Background: HIV-1 Nef is an important accessory protein with multiple effector functions. Genetic studies of the HIV-1 Nef gene show extensive genetic diversity and the functional studies have been carried out mostly with Nef derived from regions dominated by subtype B (North America & Europe).

Objective: This study was carried out to characterize genetic variations of the Nef gene from HIV-1 infected individuals from North India and to find out their functional implications.

Methods: The unique representative variants were sub-cloned in a eukaryotic expression vector and further characterized with respect to their ability to downregulate cell surface expression of CD4 and MHC-1 molecules.

Results: The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying the importance of mutations in Nef variants. Intracellular stability of Nef variants differed greatly when compared with wild type Nef B and C. There were some variants that possessed mutations in the functional domains of Nef and responsible for its differential CD4 and MHC-1 downregulation activity.

Conclusion: We observed enhanced biological activities in some of the variants, perhaps arising from amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a population to become the most abundant after a single selection event.

背景：HIV-1 Nef 是一种重要的辅助蛋白，具有多种效应功能。HIV-1 Nef 基因的遗传研究显示出广泛的遗传多样性，功能研究主要针对来自以 B 亚型为主的地区（北美和欧洲）的 Nef。

目的：本研究旨在表征来自印度北部 HIV-1 感染者的 Nef 基因的遗传变异，并找出它们的功能意义。

方法：将独特的代表性变体亚克隆到真核表达载体中，并进一步表征它们下调 CD4 和 MHC-1 分子细胞表面表达的能力。

结果：Nef 变体的系统发育分析揭示了与共有亚型 B 或 B/C 重组体的序列相似性。我们的一些变体的引导扫描分析显示与 B/C 重组体的同源性和一些与野生型 Nef B 的同源性。在大多数变体中观察到广泛的变异。dN/dS 比率显示 80% 的纯化选择和 20% 的多样化选择意味着 Nef 变体中突变的重要性。与野生型 Nef B 和 C 相比，Nef 变体的细胞内稳定性差异很大。有一些变体在 Nef 的功能域中具有突变，并导致其不同的 CD4 和 MHC-1 下调活性。

结论：我们观察到某些变体的生物活性增强，这可能是由于其功能域中的氨基酸取代所致。Nef 的 CD4 和 MHC-1 下调活性可能会带来巨大的生存优势，使种群中最稀有的基因型在单次选择事件后变得最丰富。