Adeno-Associated Virus-Mediated CRISPR-Cas13 Knockdown of Papain-like Protease from SARS-CoV-2 Virus

The COVID-19 pandemic is caused by a novel and rapidly mutating coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although several drugs are already in clinical use or under emergency authorization, there is still an urgent need to develop new drugs. Through the mining and analysis of 2776 genomes of the SARS-CoV-2 virus, we identified papain-like protease (PLpro), which is a critical enzyme required for coronavirus to generate a functional replicase complex and manipulate post-translational modifications on host proteins for evasion against host antiviral immune responses, as a conserved molecular target for the development of anti-SARS-CoV-2 therapy. We then made an infection model using the NCI-H1299 cell line stably expressing SARS-CoV-2 PLpro protein (NCI-H1299/PLpro). To investigate the effect of targeting and degrading PLpro mRNA, a compact CRISPR-Cas13 system targeting PLpro mRNA was developed and validated, which was then delivered to the aforementioned NCI-H1299/PLpro cells. The results showed that CRISPR-Cas13 mediated mRNA degradation successfully reduced the expression of viral PLpro protein. By combining the power of AAV and CRISPR-Cas13 technologies, we aim to explore the potential of attenuating viral infection by targeted degradation of important viral mRNAs via safe and efficient delivery of AAV carrying the CRISPR-Cas13 system. This study demonstrated a virus-against-virus gene therapy strategy for COVID-19 and provided evidence for the future development of therapies against SARS-CoV-2 and other RNA viral infections.