A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Figure 4
A representative example of the covariance network analysis. Network representation pair-wise covariance analysis of nonsynonymous mutations detected over the course of infection within the NS3 region (nucleotide region 4000–5499, amino acid region 1200–1800) in subject Ch_240. Nodes presented in the network are positions in the viral sequence found to have significant covariance values that indicate strong covariation between two mutation sites. In each network, the degree of connectivity is increasing from left to right. Hexagonal nodes denote mutation positions that lie within an epitope region, while those in red are mutations that have been detected as statistically significant cooccurring mutations using the Jaccard similarity coefficient. Covarying mutations, which are not shared between two or more viral variants, have their nodes colored in green.
