Williamson, C.; Moodley, C.; Magaret, C. A.; Giorgi, E. E.; Rolland, M.; Westfall, D. H.; Yssel, A.; Deng, W.; Rossenkhan, R.; Mkhize, N. N.; Chen, L. H.; Zhao, H.; Bhattacharya, T.; Pankow, A.; Murrell, B.; York, T.; Gwashu-Nyangiwe, A.; Ndabambi, N.; Thebus, R.; Cohen, P.; Lambson, B. E.; Kaldine, H.; Bhebhe, S.; Juraska, M.; Bai, H.; deCamp, A. C.; Miner, M.; Ludwig, J.; Molitor, C.; Beaume, N.; Matten, D.; Huang, Y.; Zhang, L.; Reeves, D. B.; Mayer, B.; Karuna, S. T.; Hural, J. A.; Morris, L.; Montefiori, D.; Bumgarner, R. E.; Moore, P.; Edlefsen, P. T.; Edupuganti, S.; Mgodi, N.; McElrath

In the HIV antibody mediated prevention (AMP) trials, the broadly neutralizing antibody VRC01 demonstrated protective efficacy against new diagnoses with susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, we performed deep sequencing on 172 participants in the placebo and treatment arms, generating 63,444 gag-{Delta}pol (2.5 kb) and 53,088 rev-env-{Delta}nef (3 kb) sequences. Sequences were classified into transmitted founder lineages (TFLs), and infections with multiple distinct lineages were determined. Multilineage infections were detected in ~38% of participants in both the African (HVTN 703/HPTN 081) and Americas/Europe (HVTN 704/HPTN 085) cohorts, regardless of placebo or treatment group, or cohort. The high levels of multilineage infections could be attributed to minor lineages (<5% abundance) identified in 20% of participants. Infection with VRC01 discordant viruses (IC80s >3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1mcg/ml) and resistant viruses (IC80>3mcg/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01.