A main event and multiple introductions of SARS‐CoV‐2 initiated the COVID‐19 epidemic in Greece

  1. Nikolaos Spanakis
  2. Katerina Kassela
  3. Nikolas Dovrolis
  4. Maria Bampali
  5. Elisavet Gatzidou
  6. Athanasia Kafasi
  7. Elisavet Froukala
  8. Anastasia Stavropoulou
  9. Konstantinos Lilakos
  10. Stavroula Veletza
  11. Sotirios Tsiodras
  12. Athanasios Tsakris
  13. Ioannis Karakasiliotis

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a novel coronavirus responsible for the coronavirus disease 2019 (COVID‐19) pandemic. Chains of infections starting from various countries worldwide seeded the outbreak of COVID‐19 in Athens, capital city of Greece. A full‐genome analysis of isolates from Athens' hospitals and other healthcare providers revealed the variety of SARS‐CoV‐2 that initiated the pandemic before lockdown and passenger flight restrictions. A dominant variant, encompassing the G614D amino acid substitution, spread through a major virus dispersal event, and sporadic introductions of rare variants characterized the local initiation of the epidemic. Mutations within the genome highlighted the genetic drift of the virus as rare variants emerged. An important variant contained a premature stop codon in orf7a leading to the truncation of a possibly important for viral pathogenesis domain. This study may serve as a reference for resolving future lines of infection in the area, especially after resumption of passenger flight connections to Athens and Greece during summer of 2020.

Article activity feed

  1. Version published to 10.1002/jmv.26778
  2. ScreenIT

    SciScore for 10.1101/2020.06.03.20121236: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    RandomizationA list of 94 samples was randomly formed and curated for duplicates and family acquired infections in order to better assess viral variability (Suppl.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    For this reason we used the LoFreq v.
    LoFreq
    suggested: (LoFreq, RRID:SCR_013054)
    SnpEff utilizes a genomic feature file (gff) that contains all the information on the viral protein structure and intervals on the reference sequence.
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)
    The phylogenetic tree encompassing European and European-related international isolates was constructed using FastTree v.
    FastTree
    suggested: (FastTree, RRID:SCR_015501)

    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.

  3. Version published to 10.1101/2020.06.03.20121236v1 on medRxiv