Evidence of HLA-mediated immune response driving the maintenance of CTL-escape variants in patients with undetectable viral load

Evidence of HLA-mediated immune response driving the maintenance of CTL-escape variants in patients with undetectable viral load. Dario A Dilernia, L Lourtau, L Jones, S Rodriguez, C Bautista, M Gomez-Carrillo, M Losso, and H Salomon. Immune response drives the selection of CTL-escape mutations during the course of HIV infection. After initiation of HAART, antiviral drugs exert a stronger selective force leading to a higher limitation of viral replication. Our objective was to evaluate the effectiveness of immune response as a selective force in a context of extremely reduced viral population size. Gag gene was sequenced and HLA-A and B genotyped over 108 samples from drug-naïve HIV-1 positive individuals. Associations between HLA alleles and viral polymorphisms were assessed by logistic regression. Multiple comparison corrections were addressed by the BH method (q-values). Phylogeny correction was performed by a Bayesian Markov-Chain Monte-Carlo method. Analysis of site-specific synonymous and non-synonymous substitution rate was assessed through the codon-based ML IFEL method. For four patients with viral load < 50 copies/ml (identified according to their HLA profile), RNA extraction was performed from 7 ml of plasma through an ultracentrifugation-based method and gag gene amplified through a Hi-Fi PCR. 20-40 clones were sequenced in samples obtained previously and during HAART. We found that HLA-B57 and A03 were the most efficient alleles in forcing CTL-escape, targeting mainly the previously characterized epitopes TSTLQEQIGW(p=0.0002) and RLRPGGKKK(p<10E-7), respectively. Sites under significant positive selection (p