Non-parametric geographic subdivision tests comparing pre- ASCT viruses with those at each rebound.

<p>Non-parametric geographic subdivision tests comparing pre- ASCT viruses with those at each rebound.</p

Diversity measured as average pairwise distance at longitudinal time points.

<p>APD measured pre- ASCT and during subsequent viral rebounds. Numbers in parentheses indicate the number of single genomes acquired at each time point. Significance was determined by two-tailed.</p

Inferred neighbour-joining phylogenetic tree of single genome derived HIV-1 env sequences.

<p>Two APOBEC hypermutated sequences found in the third rebound have been removed. Pre melphalan HIV DNA (-27 to -38, orange open diamonds), first rebound HIV RNA (+6, blue closed diamonds), first rebound HIV DNA (+6, blue open diamonds), second rebound HIV RNA (+515, magenta closed diamonds), third rebound HIV DNA (+643 to +958, green open diamonds). Rooted on MJ4 (black square), branches with bootstrap support > 75% are indicated by black asterisk. Overall population APD is 1.5%. The scale represents 0.005 nucleotide substitutions per site, equivalent to 4.5nt. The tips in the boxed grey area representative sequences predicted to confer CXCR4 tropism by both Geno2Pheno and Phenoseq genotypic algorithms.</p

Genotypically defined co-receptor usage following HIV rebounds.

<p>Tropism testing of the HIV V3 loop was performed in both Geno2Pheno and Phenoseq online genotypic algorithms. Percentage of CXCR4 sequences is plotted on the Y-axis. Only sequences found to be X4 in both programs were designated as X4. Significance was determined using a two-tailed Fishers Exact test.</p