Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza

Abbott, Timothy R.; Dhamdhere, Girija; Liu, Yanxia; Lin, Xueqiu; Goudy, Laine; Zeng, Leiping; Chemparathy, Augustine; Chmura, Stephen; Heaton, Nicholas S.; Debs, Robert; Pande, Tara; Endy, Drew; La Russa, Marie F.; Lewis, David B.; Qi, Lei S.

Summary The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, has highlighted the need for antiviral approaches that can target emerging viruses with no effective vaccines or pharmaceuticals. Here, we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (prophylactic antiviral CRISPR in human cells), for viral inhibition that can effectively degrade RNA from SARS-CoV-2 sequences and live influenza A virus (IAV) in human lung epithelial cells. We designed and screened CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs targeting SARS-CoV-2. This approach effectively reduced H1N1 IAV load in respiratory epithelial cells. Our bioinformatic analysis showed that a group of only six crRNAs can target more than 90% of all coronaviruses. With the development of a safe and effective system for respiratory tract delivery, PAC-MAN has the potential to become an important pan-coronavirus inhibition strategy.