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 compared the SECReTE content in SARS-CoV-2 to six other human coronaviruses, e.g. SARS-CoV, MERS-CoV, hCoV-NL63, hCoV-229E, hCoV-OC43 and hCoV-HKU1. SARS-CoV and MERS-CoV are considered potentially pandemic coronaviruses that cause severe acute respiratory syndrome, similar to SARS-CoV-2, but are less infectious and appear to result in a higher mortality rate than SARS-CoV-2 15 . The other four viruses are endemic to the human population and typically cause mild respiratory ailments with very low mortality rates 16 . Of note, hCoV-NL63 and hCoV-229E belong to the Alpha-CoV genus with a slightly shorter genome as compared to the other five CoVs, which belong to the Beta-CoV genus. All seven viruses contain SECReTE sequences in varying amounts (i.e. between 40-85 SECReTE motifs), the highest being hCoV-NL63 (Figures 1B-C and Supplementary Table S1 ). Based upon the limited data available regarding the infectivity and lethality of the different human CoVs, we did not observe an association between the number of SECReTE sequences and viral pathogenicity when comparing the three highly pathogenic (e.g. SARS-CoV, SARS-CoV-2, and MERS) to the three least pathogenic (e.g. hCoV-229E, HKU1 and OC43), particularly if the moderately pathogenic 17