Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix

  1. Gábor Kemenesi
  2. Safia Zeghbib
  3. Balázs A Somogyi
  4. Gábor Endre Tóth
  5. Krisztián Bányai
  6. Norbert Solymosi
  7. Peter M Szabo
  8. István Szabó
  9. Ádám Bálint
  10. Péter Urbán
  11. Róbert Herczeg
  12. Attila Gyenesei
  13. Ágnes Nagy
  14. Csaba István Pereszlényi
  15. Gergely Csaba Babinszky
  16. Gábor Dudás
  17. Gabriella Terhes
  18. Viktor Zöldi
  19. Róbert Lovas
  20. Szabolcs Tenczer
  21. László Kornya
  22. Ferenc Jakab

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Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019 the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of the 21th of April, 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.06.080119: (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

    Software and Algorithms
    SentencesResources
    During primary data analysis, we used RAMPART to track the sequencing process in “real-time” in order to acquire instant information regarding the quality of samples and the coverage of the amplicons.
    RAMPART
    suggested: (Rampart, RRID:SCR_016742)
    To quantify the sequence similarity, percent identity was calculated based on the BLAST 15 alignment for each paired sequence.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    All data analyses were performed using the R 3.6.2 on Linux16, for network creation, and the Igraph package was applied17.
    Igraph
    suggested: (igraph, RRID:SCR_019225)
    The sequences were aligned in MAFFT 18 with default parameters.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A positive correlation was observed between sampling time and root-to-tip genetic divergence indicating the suitability of the dataset for molecular clock analysis using the Beast v1.10.4 package.
    Beast
    suggested: (BEAST, RRID:SCR_010228)
    The datasets generated during and analysed during the current study are available in the NDEx-The Network Data Exchange repository, [http://www.ndexbio.org/#/network/2c66e15b-8eeb-11ea-aaef-0ac135e8bacf].
    http://www.ndexbio.org/#/network/2c66e15b-8eeb-11ea-aaef-0ac135e8bacf
    suggested: (Network Data Exchange (NDEx, RRID:SCR_003943)

    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

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  2. Version published to 10.1101/2020.05.06.080119v1 on bioRxiv