A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
Top Cited Papers
Open Access
- 15 September 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in American Journal of Epidemiology
- Vol. 178 (9), 1505-1512
- https://doi.org/10.1093/aje/kwt133
Abstract
The quantification of transmissibility during epidemics is essential to designing and adjusting public health responses. Transmissibility can be measured by the reproduction number R, the average number of secondary cases caused by an infected individual. Several methods have been proposed to estimate R over the course of an epidemic; however, they are usually difficult to implement for people without a strong background in statistical modeling. Here, we present a ready-to-use tool for estimating R from incidence time series, which is implemented in popular software including Microsoft Excel (Microsoft Corporation, Redmond, Washington). This tool produces novel, statistically robust analytical estimates of R and incorporates uncertainty in the distribution of the serial interval (the time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases). We applied the method to 5 historical outbreaks; the resulting estimates of R are consistent with those presented in the literature. This tool should help epidemiologists quantify temporal changes in the transmission intensity of future epidemics by using surveillance data.Keywords
This publication has 42 references indexed in Scilit:
- Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenzaProceedings of the National Academy of Sciences, 2011
- The Effective Reproduction Number of Pandemic InfluenzaEpidemiology, 2010
- Viral Shedding and Clinical Illness in Naturally Acquired Influenza Virus InfectionsThe Journal of Infectious Diseases, 2010
- Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong KongPLoS Computational Biology, 2009
- Pandemic Potential of a Strain of Influenza A (H1N1): Early FindingsScience, 2009
- Estimating Individual and Household Reproduction Numbers in an Emerging EpidemicPLOS ONE, 2007
- Smallpox transmission and control: Spatial dynamics in Great BritainProceedings of the National Academy of Sciences, 2006
- Strategies for mitigating an influenza pandemicNature, 2006
- Factors that make an infectious disease outbreak controllableProceedings of the National Academy of Sciences, 2004
- Transmission potential of smallpox in contemporary populationsNature, 2001