Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies.

Broadly neutralizing antibodies (bNAbs) show promise for HIV treatment and prevention, but are vulnerable to resistance evolution. Comprehensively understanding in vivo viral escape from individual bNAbs is necessary to design bNAb combinations that will provide durable responses. We characterize viral escape from two such bNAbs, 10-1074 and 3BNC117, using deep, longitudinal sequencing of full length HIV envelope ( env ) genes from study participants treated with bNAb monotherapy. Improved sequencing depth and computational evolutionary analyses permit us to identify in vivo routes and parallelism underlying HIV escape from each bNAb, providing new insights into this evolutionary process: 10-1074 escape is restricted to a small number of previously documented pathways, but these escape mutations 1) pre-exist in intra-host viral populations before therapy, 2) are not all equally preferred, and 3) emerge with a high degree of genetic parallelism within and across viral populations. In contrast, 3BNC117 escape follows background-specific patterns in which specific escape mutations present in one population rarely emerge or spread in other populations, but often still exhibit parallel evolutionary responses within their host. That bNAbs elicit starkly different in vivo escape profiles depending on their Env target exposes the limitations of generalizing escape patterns across therapies and highlights the substantial challenges in predicting a viral population’s bNAb susceptibility from genetic diversity alone. Significance Statement Analyses of HIV clinical trial data have long been limited by tradeoffs between sequencing at high depth and preserving genetic linkage information. Using recently developed techniques eliminating this trade off, we deeply re-sequenced samples from two clinical trials of broadly neutralizing antibody (bNAb) monotherapies. We employed novel and established computational analyses to characterize HIV populations with unprecedented resolution as they escaped these therapies. Tracking single escape mutations in the context of their genetic backgrounds, we find starkly different patterns of escape from these two bNAbs with distinct target regions, 10-1074 and 3BNC117. Our findings highlight the difficulties in evaluating pre-treatment resistance; thus, careful antibody selection for future studies will be needed to maximize the likelihood of durable efficacy.