Retracted Article: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus

Abstract

BackgroundThe 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.MethodsThe 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.ResultsThe 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.ConclusionsGenotypes 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.

In-silico Evaluation of Rare Codons and their Positions in the Structure of ATP8b1 Gene

“…We have previously modeled the structure of a number of proteins and have a good experience in homology modeling technique [33][34][35][36]. In this regard, the RCCs properties in the protein and genome of ATP8b1 was evaluated.…”

How Codon Usage Bias Affects Our Ability to Recover the Tree of Life

“…However, evidence of natural selection in Zika viruses also suggest that they evolved host-and vector-specific codon usage patterns to successfully replicate in various hosts and vectors (Butt, et al 2016). In hepatitis C, preferred codon usages did not always match the phylogenetic histories of the viruses as determined by sequence similarity, indicating that codon usage might provide additional information not identified in common phylogenomic approaches (Mortazavi, et al 2016).…”

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

“…This study was designed to make a comparative analysis of the dinucleotide signature and codon biology of the PRVs with special emphasis on the most recently discovered novel SARS-CoV-2 strain, since from the genomic view point, codon usage pattern plays a vital role in deciphering the basic biological and evolutionary processes ( Wang and Chen, 2013 ). The study of codon usage bias in viruses have been carried out to understand host adaptation of the virus, host-pathogen interaction, host immune system evasion ( Butt et al, 2016 ; Castells et al, 2017 ; Karumathil et al, 2018 ; Khandia et al, 2019 ; Mortazavi et al, 2016 ; Pinto et al, 2018 ) and translational kinetics ( Deka et al, 2019 ; Karumathil et al, 2018 ). Codon usage bias study also provides a firm understanding of the evolutionary history of virus, their phylogeny, selection pressure ( Gu et al, 2019a ; Hanson et al, 2018 ; Yao et al, 2019 ), and provides vital insight for developing medications, and new treatment regimes ( Castells et al, 2017 ; Mortazavi et al, 2016 ).…”