Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis

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Background: In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK, superseded by the omicron (B.1.1.529) variant in December, 2021.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.

Figure 1

The effect of variant on the intrinsic and household generation times Violin plots indicate posterior estimates for the alpha and delta variants. (A) The mean intrinsic generation time (the mean generation time if the supply of susceptible individuals remains constant throughout infection). (B) Overall transmissibility, β₀ (the expected number of household transmissions generated by a single, non-asymptomatic infector in an unvaccinated and otherwise entirely susceptible household, assuming that following each transmission, the infectee is removed and replaced by another susceptible individual). (C) The mean household generation time (the mean realised generation time accounting for depletion of susceptible individuals in households). (D) The SD of household generation times. Central estimates and 95% credible intervals are shown in appendix 2 (pp 24–25). Posterior estimates of the SD for the intrinsic generation time distribution, and posterior estimates of fitted model parameters, are compared between variants in appendix 2 (p 12).

Figure 2

The effect of different factors on household generation times Violin plots indicate posterior estimates of the mean household generation time depending on the vaccination status of the infector and the variant (A), the vaccination status of the infectee and the variant (B), the combination of vaccination statuses in infector–infectee pairs (eg, U–V corresponds to transmissions from unvaccinated infectors to vaccinated infectees; vaccinated defined here as individuals who have received either one or two doses) and the variant (C), the age of the infector and the variant (D), the age of the infectee and the variant (E), and the month in 2021 in which the household index case first tested positive (F). U=unvaccinated. V=vaccinated.