Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection Survey

  1. Katrina Lythgoe
  2. Tanya Golubchik
  3. Matthew Hall
  4. Thomas House
  5. Roberto Cahuantzi
  6. George MacIntyre-Cockett
  7. Helen Fryer
  8. Laura Thomson
  9. Anel Nurtay
  10. Mahan Ghafani
  11. David Buck
  12. Angie Green
  13. Amy Trebes
  14. Paolo Piazza
  15. Lorne J Lonie
  16. Ruth Studley
  17. Emma Rourke
  18. Darren Smith
  19. Matthew Bashton
  20. Andrew Nelson
  21. Matthew Crown
  22. Clare McCann
  23. Gregory R Young
  24. Rui Andre Nunes dos Santos
  25. Zack Richards
  26. Adnan Tariq
  27. Wellcome Sanger Institute COVID-19 Surveillance Team
  28. COVID-19 Infection Survey Group
  29. The COVID-19 Genomics UK (COG-UK) Consortium
  30. Christophe Fraser
  31. Ian Diamond
  32. Jeff Barrett
  33. Ann Sarah Walker
  34. David Bonsall

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Abstract

The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.

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  1. Version published to 10.1101/2022.01.05.21268323v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2022.01.05.21268323: (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
    A small number of samples (36) in our study were sequenced using Oxford Nanopore GridION or MINION.
    MINION
    suggested: (MinION, RRID:SCR_017985)
    Phylogenetics: The alignment of consensus sequences with at least 95% coverage was used for phylogenetic reconstruction using RAxML-NG version 0.9.0 [47].
    RAxML-NG
    suggested: None
    Ancestral sequence reconstruction was performed on the TreeTime divergence tree using IQ-TREE version 1.6.12 [48].
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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.

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

    About SciScore

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  3. Version published to 10.1101/2022.01.05.21268323v1 on medRxiv