Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis
This article has been Reviewed by the following groups
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- Evaluated articles (ScreenIT)
- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
Expanding the arsenal of prophylactic approaches against SARS-CoV-2 is of utmost importance, specifically those strategies that are resistant to antigenic drift in Spike. Here, we conducted a screen with over 16,000 RNAi triggers against the SARS-CoV-2 genome using a massively parallel assay to identify hyper-potent siRNAs. We selected 10 candidates for in vitro validation and found five siRNAs that exhibited hyper-potent activity with IC50<20pM and strong neutralisation in live virus experiments. We further enhanced the activity by combinatorial pairing of the siRNA candidates to develop siRNA cocktails and found that these cocktails are active against multiple types of variants of concern (VOC). We examined over 2,000 possible mutations to the siRNA target sites using saturation mutagenesis and identified broad protection against future variants. Finally, we demonstrated that intranasal administration of the siRNA cocktail effectively attenuates clinical signs and viral measures of disease in the Syrian hamster model. Our results pave the way to development of an additional layer of antiviral prophylaxis that is orthogonal to vaccines and monoclonal antibodies.
Article activity feed
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Shou-Wei Ding
Review 2: "Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis"
This preprint analyzes the usage of RNAi molecules to create a potent prophylaxis against SARS-COV-2. Reviewers deemed this study strong and reliable with the only potential limitation being the lack of studies in different animal models.
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Jian Zheng
Review 1: "Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis"
This preprint analyzes the usage of RNAi molecules to create a potent prophylaxis against SARS-COV-2. Reviewers deemed this study strong and reliable with the only potential limitation being the lack of studies in different animal models.
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Strength of evidence
Reviewers: Jian Zheng (University of Iowa) | 📗📗📗📗◻️
Shou-Wei Ding (UC Riverside) |📘📘📘📘📘 -
SciScore for 10.1101/2022.04.12.488010: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable In-vivo experiments: Male Golden Syrian hamsters age 6-8 week were treated with siRNA cocktails at days −7, −3 and −1 pre-infection. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources The HEK293FT cell-line was obtained from Thermo Scientific ( HEK293FTsuggested: RRID:CVCL_6911)Live virus experiments: Unless indicated differently, 10,000 VeroE6 cells were transfected with 100nM of siRNA treatment and infected with SARS-Cov-2 24 hours post siRNA treatment. VeroE6suggested: NoneSoftware and Algorithms Sentences Resources The gRNA was … SciScore for 10.1101/2022.04.12.488010: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable In-vivo experiments: Male Golden Syrian hamsters age 6-8 week were treated with siRNA cocktails at days −7, −3 and −1 pre-infection. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources The HEK293FT cell-line was obtained from Thermo Scientific ( HEK293FTsuggested: RRID:CVCL_6911)Live virus experiments: Unless indicated differently, 10,000 VeroE6 cells were transfected with 100nM of siRNA treatment and infected with SARS-Cov-2 24 hours post siRNA treatment. VeroE6suggested: NoneSoftware and Algorithms Sentences Resources The gRNA was modified with a phosphorothioate modification to prevent nuclease degradation and was obtained from Merck-Millipore. Merck-Milliporesuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study also has certain limitations. First, it is unclear for how long the siRNA cocktails remain effective and thus might be most appropriate in situations where high exposure risk is present, such as the case for front-line workers, immunodepression (transient or chronic), an outbreak in the household, and during the height or an infection “wave”. Second, while our siRNA cocktail protected Syrian hamsters from disease, the effect was mainly observed in the upper respiratory tract. While this is the chief site of infection and shows great promise in terms of mitigating transmission, it will require further adaptation for use in a treatment setting, which would require optimization for delivery to the lower respiratory tract and through to the lung parenchyma. Third, for the purpose of this proof-of-principle study, we adopted a pre-exposure treatment regimen that was composed of multiple days prior to infection. We aim to further optimise the regimen prior to advancing into non-human primates and ultimate clinical trials in humans. Despite these caveats, the current study substantially contributes to the global efforts to curb COVID-19, as well as future other viral pandemics of similar mortality and morbidity proportions, by illustrating the efficacy of intranasally administered siRNA cocktails as pre-exposure preventatives resilient to the likely mutational evolution of culprit pathogens. This is particularly encouraging given the alarming rate at which we are currently...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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