Maintenance of multiple Nef functions limits and dictates pathways of immune escape (VIR1P.1147)

Abstract CD8+ T lymphocytes (CD8TL) can effectively control SIV and HIV replication. CD8TL targeting of particular regions in the Nef globular core is associated with control of both viruses suggesting common mechanisms of control. Deep sequencing of SIV from nine Mamu-B*017:01+ macaques revealed distinct selection patterns in two Nef epitopes. Functional assays revealed that acute escape in one epitope impacted a conserved structural face of the Nef core and reduced MHC-I downregulation, rendering infected cells more susceptible to CD8TL against other epitopes. In contrast, acute mutations in a nearby epitope impacted Nef’s ability to downregulate Tetherin and CD28, both of which are modulated via Nef interactions with host clathrin adaptor proteins, with mutations impacting MHC-I anchor residues being most destructive. In fact, anchor residues in both epitopes are almost entirely conserved throughout primate lentiviral history, spanning more than 40 millennia suggesting selection for maintenance of function. These data suggest mechanisms by which Nef targeting CD8TL can contribute to viral control; by targeting conserved epitopes involved in fuctions that are critical for high-level viral replication in vivo. Our approach to understanding T cell mediated control of SIV revealed novel insights into Nef structure:function relationships and suggest that particular regions of the Nef protein might be attractive components of vaccines designed to induce potent CD8TL responses.