Fig. 7
Phylogenetic and HIV-1 genetic diversity analysis. a Neighbor-joining phylogenetic trees constructed using consensus sequences generated with DEEPGEN™ corresponding to the HIV-1 protease and reverse transcriptase (PR/RT), integrase (INT), and C2V3 coding regions from the 59 and 50 patient-derived viruses from St. George’s and NHS Lothian cohorts, respectively. Sequences from 16 viruses from different Group M HIV-1 subtypes, obtained from Los Alamos HIV Sequence Database (https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html), were used as reference, i.e., A1.AU.03.PS1044_Day0.DQ676872, A2.CD.97.97CDKTB48.AF286238, B.FR.83.HXB2_LAI_IIIB_BRU.K03455, C.BR.92.BR025_d.U52953, D.CD.83.ELI.K03454, F1.BE.93.VI850.AF077336, F2.CM.02.02CM_0016BBY-AY3711158, G.BE.96.DRCBL.AF084936, H.BE.93.VI991.AF190127, J.CD.97.J_97DC_KTB147.EF614151, K.CD.97.97ZR_EQTB11.AJ249235, CRF01_AE.AF.07.569M.GQ477441, CRF02_AG.CM.99.pBD6_15.AY271690, CRF03_AB.RU.97.KAL153_2.AF193276, CRF04_cpx.CY.94.94CY032_3.AF049337, and CRF05_DF.BE.93.VI961.AF076998. Bootstrap resampling (1000 data sets) of the multiple alignments tested the statistical robustness of the trees, with percentage values above 75% indicated by an asterisk. Each dot represents a patient-derived consensus sequence. b HIV-1 inter-patient genetic distances determined using the Maximum Composite Likelihood model with bootstrap as the variance estimation method (1000 replicates) within MEGA 6.06 [45]. c Intra-patient HIV-1 quasispecies diversity determined using all three PR/RT-, INT-, and C2V3- coding regions based on the p-distance model as described for deep sequencing [46]. Means ± standard deviations and statistically significant differences between both cohorts of patients (unpaired t test) are marked by ****(p < 0.0001), ***(p < 0.001), **(p < 0.01), *(p < 0.05), and n.s. (p > 0.05). n.d., not determined; SG, St. George’s; NHS, NHS Lothian