Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control

Abstract

BackgroundDespite the low level of viral replication in HIV controllers (HICs), studies have reported viral mutations related to escape from cytotoxic T-lymphocyte (CTL) response in HIV-1 plasma sequences. Thus, evaluating the dynamics of the emergence of CTL-escape mutants in HICs reservoirs is important for understanding viremia control. To analyze the HIV-1 mutational profile and dynamics of CTL-escape mutants in HICs, we selected 11 long-term non-progressor individuals and divided them into the following groups: (1) viremic controllers (VCs; n = 5) and (2) elite controllers (ECs; n = 6). For each individual, we used HIV-1 proviral DNA from PBMCs related to earliest (VE) and latest (VL) visits to obtain gag and nef sequences using the Illumina HiSeq system. The consensus of each mapped gene was used to assess viral divergence, and next-generation sequencing data were employed to identify SNPs and variations within and flanking CTL epitopes.ResultsDivergence analysis showed higher values for nef compared to gag among the HICs. EC and VC groups showed similar divergence rates for both genes. Analysis of the number of SNPs showed that VCs present more variability in both genes. Synonymous/non-synonymous mutation ratios were < 1 for gag among ECs and for nef among ECs and VCs, exhibiting a predominance of non-synonymous mutations. Such mutations were observed in regions encoding CTL-restricted epitopes in all individuals. All ECs presented non-synonymous mutations in CTL epitopes but generally at low frequency (< 1%); all VCs showed a high number of mutations, with significant frequency changes between VE and VL visits. A higher frequency of internal mutations was observed for gag epitopes, with significant changes across visits compared to Nef epitopes, indicating a pattern associated with differential genetic pressure.ConclusionsThe high genetic conservation of HIV-1 gag and nef among ECs indicates that the higher level of viremia control restricts the evolution of both genes. Although viral replication levels in HICs are low or undetectable, all individuals exhibited CTL epitope mutations in proviral gag and nef variants, indicating that potential CTL escape mutants are present in HIC reservoirs and that situations leading to a disequilibrium of the host-virus relationship can result in the spread of CTL-escape variants.Electronic supplementary materialThe online version of this article (10.1186/s12977-018-0444-z) contains supplementary material, which is available to authorized users.

Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences

“…Mapping HIV immune epitopes in different regions of the genome will further clarify this hypothesis ( Matthews et al, 2012 ; Adland et al, 2013 ). As observed previously in other studies, CTL epitope KAFSPEVIPMF was the most conserved ( Garcia-knight et al, 2016 ; Gama Caetano et al, 2018 ). This epitope has been associated with very low frequencies of CTL response selective pressures and has been a choice for many T cell-based HIV vaccines ( Hanke, 2019 ).…”

“…It is essential to state that these substitutions were identified from HIV-1 DNA sequences against plasma RNA used in a similar study ( Gounder et al, 2015 ). Proviral sequences have previously been associated with rare mutations on CTL epitopes ( Gama Caetano et al, 2018 ; Lee et al, 2019 ). These substitutions may have to be considered in designing universal and therapeutic vaccines for HIV-1 strains circulating in West African countries ( Ndung’u et al, 2019 ; Shu et al, 2020 ).…”

HIV-1 elite controllers present a high frequency of activated regulatory T and Th17 cells

“…Higher CD4 + T cell counts were observed in ECs compared with cART (p = 0.0079). Detailed CD4+ T cells/mm3 and VL profiles of the ECs and VCs during the long-term follow-up were previously described [58,59]. ECs and VCs had medians of 8.5 and 10.4 years of HIV diagnosis time, respectively.…”

A case report of HIV-1 superinfection in an HIV controller leading to loss of viremia control: a retrospective of 10 years of follow-up

“…In addition, blood was collected at each visit to isolate plasma, whole blood and peripheral blood mononuclear cell (PBMC) samples for study. Subject VC06 was initially classified as an LTNP HIV viremic controller (< 2000 cp/ml dually infected with two HIV-1 subtype B viruses (de Azevedo et al 2017) [16]. She carries a nonprotective HLA-B genotype (HLA-B*15:01/ B*48:02) but has heterozygosis for the CCR5-Δ32 mutation, which is considered a host-protective allele for disease infection and progression.…”