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Generation time of the alpha and delta SARS-CoV-2 variants : an epidemiological analysis
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Hart, W. S., Miller, E., Andrews, N. J., Waight, P., Maini, P. K., Funk, S. and Thompson, Robin N. (2022) Generation time of the alpha and delta SARS-CoV-2 variants : an epidemiological analysis. Lancet Infectious Diseases, 22 (5). pp. 603-610. doi:10.1016/S1473-3099(22)00001-9 ISSN 1473-3099.
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Official URL: https://doi.org/10.1016/S1473-3099(22)00001-9
Abstract
Background
In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK, superseded by the omicron (B.1.1.529) variant in December, 2021. The delta variant is associated with increased transmissibility compared with the alpha variant, which was the dominant variant in the UK between December, 2020, and May, 2021. To understand transmission and the effectiveness of interventions, we aimed to investigate whether the delta variant generation time (the interval between infections in infector–infectee pairs) is shorter—ie, transmissions are happening more quickly—than that of the alpha variant.
Methods
In this epidemiological analysis, we analysed transmission data from an ongoing UK Health Security Agency (UKHSA) prospective household study. Households were recruited to the study after an index case had a positive PCR test and genomic sequencing was used to determine the variant responsible. By fitting a mathematical transmission model to the data, we estimated the intrinsic generation time (which assumes a constant supply of susceptible individuals throughout infection) and the household generation time (which reflects realised transmission in the study households, accounting for susceptible depletion) for the alpha and delta variants.
Findings
Between February and August, 2021, 227 households consisting of 559 participants were recruited to the UKHSA study. The alpha variant was detected or assumed to be responsible for infections in 131 households (243 infections in 334 participants) recruited in February–May, and the delta variant in 96 households (174 infections in 225 participants) in May–August. The mean intrinsic generation time was shorter for the delta variant (4·7 days, 95% credible interval [CI] 4·1–5·6) than the alpha variant (5·5 days, 4·7–6·5), with 92% posterior probability. The mean household generation time was 28% (95% CI 0–48%) shorter for the delta variant (3·2 days, 95% CI 2·5–4·2) than the alpha variant (4·5 days, 3·7–5·4), with 97·5% posterior probability.
Interpretation
The delta variant transmits more quickly in households than the alpha variant, which can be attributed to faster depletion of susceptible individuals in households and a possible decrease in the intrinsic generation time. Interventions such as contact tracing, testing, and isolation might be less effective if transmission of the virus occurs quickly.
| Item Type: | Journal Article | |||||||||||||||
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| Subjects: | R Medicine > RA Public aspects of medicine | |||||||||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Mathematics | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | COVID-19 (Disease), COVID-19 (Disease) -- Epidemiology -- Mathematical models | |||||||||||||||
| Journal or Publication Title: | Lancet Infectious Diseases | |||||||||||||||
| Publisher: | Lancet Ltd | |||||||||||||||
| ISSN: | 1473-3099 | |||||||||||||||
| Official Date: | 1 May 2022 | |||||||||||||||
| Dates: |
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| Volume: | 22 | |||||||||||||||
| Number: | 5 | |||||||||||||||
| Page Range: | pp. 603-610 | |||||||||||||||
| DOI: | 10.1016/S1473-3099(22)00001-9 | |||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||
| Copyright Holders: | © 2022 Published by Elsevier Ltd. | |||||||||||||||
| Date of first compliant deposit: | 23 December 2021 | |||||||||||||||
| Date of first compliant Open Access: | 15 February 2022 | |||||||||||||||
| RIOXX Funder/Project Grant: |
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