Fig. 2: Association of dsRNA with vgRNA clusters.

a-b, Representative confocal images of SARS-CoV-2 infected cells display DL colocalization between dsRNA (green) and vgRNA (magenta) at both 6 hpi (a) and 24 hpi (b). c-d, Representative SR images of SARS-CoV-2 infected cells indicate association between dsRNA and vgRNA at 6 hpi (c) and short-range anti-correlation often with concentric localization at 24 hpi (d). Bottom panels, zoomed-in images of corresponding colored boxes. e, Bivariate pair-correlation functions g₁₂(r) calculated between the localizations of dsRNA and vgRNA indicate their close association at 6 hpi. f, Histogram of Rg of dsRNA clusters as determined by the BIC-GMM cluster analysis. g, Median Rg of dsRNA clusters per cell significantly decreases between 6 hpi and 24 hpi. p-value = 8·10⁻⁴, two-tailed t-test. Error bars represent mean ± standard deviation of median Rg values of dsRNA clusters in individual cells. h, Bivariate pair-correlation functions g₁₂(r) reveal nanoscale anti-correlation between dsRNA and vgRNA at 24 hpi. CSR, complete spatial randomness. Thin lines correspond to g₁₂(r) of individual cells and bold lines are the mean values of g₁₂(r) from all analyzed cells. Scale bars, 10 μm (a-b), 2 μm (c-d), 500 nm (c-d, bottom panels). Dashed lines in c and d indicate the boundary of the cell nucleus.