Resolution of viral load in mild COVID-19 patients is associated with both innate and adaptive immune responses

  1. Anbalagan Anantharaj
  2. Sunil Gujjar
  3. Nikhil Verma
  4. Naseem Ahmed Khan
  5. Heena Shaman
  6. Patil Sharanabasava
  7. Asim Das
  8. Rajesh Pandey
  9. Anil Kumar Pandey
  10. Guruprasad R. Medigeshi

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Abstract

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  1. Version published to 10.1016/j.jcv.2021.105060
  2. ScreenIT

    SciScore for 10.1101/2020.11.05.20226621: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Human Ethics: The study was approved by the Institutional ethics committees for human research at both the institutions (No. 134/A/11/16/Academics/MC/2016/134 and THS 1.8.1/ (93)).
    Consent: Informed consent was obtained from all the participants.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line AuthenticationContamination: This detects presence of 21 respiratory viruses which includes influenza A virus; influenza A(H1N1) virus (swine-lineage); influenza B virus; human rhinovirus; human coronaviruses NL63, 229E, OC43 and HKU1; human parainfluenza viruses 1, 2, 3 and 4; human metapneumoviruses A/B; human bocavirus; human respiratory syncytial viruses A/B; human adenovirus; enterovirus; human parechovirus; Mycoplasma pneumoniae and 4 bacterial species S. aureus; C. pneumoniae; H. influenzae B; S. pneumonia.

    Table 2: Resources

    Antibodies
    SentencesResources
    This was followed by incubation with secondary antibody conjugated with anti-human Alexa flour 488 (1:500; Life Technologies–A11013) for 30 min at room temperature in dark.
    anti-human Alexa flour 488
    suggested: None
    Cells were washed three times followed by incubation with antibodies against ZO-1 (Becton Dickinson), Claudin-3 (Invitrogen), SARS-CoV-2 spike antibody in IMF buffer (20 mM HEPES pH 7.5, 0.1% Triton X-100, 150 mM NaCl, 5 mM EDTA, 0.02 % sodium azide) for 1 h at RT.
    ZO-1
    suggested: None
    Claudin-3
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Indian isolates of SARS-CoV-2 was isolated from COVID-19-positive VTM samples (VTM) using Vero E6 cells (Obtained from National Centre for Cell Science, Pune, INDIA).
    Vero E6
    suggested: RRID:CVCL_XD71)
    Calu-3 and Caco-2 cells were seeded 2 days prior whereas VeroE6 were seeded a day before infection.
    Calu-3
    suggested: KCLB Cat# 30055, RRID:CVCL_0609)
    Caco-2
    suggested: None
    Software and Algorithms
    SentencesResources
    100ng of the pooled and purified library was sequenced using ONT’s MinION Mk1B platform (18).
    MinION
    suggested: (MinION, RRID:SCR_017985)
    The resulting fastq files were normalized by read length (300-500) and reads were aligned using Minimap2 (v2.17) (20) to the reference (GenBank: MN908947.3).
    Minimap2
    suggested: (Minimap2, RRID:SCR_018550)
    The fasta sequences were aligned using MUSCLE (22).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    A maximum-likehood Phylogeny was generated using FastTree 2.1.11 (23) with generalized time-reversible (GTR) substitution model and 1000 bootstrap replicates with default parameters.
    FastTree
    suggested: (FastTree, RRID:SCR_015501)
    Images were processed by background subtraction using cellSens software (Olympus).
    cellSens
    suggested: None
    Data analysis: Data was analysed and final graphs were prepared using GraphPad Prism (Version 7.0e) software.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 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.

    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.

  3. Version published to 10.1101/2020.11.05.20226621v2 on medRxiv
  4. Version published to 10.1101/2020.11.05.20226621v1 on medRxiv