Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach

Hepatitis C virus (HCV) displays excessive genetic heterogeneity and exists in several genotypes and subtypes. Characterizing these genotypes and subtypes becomes extremely important for diagnostic and epidemiological reasons. Present study analyzed HCV genome using a simple genome analysis approach. We combined manual sectioning of a reference genome alignment (RA) followed by a comprehensive comparative phylogenetic analysis. The main aim was to identify heterogeneous locations on HCV genome suitable for genotyping/subtyping. HCV reference dataset, comprising of whole genome sequences from all HCV genotypes and subtypes, was aligned into an RA. The RA was manually clipped into overlapping sections of 500 bases, each 50 bases apart. Phylogeny for each section and RA was estimated using neighbor-joining phylogenetic method. Clustering pattern between section phylogenies and RA phylogeny was compared for similarity. Sections (locations on genome) with clustering similar to whole genome were selected since it displays comparable genetic heterogeneity making these sections suitable for genotyping/subtyping. Based on this conception, we identified new genomic locations on NS3, NS4A and NS4B suitable for genotyping and subtyping. Exact genomic positions for known genotyping locations, core and NS5B were also identified. Furthermore, phylogenetic analyses at such small genomic scale provided opportunities to explore evolutionary relationships usually overlooked.