Treating Influenza and SARS-CoV-2 via mRNA-encoded Cas13a

Blanchard, Emmeline L.; Vanover, Daryll; Bawage, Swapnil Subhash; Tiwari, Pooja Munnilal; Rotolo, Laura; Beyersdorf, Jared; Peck, Hannah E.; Bruno, Nicholas C; Hincapie, Robert; Finn, M.G.; Michel, Frank; Lafontaine, Eric R.; Hogan, Robert J.; Zurla, Chiara; Santangelo, Philip J.

Here, Cas13a has been used to target and mitigate influenza virus A (IAV) and SARS-CoV-2 using a synthetic mRNA-based platform. CRISPR RNAs (crRNA) against PB1 and highly conserved regions of PB2 were screened in conjunction with mRNA-encoded Cas13a. Screens were designed such that only guides that decreased influenza RNA levels in a Cas13-mediated fashion, were valid. Cas13a mRNA and validated guides, delivered post-infection, simulating treatment, were tested in combination and across multiplicities of infection. Their function was also characterized over time. Similar screens were performed for guides against SARS-CoV-2, yielding multiple guides that significantly impacted cytopathic effect. Last, the approach was utilized in vivo, demonstrating the ability to degrade influenza RNA in a mouse model of infection, using polymer-formulated, nebulizer-based mRNA delivery. Our findings demonstrate the applicability of Cas13a in mitigating respiratory infections both in vitro and in a mouse model, paving the way for future therapeutic use.