Figure 2

Genome distribution, entropy and RT localization of OLP with significant impact on viral loads in HIV-1 clade B and C infection: The distribution of OLP with significantly elevated or reduced PR across the viral proteome is shown in A) for clade B infection (cut-off uncorrected p-value of p < 0.05) and in B) for clade C infection (cut-off q < 0.2). The entropy of beneficial and non-beneficial clade B OLP is compared in C) while in D), the entropy of beneficial OLP in HIV clade C Gag is compared to the remainder of Gag OLP (p-values based on Mann Whitney, red lines indicating median sequence entropies). In E and F, protein structures for HIV-1 reverse transcriptase (Protein databank structure ID 3IG1) were loaded into the Los Alamos HIV Database "protein feature accent" tool http://www.hiv.lanl.gov/content/sequence/PROTVIS/html/protvis.html and locations of beneficial RT OLP identified in clade B (Table 1) and in clade C (Table 2) marked by red highlights.