Repository logo

Targeting the Conserved Stem Loop 2 Motif in the SARS-CoV-2 Genome.

Accepted version



Change log


Wandel, Michal P 
Bandyra, Katarzyna J 
Ulferts, Rachel 
Wu, Mary 


RNA structural elements occur in numerous single-stranded positive-sense RNA viruses. The stem-loop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 3' untranslated region (UTR) in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts imply a key role for s2m in the viral infection cycle. Our findings indicate that the element, while stably folded, can nonetheless be invaded and remodeled 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 replication in cell culture. Our results thus permit us to suggest that the s2m element is readily targeted by ASOs, which show promise as antiviral agents. IMPORTANCE The highly conserved stem-loop 2 motif (s2m) is found in the genomes of many RNA viruses, including SARS-CoV-2. Our findings indicate that the s2m element can be targeted by antisense oligonucleotides. The antiviral potential of this element represents a promising start for further research into targeting conserved elements in RNA viruses.



LNA, SARS-CoV-2, astrovirus, coronavirus, gapmer, plus-strand RNA virus, s2m, therapeutic oligonucleotides, Animals, COVID-19, Chlorocebus aethiops, Genome, Viral, HEK293 Cells, Humans, Nucleotide Motifs, RNA Folding, RNA, Viral, SARS-CoV-2, Vero Cells, Virus Replication

Journal Title

J Virol

Conference Name

Journal ISSN


Volume Title



American Society for Microbiology


All rights reserved
Wellcome Trust (094229/Z/10/Z)
Wellcome Trust (106207/Z/14/Z)
European Research Council (646891)
Wellcome Trust (200873/Z/16/Z)
Wellcome Trust (202905/Z/16/Z)