Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy

  1. Chiyu Zhang
  2. Donald R. Forsdyke

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Abstract

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  1. Version published to 10.1016/j.compbiolchem.2021.107570
  2. Version published to 10.1101/2020.10.22.343673v3 on bioRxiv
  3. Version published to 10.1101/2020.10.22.343673v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.10.22.343673: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    These were scored for substitutable positions (whether one base could be exchanged by one of the three alternative bases) by aligning against the Wuhan prototype using Muscle software implemented in MEGA 7.0 (Edgar 2004), with manual adjustments.
    Muscle
    suggested: (MUSCLE, RRID:SCR_011812)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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: We detected the following sentences addressing limitations in the study:
    This caveat aside, we deem conservation a reliable indicator that a certain pathogen function is likely to be a suitable target for therapy. Attacking a short segment of a pathogen nucleic acid sequence is unlikely to ensnare a similar segment of its host’s nucleic acid. In any case, to militate against this, the pathogen specificity of a potential therapeutic agent can be screened against the prototypic human genomic sequence (assuming it is unlikely that patient genomes will significantly depart from this). 4.5. Concluding remarks: While prospects for the development of prophylactic vaccines against infection with SARS-CoV-2 are promising, methods to boost post-infection host immune defenses and to directly target SARS-CoV-2 are urgently needed. These require a better understanding both of viral interactions with host innate and acquired immune systems (Forsdyke 2019c), and of viral vulnerabilities. The latter enquiry proceeds in three steps: Find specific “Achilles heels.” Design therapies to exploit them. Prove their clinical effectiveness. We have here been concerned with the first step – the identification of high SI scoring regions that may then serve to focus attention on local structural details (Wacker et al., 2020; Huston et al., 2020). Although the bioinformatic technology related to this has long been available (Forsdyke 1995a), our claim to reveal viral “Achilles heels,” as promulgated in successive textbook editions (Forsdyke 2016), has only recently gained sup...

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  5. Version published to 10.1101/2020.10.22.343673v1 on bioRxiv