MOESM4 of Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays

Additional file 4. Fig. S4. Prominent species identification and elimination of potential outgrowth derived recombinant sequences. a All Pol derived consensus sequences with amplicon totals greater than 0.02% of the total amplicon number for well 5M4 (1,000,000 rCD4+ cells plated) from patient 111 were aligned and viewed in a Neighbor-Joining (NJ) phylogenetic tree. Prominent species were defined as those with amplicon totals > 2.5% of the total amplicon read number for well 5M4 and are indicated with red arrows. b Since the number of prominent species in well 5M4 were ≥ 3 the prominent sequences were aligned and viewed in a highlighter plot. The probable outgrowth derived recombinant sequence is indicated with a red X and was removed from the analysis (probable recombination area highlighted in red box). c All Pol prominent outgrowth sequences for patient 111 were viewed in a NJ tree and variants assigned based on clonality (well 5M4 indicated with red arrows)