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

Epidemics. 2019 Jun:27:12-18. doi: 10.1016/j.epidem.2018.12.002. Epub 2019 Jan 10.

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.

Keywords: Basic reproduction number; Generation interval; Infectious disease modeling.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Basic Reproduction Number
  • Disease Outbreaks / statistics & numerical data*
  • Hemorrhagic Fever, Ebola / epidemiology*
  • Humans
  • Incidence
  • Measles / epidemiology*
  • Rabies / epidemiology*
  • Time