IDENTIFICATION OF MUTATION SITES IN HEPATITIS C VIRUS GENOTYPE 3A IN NON-RESPONDERS TO COMBINATION THERAPY WITH INTERFERON- ΑLFA AND RIBAVIRIN IN RESIDENTS OF KHYBER PAKHTUNKHWA PROVINCE PAKISTAN

Authors

  • Sardar Muhammad Peshawar Medical College Peshwar
  • Mehmud ur Rehman
  • Najib ul Haq
  • Muhammad Mumtaz Khan
  • Sajjad Ahmad

Abstract

Background: This study was carried out to search for mutations in the gene encoding for Non-Structural Protein 5A, specifically in the interferon sensitivity determining region of hepatitis C virus (HCV) genotype 3a, isolated from serum samples of patients not responding to treatment with oral Ribavirin and Interferon alpha injections. Methods: This descriptive case series was conducted on HCV patients reporting in the attached teaching hospitals of Peshawar Medical College selected by consecutive sampling technique from 1st July to 31st December 2012. Amino acid sequencing was performed at the Centre of Applied Molecular Biology Lahore.  Patients showing no clinical response after 6 months of combination therapy with Injection Interferon alpha + Ribavirin and still having positive polymerase chain reaction (Declared Non-Responders) were included in this study. Results: Amino acid sequencing was performed on HCV isolates from twenty non-responder and five responder patients. All these sequences were compared with Newzealand1 (NZL1) sequence from the gene bank for mutations; 0–7 mutations were observed in responders as compared to 10–27 mutations in non-responder patients (p value <0.005). Conclusion: We were able to determine that there is a positive correlation between the number of mutations in NS5A ISDR and non-response to combination therapy. Synonymous mutations >10 and non-synonymous mutations >7 in this region suggest poor response to treatment.Keywords: ISDR; NS5A; Non Responders

Author Biography

Sardar Muhammad, Peshawar Medical College Peshwar

Assistant Professor MicrobiologyDepartment of PathologyPeshawar Medical CollegePeshawar, Pakistan

References

References

Theise DN ed. Liver and Gallbladder. In: Kumar V, Abbas AK, Aster JC: Robin and Cotran Pathological Basis of Disease 9th ed. Philadelphia, Elsevier Saunders, 2015, p. 830-835

Alter MJ: Epidemiology of C virus infection. World J Gastroenterol 2007;13:2436-2441

Shepard CW, Finelli L and Alter MJ: Global epidemiology of hepatitis C virus infection. Lancet Infect Dis 2005; 5:558-567.

Di Bisceglie A M: Hepatitis C and hepatocellular carcinoma. Hepatology 1997; 26: 34S-38S

Idrees M, Rafique S, Rehman I, Akbar H, Yousaf M Z, Butt S et al: Hepatitis C virus genotype 3a infection and hepatocellular carcinoma: Pakistan experience. World J Gastroenterol 2009; 28; 15(40): 5080-5085

Munir S, Saleem S, Idrees M, Tariq A, Butt S et al: Hepatitis C Treatment: current and future perspectives. Virology Journal 2010, 7:296

7. Simmonds P, Holmes EC, Cha TA, Chan SW, McOmish F, et al. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol1993; 74:2391–2399.

8. Zein NN, Rakela J, Krawitt EL, Reddy KR, Tominaga T, Persing DH: Hepatitis C virus genotypes in the United States: Epidemiology, Pathogenicity, and response to interferon therapy. Ann Intern Med 1996; 125:634-639

9. McOmish F, Yap PIL, Dow BC, Follett EAC, Seed C et al : Geographic distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J Clin Microbiol1994; 32: 884-92.

10. Nousbaum JB, Pol S, Nalpas B, Landais P, Berthelot P, Brechot C, the Collaborative Study Group: Hepatitis C virus type 1b (II) infection in France and Italy. Ann Intern Med 1995; 122:161-168.

11. Takada NS, Takase S, Takada A, Date T: Differences in the hepatitis C virus genotypes in different countries. J Hepatol 1993; 17:277-283.

12. Abdulkarim AS, Zein NN, Germer JJ, Kolbert CP, Kabbani L et al: Hepatitis Cvirus genotypes and hepatitis G virus in haemodialysis patients from Syria: identification of two novel hepatitis C virus subtypes. Am J Trop Med Hyg1998; 59:571-576

13. Chamberlain RW, Adams N, Saeed AA, Simmonds P, and Elliot RM: Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J Gen Virol 1997;78:1341-1347.

14. Cha TA, Kolberg J, Irvine B, Stempien M, Beall E, Yano M, Choo QL, Houghton M, Kuo G, Han JH and Urdea MS: Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma. J Clin Microbiol1992;29:2528-25

17. DeLamballerie X, Charrel RN, Attoui H, De Micco P: Classification of hepatitis C virus variants in six major types based on analysis of the envelope 1 and non structural 5B genome regions and complete polyprotein sequences. J Gen Virol1997; 78:45-51.

18. Tokita H, Okamoto H, Iizuka H, Kishimoto J, Tsuda F, Miyakawa Y, Mayumi M: The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7–9 and comparison with those in the other eight genetic groups. J Gen Virol 1998; 79:1847-1857.

Enomoto, N., I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, Y. Ogura, N. Izumi, F. Marumo, and C. Sato. 1996. Mutations in the non structural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N. Engl. J. Med. 334:77-81.

Aurora R, Donlin MJ, Cannon NA, et al. Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans.

J Clin Invest 2009; 119: 225–36.

Kohashi, T., S. Maekawa, N. Sakamoto, M. Kurosaki, H. Watanabe, Y. Tanabe, C.-H. Chen, N. Kanazawa, M, Nakagawa, S. Kakinuma et al: Site-specific mutation of the interferon sensitivity-determining region (ISDR) modulates hepatitis C virus replication. J. Viral Hepat. 2006; 13:582-590.

Idrees M and Riazuddin S: Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of Transmission. BMC Infectious Diseases 2008; 8:69

Asselah, T, Estrabaud, E, Bieche, Lapalus M I, De Muynck, S et al: Hepatitis C: viral and host factors associated with non-response to pegylated interferon plus ribavirin Liver International 2010; ISSN 1478-3223 DOI: 10.1111 / j.1478 3231. 2010. 02283.x

Pascu M, Martus P, Hohne M, Wiedenmann B, Hopf U, Schreie E, and Berg T: Sustained virological response in hepatitis C virus type 1b infected patients is predicted by the number of mutations within the NS5A ISDR: a meta- analysis focused on geographical differences. Gut 2004; 53(9):1345-1351

Bittar C, Carolina A, Yamasaki L, Quueiroz A, Carareto C, Pinho J et al : Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response. BMC Infectious Diseases 2010; 10:36

Kumthip K , Pantip C, Chusri P, Thongsawat S, Obrien A, K. Nelson K.E and Maneekarn N: Correlation between mutations in the core and NS5A genes of hepatitis C virus genotypes 1a, 1b, 3a, 3b, 6f and the response to pegylated interferon and ribavirin combination therapy. Journal of Viral Hepatitis 2011; 18, e117–e125 DOI: 10.1111 / j.1365-2893.2010.01379.x

Ali I, Khan S, Attaullah S, Niaz S, Khan J, Siraj S, Iqbal A, Swati Z and Idrees M: Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein. Virology Journal 2011; 8:258-261. Theise DN. Liver and Biliary Tract. In: Kumar V, Abbas AK, Aster JC, editors. Robin and Cotran Pathological Basis of Disease 9th ed. Philadelphia, Elsevier Saunders, 2015. p.830–5.

Alter MJ. Epidemiology of hepatitis C virus infection. World J Gastroenterol 2007;13(17):2436–41.

Shepard CW, Finelli L, Alter MJ. Global epidemiology of hepatitis C virus infection. Lancet Infect Dis 2005;5(9):558–67.

Di Bisceglie AM. Hepatitis C and hepatocellular carcinoma. Hepatology 1997;26(3 Suppl 1):S34–8.

Idrees M, Rafique S, Rehman I, Akbar H, Yousaf MZ, Butt S, et al. Hepatitis C virus genotype 3a infection and hepatocellular carcinoma: Pakistan experience. World J Gastroenterol 2009;28;15(40):5080–5.

Munir S, Saleem S, Idrees M, Tariq A, Butt S, Rauff B, et al. Hepatitis C Treatment: current and future perspectives. Virol J 2010;7:296.

Simmonds P, Holmes EC, Cha TA, Chan SW, McOmish F, Irvine B, et al. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol 1993;74(Pt 11):2391–9.

Zein NN, Rakela J, Krawitt EL, Reddy KR, Tominaga T, Persing DH. Hepatitis C virus genotypes in the United States: Epidemiology, Pathogenicity, and response to interferon therapy. Collaborative Study Group. Ann Intern Med 1996;125(8):634–9.

McOmish F, Yap PL, Dow BC, Follett EA, Seed C, Killer AJ, et al. Geographic distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J Clin Microbiol 1994;32(4):884–92.

Nousbaum JB, Pol S, Nalpas B, Landais P, Berthelot P, Brechot C. Hepatitis C virus type 1b (II) infection in France and Italy. The Collaborative Study Group. Ann Intern Med 1995;122:161–8.

Takada NS, Takase S, Takada A, Date T. Differences in the hepatitis C virus genotypes in different countries. J Hepatol 1993;17(3):277–83.

Abdulkarim AS, Zein NN, Germer JJ, Kolbert CP, Kabbani L, Krajnik KL, et al. Hepatitis C virus genotypes and hepatitis G virus in haemodialysis patients from Syria: identification of two novel hepatitis C virus subtypes. Am J Trop Med Hyg1998;59(4):571–6.

Chamberlain RW, Adams N, Saeed AA, Simmonds P, Elliot RM. Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J Gen Virol 1997;78(Pt 6):1341–7.

Cha TA, Kolberg J, Irvine B, Stempien M, Beall E, Yano M, et al. Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma. J Clin Microbiol 1992;29(11):2528–34.

de Lamballerie X, Charrel RN, Attoui H, De Micco P. Classification of hepatitis C virus variants in six major types based on analysis of the envelope 1 and nonstructural 5B genome regions and complete polyprotein sequences. J Gen Virol 1997;78(Pt 1):45–51.

Tokita H, Okamoto H, Iizuka H, Kishimoto J, Tsuda F, Miyakawa Y, et al. The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7–9 and comparison with those in the other eight genetic groups. J Gen Virol 1998;79(Pt 8):1847–57.

Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, et al. Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 1996;334(2):77–82.

Aurora R, Donlin MJ, Cannon NA, Tavis JE. Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans. J Clin Invest 2009;119(1):225–36.

Kohashi T, Maekawa S, Sakamoto N, Kurosaki M, Watanabe H, Tanabe Y, et al. Site-specific mutation of the interferon sensitivity-determining region (ISDR) modulates hepatitis C virus replication. J Viral Hepat 2006;13(9):582–90.

Idrees M, Riazuddin S. Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of Transmission. BMC Infect Dis 2008;8:69.

Asselah T, Estrabaud E, Bieche I, Lapalus M, De Muynck S, Vidaud M, et al. Hepatitis C: viral and host factors associated with non-response to pegylated interferon plus ribavirin. Liver Int 2010;30(9):1259–69.

Pascu M, Martus P, Hohne M, Wiedenmann B, Hopf U, Schreie E, et al. Sustained virological response in hepatitis C virus type 1b infected patients is predicted by the number of mutations within the NS5A ISDR: a meta- analysis focused on geographical differences. Gut 2004;53(9):1345–51.

Bittar C, Carolina AC, Yamasaki LH, Quueiroz AT, Carareto CM, Pinho JR, et al. Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response. BMC Infect Dis 2010;10:36.

Kumthip K, Pantip C, Chusri P, Thongsawat S, Obrien A, Nelson KE, et al. Correlation between mutations in the core and NS5A genes of hepatitis C virus genotypes 1a, 1b, 3a, 3b, 6f and the response to pegylated interferon and ribavirin combination therapy. J Viral Hepat 2011;18(4):e117–25.

Ali I, Khan S, Attaullah S, Khan SN, Khan J, Siraj S, et al. Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein. Virol J 2011;8:258.

Downloads

Published

2016-11-20

Most read articles by the same author(s)

<< < 1 2