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

Because of the current COVID-19 pandemic we questioned whether SECReTE elements are present in viruses, particularly those of the hCoVs, and whether they may fulfill a role in viral replication and virion production. We first determined if SARS-CoV-2 genomic RNA (gRNA) contains SECReTE motifs using the same script we used to identify SECReTEs in yeast and human mRNAs 6 . We found that the ~30kb SARS-CoV-2 gRNA contains forty motifs ( Figure 1a ). All SECReTE elements are located in protein coding sequences (CDS) and 72.5% of the SECReTE elements are encoded in either membranal or secretion-associated proteins (e.g. nsp3, nsp4, nsp6, ORF7a, ORF7b, S, M, E and N proteins). Notably, all motifs, but one, are in NNY or NYN frames ( Figure 1A & Supplementary Table S1 ). This result is similar to our findings in yeast and humans, in which mRNAs encoding secretome proteins that contain either a signal peptide (SP) or TMD, as well as mRNAs encoding secreted proteins that lack these domains, contain SECReTE elements 6 .