Crippled Coronavirus: 5’-PolyU targeted Oligo prevents development of infectious Virions

Current RNA viral pandemic of COVID-19 has been worsened by rapidly spreading viral variants. To inhibit mutation-based development of new escape variants, elements that are indispensable for the virus may be targeted. The 5’-polyU tract of the antigenome offers one such target. Host cells do not harbor 5’-polyU tracts on any of their transcripts, making the tract an attractive virus-specific target. We hypothesize that inhibiting the 5’-polyU by complementary oligonucleotide can limit the use of the tract as template for virus to generate 3’ polyA tails of RNA viruses. Here, we used a frameshift-inducing DNA oligonucleotide with 3’ polyAs to target the 5’-polyU tract of mouse coronavirus (MHV-A59). Results from assays for double stranded RNA (dsRNA) synthesis, infectivity of released virions, and syncytium formation indicate that the oligonucleotide treatment prevented generation of infectious virions. Our results show a unique mode of action of the designed 3’-polyA oligonucleotide against mouse coronavirus which leaves host cells unaffected. This strategy can be adopted for the development of novel classes of oligonucleotide-based drugs that inhibit the production of infectious RNA viruses, including the coronaviruses. Since the 5’-polyU tract is conserved and is essential for variants of coronaviruses, this strategy can potentially address coronavirus variant emergence as well.