Abstract
The distribution of the generation time (the interval between individuals becoming infected and transmitting 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 data from the early months of the COVID-19 pandemic (December 2019-March 2020) compared to existing models (Hart et al., 2021). 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 to November 2020 in the UK, we provide updated estimates of the generation time. We considered 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% credible interval 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 (5.9 days, 5.2-7.0 days) and a similar standard deviation (4.8 days, 4.0-6.3 days). As well as estimating the generation time using data from the entire study period, we also considered whether the generation time varied temporally. 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, further data collection and analysis is necessary to continue to monitor ongoing transmission and inform future public health policy decisions.
Highlights
The generation time of a SARS-CoV-2 infector-infectee pair is defined as the period of time between the infector and infectee each becoming infected (Anderson and May, 1992; Diekmann and Heesterbeek, 2000; Griffin et al, 2020; Svensson, 2007; Wallinga and Lipsitch, 2007)
Each household was recruited to the study following a confirmed SARS-CoV-2 infection, and all household members were followed to investigate whether or not they became infected
In our previous work (Hart et al, 2021), we fitted the same two models of infectiousness to data from infector-infectee transmission pairs collected in the early months of the COVID-19 pandemic
Summary
The generation time (or generation interval) of a SARS-CoV-2 infector-infectee pair is defined as the period of time between the infector and infectee each becoming infected (Anderson and May, 1992; Diekmann and Heesterbeek, 2000; Griffin et al, 2020; Svensson, 2007; Wallinga and Lipsitch, 2007). The SARS-CoV-2 generation time distribution has previously been estimated using data from known infector-infectee transmission pairs (Ferretti et al, 2020b, 2020a; Hart et al, 2021) or entire clusters of cases (Ganyani et al, 2020; Hu et al, 2021; Sun et al, 2021). These studies involved data (Cheng et al, 2020; Ferretti et al, 2020b; Ganyani et al, 2020; He et al, 2020; Xia et al, 2020; Zhang et al, 2020) collected between December 2019 and April 2020, almost entirely from countries in East and Southeast Asia (with the exception of four transmission pairs from Germany and four from Italy in (Ferretti et al, 2020b)). Two other studies found a decrease in the serial interval (the difference between symptom onset times of an infector and infectee) (Ali et al, 2020) and an increase in the proportion of presymptomatic transmissions (Bushman et al, 2021) in China over the same time period, which can be attributed to symptomatic hosts being isolated increasingly quickly over time
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