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

Human infection with Coronaviridae (CoV) viruses can result in severe acute respiratory distress leading to lethality. The recent outbreak of the SARS-CoV-2 virus emphasizes the potent ability of human coronaviruses (hCoVs) to infect and rapidly spread throughout the human population, given the absence of immune prophylaxis (e.g. vaccination) or curative treatment. SARS-CoV-2 is a positive (+) single-strand RNA [(+)ssRNA] virus comprising a genome of ~30kb encoding at least 29 viral proteins (VPs) involved in viral infection, replication, and release 1,2 . The genome is organized into a 5'untranslated region (UTR)-leader sequence, followed by a large open reading frame (ORF1ab) that encodes 16 non-structural VPs (nsp1-16), then by ORFs encoding the viral accessory proteins and structural proteins (e.g. spike (S), envelope (E), membrane (M), nucleocapsid (N)), and terminating with a 3'UTR-polyA tail. The non-structural VPs are involved in the cleavage of polypeptide1ab (NSP5), suppression of host antiviral response (nsp1), creation of the viral replication center from the endoplasmic reticulum (ER) (nsp2, 3, 4, 6) , and viral RNA replication (nsp7, 8, 9, 10, 12, 13, 14, 15, 16) . As with other members of the hCoVs, infection of the lung epithelia with SARS-CoV-2 likely induces a reticulo-vesicular network of ER-derived double membrane vesicles (DMVs) that form a discrete viral replication organelle (or center; VRC) [3] [4] [5] . VPs are translated on the VRC surface, with many (i.e. soluble and membraneanchored proteins) translocated into the membrane of the newly forming structure. VRC formation, therefore, represents an essential step for both vRNA replication and virion assembly, and hence, progressive infection upon virion release. Yet, little is known of the organellar dynamics and interactions with either the viral RNA or VPs to create the replication membrane, although morphological alteration of the ER (and, perhaps, other secretory pathway organelles, e.g. lipid droplets, Golgi, endosomes) is consistent with the secretory nature of viral replication, which first involves nsp translation and translocation.