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Estimating effective reproduction number using generation time versus serial interval, with application to covid-19 in the Greater Toronto Area, Canada

Authors
  • Knight, Jesse1, 2
  • Mishra, Sharmistha1, 2, 3, 4
  • 1 Institute of Medical Science, University of Toronto, Canada
  • 2 MAP Centre for Urban Health Solutions, Unity Health Toronto, Canada
  • 3 Division of Infectious Disease, Department of Medicine, University of Toronto, Canada
  • 4 Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Canada
Type
Published Article
Journal
Infectious Disease Modelling
Publisher
KeAi Publishing
Publication Date
Nov 01, 2020
Volume
5
Pages
889–896
Identifiers
DOI: 10.1016/j.idm.2020.10.009
PMID: 33163739
PMCID: PMC7604055
Source
PubMed Central
Keywords
License
Unknown

Abstract

background . The effective reproduction number R e ( t ) is a critical measure of epidemic potential. R e ( t ) can be calculated in near real time using an incidence time series and the generation time distribution: the time between infection events in an infector-infectee pair. In calculating R e ( t ), the generation time distribution is often approximated by the serial interval distribution: the time between symptom onset in an infector-infectee pair. However, while generation time must be positive by definition, serial interval can be negative if transmission can occur before symptoms, such as in covid-19 , rendering such an approximation improper in some contexts. methods . We developed a method to infer the generation time distribution from parametric definitions of the serial interval and incubation period distributions. We then compared estimates of R e ( t ) for covid-19 in the Greater Toronto Area of Canada using: negative-permitting versus non-negative serial interval distributions, versus the inferred generation time distribution. results . We estimated the generation time of covid-19 to be Gamma-distributed with mean 3.99 and standard deviation 2.96 days. Relative to the generation time distribution, non-negative serial interval distribution caused overestimation of R e ( t ) due to larger mean, while negative-permitting serial interval distribution caused underestimation of R e ( t ) due to larger variance. implications . Approximation of the generation time distribution of covid-19 with non-negative or negative-permitting serial interval distributions when calculating R e ( t ) may result in over or underestimation of transmission potential, respectively.

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