Hepatitis Monthly

Published by: Kowsar

Sequence and Structural Analysis of 3' Untranslated Region of Hepatitis C Virus, Genotype 3a, From Pakistani Isolates

Sadia Anjum 1 , * , Sidra Ali 1 , Tahir Ahmad 1 , Muhammad Sohail Afzal 1 , Yasir Waheed 1 , Talha Shafi 1 , Muhammad Ashraf 1 and Saadia Andleeb 1
Authors Information
1 Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
Article information
  • Hepatitis Monthly: May 01, 2013, 13 (5); e8390
  • Published Online: May 9, 2013
  • Article Type: Research Article
  • Received: September 30, 2012
  • Revised: February 7, 2013
  • Accepted: March 5, 2013
  • DOI: 10.5812/hepatmon.8390

To Cite: Anjum S, Ali S, Ahmad T, Afzal M S, Waheed Y, et al. Sequence and Structural Analysis of 3' Untranslated Region of Hepatitis C Virus, Genotype 3a, From Pakistani Isolates, Hepat Mon. 2013 ; 13(5):e8390. doi: 10.5812/hepatmon.8390.

Copyright © 2013, Kowsar Corp. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Objectives
3. Patients and Methods
4. Results
5. Discussion
  • 1. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science. 1989; 244(4902): 359-62[PubMed]
  • 2. Tsukiyama-Kohara K, Iizuka N, Kohara M, Nomoto A. Internal ribosome entry site within hepatitis C virus RNA. J Virol. 1992; 66(3): 1476-83[PubMed]
  • 3. Wang C, Le SY, Ali N, Siddiqui A. An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region. RNA. 1995; 1(5): 526-37[PubMed]
  • 4. Kolykhalov AA, Feinstone SM, Rice CM. Identification of a highly conserved sequence element at the 3' terminus of hepatitis C virus genome RNA. J Virol. 1996; 70(6): 3363-71[PubMed]
  • 5. Friebe P, Bartenschlager R. Genetic analysis of sequences in the 3' nontranslated region of hepatitis C virus that are important for RNA replication. J Virol. 2002; 76(11): 5326-38[PubMed]
  • 6. Yi M, Lemon SM. 3' nontranslated RNA signals required for replication of hepatitis C virus RNA. J Virol. 2003; 77(6): 3557-68[PubMed]
  • 7. Kolykhalov AA, Mihalik K, Feinstone SM, Rice CM. Hepatitis C virus-encoded enzymatic activities and conserved RNA elements in the 3' nontranslated region are essential for virus replication in vivo. J Virol. 2000; 74(4): 2046-51[PubMed]
  • 8. Blight KJ, Rice CM. Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA. J Virol. 1997; 71(10): 7345-52[PubMed]
  • 9. Kolykhalov AA, Agapov EV, Blight KJ, Mihalik K, Feinstone SM, Rice CM. Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA. Science. 1997; 277(5325): 570-4[PubMed]
  • 10. Choo QL, Richman KH, Han JH, Berger K, Lee C, Dong C, et al. Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci U S A. 1991; 88(6): 2451-5[PubMed]
  • 11. Romero-Lopez C, Berzal-Herranz A. A long-range RNA-RNA interaction between the 5' and 3' ends of the HCV genome. RNA. 2009; 15(9): 1740-52[DOI][PubMed]
  • 12. Banerjee R, Dasgupta A. Specific interaction of hepatitis C virus protease/helicase NS3 with the 3'-terminal sequences of viral positive- and negative-strand RNA. J Virol. 2001; 75(4): 1708-21[DOI][PubMed]
  • 13. Huang L, Hwang J, Sharma SD, Hargittai MR, Chen Y, Arnold JJ, et al. Hepatitis C virus nonstructural protein 5A (NS5A) is an RNA-binding protein. J Biol Chem. 2005; 280(43): 36417-28[DOI][PubMed]
  • 14. Zuniga S, Sola I, Cruz JL, Enjuanes L. Role of RNA chaperones in virus replication. Virus Res. 2009; 139(2): 253-66[DOI][PubMed]
  • 15. Weinlich S, Huttelmaier S, Schierhorn A, Behrens SE, Ostareck-Lederer A, Ostareck DH. IGF2BP1 enhances HCV IRES-mediated translation initiation via the 3'UTR. RNA. 2009; 15(8): 1528-42[DOI][PubMed]
  • 16. Spangberg K, Wiklund L, Schwartz S. Binding of the La autoantigen to the hepatitis C virus 3' untranslated region protects the RNA from rapid degradation in vitro. J Gen Virol. 2001; 82: 113-20[PubMed]
  • 17. Wiklund L. Role of the 3'UTR in translation and stability of HCV and HPV mRNAs. 2002;
  • 18. Kabir A, Alavian SM, Keyvani H. Distribution of hepatitis C virus genotypes in patients infected by different sources and its correlation with clinical and virological parameters: a preliminary study. Comp Hepatol. 2006; 5: 4[DOI][PubMed]
  • 19. Waheed Y, Saeed U, Anjum S, Afzal MS, Ashraf M. Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Prote in. Hepat Mon. 2012; 12(9)[DOI][PubMed]
  • 20. Alavian SM, Aalaei-Andabili SH. More risk factors of hepatitis C transmission should be considered in Pakistan. Int J Prev Med. 2011; 2(3): 188-9[PubMed]
  • 21. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31(13): 3406-15[PubMed]
  • 22. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4): 406-25[PubMed]
  • 23. Han JH, Houghton M. Group specific sequences and conserved secondary structures at the 3' end of HCV genome and its implication for viral replication. Nucleic Acids Res. 1992; 20(13): 3520[PubMed]
  • 24. Ito T, Lai MM. Determination of the secondary structure of and cellular protein binding to the 3'-untranslated region of the hepatitis C virus RNA genome. J Virol. 1997; 71(11): 8698-706[PubMed]
  • 25. Gottwein JM, Scheel TK, Callendret B, Li YP, Eccleston HB, Engle RE, et al. Novel infectious cDNA clones of hepatitis C virus genotype 3a (strain S52) and 4a (strain ED43): genetic analyses and in vivo pathogenesis studies. J Virol. 2010; 84(10): 5277-93[DOI][PubMed]
  • 26. Yamada N, Tanihara K, Takada A, Yorihuzi T, Tsutsumi M, Shimomura H, et al. Genetic organization and diversity of the 3' noncoding region of the hepatitis C virus genome. Virology. 1996; 223(1): 255-61[DOI][PubMed]
  • 27. Yanagi M, St Claire M, Emerson SU, Purcell RH, Bukh J. In vivo analysis of the 3' untranslated region of the hepatitis C virus after in vitro mutagenesis of an infectious cDNA clone. Proc Natl Acad Sci U S A. 1999; 96(5): 2291-5[PubMed]
  • 28. Tanaka T, Kato N, Cho MJ, Sugiyama K, Shimotohno K. Structure of the 3' terminus of the hepatitis C virus genome. J Virol. 1996; 70(5): 3307-12[PubMed]
  • 29. Ito T, Tahara SM, Lai MM. The 3'-untranslated region of hepatitis C virus RNA enhances translation from an internal ribosomal entry site. J Virol. 1998; 72(11): 8789-96[PubMed]
  • 30. Drexler JF, Kupfer B, Petersen N, Grotto RM, Rodrigues SM, Grywna K, et al. A novel diagnostic target in the hepatitis C virus genome. PLoS Med. 2009; 6(2)[DOI][PubMed]
  • 31. You S, Rice CM. 3' RNA elements in hepatitis C virus replication: kissing partners and long poly(U). J Virol. 2008; 82(1): 184-95[DOI][PubMed]
  • 32. Zaidi Nu, Kanwal N, Ghazal A, Fatima K, Javed F, Qadri I. Phylogenetic and structural analysis of HCV nonstructural protein 4A from Pakistani patients. Virus Genes. 2012; 44(1): 1-7[DOI][PubMed]
  • 33. Waheed Y, Tahir S, Ahmad T, Qadri I. Sequence comparison and phylogenetic analysis of core gene of hepatitis C virus from Pakistani population. Afr J Biotech. 2010; 9(29): 4561-7
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