Fig. 2
a Coverage, i.e., number of reads per nucleotide position, obtained by deep sequencing the seven patient-derived HIV-1 isolates. Near full-length HIV-1 genomes were RT-PCR amplified and deep sequenced as described in “Methods”. The position relative to the HIV-1 genome of the six overlapping amplicons used to amplify and sequence the near full-length HIV-1 genomes (HXB2 position 157 to 9428, not counting primer sequences) is indicated. b Hierarchical clustering analysis of the single nucleotides polymorphisms (SNPs) was used to group the seven patient-derived HIV-1 isolates by similarity. Dendrograms were calculated using the Euclidean distance and Complete cluster methods with 1000 bootstrap iterations as described (http://www.hiv.lanl.gov/content/sequence/HEATMAP/heatmap.html) Bootstrap values >60% are indicated by an asterisk. Green and grey blocks indicate the presence or absence of SNPs, respectively, in each HIV-1 isolate relative to the HIV-1HXB2 reference. c A Neighbor-joining phylogenetic tree was constructed using the near full-length HIV-1 consensus sequences generated for each patient-derived virus (obtained from deep sequencing reads) and rooted using the HIV-1HXB2 sequence (GenBank accession number AF033819). Bootstrap resampling (1000 data sets) of the multiple alignment tested the statistical robustness of the tree, with percentage values above 75% indicated by an asterisk. s/site substitutions per nucleotide site