title: NS4A protein as a marker of HCV history suggests that different HCV genotypes originally evolved from genotype 1b.
abstract: BACKGROUND
  The 9.6 kb long RNA genome of Hepatitis C virus (HCV) is under the control of RNA dependent RNA polymerase, an error-prone enzyme, for its transcription and replication. A high rate of mutation has been found to be associated with RNA viruses like HCV. Based on genetic variability, HCV has been classified into 6 different major genotypes and 11 different subtypes. However this classification system does not provide significant information about the origin of the virus, primarily due to high mutation rate at nucleotide level. HCV genome codes for a single polyprotein of about 3011 amino acids which is processed into structural and non-structural proteins inside host cell by viral and cellular proteases.
  
  
  RESULTS
  We have identified a conserved NS4A protein sequence for HCV genotype 3a reported from four different continents of the world i.e. Europe, America, Australia and Asia. We investigated 346 sequences and compared amino acid composition of NS4A protein of different HCV genotypes through Multiple Sequence Alignment and observed amino acid substitutions C22, V29, V30, V38, Q46 and Q47 in NS4A protein of genotype 1b. Furthermore, we observed C22 and V30 as more consistent members of NS4A protein of genotype 1a. Similarly Q46 and Q47 in genotype 5, V29, V30, Q46 and Q47 in genotype 4, C22, Q46 and Q47 in genotype 6, C22, V38, Q46 and Q47 in genotype 3 and C22 in genotype 2 as more consistent members of NS4A protein of these genotypes. So the different amino acids that were introduced as substitutions in NS4A protein of genotype 1 subtype 1b have been retained as consistent members of the NS4A protein of other known genotypes.
  
  
  CONCLUSIONS
  These observations indicate that NS4A protein of different HCV genotypes originally evolved from NS4A protein of genotype 1 subtype 1b, which in turn indicate that HCV genotype 1 subtype 1b established itself earlier in human population and all other known genotypes evolved later as a result of mutations in HCV genotype 1b. These results were further confirmed through phylogenetic analysis by constructing phylogenetic tree using NS4A protein as a phylogenetic marker.
authors.affiliation: Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Muhammad T
authors.initials: MT
authors.lastname: Sarwar
authors.forename: Humera
authors.initials: H
authors.lastname: Kausar
authors.forename: Bushra
authors.initials: B
authors.lastname: Ijaz
authors.forename: Waqar
authors.initials: W
authors.lastname: Ahmad
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ansar
authors.forename: Aleena
authors.initials: A
authors.lastname: Sumrin
authors.forename: Usman A
authors.initials: UA
authors.lastname: Ashfaq
authors.forename: Sultan
authors.initials: S
authors.lastname: Asad
authors.forename: Sana
authors.initials: S
authors.lastname: Gull
authors.forename: Imran
authors.initials: I
authors.lastname: Shahid
authors.forename: Sajida
authors.initials: S
authors.lastname: Hassan
mesh_terms: D000569:Americas; D001208:Asia; D001315:Australia; D002352:Carrier Proteins / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D005060:Europe; D019143:Evolution, Molecular; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; C455041:NS4A cofactor peptide, Hepatitis C virus; D017361:Viral Nonstructural Proteins