Intracellular assay of replication for A1664G-orange and additional mutations. The frequencies of the various genotypes are shown across various time point of the viral replication cycle from genomes isolated from inside infected cells (pellet). Time points zero and ON-Sup represent sequencing of virions from supernatant at the start and end of a passage. Each horizontal block represents a unique haplotype and is colored according to its mutations (colors coded as shown in Fig. 4a). Block height is proportional to the frequency of the haplotype. Only genotype frequencies initially higher than 5% are displayed. Genotype frequencies were inferred from Fig. 4b (Methods). a) Results from intracellular assay at MOI of 0.01, and b) Results from intracellular assay at MOI of 1. The lower panel illustrates timing of entry, replication, and packaging/lysis (see Fig. 3 legend).