Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

  1. Ray Izquierdo-Lara
  2. Goffe Elsinga
  3. Leo Heijnen
  4. Bas B. Oude Munnink
  5. Claudia M.E. Schapendonk
  6. David Nieuwenhuijse
  7. Matthijs Kon
  8. Lu Lu
  9. Frank M. Aarestrup
  10. Samantha Lycett
  11. Gertjan Medema
  12. Marion P.G. Koopmans
  13. Miranda de Graaf

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Abstract

No abstract available

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  1. Version published to 10.3201/eid2705.204410
  2. ScreenIT

    SciScore for 10.1101/2020.09.21.20198838: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Libraries from all re-sequenced samples (both Nanopore and Illumina) were generated from the same RNA as starting material.
    Nanopore
    suggested: None
    Briefly, an automated snakemake script46 was used to demultiplex fastq raw reads using Porechop (https://github.com/rrwick/Porechop), trim primers using Cutadapt47 and perform a reference-based alignment using minimap2 to GISAID sequence EPI_ISL_412973.
    Porechop
    suggested: (Porechop, RRID:SCR_016967)
    The run was monitored using RAMPART (https://artic-network.github.io/rampart/).
    RAMPART
    suggested: (Rampart, RRID:SCR_016742)
    Illumina Data Filtering, Genome assembly and Variant calling: All the processing, reference-based alignment and variant analysis of the Illumina generated data was performed using a customized workflow on the Galaxy EU server (https://usegalaxy.eu/)49.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    First, raw sequencing reads were filtered using Fastp50 to remove adaptor contamination, ambiguous bases (N), low quality reads (Phred score <30) and fragments below the length of 50 nt.
    Phred
    suggested: (Phred, RRID:SCR_001017)
    Reads were re-aligned using the leftalign utility from FreeBayes package52.
    FreeBayes
    suggested: (FreeBayes, RRID:SCR_010761)
    Our sequences were aligned with both datasets using MAFFT (https://mafft.cbrc.jp/alignment/server/).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The phylogenetic trees were visualized using Figtree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).
    Figtree
    suggested: (FigTree, RRID:SCR_008515)

    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.

    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 10.1101/2020.09.21.20198838v1 on medRxiv