Fig. 2
A Coverage, i.e., number of reads per nucleotide position, obtained by deep sequencing of cell-associated spliced HIV-1 RNA (EDITS assays) and proviral DNA from all Ugandan (n = 62) and U.S. (n = 50) HIV-infected individuals. The position relative to the HIV-1 genome of the vpu/env amplicon amplified in the nested (2nd) PCR reaction is indicated. B Neighbor-joining phylogenetic trees were constructed using the HIV-1 vpu/env consensus sequences generated for each patient-derived virus from deep sequencing reads using DEEPGEN™ Software Tool Suite [51], and rooted using the HIV-1HXB2 sequence (GenBank Accession Number AF033819). Nucleotide sequences from ten HIV-1 strains, two from each one of the HIV-1 subtypes more prevalent in Uganda and/or in the U.S., were used to subtype the patient-derived HIV-1 consensus sequences (A1.AU.03.PS1044_Day0.DQ676872, A1.RW.92.92RW008.AB253421, A2.CD.97.97CDKTB48.AF286238, A2.CM.01.01CM_1445MV.GU201516, B.HXB2_LAI_IIIB_BRU.K03455, B.NL.00.671_00T36.AY423387, C.BR.92.BR025_d.U52953, C.ET.86.ETH2220.U46016, D.CD.83.ELI.K03454, and D.CM.01.01CM_4412HAL.AY371157). HIV-1 subtype-specific clusters are depicted. 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