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

Pablo N. Perez-Guzman, Edward Knock, Natsuko Imai, Thomas Rawson, Cosmo Nazzareno Santoni, Joana Alcada, Lilith K. Whittles, Divya Thekke Kanapram, Raphael Sonabend, Katy A. M. Gaythorpe, Wes Hinsley, Richard G. FitzJohn, Erik Volz, Robert Verity, Neil M. Ferguson, Anne Cori and Marc Baguelin ()
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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
Cosmo Nazzareno Santoni: School of Public Health, Imperial College London
Joana Alcada: Royal Brompton Hospital
Lilith K. Whittles: School of Public Health, Imperial College London
Divya Thekke Kanapram: School of Public Health, Imperial College London
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

Nature Communications, 2023, vol. 14, issue 1, 1-9

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-39661-5

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