ArticlePLoS computational biology2020
Practical considerations for measuring the effective reproductive number, Rt.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 324 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
324 citing papers in PubMed, 3 syntheses or guidelines pooled it, 617 citations in OpenAlex.
- Decoding mpox: a systematic review and meta-analysis of the transmission and severity parameters of the 2022-2023 global outbreak.BMJ global health · 2025Pooled it
- Onward Virus Transmission after Measles Secondary Vaccination Failure.Emerging infectious diseases · 2024Pooled it
- Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number.Statistical methods in medical research · 2022Pooled it
- An Overview of Epidemiological Tools That Support the Progress of Foot-and-Mouth Disease Control in Southeast Asia.Pathogens (Basel, Switzerland) · 2026Review
- Multivariable Behavioral Change Modeling of Epidemics in the Presence of Undetected Infections.Statistics in medicine · 2026Article
- Real-time estimation of pathogen transmission dynamics from wastewater.Nature communications · 2026Article
- Inferring variant-specific effective reproduction numbers from combined case and sequencing data.eLife · 2026Article
- Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.PLoS computational biology · 2026Article
- Machine learning and probabilistic approaches for forecasting infectious disease transmission and cases.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2026Article
- Estimating time-varying cholera transmission and oral cholera vaccine effectiveness in Haiti and Cameroon, 2021-2023.BMJ open · 2026Article
- Unjustified Poisson assumptions lead to overconfident estimates of the effective reproductive number.Epidemiology and infection · 2026Article
- Robust estimation of the time-dependent reproduction number in the presence of weekend reporting effects.BMC global and public health · 2026Article
- A real-time early warning system to anticipate respiratory disease outbreaks using transfer learning.Nature communications · 2026Article
- Inference of latent epidemic regimes and generative simulations reveal how inequality and mobility shape COVID-19 transmission.Scientific reports · 2026Article
- Network structure induced bias in estimates of intrinsic generation times.PLoS computational biology · 2026Article
- Understanding how mobility and spatial disparities shape COVID-19 transmission under rotational and localized lockdowns.Scientific reports · 2026Article
- Estimating the generation time for SARS-CoV-2 transmission using United States household data, December 2021-May 2023.Scientific reports · 2026Article
- Reduced gravity and muon flux absence affectMicrobiology spectrum · 2026Article
- A multi-method study evaluating the inference of compartmental model parameters from a generative agent-based model.Infectious Disease Modelling · 2026Article
- Enhancing time-varying reproduction number estimates for COVID-19 with behavior and surveillance data in South Korea, 2020-2022.Archives of public health = Archives belges de sante publique · 2026Article
264 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Update of
Authors and funding
25 authors at 8 institutions in 4 countries.
Funding
Abstract
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using Rt to assess the effectiveness of interventions and to inform policy. However, estimation of Rt from available data presents several challenges, with critical implications for the interpretation of the course of the pandemic. The purpose of this document is to summarize these challenges, illustrate them with examples from synthetic data, and, where possible, make recommendations. For near real-time estimation of Rt, we recommend the approach of Cori and colleagues, which uses data from before time t and empirical estimates of the distribution of time between infections. Methods that require data from after time t, such as Wallinga and Teunis, are conceptually and methodologically less suited for near real-time estimation, but may be appropriate for retrospective analyses of how individuals infected at different time points contributed to the spread. We advise caution when using methods derived from the approach of Bettencourt and Ribeiro, as the resulting Rt estimates may be biased if the underlying structural assumptions are not met. Two key challenges common to all approaches are accurate specification of the generation interval and reconstruction of the time series of new infections from observations occurring long after the moment of transmission. Naive approaches for dealing with observation delays, such as subtracting delays sampled from a distribution, can introduce bias. We provide suggestions for how to mitigate this and other technical challenges and highlight open problems in Rt estimation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.