ArticleJournal of the Royal Society, Interface2022
Inferring the reproduction number using the renewal equation in heterogeneous epidemics.
Article in Journal of the Royal Society, Interface, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.PLoS computational biology · 2026Article
- Unjustified Poisson assumptions lead to overconfident estimates of the effective reproductive number.Epidemiology and infection · 2026Article
- TheCommunications physics · 2026Article
- Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers.PLoS computational biology · 2025Article
- The time-dependent reproduction number for epidemics in heterogeneous populations.Journal of the Royal Society, Interface · 2025Article
- A novel approach to estimatingFrontiers in public health · 2025Article
- Epidemiological impact of revoking mask-wearing recommendation on COVID-19 transmission in Tokyo, Japan.Infectious Disease Modelling · 2024Article
- Emergence of the reproduction matrix in epidemic forecasting.Journal of the Royal Society, Interface · 2024Article
- Advancements in Defining and Estimating the Reproduction Number in Infectious Disease Epidemiology.China CDC weekly · 2023Article
- Risk averse reproduction numbers improve resurgence detection.PLoS computational biology · 2023Article
- Enhancing global preparedness during an ongoing pandemic from partial and noisy data.PNAS nexus · 2023Article
- Correlation of viral loads in disease transmission could affect early estimates of the reproduction number.Journal of the Royal Society, Interface · 2023Article
- Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges.PLOS digital health · 2022Article
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Authors and funding
3 authors.
Funding
Abstract
Real-time estimation of the reproduction number has become the focus of modelling groups around the world as the SARS-CoV-2 pandemic unfolds. One of the most widely adopted means of inference of the reproduction number is via the renewal equation, which uses the incidence of infection and the generation time distribution. In this paper, we derive a multi-type equivalent to the renewal equation to estimate a reproduction number which accounts for heterogeneity in transmissibility including through asymptomatic transmission, symptomatic isolation and vaccination. We demonstrate how use of the renewal equation that misses these heterogeneities can result in biased estimates of the reproduction number. While the bias is small with symptomatic isolation, it can be much larger with asymptomatic transmission or transmission from vaccinated individuals if these groups exhibit substantially different generation time distributions to unvaccinated symptomatic transmitters, whose generation time distribution is often well defined. The bias in estimate becomes larger with greater population size or transmissibility of the poorly characterized group. We apply our methodology to Ebola in West Africa in 2014 and the SARS-CoV-2 in the UK in 2020-2021.
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