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

Liu, Zongzhi1,2,3,4; Gao, Xiang5; Kan, Chuanwen3,6; Li, Lingyu1,2,3,4; Zhang, Yuan7; Gao, Yibo8; Zhang, Shengyuan5; Zhou, Liangji7; Zhao, Hui7,9,10; Li, Mingkun3,11; Zhang, Zheng5,12; Sun, Yingli1,2,3,4

2023-02-01

10.1002/mco2.208

MEDCOMM   Impact Factor & Quartile

2688-2663

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.

CRISPR-Cas system gene editing RNAi therapy SARS-CoV-2

ESCI

English

Corresponding

National Key R&D Program of China["2019YFC1315701","2018YFC1312100","2017YFC1311000"] ; Chinese Academy of Sciences[KJZD-EW-L14] ; Shenzhen Science and Technology Program["SZSM201612097","SZSM201812062"] ; Cancer Hospital, Chinese Academy of Medical Sciences, Shenzhen Center/Shenzhen Cancer Hospital Research Project[SZ2020ZD004] ; Shenzhen Science and Technology Program[KCXFZ20201221173008022] ; Sanming Project of Medicine in Shenzhen["SZSM201612097","SZSM201812062"] ; Shenzhen Key Medical Discipline Construction Fund[SZXK075]

Research & Experimental Medicine

Medicine, Research & Experimental

WOS:000922075600001

WILEY

Web of Science

1.Chinese Acad Med Sci & Peking Union Med Coll, Canc Hosp, Cent Lab, Natl Cannc Ctr,Natl Clin Res Ctr Canc, Shenzhen, Peoples R China
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7.Chinese Univ Hong Kong, Fac Med, Sch Biomed Sci, Key Lab Regenerat Med,Minist Educ, Hong Kong, Peoples R China
8.Chinese Acad Med Sci & Peking Union Med Coll, Natl Clin Res Ctr Canc, Canc Hosp, Natl Canc Ctr, Beijing, Peoples R China
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12.Southern Univ Sci & Technol, Shenzhen Peoples Hosp 3, Affiliated Hosp 2, Inst Hepatol,Sch Med, Shenzhen 518112, Guangdong, Peoples R China

Liu, Zongzhi,Gao, Xiang,Kan, Chuanwen,et al. CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection[J]. MEDCOMM,2023,4(1).

Liu, Zongzhi.,Gao, Xiang.,Kan, Chuanwen.,Li, Lingyu.,Zhang, Yuan.,...&Sun, Yingli.(2023).CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection.MEDCOMM,4(1).

Liu, Zongzhi,et al."CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection".MEDCOMM 4.1(2023).