Sequence analysis of travel-related SARS-CoV-2 cases in the Greater Geelong region, Australia

  1. Tarka Raj Bhatta
  2. Anthony Chamings
  3. Kwee-Chin Liew
  4. Freya Langham
  5. Rudi Gasser
  6. Owen Harris
  7. Andrew Gador-Whyte
  8. John Stenos
  9. Eugene Athan
  10. Soren Alexandersen

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Abstract

This study reports the sequence analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from infected individuals within the Greater Geelong region, Victoria, Australia. All but one individual had recently returned from travelling abroad, and all had clinical signs consistent with SARS-CoV-2 infection. SARS-CoV-2 belonging to three lineages were detected and represent separate introductions of the virus into the region. Sequence data were consistent with the recent travel history of each case. Full virus genome sequencing can play an important role in supporting local epidemiological tracing and monitoring for community transmission. Quality of the SARS-CoV-2 sequences obtained was highly dependent on appropriate sample collection and handling.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.08.20125898: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Samples were collected for this study with approval from the Barwon Health Human Research Ethics Committee (Ref HREC 20/56), and all participants gave their informed consent for their samples and case description to be included.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The sequence reads generated were mapped to a SARS-CoV-2 reference genome (NCBI GenBank accession number MN908947) 1 using the TMAP software included in the Torrent Suite 5.10.1 17, and visualized in Integrative Genomic Viewer 18 (IGV 2.6.3) (Broad Institute, Cambridge, MA, USA).
    TMAP
    suggested: (TMAP, RRID:SCR_000687)
    Near complete and partial SARS-CoV-2 genomes were aligned using Clustal-W 19 in MEGA 7 software 20.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.

    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.

  2. Version published to 10.1101/2020.06.08.20125898v1 on medRxiv