University of Rome Tor Vergata, Via Montpellier 1, Rome, Italy.
Retrovirology. 2011 May 12;8:33. doi: 10.1186/1742-4690-8-33.
The third variable loop (V3) of the HIV-1 gp120 surface protein is a major determinant of cellular co-receptor binding. However, HIV-1 can also modulate its tropism through other regions in gp120, such as V1, V2 and C4 regions, as well as in the gp41 protein. Moreover, specific changes in gp41 are likely to be responsible for of damage in gp120-CCR5 interactions, resulting in potential resistance to CCR5 inhibitors.In order to genetically characterize the two envelope viral proteins in terms of co-receptor usage, we have analyzed 526 full-length env sequences derived from HIV-1 subtype-B infected individuals, from our and public (Los Alamos) databases. The co-receptor usage was predicted by the analysis of V3 sequences using Geno2Pheno (G2P) algorithm. The binomial correlation phi coefficient was used to assess covariation among gp120V3 and gp41 mutations; subsequently the average linkage hierarchical agglomerative clustering was performed.
According to G2P false positive rate (FPR) values, among 526 env-sequences analyzed, we further characterized 196 sequences: 105 with FPR <5% and 91 with FPR >70%, for X4-using and R5-using viruses, respectively.Beyond the classical signatures at 11/25 V3 positions (S11S and E25D, R5-tropic viruses; S11KR and E25KRQ, X4-tropic viruses), other specific V3 and gp41 mutations were found statistically associated with the co-receptor usage. Almost all of these specific gp41 positions are exposed on the surface of the glycoprotein. By the covariation analysis, we found several statistically significant associations between V3 and gp41 mutations, especially in the context of CXCR4 viruses. The topology of the dendrogram showed the existence of a cluster associated with R5-usage involving E25DV3, S11SV3, T22AV3, S129DQgp41 and A96Ngp41 signatures (bootstrap = 0.88). Conversely, a large cluster was found associated with X4-usage involving T8IV3, S11KRV3, F20IVYV3, G24EKRV3, E25KRV3, Q32KRV3, A30Tgp41, A189Sgp41, N195Kgp41 and L210Pgp41 mutations (bootstrap = 0.84).
Our results show that gp120V3 and several specific amino acid changes in gp41 are associated together with CXCR4 and/or CCR5 usage. These findings implement previous observations that determinants of tropism may reside outside the V3-loop, even in the gp41. Further studies will be needed to confirm the degree to which these gp41 mutations contribute directly to co-receptor use.
HIV-1 gp120 表面蛋白的第三个可变环 (V3) 是细胞共受体结合的主要决定因素。然而，HIV-1 也可以通过 gp120 中的其他区域（如 V1、V2 和 C4 区域）以及 gp41 蛋白来调节其嗜性。此外，gp41 中的特定变化可能导致 gp120-CCR5 相互作用的损伤，从而导致对 CCR5 抑制剂的潜在耐药性。
为了从遗传角度表征两种包膜病毒蛋白的共受体使用情况，我们分析了来自我们和公共（洛斯阿拉莫斯）数据库中感染 HIV-1 亚型-B 的个体的 526 个全长 env 序列。使用 Geno2Pheno (G2P) 算法分析 V3 序列来预测共受体使用情况。使用二项式相关 phi 系数评估 gp120V3 和 gp41 突变之间的共变；随后进行平均链接层次凝聚聚类。
根据 G2P 假阳性率 (FPR) 值，在分析的 526 个 env 序列中，我们进一步对 196 个序列进行了特征描述：FPR<5% 的有 105 个，FPR>70% 的有 91 个，分别为 X4 使用和 R5 使用病毒。除了 11/25 V3 位置的经典特征（S11S 和 E25D，R5-嗜性病毒；S11KR 和 E25KRQ，X4-嗜性病毒）外，还发现了其他与共受体使用情况相关的特定 V3 和 gp41 突变。这些特定的 gp41 位置几乎都暴露在糖蛋白的表面。通过共变分析，我们发现 V3 和 gp41 突变之间存在几个具有统计学意义的关联，尤其是在 CXCR4 病毒的情况下。树状图的拓扑结构显示存在一个与 R5 使用相关的簇，涉及 E25DV3、S11SV3、T22AV3、S129DQgp41 和 A96Ngp41 特征（自举=0.88）。相反，发现一个与 X4 使用相关的大簇，涉及 T8IV3、S11KRV3、F20IVYV3、G24EKRV3、E25KRV3、Q32KRV3、A30Tgp41、A189Sgp41、N195Kgp41 和 L210Pgp41 突变（自举=0.84）。
我们的结果表明，gp120V3 和 gp41 中的几个特定氨基酸变化与 CXCR4 和/或 CCR5 使用相关。这些发现证实了以前的观察结果，即嗜性决定因素可能位于 V3 环之外，甚至在 gp41 中。需要进一步的研究来证实这些 gp41 突变在多大程度上直接导致共受体的使用。
