Extended Data Fig. 5: Phylogenetic env trees and TZM-bl neutralization curves for individuals with viral blips.

a, Circulating reservoir and viral rebound in study participants with detectable viraemia at week −2 or day 0. Maximum likelihood phylogenetic trees of full-length env sequences of viruses isolated from week −2 Q²VOA cultures, rebound plasma SGA and rebound outgrowth from the four participants with viral blips. Open black rectangles indicate Q²VOA-derived viruses from week −2. Viruses obtained at the time of rebound are indicated by red rectangles (plasma SGA) and red stars (rebound PBMC outgrowth cultures), respectively. Asterisks indicate nodes with significant bootstrap values (bootstrap support ≥70%). Clones are denoted by coloured lines. Boxes indicate IC₈₀ values (μg ml⁻¹) of 3BNC117 and 10-1074 against individual clones, with asterisks indicating IC₁₀₀ > 50 μg ml⁻¹. b, Latent reservoir virus TZM-bl neutralization curves for two participants that had a viral load of >20 copies per ml at day 0 (9248 and 9250). Curves show neutralization titres by 3BNC117 (blue), 10-1074 (red) and other bNAbs, when available, for week −2 Q²VOA-derived viruses present in the circulating reservoir. Three representative viruses from 9248 (left) and 9250 (right) are shown. Although these viruses had low 3BNC117 and 10-1074 IC₅₀ or IC₈₀ titres, the IC₁₀₀ (black dotted line) is reached only at a high concentration or not reached at all. The neutralization titre was measured by TZM-bl neutralization assay using a five-parameter curve fit method.