CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection

The emergence of SARS-CoV-2 variants of concern (VOCs) underscores the need for antiviral strategies beyond vaccines and small-molecule therapeutics. We demonstrate that a CRISPR-Cas13d approach can effectively degrade SARS-CoV-2 RNA. Using cytological infection models, we designed and screened CRISPR-associated RNAs (crRNAs) targeting conserved viral regions and validated functional guides in vitro. Reprogrammed Cas13d effectors targeting NSP13, NSP14, and nucleocapsid transcripts achieved greater than 99% silencing efficiency in human cells infected with SARS-CoV-2, including variants circulating over the past two years. Bioinformatic analyses of SARS-CoV-2 genomic sequences showed these crRNAs target nearly 100% of the SARS-CoV-2 family, including Omicron. The Cas13d system exhibited high specificity, efficiency, and rapid redeployability, supporting its potential as an antiviral modality to protect against current and unexpected SARS-CoV-2 variants carrying multiple mutations.

Zongzhi Liu, Xiang Gao, Chuanwen Kan, Lingyu Li, Yuan Zhang, Yibo Gao, Shengyuan Zhang, Liangji Zhou, Hui Zhao, Mingkun Li, Yingli Sun, Zheng Zhang