High-throughput screening of neutralizing epitopes on HIV particles using single-virus droplet microfluidics. MiSeq 250 NGS raw data of WT-Env and T303-Env sequencing reads from microfluidic experiments.

Analyzing surface epitopes of single HIV particles holds great potential for the development of vaccine candidates. However, existing technologies do not allow corresponding screens at high-throughput. We present here a single-virus droplet-based microfluidics platform enabling sorting of HIV-1 particles at a throughput of >200 per second based on the expression of epitopes recognized by broadly neutralizing antibodies. We show that virus particles displaying these epitopes can be identified, sorted and analyzed by next generation sequencing (NGS): an approximately 1.5 × 10^7 fold enrichment of viral particles displaying neutralizing epitopes could be obtained in a single sort, thus opening the way for screening diverse virus libraries with optimal antigenic features for HIV vaccine candidates.