Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2

Abstract

Influenza A virus's (IAV's) frequent genetic changes challenge vaccine strategies and engender resistance to current drugs. We sought to identify conserved and essential RNA secondary structures within IAV's genome that are predicted to have greater constraints on mutation in response to therapeutic targeting. We identified and genetically validated an RNA structure (packaging stem-loop 2 (PSL2)) that mediates in vitro packaging and in vivo disease and is conserved across all known IAV isolates. A PSL2-targeting locked nucleic acid (LNA), administered 3 d after, or 14 d before, a lethal IAV inoculum provided 100% survival in mice, led to the development of strong immunity to rechallenge with a tenfold lethal inoculum, evaded attempts to select for resistance and retained full potency against neuraminidase inhibitor-resistant virus. Use of an analogous approach to target SARS-CoV-2, prophylactic administration of LNAs specific for highly conserved RNA structures in the viral genome, protected hamsters from efficient transmission of the SARS-CoV-2 USA_WA1/2020 variant. These findings highlight the potential applicability of this approach to any virus of interest via a process we term 'programmable antivirals', with implications for antiviral prophylaxis and post-exposure therapy.

In vivo secondary structural analysis of Influenza A virus genomic RNA

“…Multiple studies suggest that biologically functional RNA motifs exist in regions of strong primary sequence conservation and that suppression of synonymous codon usage may be a result of maintaining RNA structure [ 82 – 84 ]. Additionally, the introduction of synonymous mutations within conserved regions of vRNA packaging signals has been shown to dramatically reduce genome assembly [ 83 , 85 , 86 ].…”

Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses

“…Is frequent re-boosting a viable vaccine option, e.g., via self-administered home nasal vaccines? Also to be considered are possible ancillary roles for prophylactic antivirals, including “programmable antivirals” targeting conserved structures, 142 antibodies, including therapeutic IgA 143 and innate immunity stimulators as adjuncts to imperfect vaccines. It remains to be seen if vaccination and prophylaxis can be effectively combined at the population level.…”

Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors

“…Two ASOs, LNA-12.8 and LNA-14.3, targeting the RNA motif of N and 5′UTR/ORF1ab, respectively, significantly reduced the viral titer of SARS-CoV-2. The experiments conducted on Syrian hamsters showed that LNA-12.8 prevents or mitigates SARS-CoV-2 transmission, diminishing virus titer in the lungs [ 87 ].…”

“…The influenza virus mutates rapidly and can develop resistance to antiviral drugs. The group of Hagey et al characterized the loop-stalk structure of PSL2 RNA, which serves as a packaging signal for the PB2 segment [ 87 ]. First, the secondary RNA structure in PB2 that mediates the packaging was mapped.…”

“…It appeared that the ASO targeting PSL2 also enabled mice to develop resistance. This approach may be used against vaccine-resistant virus strains in the future [ 87 ].…”