Neutralization profiles of HIV-1 subtype C breakthrough viruses from the Southern African VRC01 AMP trial

Background: HIV-1 Env reference panels are used to guide the clinical development of broadly neutralizing antibodies (bNAbs) but need to be updated periodically as genetic drift may impact neutralization phenotypes. We assessed the neutralization sensitivity of breakthrough viruses from the southern African VRC01 AMP trial (HVTN 703/HPTN 081) as geographically relevant, current subtype C transmitted/founder viruses. Methods: Envelope sequences of breakthrough infections from 30 women in the AMP trial (prior to unblinding) were used to produce transmitted/founder (T/F) pseudotyped viruses. These were tested against 14 bNAbs targeting the CD4bs (n = 4), V3-glycan (n = 3), V2-apex (n = 3), gp120-gp41 interface (n = 2) and the MPER (n = 2) in the TZM-bl neutralization assay. Single bNAb neutralization data was used in the Loewe additive model (CombiNAber) to model the efficacy of bNAb combinations. Weakly neutralizing antibodies targeting normally occluded epitopes on HIV Env (V3, CD4i, V2 and gp41) were included to assess the tier phenotype of the viruses. Results: All breakthrough viruses were of the tier 2 phenotype, typical of T/F viruses. At a concentration of 1 [micro]g/ml at [IC.sub.50], 91% of viruses were neutralized by VRC07-523LS (GMT [IC.sub.50]=0.16) representing the best coverage by a single bNAb. Combinations of two to four bNAbs increased the number of viruses neutralized with the 4 bNAb combination (CAP256-VRC26.25/PGT121/VRC07-523LS/35022) neutralizing 100% of viruses (GMT [IC.sub.50]=0.01). The best-in-class 3 bNAb combination (CAP256-VRC26.25/PGT121/35022) provided 97% coverage (GMT [IC.sub.50]=0.01). Clinically advanced triple combinations such as CAP256-VRC26.25.25/PGT121/VRC07-523LS and/PGDM1400/PGT121/VRC07-523LS both resulted in a coverage of 97% (GMT IC50 = 0.02) against this panel of 30 subtype C breakthrough viruses. Conclusions: Our data confirm the need to use combination bNAbs in passive immunization trials to improve coverage of subtype C viruses. The exposure of a subset of these breakthrough viruses to VRC01 may have affected their phenotype, and this will be investigated when the AMP trial data is unblinded. Overall, these breakthrough viruses represent a unique resource for defining the sensitivity of contemporaneous circulating viral isolates to bNAbs.