FIG 2.

Characterization of CHIKV D-RNA populations using differential expression approaches. Three replicates each of intracellular (blue) and resulting virion (pink) RNA from CHIKV infected Vero cells and supernatant, respectively, were sequenced and evaluated for defective RNA (D-RNA) expression using ViReMa v1.5. Count tables of D-RNAs abundance were passed to DESeq2 for subsequent analyses. (A) Two-dimensional principal-component analysis; (B) differential expression of all D-RNA species; (C) hierarchical clustering of CHIKV D-RNA species expression (using normalized count number from DESeq2 output with Cluster 3.0 and Treeview).