Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa.
National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Virol J. 2022 Mar 28;19(1):56. doi: 10.1186/s12985-022-01772-8.
Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection.
Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at [Formula: see text] 5% were detected using low-frequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 CTL epitopes.
Fifty-two participants were enrolled in the study. Their median age was 28 years (interquartile range: 24-32 years) and majority of participants (92.3%) were female. Illumina minority variant analysis identified a significantly higher number of CTL epitopes (n = 65) compared to epitopes (n = 8) identified through Sanger sequencing. Most of the identified epitopes mapped to reverse transcriptase (RT) and integrase (IN) regardless of sequencing method. There was a significantly higher proportion of minority variant epitopes in RT (n = 39, 60.0%) compared to IN (n = 17, 26.2%) and PR (n = 9, 13.8%), p = 0.002 and < 0.0001, respectively. However, no significant difference was observed between the proportion of minority variant epitopes in IN versus PR, p = 0.06. Some epitopes were detected in either early or chronic HIV-1 infection whereas others were detected in both stages. Different distribution patterns of minority variant epitopes were observed in sample pairs; with some increasing or decreasing over time, while others remained constant. Some of the identified epitopes have not been previously reported for HIV-1 subtype C. There were also variants that could not be mapped to reported CTL epitopes in the Los Alamos HIV database.
Deep sequencing revealed many Pol CTL epitopes, including some not previously reported for HIV-1 subtype C. The findings of this study support the inclusion of RT and IN epitopes in HIV-1 vaccine candidates as these proteins harbour many CTL epitopes.
尽管已经进行了多次尝试，但目前仍没有有效的 HIV-1 疫苗。HIV-1 聚合酶（pol）基因高度保守，编码细胞毒性 T 淋巴细胞（CTL）表位。本研究的目的是在感染的早期和慢性阶段获得的大多数样本对中，对 HIV-1 Pol CTL 表位进行特征描述。
对所有样本进行 Illumina 深度测序，而仅对基线样本进行 Sanger 测序。使用 MEGA 计算非同义与同义突变比来评估受免疫选择压力的密码子。使用 CLC Genomics 的低频变异工具检测发生频率在 [Formula: see text] 5%的少数 CTL 表位变异。使用 Los Alamos HIV 数据库将突变映射到已知的 HIV-1 CTL 表位。
本研究纳入了 52 名参与者。他们的中位年龄为 28 岁（四分位间距：24-32 岁），大多数参与者（92.3%）为女性。Illumina 少数变体分析鉴定出的 CTL 表位数量明显多于通过 Sanger 测序鉴定出的表位数量（n=65 比 n=8）。无论测序方法如何，大多数鉴定出的表位都映射到逆转录酶（RT）和整合酶（IN）。在 RT（n=39，60.0%）中少数变异表位的比例明显高于 IN（n=17，26.2%）和 PR（n=9，13.8%），p=0.002 和 <0.0001，分别。然而，IN 中少数变异表位的比例与 PR 之间没有显著差异，p=0.06。一些表位在 HIV-1 感染的早期或慢性期均有检出，而其他表位仅在其中一个阶段检出。在样本对中观察到少数变异表位的分布模式不同；有些随着时间的推移而增加或减少，而有些则保持不变。鉴定出的一些表位以前没有报道过 HIV-1 亚型 C。也有一些变体无法映射到 Los Alamos HIV 数据库中报道的 CTL 表位。
深度测序揭示了许多 Pol CTL 表位，包括一些以前没有报道过的 HIV-1 亚型 C。本研究的结果支持将 RT 和 IN 表位纳入 HIV-1 疫苗候选物中，因为这些蛋白含有许多 CTL 表位。
