Synthetically inducing G-quadruplexes in coronavirus genome reduces infectivity

RNA G-quadruplexes (rG4s) are unusual RNA secondary structures formed by stacking arrays of guanine tetrads. Although thousands of potential rG4-forming motifs occur throughout the mammalian transcriptome, many single-stranded RNA (ssRNA) viruses are thought to be depleted of rG4-forming sequences. Using in silico methods, we examine rG4-forming potential in single-stranded RNA (ssRNA) viruses and observe that, while canonical rG4 motifs are depleted, non-canonical rG4 motifs occur at comparable or higher frequencies relative to the mammalian transcriptome. We ask if the non-canonical rG4's can be leveraged to block viral replication and control infection using OC43, the coronavirus believed to be responsible for the 1889 "Russian Flu" pandemic. Profiling with "d-rG4-seq" confirms a dearth of folded rG4 in the OC43 RNA genome during natural infection. Intriguingly, rG4 ligands induce synthetic rG4 structures of a non-canonical nature. Significantly, induced rG4 inhibits viral replication and reduces infectivity. We show that the rG4 ligands act by disrupting the unique pattern of OC43 "discontinuous transcription". Thus, rG4-targeting compounds present a potential therapeutic approach for targeting ssRNA viruses.