Abstract
BackgroundIn May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK, superseded by the omicron (B.1.1.529) variant in December, 2021.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.MethodsIn 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.FindingsBetween 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.InterpretationThe 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.FundingNational Institute for Health Research, UK Health Security Agency, Engineering and Physical Sciences Research Council, and UK Research and Innovation.
Highlights
Where sequencing data were unavailable, we assumed that the alpha variant was responsible for infections in households in which the index case first tested positive before May, 2021, and the delta variant was responsible for infections in households in which the index case first tested positive after May, 2021
The mean intrinsic generation time was estimated to be 4·7 days for the delta variant and 5·5 days (4·7–6·5) for the alpha variant
Comparing the posterior estimates suggests that the mean intrinsic generation time is 15% shorter for the delta variant than the alpha variant, with 92% posterior probability that the delta variant has the shorter mean intrinsic generation time of the two variants
Summary
In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK1 and globally. This variant presents a higher risk of severe disease compared with previous variants, vaccination is still protective. The delta variant led to an increase in the growth rate of COVID-19 cases in the UK, outcompeting other variants. This growth was attributed to increased transmissibility, with a study suggesting that the delta variant was 43–68% more transmissible than the alpha (B.1.1.7) variant, which was first identified in a sample from September, 2020.6One way to characterise transmission of a SARS-CoV-2 variant is to measure its speed and strength. Speed refers to how quickly the variant grows at the populationlevel, which is measured by the exponential growth rate and is inferable from disease incidence data. Strength reflects the variant’s transmissibility and is typically measured by the time-dependent reproduction number (ie, the number of people that each infected person is expected to infect). In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK1 and globally.. In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK1 and globally.2 This variant presents a higher risk of severe disease compared with previous variants, vaccination is still protective.. The delta variant led to an increase in the growth rate of COVID-19 cases in the UK, outcompeting other variants.. One way to characterise transmission of a SARS-CoV-2 variant is to measure its speed and strength.. Speed refers to how quickly the variant grows at the populationlevel, which is measured by the exponential growth rate and is inferable from disease incidence data.. An increased growth rate of COVID-19 cases, as observed for the delta variant, is attributable to increased transmissibility, a shorter generation time, or both of these factors. The generation time (ie, the time between infection events in infector–infectee pairs) determines the relationship between a variant’s speed and its strength and is an input used in models to estimate the reproduction number from case notification data. In principle, an increased growth rate of COVID-19 cases, as observed for the delta variant, is attributable to increased transmissibility, a shorter generation time, or both of these factors.
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