Targeting the Conserved Stem Loop 2 Motif in the SARS-CoV-2 Genome
This article has been Reviewed by the following groups
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- Evaluated articles (ScreenIT)
- Evaluated articles (Rapid Reviews Infectious Diseases)
Abstract
The highly conserved stem-loop 2 motif (s2m) is found in the genomes of many RNA viruses, including SARS-CoV-2. Our findings indicate that the s2m element can be targeted by antisense oligonucleotides. The antiviral potential of this conserved element represents a promising start for further research into targeting conserved elements in RNA viruses.
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Strength of evidence
Reviewers: Hasan Cubuk (Istanbul Arel University) | 📗📗📗📗 ◻️
Anders Näär (UC Berkeley) | 📒📒📒 ◻️ ◻️
Valerio Orlando (KAUST) | 📒📒📒 ◻️ ◻️ -
Anders Näär
Review 2: "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation"
This manuscript offers a gapmer-based therapeutic strategy targeting the highly conserved s2m element present in the SARS-CoV-2 genome. While potentially informative, the study's claims require testing with wildtype SARS-CoV-2 virus and animal models to be substantiated.
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Valerio Orlando
Review 3: "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation"
This manuscript offers a gapmer-based therapeutic strategy targeting the highly conserved s2m element present in the SARS-CoV-2 genome. While potentially informative, the study's claims require testing with wildtype SARS-CoV-2 virus and animal models to be substantiated.
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Hasan Cubuk
Review 1: "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation"
This manuscript offers a gapmer-based therapeutic strategy targeting the highly conserved s2m element present in the SARS-CoV-2 genome. While potentially informative, the study's claims require testing with wildtype SARS-CoV-2 virus and animal models to be substantiated.
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SciScore for 10.1101/2020.09.18.304139: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication Contamination: All cell lines tested negative for mycoplasma. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HEK293ET, HeLa and A459 cells, as well as all stable cell lines, were grown in IMDM medium supplemented with 10% FCS at 37 °C in 5% CO2. HEK293ETsuggested: RRID:CVCL_6996)HeLasuggested: NoneA459suggested: RRID:CVCL_A459)To examine the effect of gapmers on GFP expression, HeLa or A549 cells with a stably integrated GFP-s2m/s2m_scr reporter were seeded at 5 × 104 cells per well in 24-well … SciScore for 10.1101/2020.09.18.304139: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication Contamination: All cell lines tested negative for mycoplasma. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HEK293ET, HeLa and A459 cells, as well as all stable cell lines, were grown in IMDM medium supplemented with 10% FCS at 37 °C in 5% CO2. HEK293ETsuggested: RRID:CVCL_6996)HeLasuggested: NoneA459suggested: RRID:CVCL_A459)To examine the effect of gapmers on GFP expression, HeLa or A549 cells with a stably integrated GFP-s2m/s2m_scr reporter were seeded at 5 × 104 cells per well in 24-well plates. A549suggested: NoneHuh7.5.1 and HEK293T cells were transfected in triplicate with Lipofectamine 2000 reagent (Invitrogen), using the protocol in which suspended cells are added directly to the RNA complexes in 96-well plates. Huh7.5.1suggested: RRID:CVCL_E049)HEK293Tsuggested: NoneSARS-CoV-2 infection assay: Vero E6 cells (NIBC, UK) were grown in DMEM (containing 10 % FBS) at 37 °C and 5 % CO2 in 96 well imaging plates (Greiner 655090). Vero E6suggested: NoneSoftware and Algorithms Sentences Resources Quantitative Gel Analysis and SHAPE Reactivity Calculation: Signal intensity of each band on the PAGE gel was detected using ImageQuant TL software and normalized to the total signal of the whole lane. ImageQuantsuggested: (ImageQuant, RRID:SCR_014246)Motion correction, ctf estimation and particle-picking were performed in Warp (Tegunov and Cramer, 2019) and 2D/3D alignments and averaging were carried out with cryoSPARC 2.15 (Punjani et al., 2017) cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Data were analysed in FlowJo (v10.7.1). FlowJosuggested: (FlowJo, RRID:SCR_008520)Results 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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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: Please consider improving the rainbow (“jet”) colormap(s) used on page 33. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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.
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