Complete mapping of viral escape from neutralizing antibodies
(A) Libraries of viruses carrying all amino-acid point mutants of a protein that support viral replication are incubated with or without antibody, and used to infect cells. Viral RNA is extracted from cells and accurately deep sequenced to quantify the frequency of each mutation in the antibody-selected and no-antibody control samples. (B) Differential selection is defined as the logarithm of the enrichment of each mutation in the antibody-selected sample versus the control. In the logo plots, the height of each letter is proportional to the differential selection for that amino-acid. The site differential selection is the total height of the logo stack at that site (the sum of mutation differential selection values). Only positive differential selection (corresponding to mutations enriched by selection) is shown. Logo plot letters are colored by physicochemical properties of amino-acids.