Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma

Figure 4

Phylogenetic tree analysis of all PBMC- and plasma-derived HCV IRES sequences. The evolutionary history was inferred by using the Maximum Likelihood method based on the Kimura 2-parameter model. The tree with the highest log likelihood (-1129.7196) is shown. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 450 nucleotide sequences. PBMC-derived HCV IRES nucleotide sequences (n=225; coloured in blue) and plasma-derived HCV IRES nucleotide sequences (n=225; coloured in red) (a). HCV IRESes with the triple adenine variant (A-A-A) in PBMC (n=36; blue triangles) and in plasma (n=26; red triangles) (b). All positions containing gaps and missing data were eliminated. There were a total of 200 positions (nt 100 to 300) in the final dataset. The bootstrap values along the branches indicate percent confidence of branches. Bootstrap values greater than 70% are shown. The scale bar corresponds to 0.01 substitutions per site. Evolutionary analyses were conducted in MEGA6.

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