Longitudinal Evolutionary Dynamics of HIV Escape from Broadly Neutralizing Antibodies

Abstract

We conducted experimental in vivo evolution of HIV to understand how the virus mutates to resist broadly neutralizing antibodies (bNAbs). In the first part, we longitudinally sequenced HIV escape from bNAbs in humanized mouse models. We found that HIV could escape in vivo from many bNAbs with a single point mutation, but we found one CD4-binding site bNAb that partially suppressed HIV. For this bNAb, we found that HIV had a constrained multi-step path of escape. We then used mathematical modeling to explain the tradeoffs between intrinsic replicative fitness and antibody resistance that HIV faced when escaping bNAb pressure. In the second part, we engineered HIV with two "barcodes," one at either side of its envelope gene. Each virion produced in this ~10^4 library had two unique sequences. We found that barcoded HIV remained replication competent, and we used it to measure three in vivo biological phenomena in humanized mouse models. We first compared the relative efficiency of intravenous versus intravaginal infection, by comparing the barcode diversity of the established infection. Second, by measuring the temporal loss of genetic linkage between the two barcodes, we found that HIV had a recombination rate that was comparable to its mutation rate. Lastly, we found that different bNAbs genetically bottlenecked the HIV population to different degrees. For some bNAbs, diversity of barcode lineages was only partially reduced, suggesting easier escape with independent mutations arising de novo on many lineages. For other bNAbs, the diversity was greatly reduced, suggesting more difficult escape from a few origins. Thus, barcode diversity reduction is a measure of in vivo bNAb "escapability" and a means to rank bNAbs for clinical evaluation.