FIG 6.

Characterization of alphavirus D-RNA populations using differential expression approaches. Three replicates each of intracellular (blue) and resulting virion (pink) RNA from Mayaro virus-infected (A, D, and G), Sindbis virus-infected (B, E, and H), and Aura virus-infected (C, F, and I) cells and supernatant was sequenced and evaluated for defective RNA (D-RNA) expression using ViReMa v1.5. DESeq2 was then used to concatenate and normalize count data for subsequent analyses. (A through C) Shannon’s diversity index H; (D through F) differential expression of all D-RNA species; (G through I) principal-component analyses. *, P < 0.05; **, P < 0.01; ***, P < 0.001.