Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021

  1. Charles N. Agoti
  2. George Githinji
  3. Khadija S. Mohammed
  4. Arnold W. Lambisia
  5. Zaydah R. de Laurent
  6. Maureen W. Mburu
  7. Edidah M. Ong’era
  8. John M. Morobe
  9. Edward Otieno
  10. Hamza Abdou Azali
  11. Kamal Said Abdallah
  12. Abdoulaye Diarra
  13. Ali Ahmed Yahaya
  14. Peter Borus
  15. Nicksy Gumede Moeletsi
  16. Dratibi Fred Athanasius
  17. Benjamin Tsofa
  18. Philip Bejon
  19. D. James Nokes
  20. Lynette Isabella Ochola-Oyier

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Abstract

Background. Genomic data is key in understanding the spread and evolution of SARS-CoV-2 pandemic and informing the design and evaluation of interventions. However, SARS-CoV-2 genomic data remains scarce across Africa, with no reports yet from the Indian Ocean islands.

Methods. We genome sequenced six SARS-CoV-2 positive samples from the first major infection wave in the Union of Comoros in January 2021 and undertook detailed phylogenetic analysis.

Results. All the recovered six genomes classified within the 501Y.V2 variant of concern (also known as lineage B.1.351) and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30 th Oct-2020 (95% Credibility Interval: 06 th Sep-2020 to 10 th Dec-2020). Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte (part of the Comoros archipelago and a France, Overseas Department).

Conclusions. The recovered genomes, albeit few, confirmed local transmission following probably multiple introductions of the SARS-CoV-2 501Y.V2 variant of concern during the Comoros’s first major COVID-19 wave. These findings demonstrate the importance of genomic surveillance and have implications for ongoing control strategies on the islands.

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  1. Version published to 10.12688/wellcomeopenres.16889.1
  2. ScreenIT

    SciScore for 10.1101/2021.04.08.21254321: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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

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  3. Version published to 10.1101/2021.04.08.21254321 on medRxiv