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Due to the rapid mutations of SARS-CoV-2, specific and effective prevention and treatment by CRISPR toolkits for coronavirus disease 2019 (COVID-19) are urgently needed to control the current pandemic spread. Here, we designed Type III CRISPR endonuclease antivirals for coronaviruses (TEAR-CoV) as a therapeutic to combat SARS-CoV-2 infection. We provided a proof of principle demonstration that TEAR-CoV-based RNA engineering approach leads to RNA-guided transcript degradation both in vitro and in eukaryotic cells, which could be used to broadly target RNA viruses. We report that TEAR-CoV not only cleaves SARS-CoV-2 genome and mRNA transcripts, but also degrades live influenza A virus (IAV), impeding viral replication in cells and in mice. Moreover, bioinformatics screening of gRNAs along RNA sequences reveals that a group of five gRNAs (hCoV-gRNAs) could potentially target 99.98% of human coronaviruses. TEAR-CoV also exerted specific targeting and cleavage of common human coronaviruses. The fast design and broad targeting of TEAR-CoV may represent a versatile antiviral approach for SARS-CoV-2 or potentially other emerging human coronaviruses.<\/jats:p>","DOI":"10.1093\/nar\/gkac016","type":"journal-article","created":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T12:22:28Z","timestamp":1643631748000},"page":"e47-e47","source":"Crossref","is-referenced-by-count":15,"title":["Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses"],"prefix":"10.1093","volume":"50","author":[{"given":"Ping","family":"Lin","sequence":"first","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing\u00a0400715, China"},{"name":"Wound Trauma Medical Center, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanwang","family":"Shen","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing\u00a0400715, China"},{"name":"State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shugang","family":"Qin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinqin","family":"Pu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhihan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pan","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenwei","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadeem","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Jiang","sequence":"additional","affiliation":[{"name":"Wound Trauma Medical Center, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingyou","family":"Xia","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing\u00a0400715, China"},{"name":"State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1205-982X","authenticated-orcid":false,"given":"Min","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,2,15]]},"reference":[{"key":"2022050521364223300_B1","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in china","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"2022050521364223300_B2","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in china, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2022050521364223300_B3","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1056\/NEJMoa2001316","article-title":"Early transmission dynamics in wuhan, china, of novel coronavirus\u2013infected pneumonia","volume":"382","author":"Li","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2022050521364223300_B4","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1126\/science.abc1932","article-title":"Development of an inactivated vaccine candidate for SARS-CoV-2","volume":"369","author":"Gao","year":"2020","journal-title":"Science"},{"key":"2022050521364223300_B5","doi-asserted-by":"crossref","first-page":"104260","DOI":"10.1016\/j.meegid.2020.104260","article-title":"Genetic diversity and evolution of SARS-CoV-2","volume":"81","author":"Phan","year":"2020","journal-title":"Infect. Genet. 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Sci."},{"key":"2022050521364223300_B20","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2022050521364223300_B21","doi-asserted-by":"crossref","first-page":"3728","DOI":"10.1038\/s41467-019-11695-8","article-title":"High-throughput screen reveals sRNAs regulating crRNA biogenesis by targeting CRISPR leader to repress rho termination","volume":"10","author":"Lin","year":"2019","journal-title":"Nat. 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Iimmun."},{"key":"2022050521364223300_B24","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1096\/fj.201801085R","article-title":"TRPC1 intensifies house dust mite\u2013induced airway remodeling by facilitating epithelial-to-mesenchymal transition and STAT3\/NF-\u03baB signaling","volume":"33","author":"Pu","year":"2019","journal-title":"FASEB J."},{"key":"2022050521364223300_B25","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1126\/science.aao0100","article-title":"A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems","volume":"357","author":"Kazlauskiene","year":"2017","journal-title":"Science"},{"key":"2022050521364223300_B26","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.molcel.2017.12.007","article-title":"Rapid and scalable characterization of CRISPR technologies using an e. coli cell-free transcription-translation system","volume":"69","author":"Marshall","year":"2018","journal-title":"Mol. 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Commun."},{"key":"2022050521364223300_B28","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1080\/15476286.2020.1813411","article-title":"Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic sulfolobales and the evasion of lethal gene silencing","volume":"18","author":"Zink","year":"2021","journal-title":"RNA Biol."},{"key":"2022050521364223300_B29","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1089\/crispr.2020.0032","article-title":"Targeted RNA knockdown by a type III CRISPR-Cas complex in zebrafish","volume":"3","author":"Fricke","year":"2020","journal-title":"CRISPR J."},{"key":"2022050521364223300_B30","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/j.cell.2020.03.045","article-title":"Structural and functional basis of SARS-CoV-2 entry by using human ACE2","volume":"181","author":"Wang","year":"2020","journal-title":"Cell"},{"key":"2022050521364223300_B31","doi-asserted-by":"crossref","first-page":"179","DOI":"10.3390\/v8070179","article-title":"Replication-competent influenza a viruses expressing reporter genes","volume":"8","author":"Breen","year":"2016","journal-title":"Viruses"},{"key":"2022050521364223300_B32","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","article-title":"SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor","volume":"181","author":"Hoffmann","year":"2020","journal-title":"Cell"},{"key":"2022050521364223300_B33","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1126\/science.abb2762","article-title":"Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2","volume":"367","author":"Yan","year":"2020","journal-title":"Science"},{"key":"2022050521364223300_B34","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cell.2020.02.058","article-title":"Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein","volume":"181","author":"Walls","year":"2020","journal-title":"Cell"},{"key":"2022050521364223300_B35","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","article-title":"Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor","volume":"581","author":"Lan","year":"2020","journal-title":"Nature"},{"key":"2022050521364223300_B36","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1126\/science.abc1560","article-title":"Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir","volume":"368","author":"Yin","year":"2020","journal-title":"Science"},{"key":"2022050521364223300_B37","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/s41422-020-0290-0","article-title":"Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses","volume":"30","author":"Nguyen","year":"2020","journal-title":"Cell Res."},{"key":"2022050521364223300_B38","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/s41422-019-0151-x","article-title":"Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry","volume":"29","author":"Guo","year":"2019","journal-title":"Cell Res."},{"key":"2022050521364223300_B39","first-page":"01135","article-title":"HIV-1 employs multiple mechanisms to resist Cas9\/single guide RNA targeting the viral primer binding site","volume":"92","author":"Wang","year":"2018","journal-title":"J. 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U.S.A."},{"key":"2022050521364223300_B52","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1517\/17425247.2016.1121990","article-title":"Clinical potential of electroporation for gene therapy and DNA vaccine delivery","volume":"13","author":"Lambricht","year":"2016","journal-title":"Expert Opin. Drug Deliv."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/8\/e47\/43546938\/gkac016.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/8\/e47\/43546938\/gkac016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T21:41:21Z","timestamp":1651786881000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/8\/e47\/6528908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,15]]},"references-count":52,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,2,15]]},"published-print":{"date-parts":[[2022,5,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac016","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5,6]]},"published":{"date-parts":[[2022,2,15]]}}}