Tetherin downmodulation by SIVmac Nef lost with the H196Q escape variant is restored by an upstream variant

The H(196) residue in SIVmac239 Nef is conserved across the majority of HIV and SIV isolates, lies immediately adjacent to the AP-2 (adaptor protein 2) binding di-leucine domain (ExxxLM(195)), and is critical for several described AP-2 dependent Nef functions, including the downregulation of tetherin (BST-2/CD317), CD4, and others. Surprisingly, many stocks of the closely related SIVmac251 swarm virus harbor a nef allele encoding a Q(196). In SIVmac239, this variant is associated with loss of multiple AP-2 dependent functions. Publicly available sequences for SIVmac251 stocks were mined for variants linked to Q(196) that might compensate for functional defects associated with this residue. Variants were engineered into the SIVmac239 backbone and in Nef expression plasmids and flow cytometry was used to examine surface tetherin expression in primary CD4 T cells and surface CD4 expression in SupT1 cells engineered to express rhesus CD4. We found that SIVmac251 stocks that encode a Q(196) residue in Nef uniformly also encode an upstream R(191) residue. We show that R(191) restores the ability of Nef to downregulate tetherin in the presence of Q(196) and has a similar but less pronounced impact on CD4 expression. However, a published report showed Q(196) commonly evolves to H(196) in vivo, suggesting a fitness cost. R(191) may represent compensatory evolution to restore the ability to downregulate tetherin lost in viruses harboring Q(196).