Context-specific emergence and growth of the SARS-CoV-2 Delta variant

  1. John T. McCrone
  2. Verity Hill
  3. Sumali Bajaj
  4. Rosario Evans Pena
  5. Ben C. Lambert
  6. Rhys Inward
  7. Samir Bhatt
  8. Erik Volz
  9. Christopher Ruis
  10. Simon Dellicour
  11. Guy Baele
  12. Alexander E. Zarebski
  13. Adam Sadilek
  14. Neo Wu
  15. Aaron Schneider
  16. Xiang Ji
  17. Jayna Raghwani
  18. Ben Jackson
  19. Rachel Colquhoun
  20. Áine O’Toole
  21. Thomas P. Peacock
  22. Kate Twohig
  23. Simon Thelwall
  24. Gavin Dabrera
  25. Richard Myers
  26. The COVID-19 Genomics UK (COG-UK) Consortium
  27. Nuno R. Faria
  28. Carmen Huber
  29. Isaac I. Bogoch
  30. Kamran Khan
  31. Louis du Plessis
  32. Jeffrey C. Barrett
  33. David M. Aanensen
  34. Wendy S. Barclay
  35. Meera Chand
  36. Thomas Connor
  37. Nicholas J. Loman
  38. Marc A. Suchard
  39. Oliver G. Pybus
  40. Andrew Rambaut
  41. Moritz U. G. Kraemer

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Abstract

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide 1,2 . The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing—and not the number of importations—were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

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  1. Version published to 10.1038/s41586-022-05200-3
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    SciScore for 10.1101/2021.12.14.21267606: (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
    For subtree an empirical distribution of time trees was estimated independently using a recently implemented model in BEAST v1.1081 (commit:d1a45) which replaces the substitution model in classical analyses.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Model convergence and proper statistical mixing were verified in Tracer v1.784.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    Visualisations were made using a custom Python script.
    Python
    suggested: (IPython, RRID:SCR_001658)

    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.

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

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  3. Version published to 10.1101/2021.12.14.21267606 on medRxiv
  4. Version published to 10.21203/rs.3.rs-1159614/v1 on Research Square