A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa

  1. Tulio de Oliveira
  2. Silvia Lutucuta
  3. John Nkengasong
  4. Joana Morais
  5. Joana Paula Paixão
  6. Zoraima Neto
  7. Pedro Afonso
  8. Julio Miranda
  9. Kumbelembe David
  10. Luzia Inglês
  11. Amilton Pereira Agostinho Paulo Raisa Rivas Carralero
  12. Helga Reis Freitas
  13. Franco Mufinda
  14. Sofonias Kifle Tessema
  15. Houriiyah Tegally
  16. Emmanuel James San
  17. Eduan Wilkinson
  18. Jennifer Giandhari
  19. Sureshnee Pillay
  20. Marta Giovanetti
  21. Yeshnee Naidoo
  22. Aris Katzourakis
  23. Mahan Ghafari
  24. Lavanya Singh
  25. Derek Tshiabuila
  26. Darren Martin
  27. Richard J Lessells

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Abstract

At the end of 2020, the Network for Genomic Surveillance in South Africa (NGS-SA) detected a SARS-CoV-2 variant of concern (VOC) in South Africa (501Y.V2 or PANGO lineage B.1.351)1. 501Y.V2 is associated with increased transmissibility and resistance to neutralizing antibodies elicited by natural infection and vaccination2,3. 501Y.V2 has since spread to over 50 countries around the world and has contributed to a significant resurgence of the epidemic in southern Africa. In order to rapidly characterize the spread of this and other emerging VOCs and variants of interest (VOIs), NGS-SA partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance across the region.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.30.21254323: (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: 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.

  2. Version published to 10.1101/2021.03.30.21254323 on medRxiv