Background
Broadly neutralizing antibodies (bNAbs) against HIV-1 have re-invigorated research into antibody therapies and vaccination strategies for prevention, treatment, and cure of HIV-1 because of their unique ability to neutralize diverse HIV-1 strains. While many HIV-1 isolates are initially susceptible to bNAbs, their ability to acquire resistance is unknown. Understanding the evolutionary barriers to bNAb resistance will inform the feasibility of using bNAbs as HIV-1 prevention, treatment, and cure.
Methods
We developed a cell-culture based system to understand the evolutionary barriers to escape from neutralization by the bNAb 3BNC117. We performed numerous parallel selection experiments to capture the array of escape pathways available to a range of HIV-1 strains. We isolated 375 viruses that replicated in the presence of 3BNC117 from 16 starting viral strains. Each viral variant isolated by our assay was confirmed to be resistant to 3BNC117 and sequenced using Illumina-based short read sequencing. We developed a statistical model to distinguish mutations conferring bNAb resistance from passanger mutations and confirmed these predictions using a pseudotype neutralization assay. We performed this procedure on numerous group M HIV-1 isolates of various subtypes that capture the worldwide diversity of HIV-1.
Results
3BNC117-resistant variants were isolated from all HIV-1 strains tested. Some viral strains demonstrated many different mutational escape pathways, while others demonstrated only a single dominant escape mutation that was selected in several different resistant isolates. The vast majority of HIV-1 strains required only a single nucleotide substitution to escape 3BNC117 neutralization. These resistance mutations existed in the viral quasispecies prior to selection at variable frequencies, ranging from 1 in 102 viruses (common) to less than 1 in 106 viruses (rare). Each resistance mutation was tested in a pseudotype assay against a panel of bNAbs, demonstrating that some, but not all 3BNC117 escape mutations were able to confer resistance to additional CD4 binding site bNAbs.
Conclusions
This study demonstrates that various pathways exist for escape from a CD4 binding site bNAb 3BNC117 among divergent HIV-1 isolates. Understanding the pathways enabling escape from bNAb neutralization as well as the frequency at which they are maintained in the population will help to tailor these antibody-based therapies and inform the design of vaccines that aim to elicit bNAb-like antibodies.
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