Identification and enrichment of SECReTE cis-acting RNA elements in the Coronaviridae and other (+) single-strand RNA viruses

Gal Haimovich; Tsviya Olender; Camila Baez; Jeffrey E Gerst

Next, we expanded our analysis to 2993 genomes of Coronaviridae viruses and strains that were organized by similarity to the hCoVs 18 or by their genera (Supplementary Table S4 ). We plotted the SECReTE score (SECReTE number/kb) vs. %CT based on these two groupings and found a good correlation between the SECReTE and %CT . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.050088 doi: bioRxiv preprint in at least some of the groups (R 2 = 0.6830, 0.8637, 0.5763 for Alpha-CoV, Beta-CoV, Delta-CoV, respectively) and a low correlation (R 2 = 0.04333) with Gamma-CoV) (Figure 2A ). For 229E-like, HKU1-like, NL63-like, OC43-like, MERS-like, SARS-like and SARS-2-like, respectively, the R 2 values were 0.1794, 0.7710, 0.6801, 0.6982, 0.8759, 0.01020 and 0.003998 ( Figure 2B ). Notably, for some CoV families/genera we observe a wide variability in SECReTE scores that at the same %CT, which might arise via non-random occurrences (see below).