학술논문
Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis.
Document Type
Academic Journal
Author
Hart WS; Mathematical Institute, University of Oxford, Oxford, UK.; Miller E; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; Immunisation and Countermeasures Division, UK Health Security Agency, London, UK.; Andrews NJ; Data and Analytical Sciences, UK Health Security Agency, London, UK.; Waight P; Immunisation and Countermeasures Division, UK Health Security Agency, London, UK.; Maini PK; Mathematical Institute, University of Oxford, Oxford, UK.; Funk S; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.; Thompson RN; Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK. Electronic address: robin.n.thompson@warwick.ac.uk.
Source
Publisher: Elsevier Science Country of Publication: United States NLM ID: 101130150 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1474-4457 (Electronic) Linking ISSN: 14733099 NLM ISO Abbreviation: Lancet Infect Dis Subsets: MEDLINE
Subject
Language
English
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Background: In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK, superseded by the omicron (B.1.1.529) variant in December, 2021.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.
Funding: National Institute for Health Research, UK Health Security Agency, Engineering and Physical Sciences Research Council, and UK Research and Innovation.
Competing Interests: Declaration of interests We declare no competing interests. WSH, SF, and RNT report participation in discussions of the UK Government's Scientific Pandemic Influenza Group on Modelling, Operational subgroup.
(Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.)
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.
Funding: National Institute for Health Research, UK Health Security Agency, Engineering and Physical Sciences Research Council, and UK Research and Innovation.
Competing Interests: Declaration of interests We declare no competing interests. WSH, SF, and RNT report participation in discussions of the UK Government's Scientific Pandemic Influenza Group on Modelling, Operational subgroup.
(Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.)