Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil.
Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil.
Retrovirology. 2018 Sep 10;15(1):62. doi: 10.1186/s12977-018-0444-z.
Despite 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 (V) and latest (V) 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.
Divergence 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 V and V 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.
The 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.
尽管 HIV 控制者（HIC）体内的病毒复制水平较低，但已有研究报告称，在 HIV-1 血浆序列中存在与细胞毒性 T 淋巴细胞（CTL）反应逃逸相关的病毒突变。因此，评估 HIC 储库中 CTL 逃逸突变体的出现动态对于理解病毒血症控制至关重要。为了分析 HIC 中 HIV-1 的突变特征和 CTL 逃逸突变体的动态，我们选择了 11 名长期非进展者个体，并将他们分为以下两组：（1）病毒血症控制者（VCs；n=5）和（2）精英控制者（ECs；n=6）。对于每个个体，我们使用与最早（V）和最晚（V）就诊相关的 PBMC 中的 HIV-1 前病毒 DNA，使用 Illumina HiSeq 系统获得 gag 和 nef 序列。每个映射基因的共识用于评估病毒分化，下一代测序数据用于鉴定 CTL 表位内和侧翼的 SNP 和变异。
分化分析显示，HIC 中 nef 与 gag 相比具有更高的值。EC 和 VC 组在这两个基因上显示出相似的分化率。对 SNP 数量的分析表明，VCs 在两个基因中都表现出更多的变异性。EC 中 gag 和 ECs 及 VCs 中的 nef 的同义/非同义突变比均<1，表现出非同义突变的优势。所有个体的 CTL 限制性表位编码区都观察到这种突变。所有 EC 都在 CTL 表位中出现非同义突变，但通常频率较低（<1%）；所有 VCs 都显示出大量突变，在 V 和 V 就诊之间有显著的频率变化。gag 表位的内部突变频率更高，与 Nef 表位相比，各次就诊之间的变化具有显著意义，表明存在与差异遗传压力相关的模式。
EC 中 HIV-1 gag 和 nef 的高度遗传保守性表明，更高水平的病毒血症控制限制了这两个基因的进化。尽管 HIC 中的病毒复制水平较低或无法检测到，但所有个体的前病毒 gag 和 nef 变体中均存在 CTL 表位突变，表明潜在的 CTL 逃逸突变体存在于 HIC 储库中，并且导致宿主-病毒关系失衡的情况可能导致 CTL 逃逸变异体的传播。
