CRISPR‐Cas13d effectively targets SARS‐CoV‐2 variants, including Delta and Omicron, and inhibits viral infection
Zongzhi Liu,
Xiang Gao,
Chuanwen Kan,
Lingyu Li,
Yuan Zhang,
Yibo Gao,
Shengyuan Zhang,
Liangji Zhou,
Hui Zhao,
Mingkun Li,
Zheng Zhang,
Yingli Sun
Affiliations
Zongzhi Liu
Central Laboratory National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China
Xiang Gao
Institute of Hepatology National Clinical Research Center for Infectious Disease School of Medicine Shenzhen Third People's Hospital The Second Affiliated Hospital Southern University of Science and Technology Shenzhen Guangdong China
Chuanwen Kan
University of Chinese Academy of Sciences Beijing China
Lingyu Li
Central Laboratory National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China
Yuan Zhang
Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong
Yibo Gao
National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
Shengyuan Zhang
Institute of Hepatology National Clinical Research Center for Infectious Disease School of Medicine Shenzhen Third People's Hospital The Second Affiliated Hospital Southern University of Science and Technology Shenzhen Guangdong China
Liangji Zhou
Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong
Hui Zhao
Key Laboratory for Regenerative Medicine Ministry of Education School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Hong Kong
Mingkun Li
University of Chinese Academy of Sciences Beijing China
Zheng Zhang
Institute of Hepatology National Clinical Research Center for Infectious Disease School of Medicine Shenzhen Third People's Hospital The Second Affiliated Hospital Southern University of Science and Technology Shenzhen Guangdong China
Yingli Sun
Central Laboratory National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China
Abstract The recent pandemic of variants of concern (VOC) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) highlights the need for innovative anti‐SARS‐CoV‐2 approaches in addition to vaccines and antiviral therapeutics. Here, we demonstrate that a CRISPR‐Cas13‐based strategy against SARS‐CoV‐2 can effectively degrade viral RNA. First, we conducted a cytological infection experiment, screened CRISPR‐associated RNAs (crRNAs) targeting conserved regions of viruses, and used an in vitro system to validate functional crRNAs. Reprogrammed Cas13d effectors targeting NSP13, NSP14, and nucleocapsid transcripts achieved >99% silencing efficiency in human cells which are infected with coronavirus 2, including the emerging variants in the last 2 years, B.1, B.1.1.7 (Alpha), D614G B.1.351 (Beta), and B.1.617 (Delta). Furthermore, we conducted bioinformatics data analysis. We collected the sequence information of COVID‐19 and its variants from China, and phylogenetic analysis revealed that these crRNA oligos could target almost 100% of the SARS‐CoV family, including the emerging new variant, Omicron. The reprogrammed Cas13d exhibited high specificity, efficiency, and rapid deployment properties; therefore, it is promising for antiviral drug development. This system could possibly be used to protect against unexpected SARS‐CoV‐2 variants carrying multiple mutations.
