Official Journal of Research Center for Gastroenterology and Liver Diseases
Authors
4, Saeed Gholamzadeh3,*, Abdorrasoul Malekpour3,**, Mohammad Ghorbani5, Masoud Torkzadeh Mahani1, Safa Lotfi1, Ali Fakhrzad2The hepatitis C virus (HCV) has six major genotypes. The purpose of this study was to phylogenetically investigate the differences between the genotypes of HCV, and to determine the types of amino acid codon usage in the structure of the virus in order to discover new methods for treatment regimes.
The codon usage of the six genotypes of the HCV nucleotide sequence was investigated through the online application available on the website Gene Infinity. Also, phylogenetic analysis and the evolutionary relationship of HCV genotypes were analyzed with MEGA 7 software.
The six genotypes of HCV were divided into two groups based on their codon usage properties. In the first group, genotypes 1 and 5 (74.02%), and in the second group, genotypes 2 and 6 (72.43%) were shown to have the most similarity in terms of codon usage. Unlike the results with respect to determining the similarity of codon usage, the phylogenetic analysis showed the closest resemblance and correlation between genotypes 1 and 4. The results also showed that HCV has a GC (guanine-cytosine) abundant genome structure and prefers codons with GC for translation.
Genotypes 1 and 4 demonstrated remarkable similarity in terms of genome sequences and proteins, but surprisingly, in terms of the preferred codons for gene expression, they showed the greatest difference. More studies are therefore needed to confirm the results and select the best approach for treatment of these genotypes based on their codon usage properties.
Copyright © 2016, 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.
Alavian SM. Retraction Note: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon. 2020;20(1):e101548. doi: https://doi.org/10.5812/hepatmon.101548
Alavian SM. Corrigendum to: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon. 2019;19(11):e99558. doi: https://doi.org/10.5812/hepatmon.99558
Salehi Moghadam F, Mohebbi SR, Hosseini SM, Damavand B, Zali MR. A New Subtype of Hepatitis C Virus Genotype 3: Analysis of Available Evidence. Hepat Mon. 2013;13(8):e13380. doi: https://doi.org/10.5812/hepatmon.13380
Waheed Y, Saeed U, Anjum S, Afzal M, Ashraf M. Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Protein. Hepat Mon. 2012;12(9):6142. doi: https://doi.org/10.5812/hepatmon.6142
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