One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

  1. Fatiha M. Benslimane
  2. Hebah A. Al Khatib
  3. Ola Al-Jamal
  4. Dana Albatesh
  5. Sonia Boughattas
  6. Ayeda A Ahmed
  7. Meryem Bensaad
  8. Shameem Younuskunju
  9. Yasmin A. Mohamoud
  10. Mashael Al Badr
  11. Abdalla A. Mohamed
  12. Reham A. El-Kahlout
  13. Tasneem Al-Hamad
  14. Dina Elgakhlab
  15. Fatima H. Al-Kuwari
  16. Chadi Saad
  17. Andrew Jeremijenko
  18. Abdullatif Al-Khal
  19. Muna A. Al-Maslamani
  20. Roberto Bertollini
  21. Einas A. Al-Kuwari
  22. Hamad E. Al-Romaihi
  23. Salih Al-Marri
  24. Mohammed Al-Thani
  25. Radja M. Badji
  26. Hamdi Mbarek
  27. Yasser Al-Sarraj
  28. Joel A. Malek
  29. Said I. Ismail
  30. Laith J. Abu-Raddad
  31. Peter V. Coyle
  32. Asmaa A. Al Thani
  33. Hadi M. Yassine

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Abstract

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

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  1. Version published to 10.3389/fcimb.2021.768883
  2. ScreenIT

    SciScore for 10.1101/2021.05.19.21257433: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics statement: The study was approved by the Institutional Review Board (IRB) committees of Qatar University (QU-IRB 1289-EA/20) and Hamad Medical Corporation (MRC-01-20-145) ethical boards.
    Consent: Samples collected were retrospective as such, following the national legislation and the institutional requirements, written informed consent for participants was not required for this study. 2.2.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Bioinformatics analysis: For ONT reads, MinKNOW software was used for base calling and reads with a minimum Q score of 7 were considered for downstream analysis.
    MinKNOW
    suggested: None
    For Illumina reads, sequences were quality/adapter trimmed with CUTADAPT, primer sequences removed with FGBIO, aligned with BWA-MEM and SNPs called with SAMTOOLS as previously described [14, 16].
    CUTADAPT
    suggested: (cutadapt, RRID:SCR_011841)
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    SAMTOOLS
    suggested: (SAMTOOLS, RRID:SCR_002105)
    A Maximum Likelihood (ML) phylogeny was generated using IQTree v2.1.3 under a GTR model of nucleotide substitution with empirical codon frequencies plus the FreeRate model [20].
    IQTree
    suggested: None
    Phylogenetic trees were edited and visualized using Figtree software v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/). root-to-tip regression analyses of B.1.1.7 and B.1.351 genomes were performed using TempEst v1.5.3 to investigate the temporal signal of the datasets [22].
    Figtree
    suggested: (FigTree, RRID:SCR_008515)
    TempEst
    suggested: (TempEst, RRID:SCR_017304)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.05.19.21257433v1 on medRxiv
  4. Version published to 10.1101/2021.05.19.21257433v2 on medRxiv