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Figure 2 | Retrovirology

Figure 2

From: Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

Figure 2

Validation of reconstructed haplotypes from subject 9213. (A) Neighbor-joining phylogenetic tree generated from the global alignment of the vif genes extracted from the 6 haplotypes reconstructed from the day 59 data (red) and the SGA vif gene sequences (black) obtained from [11]. (B) The predicted haplotype frequencies for subject 9213 plotted for each sample (day 0, day 3, day 59, day 165, day 476, and day 1543). Note that the variation in read coverage (667.7, 724.4, 750.5, 299.7, 227.6 and 540.7, respectively) does not seem to influence the number of predicted haplotypes. (C) Comparison of the epitope frequencies estimated from reconstructed haplotypes and those from the local analysis of sequencing reads described in [11]. Markers represent different days. Variants of each epitope are represented as different observations. Several epitope variants with 100% read frequency and a 100% predicted frequency in reconstructed haplotypes appear as overlapping points in the upper right corner on the diagonal. The overlapping points were not considered for the correlation analysis. The Spearman’s rank correlation coefficient between predicted epitope frequencies extracted from complete genome haplotypes and the local read frequencies was ρ = 0.85 (p-value < 10-15).

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