Ranking of predicted RNA-RNA base-pairing interactions.

Predicted long-range RNA-RNA base-pairing interactions between the Spike region the full genome for both SARS-CoV-1 and SARS-CoV-2 using IntaRNA software package. See Materials and Methods for details. There was a total of 69 independent hits across both genomes. Column SARS-CoV denotes the strain. Column TotalLength denotes length of the interacting regions (query + target). Ranking is according to residual values against the generalized linear model where length of interaction was used to estimate interaction energy. The built-in function glm(energy~length, data = data, family = "gaussian")in R programming language was used to fit the model. Length coefficient = -0.03190. Length was a significant factor in the model. (Pr(>|t|) for length = 0.00067. Median of residuals = -0.2287). 1-Quantile of residuals = -2.1536. SARS-CoV-2 hits are shown as bold. Rank 11 also shown with * denotes the SARS-CoV-2 Spike-ORF8 interaction.
(CSV)