Analysis of genetic diversity and VRC01 pressure on HIV-1 breakthrough viruses from the AMP trial

Background: The Antibody Mediated Prevention (AMP) trial evaluated if VRC01, a CD4 binding site broadly neutralizing antibody, could prevent HIV-1 acquisition. To inform our understanding of how prevention efficacy depended on viral env gene charateristics, viral quasis-pecies and neutralization sensitivity of HIV-1 breakthrough infections were analyzed. Methods: The trial evaluated VRC01 in women from sub-Saharan Africa (703/081); and men and transgender persons who have sex with men (704/085), from the Americas. Control samples from Thailand, Kenya and South Africa are being used for calibrating infection timing using sequence data. Rev-env-nef (REN) sequences were generated using Sanger and PacBio Single Molecule Real-Time (SMRT) sequencing platforms. To improve PacBio accuracy and enable quantitation, each viral RNA molecule was labelled with a unique molecular identifier (SMRT-UMI). Rev-env genes from imputed founder viruses were synthesized for pseudovirus production and in vitro sensitivity to VRC01 determined using the TZM-bl assay. Results: Approximately 84 000 unique REN sequences were generated from the first HIV-1 positive visit from 218 infected individuals in both trials, and two to four weeks later from a subset of individuals, providing a median of 174 unique env sequences per participant per time point. In approximately 2/3 of individuals, viral diversity was low, consistent with infection with a single founder virus. Of the 1/3 of individuals with higher viral diversity, consistent with infection with multiple founders, a third had low frequency variants (