Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences

  1. M. Shaminur Rahman
  2. M. Rafiul Islam
  3. A. S. M. Rubayet Ul Alam
  4. Israt Islam
  5. M. Nazmul Hoque
  6. Salma Akter
  7. Md. Mizanur Rahaman
  8. Munawar Sultana
  9. M. Anwar Hossain

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

The emerging novel coronavirus SARS-CoV-2 has created a global confusing pandemic health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis and containment. We explored 61,485 sequences of the Nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in RT-PCR based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally. Of these mutations, 367 occupy primer binding sites including 3’-end mismatch to primer-pair of 11 well characterized primer sets. Noteworthy, CDC (USA) recommended N2 primer set contained lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain (CTD), respectively. Moreover, 11 in-frame deletions were revealed, mostly (n =10) within the highly flexible linker region, and the rest within the NTD region. Furthermore, we predicted the possible consequences of high-frequency mutations (≥ 20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that high frequency (67.94% of mutated sequences) coevolving mutations (R203K and G204R) destabilized and decreased overall structural flexibility. Despite being proposed as the alternate target to spike protein for vaccine and therapeutics, ongoing nonsynonymous evolution of the N protein may challenge the endeavors, thus need further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.08.05.237339: (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
    The 3D structure was validated using the Ramachandran plot (>90 restudies were allowed region) in PROCHECK v3.5 server (https://servicesn.mbi.ucla.edu/PROCHECK/
    PROCHECK
    suggested: (PROCHECK, RRID:SCR_019043)
    Finally, the energy minimized and validated 3D structure was visualized by PyMol v2.4 (DeLano, 2002).
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)
    For two or more mutational effect prediction, we used FoldX v.
    FoldX
    suggested: (FoldX, RRID:SCR_008522)
    5.0 with their default parameters and three times run (Delgado et al., 2019) plugin in YASARA.
    YASARA
    suggested: (YASARA, RRID:SCR_017591)

    Results from OddPub: Thank you for sharing your data.

    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: 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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.08.05.237339v1 on bioRxiv