Inference of SARS-CoV-2 generation times using UK household data

Abstract

The distribution of the generation time (the interval between individuals becoming infected and passing on the virus) characterises changes in the transmission risk during SARS-CoV-2 infections. Inferring the generation time distribution is essential to plan and assess public health measures. We previously developed a mechanistic approach for estimating the generation time, which provided an improved fit to SARS-CoV-2 data from January-March 2020 compared to existing models. However, few estimates of the generation time exist based on data from later in the pandemic. Here, using data from a household study conducted from March-November 2020 in the UK, we provide updated estimates of the generation time. We consider both a commonly used approach in which the transmission risk is assumed to be independent of when symptoms develop, and our mechanistic model in which transmission and symptoms are linked explicitly. Assuming independent transmission and symptoms, we estimated a mean generation time (4.2 days, 95% CrI 3.3-5.3 days) similar to previous estimates from other countries, but with a higher standard deviation (4.9 days, 3.0-8.3 days). Using our mechanistic approach, we estimated a longer mean generation time (6.0 days, 5.2-7.0 days) and a similar standard deviation (4.9 days, 4.0-6.3 days). Both models suggest a shorter mean generation time in September-November 2020 compared to earlier months. Since the SARS-CoV-2 generation time appears to be changing, continued data collection and analysis is necessary to inform future public health policy decisions.

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

“…In this model, each infection is divided into three successive stages (the duration of time in each stage followed independent distributions): latent, presymptomatic and infectious, and symptomatic and infectious. 17 , 18 Unlike standard methods for estimating the generation time, 15 , 16 this approach links an infected host's infectivity profile to the time at which they develop symptoms .…”

“…Previous studies have estimated the SARS-CoV-2 generation time, 15 , 16 , 17 , 18 , 19 , 20 with most estimates using data collected early in the COVID-19 pandemic. A household study 18 from the UK Health Security Agency (UKHSA) indicated that the generation time of SARS-CoV-2 became shorter between September and November, 2020, compared with the earlier months.…”

“…Previous studies have estimated the SARS-CoV-2 generation time, 15 , 16 , 17 , 18 , 19 , 20 with most estimates using data collected early in the COVID-19 pandemic. A household study 18 from the UK Health Security Agency (UKHSA) indicated that the generation time of SARS-CoV-2 became shorter between September and November, 2020, compared with the earlier months. However, although this period coincided with emergence of the alpha variant, that variant was responsible for infections in only two households in the UKHSA study, and the delta variant had not yet emerged.…”

“…However, although this period coincided with emergence of the alpha variant, that variant was responsible for infections in only two households in the UKHSA study, and the delta variant had not yet emerged. 18 Therefore, in this epidemiological analysis we compared the effect of these variants on the SARS-CoV-2 generation time using data from an ongoing household study in the UK.…”

Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model

“…The value of G, the time period considered as measured in mean generation times, is going to be a subjective decision. Estimates for the generation time are variable between studies, but typically around 4-6 days [34][35][36]. We take G = 15 by default, corresponding to a time window of two to three months.…”