Early protease inhibitor (PI) based antiretroviral therapy (ART) is recommended in vertically infected children, bringing immediate clinical benefit and limiting the reservoir size, which may impact on future chances of cure. We previously reported linked multi-class drug resistance (MDR) in children that received nevirapine prophylaxis and failed early PI based ART (Lange et al, JAIDS 2015). Here we report evolutionary histories of drug resistant lineages in these children.
Single genome sequencing was used to characterise genetically linked MDR in HIV-1 protease and reverse transcriptase from longitudinal plasma samples. Sequences were obtained from the pre-ART populations, during suppressive therapy, treatment failure, treatment interruption and re-started ART. The mean pairwise genetic distances (MPDs) between these populations were calculated. The evolution and population diversity of MDR lineages were analysed by Maximum Likelihood (ML) phylogenetic reconstruction.
442 sequences were obtained from 2/10 children: n=249 from 7 time points in the first child; n=193 from 5 time points in the second child. Sampling depth was estimated as ≥ 5-10% of the viral population. ML trees showed multiple emergences of MDR on distinct intra-patient lineages. One child had a clonally expanded MDR lineage persisting for 85 weeks of ART. Accordingly, MPD at weeks 12, 40, 72 and 96 of ART were significantly lower than at baseline (0.6%, 0.5%, 0.2% and 0.3% vs 0.7% respectively; p<0.0001). In stark contrast the ML tree of the second child indicated temporal stepwise accumulation of resistance mutations. In this scenario the MPD at weeks 40 and 96 of ART and at week 60 of re-started ART were significantly higher than at baseline (0.3%, 0.4% and 0.3% vs 0.1% respectively; p<0.0001). MDR populations with PI resistance most frequently evolved from RT M184V mutated viral populations in both children.
We report distinct patterns of multiple class HIV-1 drug resistance acquisition over time in children treated with early PI based ART: firstly clonal expansion from an MDR reservoir, and secondly through stepwise accumulation of major resistance mutations.