VirScan data analysis
infection
INFECTION
Longitudinal samples for each participant were included on the same 96-well immunoprecipitation plate. Each plate included 7-8 mock reactions (beads only; negative controls) and a positive control sample in triplicate (pooled plasma from 10 HPTN 071 participants with infection duration >2 years and VL >2,000 copies/mL). Antibody reactivity data for individual peptides were reported as raw read counts, fold change values (compared to read counts in observed mock reactions), and associated p-values. Raw read counts for each peptide were determined via exact matching of the first 50 nucleotides of peptide coding DNA, with one added read count for each peptide. Fold changes and p-values were determined using the exact test for the negative binomial distribution implemented in the edgeR package (Viral aggregate reactivity scores (VARscores) are a measure of the overall level and breadth of antibody reactivity across a viral genome. In this study, VARscores and associated p-values were calculated by comparing mean log