Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

  1. Ana da Silva Filipe
  2. James G. Shepherd
  3. Thomas Williams
  4. Joseph Hughes
  5. Elihu Aranday-Cortes
  6. Patawee Asamaphan
  7. Shirin Ashraf
  8. Carlos Balcazar
  9. Kirstyn Brunker
  10. Alasdair Campbell
  11. Stephen Carmichael
  12. Chris Davis
  13. Rebecca Dewar
  14. Michael D. Gallagher
  15. Rory Gunson
  16. Verity Hill
  17. Antonia Ho
  18. Ben Jackson
  19. Edward James
  20. Natasha Jesudason
  21. Natasha Johnson
  22. E. Carol McWilliam Leitch
  23. Kathy Li
  24. Alasdair MacLean
  25. Daniel Mair
  26. David A. McAllister
  27. John T. McCrone
  28. Sarah E. McDonald
  29. Martin P. McHugh
  30. A. Keith Morris
  31. Jenna Nichols
  32. Marc Niebel
  33. Kyriaki Nomikou
  34. Richard J. Orton
  35. Áine O’Toole
  36. Massimo Palmarini
  37. Benjamin J. Parcell
  38. Yasmin A. Parr
  39. Andrew Rambaut
  40. Stefan Rooke
  41. Sharif Shaaban
  42. Rajiv Shah
  43. Joshua B. Singer
  44. Katherine Smollett
  45. Igor Starinskij
  46. Lily Tong
  47. Vattipally B. Sreenu
  48. Elizabeth Wastnedge
  49. The COVID-19 Genomics UK (COG-UK) Consortium
  50. Matthew T. G. Holden
  51. David L. Robertson
  52. Kate Templeton
  53. Emma C. Thomson

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  1. ScreenIT

    SciScore for 10.1101/2020.06.08.20124834: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    Reads were size filtered, demultiplexed and trimmed with Porechop (https://github.com/rrwick/Porechop), and mapped against reference strain Wuhan-Hu-1 (MN908947).
    Wuhan-Hu-1
    suggested: None
    Software and Algorithms
    SentencesResources
    Sequencing was conducted in MinKNOW version 19.12.5.
    MinKNOW
    suggested: None
    RAMPART v1.0.5 was used to visualise read mapping in real-time.
    RAMPART
    suggested: (Rampart, RRID:SCR_016742)
    Reads were size filtered, demultiplexed and trimmed with Porechop (https://github.com/rrwick/Porechop), and mapped against reference strain Wuhan-Hu-1 (MN908947).
    Porechop
    suggested: (Porechop, RRID:SCR_016967)
    Variants were called using Nanopolish 0.11.3 and accepted if they had a log-likelihood score of greater than 200 and minimum read coverage of 20.
    Nanopolish
    suggested: (Nanopolish, RRID:SCR_016157)
    Reads were trimmed with trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped with BWA (17) to the Wuhan-Hu-1 (MN908947) reference sequence, followed by primer trimming and consensus calling with iVar (18) and a minimum read coverage of 10.
    http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
    suggested: (Trim Galore, RRID:SCR_011847)
    BWA
    suggested: (BWA, RRID:SCR_010910)
    All consensus genomes are available from the GISAID database (https://www.gisaid.org), the COG-UK consortium website (https://www.cogconsortium.uk/data/) and BAM files from the European Nucleotide Archive’s Sequence Read Archive service, BioProject PRJEB37886 (https://www.ebi.ac.uk/ena/data/view/PRJEB37886).
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Consensus sequences were aligned using MAFFT (19).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A maximum-likelihood phylogenetic tree was constructed using IQ-TREE with the HKY nucleotide substitution model as determined by modeltest-NG (20, 21) and visualised with Figtree.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Figtree
    suggested: (FigTree, RRID:SCR_008515)

    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 10.1038/s41564-020-00838-z
  3. ScreenIT

    SciScore for 10.1101/2020.06.08.20124834: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.RandomizationUp to 300 samples per week were selected prospectively following ethical approval from the relevant national biorepository authorities ( 16/WS/0207NHS and10/S1402/33 ) between 1st March and 1st April 2020 . 50 % of samples were randomly selected to achieve a representative target for all Scottish health boards and 50 % to cover suspected healthcarerelated nosocomial infections as they occurred.Blindingnot detected.Power Analysisnot detected.Sex as a biological variableThe first case of COVID-19 in Scotland was a 51-year-old male from Tayside with mild respiratory symptoms who was tested on the 28th February 2020 ( and reported positive on the 1st March 2020) .

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequencing was conducted in MinKNOW version 19.12.5 .
    MinKNOW
    suggested: None
    RAMPART v1.0.5 was used to visualise read mapping in real-time.
    RAMPART
    suggested: (Rampart, SCR_016742)
    Reads were size filtered , demultiplexed and trimmed with Porechop ( https://github.com/rrwick/Porechop) , and mapped against reference strain Wuhan-Hu-1 ( MN908947) .
    Porechop
    suggested: (Porechop, SCR_016967)
    Variants were called using Nanopolish 0.11.3 and accepted if they had a log-likelihood score of greater than 200 and minimum read coverage of 20 .
    Nanopolish
    suggested: (Nanopolish, SCR_016157)
    Reads were trimmed with trim_galore ( http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ) and mapped with BWA ( 17 ) to the Wuhan-Hu-1 ( MN908947 ) reference sequence , followed by primer trimming and consensus calling with iVar ( 18 ) and a minimum read coverage of 10 . Sequence Data .
    http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
    suggested: (Trim Galore, SCR_011847)
          <div style="margin-bottom:8px">
        <div><b>BWA</b></div>
        <div>suggested: (BWA, <a href="https://scicrunch.org/resources/Any/search?q=SCR_010910">SCR_010910</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All consensus genomes are available from the GISAID database ( https://www.gisaid.org) , the COG-UK consortium website ( https://www.cogconsortium.uk/data/ ) and BAM files from the European Nucleotide Archive’s Sequence Read Archive service , BioProject PRJEB37886 ( https://www.ebi.ac.uk/ena/data/view/PRJEB37886).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>BioProject</b></div>
        <div>suggested: (NCBI BioProject, <a href="https://scicrunch.org/resources/Any/search?q=SCR_004801">SCR_004801</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Consensus sequences were aligned using MAFFT ( 19) .</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>MAFFT</b></div>
        <div>suggested: (MAFFT, <a href="https://scicrunch.org/resources/Any/search?q=SCR_011811">SCR_011811</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A maximum-likelihood phylogenetic tree was constructed using IQTREE with the HKY nucleotide substitution model as determined by modeltest-NG ( 20 , 21 ) and visualised with Figtree.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Figtree</b></div>
        <div>suggested: (FigTree, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008515">SCR_008515</a>)</div>
      </div>
    </td></tr></table>

    Results from OddPub: Thank you for sharing your data.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.06.08.20124834v1 on medRxiv