A rapid and efficient platform for antiviral crRNA screening using CRISPR-Cas13a-based nucleic acid detection

Lan Yang; Youcui Zhang; Wenyanbo Yi; Xue Dong; Mengwei Niu; Yingjie Song; Yao Han; Hao Li; Yansong Sun

doi:10.3389/fimmu.2023.1116230

A rapid and efficient platform for antiviral crRNA screening using CRISPR-Cas13a-based nucleic acid detection

Front Immunol. 2023 May 9:14:1116230. doi: 10.3389/fimmu.2023.1116230. eCollection 2023.

Authors

Lan Yang¹, Youcui Zhang^{1

2}, Wenyanbo Yi¹, Xue Dong¹, Mengwei Niu¹, Yingjie Song¹, Yao Han¹, Hao Li¹, Yansong Sun¹

Affiliations

¹ State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
² College of Life Sciences, Fujian Agriculture and Forestry University, Fujian, China.

Abstract

Introduction: Rapid and high-throughput screening of antiviral clustered regularly interspaced short palindromic repeat (CRISPR) RNAs (crRNAs) is urgently required for the CRISPR-Cas13a antiviral system. Based on the same principle, we established an efficient screening platform for antiviral crRNA through CRISPR-Cas13a nucleic acid detection.

Method: In this study, crRNAs targeting PA, PB1, NP, and PB2 of the influenza A virus (H1N1) were screened using CRISPR-Cas13a nucleic acid detection, and their antiviral effects were confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The RNA secondary structures were predicted by bioinformatics methods.

Results: The results showed that crRNAs screened by CRISPR-Cas13a nucleic acid detection could effectively inhibit viral RNA in mammalian cells. Besides, we found that this platform for antiviral crRNA screening was more accurate than RNA secondary structure prediction. In addition, we validated the feasibility of the platform by screening crRNAs targeting NS of the influenza A virus (H1N1).

Discussion: This study provides a new approach for screening antiviral crRNAs and contributes to the rapid advancement of the CRISPR-Cas13a antiviral system.

Keywords: CRISPR/Cas13a; antiviral; crRNA screening; influenza A(H1N1); nucleic acid detection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Clustered Regularly Interspaced Short Palindromic Repeats* / genetics
Influenza A Virus, H1N1 Subtype* / genetics
Mammals / genetics
RNA, Guide, CRISPR-Cas Systems
RNA, Viral / genetics

Substances

RNA, Guide, CRISPR-Cas Systems
RNA, Viral

Grants and funding

This work was supported by the National Natural Science Foundation of China (grant number 31901051); and the National Science and Technology Major Project of China (grant number 2018ZX10301407).