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Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

Author

Listed:
  • Pablo N. Perez-Guzman

    (School of Public Health, Imperial College London)

  • Edward Knock

    (School of Public Health, Imperial College London)

  • Natsuko Imai

    (School of Public Health, Imperial College London)

  • Thomas Rawson

    (School of Public Health, Imperial College London)

  • Yasin Elmaci

    (School of Public Health, Imperial College London)

  • Joana Alcada

    (Royal Brompton Hospital
    Faculty of Medicine, Imperial College London)

  • Lilith K. Whittles

    (School of Public Health, Imperial College London)

  • Divya Thekke Kanapram

    (School of Public Health, Imperial College London
    University of Cambridge)

  • Raphael Sonabend

    (School of Public Health, Imperial College London)

  • Katy A. M. Gaythorpe

    (School of Public Health, Imperial College London)

  • Wes Hinsley

    (School of Public Health, Imperial College London)

  • Richard G. FitzJohn

    (School of Public Health, Imperial College London)

  • Erik Volz

    (School of Public Health, Imperial College London)

  • Robert Verity

    (School of Public Health, Imperial College London)

  • Neil M. Ferguson

    (School of Public Health, Imperial College London)

  • Anne Cori

    (School of Public Health, Imperial College London)

  • Marc Baguelin

    (School of Public Health, Imperial College London
    National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Modelling and Health Economics
    London School of Hygiene & Tropical Medicine)

Abstract

As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.4 (95% credible interval (CrI) 7.8-9.1). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (3.0%, 95% CrI 2.8-3.2), followed by Delta (2.1%, 95% CrI 1.9–2.4), Wildtype (1.2%, 95% CrI 1.1–1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.

Suggested Citation

  • Pablo N. Perez-Guzman & Edward Knock & Natsuko Imai & Thomas Rawson & Yasin Elmaci & Joana Alcada & Lilith K. Whittles & Divya Thekke Kanapram & Raphael Sonabend & Katy A. M. Gaythorpe & Wes Hinsley &, 2023. "Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39661-5
    DOI: 10.1038/s41467-023-39661-5
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    References listed on IDEAS

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    1. Jeffrey D Sachs & Salim S Abdool Karim & Lara Aknin & Joseph Allen & Kirsten Brosbol & Francesca Colombo & Gabriela Cuevas Barron & Maria Fernanda Espinosa & Vitor Gaspar & Alejandro Gaviria & Andy Ha, 2022. "The Lancet Commission on lessons for the future from the COVID-19 pandemic," DEOS Working Papers 2226, Athens University of Economics and Business.
    2. Natalie Dean, 2022. "Tracking COVID-19 infections: time for change," Nature, Nature, vol. 602(7896), pages 185-185, February.
    3. Joël Mossong & Niel Hens & Mark Jit & Philippe Beutels & Kari Auranen & Rafael Mikolajczyk & Marco Massari & Stefania Salmaso & Gianpaolo Scalia Tomba & Jacco Wallinga & Janneke Heijne & Malgorzata Sa, 2008. "Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases," PLOS Medicine, Public Library of Science, vol. 5(3), pages 1-1, March.
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    1. Lloyd A. C. Chapman & Maite Aubry & Noémie Maset & Timothy W. Russell & Edward S. Knock & John A. Lees & Henri-Pierre Mallet & Van-Mai Cao-Lormeau & Adam J. Kucharski, 2023. "Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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