The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
Open accessAbstract
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.
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Cites
Infectious Diseases of Humans: Dynamics and Control
(1992) · Annals of Internal Medicine · doi:10.7326/0003-4819-117-2-174_4 · Cited by 7,819
Infectious Diseases of Humans: Dynamics and Control
Anderson, R. M., & May, R. M. (1991) · doi:10.1093/oso/9780198545996.001.0001 · Cited by 6,179
A Major Outbreak of Severe Acute Respiratory Syndrome in Hong Kong
Lee, N. L. S., Hui, D. S. C., Wu, A. K. L., Chan, P. K. S., Cameron, P. A., Joynt, G. M., Ahuja, A. T., Yung, M. Y., Leung, C. B., To, K. F., et al. (2003) · New England Journal of Medicine · doi:10.1056/nejmoa030685 · Cited by 2,638
Peiris, J., Chu, C., Cheng, V., Chan, K., Hung, I., Poon, L., Law, K., Tang, B., Hon, T., Chan, C., et al. (2003) · The Lancet · doi:10.1016/s0140-6736(03)13412-5 · Cited by 2,375
Strategies for mitigating an influenza pandemic
Ferguson, N. M., Cummings, D. A. T., Fraser, C., Cajka, J. C., Cooley, P. C., & Burke, D. S. (2006) · Nature · doi:10.1038/nature04795 · Cited by 2,203
Self-citationPandemic Potential of a Strain of Influenza A (H1N1): Early Findings
Fraser, C., Donnelly, C. A., Cauchemez, S., Hanage, W. P., Kerkhove, M. D. V., Hollingsworth, T. D., Griffin, J. T., Baggaley, R. F., Jenkins, H. E., Lyons, E., et al. (2009) · Science · doi:10.1126/science.1176062 · Cited by 1,915
Self-citationStrategies for containing an emerging influenza pandemic in Southeast Asia
Ferguson, N. M., Cummings, D. A. T., Cauchemez, S., Fraser, C., Riley, S., Meeyai, A. C., Iamsirithaworn, S., & Burke, D. S. (2005) · Nature · doi:10.1038/nature04017 · Cited by 1,820
Self-citation(1988) · World Health Organization eBooks · Cited by 1,574
Transmission Dynamics and Control of Severe Acute Respiratory Syndrome
Lipsitch, M., Cohen, T., Cooper, B. S., Robins, J. M., Ma, S., James, L., Gopalakrishna, G., Chew, S. K., Tan, C. C., Samore, M. H., et al. (2003) · Science · doi:10.1126/science.1086616 · Cited by 1,485
Elwood, J. M. (1989) · Journal of Epidemiology & Community Health · doi:10.1136/jech.43.1.92 · Cited by 1,412
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Self-citationPan, A., Liu, L., Wang, C., Guo, H., Hao, X., Wang, Q., Huang, J., He, N., Yu, H., Lin, X., et al. (2020) · JAMA · doi:10.1001/jama.2020.6130 · Cited by 1,931
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Metadata
- Authors
- Cori, A., Ferguson, N. M., Fraser, C., & Cauchemez, S.
- Affiliations
- Imperial College London (GB)
- University of Oxford (GB)
- Institut Pasteur (FR)
- Corresponding author
- Cori, Anne
- Venue
- American Journal of Epidemiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-09-15
- Volume
- 178
- Issue
- 9
- Pages
- 1505-1512
- ISSN
- 0002-9262 (ISSN-L)
- 1476-6256
- PMC
- PMC3816335
- OpenAlex
- W2097446414
- Cited by
- 1,530
- References
- 45
- Citations by year
- 2026: 94 · 2025: 141 · 2024: 161 · 2023: 199 · 2022: 268 · 2021: 328 · 2020: 262 · 2019: 21 · 2018: 16 · 2017: 16 · 2016: 16 · 2015: 3 · 2014: 4 · 2013: 1
- FWCI
- 8.33
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- American Journal of Epidemiology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Royal Society
- Imperial College London
- Medical Research Council (MR/K010174/1, G0800596)
- National Institute of General Medical Sciences
- Topics
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Physical Sciences › Mathematics › Applied Mathematics › Mathematical and Theoretical Epidemiology and Ecology Models
- Health Sciences › Medicine › Epidemiology › Data-Driven Disease Surveillance
- Keywords
- time-varying reproduction number, analytical estimation, transmission intensity, public health response
- MeSH terms
- Humans, Software, Time Factors, Virus Diseases, Models, Statistical, Incidence, Epidemics
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