Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
Fundación Huésped, Buenos Aires, Argentina.
Vaccine. 2018 Jun 27;36(28):4142-4151. doi: 10.1016/j.vaccine.2018.04.086. Epub 2018 May 22.
Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection.
160 singlegag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient). Sanger sequencing and NGS SMRT technology (Pacific Biosciences) were implemented to sequence the amplicons. Phylogenetic analysis was performed by using MEGA 6.06. HLA-I (A and B) typing was performed by SSOP-PCR method. The chromatograms were analyzed with Sequencher 4.10. Epitopes and immune-proteosomal cleavages prediction was performed with CBS prediction server for the 30 HLA-A and -B alleles most prevalent in our population with peptide lengths from 8 to 14 mer. Cytotoxic response prediction was performed by using IEDB Analysis Resource.
After implementing epitope prediction analysis, we identified a total number of 325 possible viral epitopes present in two or more acute or chronic patients. 60.3% (n = 196) of them were present only in acute infection (prevalent acute epitopes) while 39.7% (n = 129) were present only in chronic infection (prevalent chronic epitopes). Within p24, the difference was equally dramatic with 59.4% (79/133) being acute epitopes (p < 0.05). This is consistent with progressive viral adaptation to immune response in time and further supported by the fact that cytotoxic responses prediction showed that acute epitopes are more likely to generate immune response than chronic epitopes. Interestingly, only 27.5% of acute epitopes match the population-level consensus sequence of the virus.
Our results indicate that certain non-consensus viral residues might be transmitted more frequently than consensus-residues when located in immunological relevant positions (epitopes). This observation might be relevant to the rationale behind development of an effective vaccineto reduce viral reservoir and induce functional cure of HIV infection based in prevalent acute epitopes.
最近的研究表明，与更高病毒适应性相关的病毒多态性的传播存在选择偏倚。此外，在病毒传播并在受者中产生特定免疫反应之前，病毒会经历多次回复突变，从而增加其复制能力。这些方面以及其他方面都会影响早期急性感染中病毒群体的特征。
通过对 8 名早期急性感染（<30 天，平均 22 天）和 8 名感染时间约为一年的 ARV 初治患者的血浆样本进行限制稀释 RT-PCR，获得了 160 个单基因扩增子。对扩增子进行 Sanger 测序和 NGS SMRT 技术（太平洋生物科学公司）测序。利用 MEGA 6.06 进行系统发育分析。采用 SSOP-PCR 法对 HLA-I（A 和 B）进行分型。使用 Sequencher 4.10 对色谱图进行分析。利用 CBS 预测服务器对 30 个在我国人群中最常见的 HLA-A 和 -B 等位基因进行 8-14 个氨基酸长度的肽段进行免疫保护酶切预测和表位预测。利用 IEDB 分析资源进行细胞毒性反应预测。
在实施表位预测分析后，我们在两个或多个急性或慢性患者中总共鉴定出 325 个可能的病毒表位。其中 60.3%（n=196）仅存在于急性感染中（流行急性表位），而 39.7%（n=129）仅存在于慢性感染中（流行慢性表位）。在 p24 中，差异同样显著，其中 59.4%（79/133）为急性表位（p<0.05）。这与病毒随时间逐渐适应免疫反应的情况一致，进一步证实了细胞毒性反应预测的结果，即急性表位比慢性表位更有可能产生免疫反应。有趣的是，只有 27.5%的急性表位与病毒的人群共识序列匹配。
我们的结果表明，在免疫相关位置（表位）处，某些非共识病毒残基的传播频率可能高于共识残基。这一观察结果可能与开发有效疫苗以减少病毒库并诱导 HIV 感染功能性治愈的基本原理有关，该疫苗基于流行的急性表位。
