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

dard reference set, and the dotted lines are using reference data from all public databases. In each of the fourth rows we display the average RMSE at each site for different D B as defined in the key. Source data are provided as a Source Data file. 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. Figure 15 : Summary of HLA-B associated selection in protease. 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 16 : Summary of HLA-C associated selection in protease. 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 17 : Summary of HLA-A 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 l