major genotypes,


[1]  D. B. Strader, T. Wright, D. L. Thomas, and L. B. Seeff, “Diagnosis, management, and treatment of hepatitis C,” Hepatology, vol. 39, no. 4, pp. 1147–1171, 2004.
[2]  S. Klimashevskaya, A. Obriadina, T. Ulanova et al., “Distinguishing acute from chronic and resolved hepatitis C virus (HCV) infections by measurement of anti-HCV immunoglobulin G avidity index,” Journal of Clinical Microbiology, vol. 45, no. 10, pp. 3400–3403, 2007.
[3]  A. C. Araujo, I. V. Astrakhantseva, H. A. Fields, and S. Kamili, “Distinguishing acute from chronic hepatitis C virus (HCV) infection based on antibody reactivities to specific HCV structural and nonstructural proteins,” Journal of Clinical Microbiology, vol. 49, no. 1, pp. 54–57, 2011.
[4]  L. Stuyver, W. van Arnhem, A. Wyseur, F. Hernandez, E. Delaporte, and G. Maertens, “Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 21, pp. 10134–10138, 1994.
[5]  J. Bukh, R. H. Miller, and R. H. Purcell, “Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes,” Seminars in Liver Disease, vol. 15, no. 1, pp. 41–63, 1995.
[6]  T. Sy and M. M. Jamal, “Epidemiology of hepatitis C virus (HCV) infection,” International Journal of Medical Sciences, vol. 3, no. 2, pp. 41–46, 2006.
[7]  J. Pawlotsky, “Mechanisms of antiviral treatment efficacy and failure in chronic hepatitis C,” Antiviral Research, vol. 59, no. 1, pp. 1–11, 2003.
[8]  M. Nafees, M. S. Bhatti, and I. U. Haq, “Sero-prevalence of HCV Antibodies in population attending Madina Teaching hospital, Faisalabad,” Annals of King Edward Medical University, vol. 13, no. 4, pp. 57–62, 2010.
[9]  S. Akhtar, T. Moatter, S. I. Azam, M. H. Rahbar, and S. Adil, “Prevalence and risk factors for intrafamilial transmission of hepatitis C virus in Karachi, Pakistan,” Journal of Viral Hepatitis, vol. 9, no. 4, pp. 309–314, 2002.
[10]  N. S. Ali, K. Jamal, and R. Qureshi, “Hepatitis B vaccination status and identification of risk factors for hepatitis B in health care workers,” Journal of the College of Physicians and Surgeons. Pakistan, vol. 15, no. 5, pp. 257–260, 2005.
[11]  T. Ohno, M. Mizokami, R. Wu et al., “New hepatitis C virus (HCV) genotyping system that allows for identification of HCV genotypes 1a, 1b, 2a, 2b, 3a, 3b, 4, 5a, and 6a,” Journal of Clinical Microbiology, vol. 35, no. 1, pp. 201–207, 1997.
[12]  Y. S. Lee, S. K. Yoon, E. S. Chung et al., “The relationship of histologic activity to serum ALT, HCV genotype and HCV RNA titers in chronic hepatitis C,” Journal of Korean Medical Science, vol. 16, no. 5, pp. 585–591, 2001.
[13]  X. Forns, M. D. Maluenda, F. X. López-Labrador et al., “Comparative study of three methods for genotyping hepatitis C virus strains in samples from Spanish patients,” Journal of Clinical Microbiology, vol. 34, no. 10, pp. 2516–2521, 1996.
[14]  K. Nagayama, M. Kurosaki, N. Enomoto, Y. Miyasaka, F. Marumo, and C. Sato, “Characteristics of hepatitis C viral genome associated with disease progression,” Hepatology, vol. 31, no. 3, pp. 745–750, 2000.
[15]  J. Pawlotsky, L. Prescott, P. Simmonds et al., “Serological determination of hepatitis C virus genotype: comparison with a standardized genotyping assay,” Journal of Clinical Microbiology, vol. 35, no. 7, pp. 1734–1739, 1997.
[16]  H. Okamoto, Y. Sugiyama, S. Okada et al., “Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources,” Journal of General Virology, vol. 73, part 3, pp. 673–679, 1992.
[17]  M. T. Pyne, E. Q. Konnick, A. Phansalkar, and D. R. Hillyard, “Evaluation of the abbott investigational use only RealTime hepatitis C virus (HCV) assay and comparison to the roche TaqMan HCV analyte-specific reagent assay,” Journal of Clinical Microbiology, vol. 47, no. 9, pp. 2872–2878, 2009.
[18]  N. Muhammad and M. A. Jan, “Epidemiology of hepatitis C virus (HCV) infection,” Journal of the College of Physicians and Surgeons. Pakistan, vol. 15, no. 1, p. 11, 2005.
[19]  M. Idrees and S. Riazuddin, “Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission,” BMC Infectious Diseases, vol. 8, article 69, 2008.
[20]  J. R. Oubi?a, J. F. Quarleri, M. A. Sawicki et al., “Hepatitis C virus and GBV-C/hepatitis G virus in Argentine patients with porphyria cutanea tarda,” Intervirology, vol. 44, no. 4, pp. 215–218, 2001.
[21]  V. Alfonso, D. Flichman, S. Sookoian, V. A. Mbayed, and R. H. Campos, “Phylogenetic characterization of genotype 4 hepatitis C virus isolates from Argentina,” Journal of Clinical Microbiology, vol. 39, no. 5, pp. 1989–1992, 2001.
[22]  S. Attaullah, S. Khan, and I. Ali, “Hepatitis C virus genotypes in Pakistan: a systemic review,” Virology Journal, vol. 8, article 433, 2011.
[23]  Y.-W. Hu, E. Balaskas, M. Furione et al., “Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections,” Journal of Clinical Microbiology, vol. 38, no. 8, pp. 2807–2813, 2000.
[24]  J.-S. Li, L. Vitvitski, S.-P. Tong, and C. Trepo, “Identification of the third major genotype of hepatitis C virus in France,” Biochemical and Biophysical Research Communications, vol. 199, no. 3, pp. 1474–1481, 1994.
[25]  J. Albadalejo, R. Alonso, R. Antinozzi et al., “Multicenter evaluation of the COBAS AMPLICOR HCV assay, an integrated PCR system for rapid detection of hepatitis C virus RNA in the diagnostic laboratory,” Journal of Clinical Microbiology, vol. 36, no. 4, pp. 862–865, 1998.


comments powered by Disqus