Retracted Article: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus

authors:

avatar Mojtaba Mortazavi 1 , avatar Mohammad Zarenezhad 2 , 3 , avatar Seyed Moayed Alavian ORCID 4 , avatar Saeed Gholamzadeh 3 , * , avatar Abdorrasoul Malekpour 3 , ** , avatar Mohammad Ghorbani 5 , avatar Masoud Torkzadeh Mahani 1 , avatar Safa Lotfi 1 , avatar Ali Fakhrzad 2

Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
Baqiyatallah Research Center for Gastroenterology and Liver Disease, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
Department of Pathology, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran
Corresponding Authors:
Hepatitis Monthly: Vol.16, issue 10; e39196
published online: September 10, 2016
article type: Research Article
received: May 14, 2016
revised: July 16, 2016
accepted: August 31, 2016
DOI: https://doi.org/10.5812/hepatmon.39196

how to cite: Mortazavi M, Zarenezhad M, Alavian S M, Gholamzadeh S, Malekpour A, et al. Retracted Article: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon. 2016;16(10):e39196. https://doi.org/10.5812/hepatmon.39196.

Abstract

Background:

The 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.

Methods:

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.

Results:

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.

Conclusions:

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.