A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection

  1. Sarena Banu
  2. Ramakrishnan Nagaraj
  3. Mohammed M. Idris

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Abstract

Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2, in India, during the early days of the pandemic in 2020, by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.

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  1. Version published to 10.1371/journal.pone.0279998
  2. ScreenIT

    SciScore for 10.1101/2021.12.06.471525: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Real-time PCR analysis was performed for the selected list of the gene using Applied BiosystemsViiA™ 7 Real-Time PCR System (USA) with gene-specific primers (Table 3).
    Applied BiosystemsViiA™
    suggested: None
    All primers were synthesized using Primer3 software and, the GAPDH gene was used for the data normalization.
    Primer3
    suggested: (Primer3, RRID:SCR_003139)
    The obtained spot patterns were densitometrically analyzed using ImageJ software to estimate the expression level of cytokines in SARS-CoV-2 infection.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    GAPDH was used as a housekeeping protein. 5. Pathway Analysis: The proteins and genes selected for the study were analyzed for network and pathway analysis using Ingenuity Pathway Analysis software-based.
    Ingenuity Pathway Analysis
    suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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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  3. Version published to 10.1101/2021.12.06.471525v1 on bioRxiv