Computational protocol: NS4A protein as a marker of HCV history suggests that different HCV genotypes originally evolved from genotype 1b

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Protocol publication

[…] Total of 346 nucleotide sequences were randomly selected and downloaded from Hepatitis C Virus Database http://www.hcvdb.org and GenBank http://www.ncbi.nlm.nih.gov representing 6 different HCV genotypes. The 346 sequences included in this study were reported from all over the world; France, Germany, UK, Switzerland, Ireland, Belgium, Spain, Portugal, Denmark, Sweden, Russia, Japan, China, Korea, Indonesia, Hong Kong, Thailand, Viet Nam, Pakistan, Singapore, India, Australia, USA, Canada, Algeria, Egypt, Cameroon and South Africa representing Europe, Asia, North America and Africa (Table ). These nucleotide sequences were then adjusted for NS4A gene region using BioEdit software http://www.mbio.ncsu.edu/bioedit/bioedit.html and isolated H77 as a reference sequence http://www.hcvdb.org/gene_detail.asp?gene_id=64592. Amino acid sequences were deduced for these sequences using EXPASY protein translate tool http://expasy.org/tools/dna.html. The amino acid sequences were then fed to CLC sequence viewer 6 http://www.clcbio.com/index.php?id=28 for Multiple Sequence Alignment (MSA) to be performed. CLC sequence a viewer 6 is freely available software.First of all MSA was performed for 56 sequences from genotype 3 subtype 3a. After that single MSA was done for all the 346 sequences. Then MSA was performed for 73 sequences from genotype 1 subtype 1b and 3 sequences from genotype 1 subtype 1c. Furthermore, MSA was performed for the 73 sequences from genotype 1 subtype 1b with 64 sequences from genotype 1 subtype 1a, 35 sequences from genotype 5, 37 sequences from genotype 4, 58 sequences from genotype 3 and 58 sequences from genotype 2 respectively. Finally a single phylogenetic tree was constructed for all the 346 sequences using UPGMA method using CLC sequence software http://www.clcbio.com/index.php?id=28. […]

Pipeline specifications

Software tools BioEdit, CLC Sequence Viewer, CLC Assembly Cell
Databases HCVDB
Application Phylogenetics
Organisms Hepacivirus C, Homo sapiens
Diseases Hepatitis C