A practical generation-interval-based approach to inferring the strength of epidemics from their speed

Epidemics
Sang Woo ParkJonathan Dushoff

Abstract

Infectious disease outbreaks are often characterized by the reproduction number R and exponential rate of growth r. R provides information about outbreak control and predicted final size, but estimating R is difficult, while r can often be estimated directly from incidence data. These quantities are linked by the generation interval - the time between when an individual is infected by an infector, and when that infector was infected. It is often infeasible to obtain the exact shape of a generation-interval distribution, and to understand how this shape affects estimates of R. We show that estimating generation interval mean and variance provides insight into the relationship between R and r. We use examples based on Ebola, rabies and measles to explore approximations based on gamma-distributed generation intervals, and find that use of these simple approximations are often sufficient to capture the r-R relationship and provide robust estimates of R.

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Citations

Sep 24, 2019·BMJ Global Health·Cyrus ShahparThomas R Frieden
Jun 24, 2020·Journal of the Royal Society, Interface·Sang Woo ParkJonathan Dushoff
Apr 27, 2019·Virus Evolution·Joshua S WeitzRachel J Whitaker
Dec 11, 2020·PLoS Computational Biology·Katelyn M GosticSarah Cobey
Dec 29, 2020·Proceedings of the National Academy of Sciences of the United States of America·Sang Woo ParkJonathan Dushoff
Dec 2, 2020·Transboundary and Emerging Diseases·AshleyG JordanBrendanD Cowled
Nov 21, 2020·Annals of Surgery·Mohammad HusseinJuan Duchesne
Mar 25, 2021·Proceedings. Biological Sciences·Jonathan Dushoff, Sang Woo Park
May 26, 2021·Scientific Reports·G B AlmeidaC M C B Fortaleza
Jul 18, 2020·Journal of the American Medical Directors Association·Gil CaspiOren Caspi
Aug 15, 2021·Journal of Theoretical Biology·Shi ZhaoMaggie H Wang
Sep 26, 2021·Proceedings of the National Academy of Sciences of the United States of America·Odo DiekmannMartin C J Bootsma
Nov 23, 2021·Journal of Biological Dynamics·Milan Batista

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