The genomic epidemiology of SARS-CoV-2 in Palestine

  1. Nouar Qutob
  2. Zaidoun Salah
  3. Damien Richard
  4. Hisham Darwish
  5. Husam Sallam
  6. Issa Shtayeh
  7. Osama Najjar
  8. Mahmoud Ruzayqat
  9. Dana Najjar
  10. François Balloux
  11. Lucy van Dorp

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause significant public health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with isolated viral samples from patients in Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020 - 19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales.

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    SciScore for 10.1101/2020.10.26.355677: (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
    Variants were then called using Freebayes v1.2231.
    Freebayes
    suggested: (FreeBayes, RRID:SCR_010761)
    The 54,793 SARS-CoV-2 assemblies were profile aligned against Wuhan-Hu-1 (MN908947.3) using MAFFT v.7.20533.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Phylogenetic reconstruction: The 69 aligned Palestinian sequences generated herein and 54,793 strains from the worldwide diversity were concatenated and a maximum likelihood tree built using IQ-TREE 2.1.0 Covid release34.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Trees were queried and plotted using the R packages Ape v5.4 36 and ggtree v1.16.637.
    Ape
    suggested: (APE, RRID:SCR_009122)
    The number of SNPs differing between viral assemblies within Palestine and across global datasets was assessed using SNP-sites38 and SNP-dists (https://github.com/tseemann/snp-dists) with heatmaps plotted using ComplexHeatMap v2.1.239.
    ComplexHeatMap
    suggested: (ComplexHeatmap, RRID:SCR_017270)
    Following confirmation of significant temporal signal we applied dater() within the TreeDater package v0.50 specifying a strict clock model and assessed confidence intervals following 100 iterations of the parboot() parametric bootstrap fitting method.
    TreeDater
    suggested: None

    Results from OddPub: Thank you for sharing your code and 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.

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  2. Version published to 10.1101/2020.10.26.355677v3 on bioRxiv
  3. Version published to 10.1101/2020.10.26.355677v2 on bioRxiv
  4. Version published to 10.1101/2020.10.26.355677v1 on bioRxiv