A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Figure 2
Phylogenetic tree representation of viral sequences obtained from Ch_240. Phylogenetic tree of circulating HCV variants from sequences derived from the NS3 region (nucleotide region 4000–5499, amino acid region 1200–1800). This tree shows the significant rapid evolution of HCV genome over the course of the infection from acute phase (in red viral sequences from 44 DPI, in pink those for 57 DPI) through the chronic phase of infection (in green sequences from 220 DPI, and in blue from 538 DPI). The infection is characterized by two sequential genetic bottlenecks, one soon after the acute phase of infection, the other after 220 DPI, both indicating substantial changes in the circulating viral populations. The label H_44D_0 indicates the transmitted/founder virus used to root the phylogenetic tree. The numbers at branches indicate the bootstrap value after resampling 1000 times. Viral Dynamics plot (b) shows the viral load (grey shading) over time, while the orange diamonds indicate available deep sequence data (from left to right: 44, 57, 220, 538 DPI). Shannon entropy calculated from the full distribution of HCV genomic mutations and the one from the distribution of nonsynonymous mutations only are indicated by a purple line and red line, respectively.
