A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture

► A real-time PCR assay to differentially quantify HIV-1 production in competitions. ► A mathematical method to estimate fitness impact of AA substitutions. ► Determination of the fitness impact of 8 AA substitutions in HIV-1 Gag and Env.