HIV-1 sequencing of patients failing 2nd-line regimens

Prolonged virologic failure on 2nd-line protease inhibitor (PI) based ART without emergence of major protease mutations is well recognised and provides an opportunity to study within-host evolution in long-term viraemic individuals. Using next-generation sequencing and in silico haplotype reconstruction we analysed whole genome sequences from longitudinal plasma samples of eight chronically infected HIV-1 individuals failing 2nd-line regimens from the ANRS 12249 TasP trial. On non-suppressive ART, there were large fluctuations in synonymous and non-synonymous variant frequencies despite stable viraemia. Reconstructed haplotypes provided evidence for selective sweeps during periods of partial adherence, and viral population competition during periods of low drug exposure. Drug resistance mutations in RT can be used as markers of viral populations in the reservoir and there was evidence of linkage disequilibrium decay, indicative of recombination. With years of PI exposure within the context of large stable populations displaying ongoing selective competition, the lacking emergence of major PI resistance mutations indicates that there are significant fitness costs for these mutations.