Molecular epidemiology of SARS-CoV-2 in Cyprus

  1. Jan Richter
  2. Pavlos Fanis
  3. Christina Tryfonos
  4. Dana Koptides
  5. George Krashias
  6. Stavros Bashiardes
  7. Andreas Hadjisavvas
  8. Maria Loizidou
  9. Anastasis Oulas
  10. Denise Alexandrou
  11. Olga Kalakouta
  12. Mihalis I. Panayiotidis
  13. George M. Spyrou
  14. Christina Christodoulou

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Abstract

Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.

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  1. Version published to 10.1371/journal.pone.0248792
  2. ScreenIT

    SciScore for 10.1101/2021.03.16.21252974: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was approved by the Cyprus National Bioethics committee (EEBK 21.1.01.03)
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Mapping, alignment and lineage assignment: The Burrows-Wheeler Aligner (BWA), version: 0.7.15 was used to map the raw reads to the coronavirus reference genome Wuhan-Hu-1 (NCBI ID:NC_045512.2) [8].
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Duplicate reads, which are likely to be the results of PCR bias, were marked using Picard version: 2.6.0 (http://broadinstitute.github.io/picard/).
    Picard
    suggested: (Picard, RRID:SCR_006525)
    Samtools, version: 0.1.19, was used for additional BAM/SAM file manipulations [9].
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Phylogenetic analysis: All phylogenetic analyses were conducted in MEGA7 [13].
    MEGA7
    suggested: None
    The alignment of consensus sequences was performed using MUSCLE.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    In addition, jModelTest [14] was used for evaluating the best fitting nucleotide substitution model under BIC yielding the same result (TN93model + gamma distributed rates).
    jModelTest
    suggested: (jModelTest, RRID:SCR_015244)

    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 10.1101/2021.03.16.21252974 on medRxiv