title: Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus.
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 websiteGene 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.
authors.affiliation: Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran.
authors.forename: Mojtaba
authors.initials: M
authors.lastname: Mortazavi
authors.affiliation: Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran; Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Zarenezhad
authors.affiliation: Baqiyatallah Research Center for Gastroenterology and Liver Disease, Baqiyatallah University of Medical Sciences, Tehran, IR Iran.
authors.forename: Seyed Moayed
authors.initials: SM
authors.lastname: Alavian
authors.affiliation: Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran.
authors.forename: Saeed
authors.initials: S
authors.lastname: Gholamzadeh
authors.affiliation: Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran.
authors.forename: Abdorrasoul
authors.initials: A
authors.lastname: Malekpour
authors.affiliation: Department of Pathology, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ghorbani
authors.affiliation: Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran.
authors.forename: Masoud
authors.initials: M
authors.lastname: Torkzadeh Mahani
authors.affiliation: Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran.
authors.forename: Safa
authors.initials: S
authors.lastname: Lotfi
authors.affiliation: Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Fakhrzad
keywords: Bioinformatic Study; Codon Usage; Hepatitis C Virus; Phylogenetic Analysis