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Molecular and Genetic Characterization of Natural Variants of HIV-1 Nef Gene from North India and its Functional Implication in Down-Regulation of MHC-I and CD-4

[ Vol. 19 , Issue. 2 ]


J. Singh*, L. Ronsard, M. Pandey, R. Kapoor, V. G. Ramachandran and A. C. Banerjea   Pages 172 - 187 ( 16 )


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.


Cluster of Differentiation-4 (CD4), functional domain, genetic variations, human immunodeficiency virus (HIV), major histocompatibility complex-1 (MHC-1), Nef.


National Institute of Immunology, New Delhi, National Institute of Immunology, New Delhi, King George`s Medical University, National Institute of Immunology, New Delhi, Department of Virology, National Institute of Immunology, New Delhi-110067, Department of Virology, National Institute of Immunology, New Delhi-110067

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