Genomic profiles of vaccine breakthrough SARS-CoV-2 strains from Odisha, India

  1. Arup Ghosh
  2. Safal Walia
  3. Roma Rattan
  4. Amol Kanampalliwar
  5. Atimukta Jha
  6. Shifu Aggarwal
  7. Sana Fatma
  8. Niyati Das
  9. Nirupama Chayani
  10. Punit Prasad
  11. Sunil K. Raghav
  12. Ajay Parida

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Abstract

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  1. Version published to 10.1016/j.ijid.2022.03.042
  2. ScreenIT

    SciScore for 10.1101/2021.08.16.21261912: (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
    After demultiplexing, non-Host (Human) extracted reads using Kraken2 taxonomic classifier [5], were aligned using BWA against the Wuhan-Hu-1 (NC_045512.2) reference genome.
    Kraken2
    suggested: None
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Single nucleotide variants and short INDELs were called using GATK4 Haplotypecaller using ploidy 1 followed by removal of low-quality variants (Quality by depth, QD < 5) by GATK VariantFiltration.
    GATK
    suggested: (GATK, RRID:SCR_001876)

    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 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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.08.16.21261912v1 on medRxiv