Fig. 4: Conserved short- and long-range interactions in SARS-CoV-2 WT and Omicron genomes.

a Arc plots showing the top 40 pair-wise RNA-RNA interactions along the SARS-CoV-2 WT and Omicron genomes. Shared interactions between the WT and Omicron variants are highlighted in green. Unique interactions in WT (blue) and in Omicron (red) are plotted on the top and bottom panels, respectively. N = 2 independent experiments (total 4 replicates for each variant). b Bar-chart showing the abundance of SPLASH interactions that span different lengths along the WT and Omicron genomes. Interactions that span a distance longer than 1 kb are classified as long-range interactions and comprise 59.6% of all interactions in WT and 43.2% in Omicron, respectively. c Venn diagram showing the overlap of SPLASH interactions between SARS-CoV-2 WT (grey) and Omicron (pink) identified in infected Vero-E6/TMPRSS2 cells. d Multilevel doughnut chart showing unique or shared SPLASH interactions of SARS-CoV-2 WT and Omicron that span different distances along the genome. e Bar-chart showing interactions per base for short- (≤ 1 kb) and long-range (> 1 kb) interacting regions that fall within structurally conserved or non-conserved regions in WT and Omicron variants, respectively. f Bar-chart showing the number of RNA-RNA interactions between virus and host per base in structurally conserved and non-conserved regions. g Bar-chart showing the frequency of conserved interactions and conserved interactions with SNVs in WT and Omicron variants. h Bar-chart showing the frequency of conserved interactions with SNV that span short-range (≤ 1 kb) and long-range (> 1 kb) along the virus genome. P-values were calculated using a one-sided chi-square test. i Venn diagrams showing the intersection of RNA-RNA interactions that were experimentally identified from WT and Omicron-infected cells by SPLASH, as well as predicted interactions in all VOCs based on sequence conservation. Source data are provided as a Source Data file.