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. 2017 Sep 13;22(3):400–410.e5. doi: 10.1016/j.chom.2017.08.003

Figure 2.

Figure 2

Hotspots for Intrahost Diversity in the DENV-3 Genome

(A) Percent intrahost codon diversity (y axis) across the coding region of DENV-3 (x axis) in 68 PBMC (top panel) and 31 plasma (bottom panel) samples; each data point is colored according to the number of samples in which ≥1% intrahost diversity is detected at that locus.

(B) Major variants at the hotspot loci in prM/M (top) and E (bottom). Red asterisk, furin cleavage site.

(C) Prevalence of major hotspot loci (i.e., loci with ≥1% variant abundance in ≥50% of samples) in 68 plasma (right panel) and 31 PBMC (left panel) samples in both read orientations (read 1 in yellow and read 2 in red).

(D) Percent samples with diversity at each hotspot locus, shown for increasing cutoffs for percent intrahost codon diversity, in the 68 PBMC (left panel) and 31 plasma (right panel) datasets.

(E) Average percent intrahost (yellow) and percent interhost (red) diversity in codon (left panel) or amino acid (right panel) coordinates for each hotspot locus. Interhost diversity was calculated across all global DENV-3 isolates for which full-genome sequences were available (n = 690).