High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India

  1. Tanmay Dharmadhikari
  2. Vinay Rajput
  3. Rakeshkumar Yadav
  4. Radhika Boargaonkar
  5. Dhawal Patil
  6. Saurabh Kale
  7. Sanjay P. Kamble
  8. Syed G. Dastager
  9. Mahesh S. Dharne

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Abstract

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  1. Version published to 10.1016/j.scitotenv.2021.151038
  2. ScreenIT

    SciScore for 10.1101/2021.06.08.21258563: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: 2.1 Sample Collection and Processing: The Sampling site Deccan (18.506492,73.836359; Kothrud Basin) and Near Deccan (18.512711,73.840699; Prabhat Road Basin) are open wastewater drains entering the Mutha river near the sample collection site.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    , 5X Q5 Reaction Buffer (New England Biolabs; M0491S), dNTPs mix (New England Biolabs; N0447S) and primer pools 40 U/ul SARS-CoV-2 primers (Pool A & B) 100uM (ARCTIC) (New England Biolabs; GTR_066_COVID25).
    New England Biolabs
    suggested: (New England Biolabs, RRID:SCR_013517)
    The barcoded samples were pooled together, and the run was set up on the MinION device (Oxford Nanopore Technologies).
    MinION
    suggested: (MinION, RRID:SCR_017985)

    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.

    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 10.1101/2021.06.08.21258563v1 on medRxiv