Shedding dynamics of a DNA virus population during acute and long-term persistent infection
Fig 5
Diversity of barcode repertoire decreases after early times of infection.
Shown is the Shannon entropy, which is a measure of complexity (blue line). Shannon entropy captures both the richness (number of barcodes) and evenness (how uniformly barcode abundances are distributed) within the viral population. Overlaid is a plot showing a separate analysis for the number of barcodes it takes to account for 75% of total bulk shed genomes at any single time point (gold). This measure provides a complementary view of diversity by focusing on how many dominant barcodes contribute to the majority of viral DNA at each timepoint. Note, both measures show similar trends of diversity decreasing after the early times post-infection and then stabilizing.