The stem loop 2 motif is a site of vulnerability for SARS-CoV-2

• Published in: bioRxiv 2021-03
• Main Authors: Lulla, Valeria, Wandel, Michal P, Bandyra, Katarzyna J, Ulferts, Rachel, Wu, Mary, Dendooven, Tom, Yang, Xiaofei, Doyle, Nicole, Oerum, Stephanie, Beale, Rupert, Sara M O’rourke, Randow, Felix, Maier, Helena J, Scott, William, Ding, Yiliang, Firth, Andrew E, Bloznelyte, Kotryna, Luisi, Ben F
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; Antisense oligonucleotides; Antiviral agents; Cell culture; Conserved sequence; Coronaviruses; Evolutionary conservation; Genomes; Nucleotide sequence; RNA viruses; Severe acute respiratory syndrome coronavirus 2; Viral infections
• DOI: 10.1101/2020.09.18.304139

Summary RNA structural elements occur in numerous single stranded (+)-sense RNA viruses. The stemloop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 3’ UTR in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including SARS-CoV and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts implicates a key role of s2m in the viral infection cycle. Our findings indicate that the element, while stably folded, can nonetheless be invaded and remodelled spontaneously by antisense oligonucleotides (ASOs) that initiate pairing in exposed loops and trigger efficient sequence-specific RNA cleavage in reporter assays. ASOs also act to inhibit replication in an astrovirus replicon model system in a sequence-specific, dose-dependent manner and inhibit SARS-CoV-2 infection in cell culture. Our results thus permit us to suggest that the s2m element is a site of vulnerability readily targeted by ASOs, which show promise as anti-viral agents. Competing Interest Statement The authors have declared no competing interest. Footnotes * ↵* These joint-first authors made complementary and equivalent contributions * Cell culture data for SARS-CoV-2