Dingyao Zhang1,2, Jingru Tian1,2, Yadong Wang1,2,3, Jun Lu1,2,3,4. 1. Yale Stem Cell Center, New Haven, CT, 06520, USA. 2. Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA. 3. Yale Center for RNA Science and Medicine, Yale Cancer Center, New Haven, CT, 06520, USA. 4. Yale Cooperative Center of Excellence in Hematology, New Haven, CT, 06520, USA.
Abstract
MOTIVATION: The COVID-19 pandemic has highlighted the threat of emerging respiratory viruses and has exposed the lack of availability of off-the-shelf therapeutics against new RNA viruses. Previous research has established the potential that siRNAs and RNA-targeting CRISPR have in combating known RNA viruses. However, the feasibility and tools for designing anti-viral RNA therapeutics against future RNA viruses have not yet been established. RESULTS: We develop the Evitar (Emerging-Virus-Targeting RNA) pipeline for designing anti-viral siRNAs and CRISPR Cas13a guide RNA (gRNA) sequences. Within Evitar, we develop Greedy Algorithm with Redundancy (GAR) and Similarity-weighted Greedy Algorithm with Redundancy (SGAR) to enhance the performance. Time simulations using known coronavirus genomes deposited as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. Additionally, among the top 19 pre-designed gRNAs, there are three SARS-CoV-2-targeting Cas13a gRNAs that could be predicted using information from 2011. Before-the-outbreak design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Designed siRNAs are further shown to suppress SARS-CoV-2 viral sequences using in vitro reporter assays. Our results support the utility of Evitar to pre-design anti-viral siRNAs/gRNAs against future viruses. Therefore, we propose the development of a collection consisting of roughly 30 pre-designed, safety-tested, and off-the-shelf siRNA/CRISPR therapeutics that could accelerate responses to future RNA virus outbreaks. AVAILABILITY: Codes are available at GitHub (https://github.com/dingyaozhang/Evitar). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The COVID-19 pandemic has highlighted the threat of emerging respiratory viruses and has exposed the lack of availability of off-the-shelf therapeutics against new RNA viruses. Previous research has established the potential that siRNAs and RNA-targeting CRISPR have in combating known RNA viruses. However, the feasibility and tools for designing anti-viral RNA therapeutics against future RNA viruses have not yet been established. RESULTS: We develop the Evitar (Emerging-Virus-Targeting RNA) pipeline for designing anti-viral siRNAs and CRISPR Cas13a guide RNA (gRNA) sequences. Within Evitar, we develop Greedy Algorithm with Redundancy (GAR) and Similarity-weighted Greedy Algorithm with Redundancy (SGAR) to enhance the performance. Time simulations using known coronavirus genomes deposited as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. Additionally, among the top 19 pre-designed gRNAs, there are three SARS-CoV-2-targeting Cas13a gRNAs that could be predicted using information from 2011. Before-the-outbreak design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Designed siRNAs are further shown to suppress SARS-CoV-2 viral sequences using in vitro reporter assays. Our results support the utility of Evitar to pre-design anti-viral siRNAs/gRNAs against future viruses. Therefore, we propose the development of a collection consisting of roughly 30 pre-designed, safety-tested, and off-the-shelf siRNA/CRISPR therapeutics that could accelerate responses to future RNA virus outbreaks. AVAILABILITY: Codes are available at GitHub (https://github.com/dingyaozhang/Evitar). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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