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Naturally-arising amino acid polymorphisms of HIV-1 Nef that differentially modulate downregulation of HLA-A and HLA-B molecules


Differential Nef-mediated down-regulation of HLA-Aand HLA-B has been reported in laboratory-adapted Nef strains [1]. Whether naturally-occurring Nef proteins exhibit differential HLA class I (HLA-I) down-regulation activities remains unknown.

Materials and methods

Plasma HIV RNA-derived Nef clones (one per patient) were isolated from 45 chronically-infected subjects and inserted into the pNL43 proviral vector. Recombinant viruses were prepared and used to infect the HLA-l-deficient cell line 721.221 ectopically expressing either HLA-A*24 or HLA-B*35. Following infection, cell-surface HLA-I expression of virus-infected cells was evaluated by flow cytometry using a pan HLA-I specific antibody [2, 3].


Cell-surface HLA-I expression levels differed following infection with recombinant viruses expressing patient-derived Nef, with median [IQR] expression levels of HLA-A*24 and HLA-B*35 of 38.9 [23.4-76.9] % and 50.7 [39.9-81.9] %, respectively, compared to those of uninfected cells as 100% (p <0.001). Thus, downregulation of HLA-A by patient-derived Nef clones was significantly more efficient than that of HLA-B, consistent with the previous observations made by laboratory-adapted strains. However, ratios of downregulation activity of HLA-A/HLA-B were median [IQR] 1.25 [0.81-2.37], while that of control strain SF2 was 1.21, indicating a relatively broad range of HLA-A and HLA-B downregulation activities among naturally-isolated Nef clones. Codon-function analysis of HLA-A/HLA-B downregulation ratios identified amino acid polymorphisms at position158 and 202 as being significantly associated (p <0.01, q <0.2) with relative abilities to downregulate alleles of HLA-A vs. B loci.


Despite a broad range of observed function, Nef-mediated ability to downregulate HLA-A exceeded that of HLA-B in 45 Nef clones in chronic infection. We identified for the first time two Nef amino acid polymorphisms at position 158 and 202 that differentially influence HLA-A and HLA-B downregulation, suggesting that they play a role in differential interaction between Nef and allelic polymorphisms of HLA-I cytoplasmic tail.


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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Mahiti, M., Mwimanzi, P., Ogata, Y. et al. Naturally-arising amino acid polymorphisms of HIV-1 Nef that differentially modulate downregulation of HLA-A and HLA-B molecules. Retrovirology 10 (Suppl 1), P54 (2013).

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