Fig. 1.

Inferring the direction of transmission from HIV-1 deep-sequence data. a The principles of deep-sequence viral phylogenetic analysis are illustrated on data from male M1 (turquoise) who initially reported partnership with female F1 (green), and later with female F2 (blue). We also included data from another male M2 whose virus was genetically close to that of F1, although a partnership was not reported (see Supplementary Figure 2). b Viral genomes from all individuals were deep-sequenced, generating short viral sequence fragments (reads) that cover the genome. Reads were mapped against HIV-1 reference sequences, and are shown as horizontal coloured lines. Genomic windows covering the whole genome were defined; one is highlighted in black. For each window, overlapping reads were extracted, aligned, and a phylogeny was reconstructed using standard methods. c Each phylogeny contained many unique reads per individual that tended to cluster in the phylogeny. This enabled us to reconstruct parts of the tree (subgraphs) in which virus was inferred to be in each individual (colours label individuals; diamonds indicate unique read fragments, and the size of diamonds reflects copy number). In the phylogeny shown, virus from M1 (turquoise) was phylogenetically ancestral to that from F2 (blue), suggesting that transmission occurred from M1 to F2. Similarly, virus from F1 (green) was phylogenetically ancestral to that from M2 (purple), suggesting that transmission occurred from F1 to M2. For ease of illustration, only a part of the entire reconstructed deep-sequence phylogeny is shown. HIV-1 reference sequences and virus from another phylogenetically distant individual that is in-between the F1−M2 and M1−F2 pair are shown in black. d Viral deep-sequence phylogenies were reconstructed for each 250 bp genomic window to determine the statistical support of inferences on transmission and the direction of transmission. For each pair of individuals, the scan plots show the shortest patristic distance between subgraphs of both individuals (y-axis) and the topological relationship between subgraphs of both individuals (colours) across the genome. Deep-sequence data of sufficient quality were available for the HIV-1 gag gene, and the genomic position on the x-axis indicates the start of each 250 bp read alignment