An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies

Abstract

Anti-HIV broadly neutralizing antibodies (bnAbs) have revealed vaccine targets on the virus's Env protein and are themselves promising immunotherapeutics. The efficacy of bnAb-based therapies and vaccines depends in part on how readily the virus can escape neutralization. While structural studies can define contacts between bnAbs and Env, only functional studies can define mutations that confer escape. Here we map how all single amino-acid mutations to Env affect neutralization of HIV by nine bnAbs targeting five epitopes. For most bnAbs, mutations at only a small fraction of structurally defined contact sites mediated escape, and most escape occurred at sites that are near but do not directly contact the antibody. The mutations selected by two pooled bnAbs were similar to those expected from the combination of the bnAbs' independent action. Overall, our mutation-level antigenic atlas provides a comprehensive dataset for understanding viral immune escape and refining therapies and vaccines.

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

“…Conversely, there were instances where previous studies had defined sites on Env with close proximity and hydrogen bonding to the antibody by X-ray crystallography, such as residues 595 to 609 for F240 19 , but we did not observe strong negative selection taking place at sites 595, 596, or 605 -609. Other studies have demonstrated that side chain proximity does not necessarily predict the contribution of a site to the formation of a protein-protein complex [25][26][27][28][29][30][31][32] , and this case with F240 further illustrates how analysis by Phage-DMS can yield information on the critical binding interactions of an antibody distinct from the identity of interfacing sites obtained by structural studies.…”

Mycobacterium tuberculosisdisease associates with higher HIV-1-specific antibody responses

“…Antibodies that target conserved structures on the HIV-1 Env generally impart broad and potent nAb responses (47). Changes at specific amino acid sites that affect this conserved structure account for escape from bnAbs.…”

Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide

“…To identify resistance mutations, we incubated the mutant virus libraries with or without enfuvirtide, infected cells, and then identified the mutant viruses that were enriched upon drug selection using deep sequencing. This approach is similar to the mutational antigenic profiling process we have previously used to map antibody escape [10,11]. Briefly, 5×10 5 to 1×10 6 infectious units of three independent mutant virus libraries were incubated in the presence of 8ug/mL of enfuvirtide, then infected into 1×10 6 SupT1.CCR5 cells in R10 (RPMI with 10% FBS, 1% 200 mM L-glutamine, and 100 units/mL of penicillin and streptomycin), containing 100ug/mL DEAE-dextran.…”

“…Selected and mock-selected viral cDNA was then sequenced with a barcoded subamplicon sequencing approach as previously described [8], which introduces unique molecular identifiers used to correct sequencing errors. The amount of virus library that entered cells was quantified via qPCR [11].…”