Mapping the drivers of within-host pathogen evolution using massive data sets

Palmer, Duncan S.; Turner, Isaac; Fidler, Sarah; Frater, John; Goedhals, Dominique; Goulder, Philip; Huang, Kuan-Hsiang Gary; Oxenius, Annette; Phillips, Rodney; Shapiro, Roger; Vuuren, Cloete van; McLean, Angela R.; McVean, Gil

ines refers to the A-list [45] and B-list [46] which are coloured purple and pink respectively. In addition, we colour sites of known escape variants within the A-list epitopes in yellow. Source data are provided as a Source Data file. Figure 18 : Summary of HLA-C associated selection in reverse transcriptase. We display a summary of all the results of each of our MCMC runs applied to protease. Inference results on the grey horizontal strips are coloured as shown in the key. Two grey strips per HLA show selection away from C = B and C = C respectively. Bar plots to the right show HLA frequencies. The two lowest strips summarise median ω according to the colour bar. Blue vertical lines denote drug resistance sites. Green vertical lines denote sites at which there is an amino acid difference between the subtype B and subtype C consensus viral sequence. Colouring of epitopes plotted above the grey lines refers to the A-list [45] and B-list [46] which are coloured purple and pink respectively. In addition, we colour sites of known escape variants within the A-list epitopes in yellow. Source data are provided as a Source Data file. Figure 19 : Estimated recombination probabilities between sites across protease and reverse transcriptase. The mean estimate is plotted in black, the median is plotted in red. The white band denotes the 50% credible interval within the 95% credible interval denoted by the grey band. Blue vertical lines denote drug resistance sites. Green vertical lines denote sites at which there is an amino acid difference between the subtype B and subtype C consensus viral sequence. Source data are provided as a Source Data file. The impact of HLA alleles on differentiation between HIV-1 subtypes. Let C B and C B be the subtype B and subtype C viral sequence consensus respectively. Let H B and H C be the distribution of HLA types in individuals harbouring subtype B and subtype C viruses as defined by RIP [47] in the query data set. The panels display comparisons of HLA-associated selection pressure away from C B and C C by H B and H C . The first row shows results for protease, and the second row shows results for reverse transcriptase. Sites that distinguish subtype B and subtype C at the amino acid level are highlighted in red. Source data are provided as a Source Data file.