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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.

Published onNov 05, 2020
Review 3: "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation"
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Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation
Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation
Description

Summary The SARS-CoV-2 virus contains an unusually large, single-stranded RNA genome that is punctuated with structured elements of unknown function, such as the s2m element located in the 3’ untranslated region. The evolutionary conservation of the s2m element and its occurrence in all viral subgenomic transcripts implicates a key role in the viral infection cycle. In order to exploit this element as a potential therapeutic target, we have designed antisense “gapmer” oligonucleotides that efficiently base-pair to the s2m region. These oligonucleotides, composed of locked nucleic acids (LNA) flanking a central DNA core, successfully remodel the s2m structure and induce sequence-specific RNA cleavage by RNase H in vitro. Gapmers are also effective in human cells as they reduce the fluorescence signal in GFP reporter assays and cause a dose-dependent reduction in replication in a model replicon system based on a human astrovirus. Overall, these oligonucleotides show promise as anti-viral agents and may serve as a helpful starting point to develop treatments for COVID-19.

RR:C19 Evidence Scale rating by reviewer:

  • Potentially informative. The main claims made are not strongly justified by the methods and data, but may yield some insight. The results and conclusions of the study may resemble those from the hypothetical ideal study, but there is substantial room for doubt. Decision-makers should consider this evidence only with a thorough understanding of its weaknesses, alongside other evidence and theory. Decision-makers should not consider this actionable, unless the weaknesses are clearly understood and there is other theory and evidence to further support it.

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Review:

The work by Lulla et al. describes an AntiSense-Oligo (ASO) approach to target COVID-19 RNA. The rationale is to use LNA ASO to target specific portions of the viral genome to inhibit its replication.

LNA technology is well known and its use has become a promising strategy in clinics. Advantage is mainly the long term stability of LNA oligos as they are not degraded by endogenous RNAi machinery.

By computational approach authors identify a critical, conserved portion of the 5’end of SARS-CoV-2 genome. In vitro assays (SHAPE) demonstrate the effectiveness of specific set of the designed LNAs in targeting predicted single strand RNA regions (s2m) of the viral genome.

Using a tissue-culture based assay, the authors convincingly show the ability of s2mLNA to target and degrade a gene expression reporter construct.

Authors complete their analysis by moving to an Astrovirus replication in culture system. Data show ability of selected gap-mers to inhibit viral replication in the nM linear range (0,5-500).

Overall, within the limits of the assays used, the results are consistent with the rationale of the hypothesized knock down strategy. As indicated in the discussion, the work represents a promising preliminary set of data towards preclinical large-scale screening of in vivo effective gap-mers to be used in real pathological contexts.

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