Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus

Authors Information
Article Notes and Dates
To Cite : Mortazavi M, Zarenezhad M, Alavian S M, Gholamzadeh S, Malekpour A, et al. Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus, Hepat Mon. 2016 ;16(10):e39196. doi: 10.5812/hepatmon.39196.
Copyright: Copyright © 2016, Hepatitis Monthly. 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..
Abstract
1. Background
2. Objectives
3. Methods
4. Results
5. Discussion
Acknowledgements
Footnotes
References
  • 1. Lauer GM, Walker BD. Hepatitis C virus infection. N Engl J Med. 2001; 345(1): 41-52[DOI][PubMed]
  • 2. Feinstone SM, Kapikian AZ, Purcell RH, Alter HJ, Holland PV. Transfusion-associated hepatitis not due to viral hepatitis type A or B. N Engl J Med. 1975; 292(15): 767-70[DOI][PubMed]
  • 3. Vaudin M, Wolstenholme AJ, Tsiquaye KN, Zuckerman AJ, Harrison TJ. The complete nucleotide sequence of the genome of a hepatitis B virus isolated from a naturally infected chimpanzee. J Gen Virol. 1988; 69 ( Pt 6): 1383-9[DOI][PubMed]
  • 4. 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[DOI][PubMed]
  • 5. Gower E, Estes C, Blach S, Razavi-Shearer K, Razavi H. Global epidemiology and genotype distribution of the hepatitis C virus infection. J Hepatol. 2014; 61(1 Suppl)-57[DOI][PubMed]
  • 6. Chambers TJ, Hahn CS, Galler R, Rice CM. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol. 1990; 44: 649-88[DOI][PubMed]
  • 7. Esteban R. Epidemiology of hepatitis C virus infection. J Hepatol. 1993; 17 Suppl 3-71[PubMed]
  • 8. de Oliveria Andrade LJ, D'Oliveira A, Melo RC, De Souza EC, Costa Silva CA, Parana R. Association between hepatitis C and hepatocellular carcinoma. J Glob Infect Dis. 2009; 1(1): 33-7[DOI][PubMed]
  • 9. Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002. CA Cancer J Clin. 2005; 55(2): 74-108[PubMed]
  • 10. Alberti A, Chemello L, Benvegnu L. Natural history of hepatitis C. J Hepatol. 1999; 31 Suppl 1: 17-24[PubMed]
  • 11. Peters MG. End-stage liver disease in HIV disease. Top HIV Med. 2009; 17(4): 124-8[PubMed]
  • 12. Norder H, Courouce AM, Magnius LO. Complete genomes, phylogenetic relatedness, and structural proteins of six strains of the hepatitis B virus, four of which represent two new genotypes. Virology. 1994; 198(2): 489-503[DOI][PubMed]
  • 13. Roque-Afonso AM, Ducoulombier D, Di Liberto G, Kara R, Gigou M, Dussaix E, et al. Compartmentalization of hepatitis C virus genotypes between plasma and peripheral blood mononuclear cells. J Virol. 2005; 79(10): 6349-57[DOI][PubMed]
  • 14. Sharp PM, Emery LR, Zeng K. Forces that influence the evolution of codon bias. Philos Trans R Soc Lond B Biol Sci. 2010; 365(1544): 1203-12[DOI][PubMed]
  • 15. Nirenberg MW, Matthaei JH, Jones OW, Martin RG, Barondes SH. Approximation of genetic code via cell-free protein synthesis directed by template RNA. Fed Proc. 1963; 22: 55-61[PubMed]
  • 16. Grantham R, Gautier C, Gouy M, Mercier R, Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980; 8(1)-62[PubMed]
  • 17. Lloyd AT, Sharp PM. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res. 1992; 20(20): 5289-95[PubMed]
  • 18. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985; 2(1): 13-34[PubMed]
  • 19. Shepard CW, Finelli L, Alter MJ. Global epidemiology of hepatitis C virus infection. Lancet Infect Dis. 2005; 5(9): 558-67[DOI][PubMed]
  • 20. Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, et al. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology. 2014; 59(1): 318-27[DOI][PubMed]
  • 21. Zein NN. Clinical significance of hepatitis C virus genotypes. Clin Microbiol Rev. 2000; 13(2): 223-35[PubMed]
  • 22. Fattahi M, Malekpour A, Mortazavi M, Safarpour A, Naseri N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J Dig Dis. 2014; 6(4): 214-27[PubMed]
  • 23. Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 2000; 28(6): 1102[PubMed]
  • 24. Minitab I. MINITAB statistical software. Minitab Release. 2000; 13
  • 25. Puigbo P, Bravo IG, Garcia-Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct. 2008; 3: 38[DOI][PubMed]
  • 26. Fattovich G, Stroffolini T, Zagni I, Donato F. Hepatocellular carcinoma in cirrhosis: incidence and risk factors. Gastroenterology. 2004; 127(5 Suppl 1)-50[PubMed]
  • 27. Bennetzen JL, Hall BD. Codon selection in yeast. J Biol Chem. 1982; 257(6): 3026-31[PubMed]
  • 28. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics. 2012; 28(11): 1438-45[DOI][PubMed]
  • 29. Belalov IS, Lukashev AN. Causes and implications of codon usage bias in RNA viruses. PLoS One. 2013; 8(2)[DOI][PubMed]
  • 30. Allner O, Nilsson L. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA. 2011; 17(12): 2177-88[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Search Relations:

Author(s):

Article(s):

Create Citiaion Alert via Google Reader

Cited By:

Hepatitis Monthly accepts terms & conditions of:

International Committee of Medical Journal Editors (ICMJE) Citedby Linking DOI enabled Crossref iThenticate COPE Cross Check