title: Intrinsic and realized generation intervals in infectious-disease transmission.
abstract: The generation interval is the interval between the time when an individual is infected by an infector and the time when this infector was infected. Its distribution underpins estimates of the reproductive number and hence informs public health strategies. Empirical generation-interval distributions are often derived from contact-tracing data. But linking observed generation intervals to the underlying generation interval required for modelling purposes is surprisingly not straightforward, and misspecifications can lead to incorrect estimates of the reproductive number, with the potential to misguide interventions to stop or slow an epidemic. Here, we clarify the theoretical framework for three conceptually different generation-interval distributions: the 'intrinsic' one typically used in mathematical models and the 'forward' and 'backward' ones typically observed from contact-tracing data, looking, respectively, forward or backward in time. We explain how the relationship between these distributions changes as an epidemic progresses and discuss how empirical generation-interval data can be used to correctly inform mathematical models.
authors.affiliation: School of Computational Science and Engineering, McMaster University, Hamilton, Canada L8S 4L8 david.champredon@gmail.com.
authors.forename: David
authors.identifier: 0000-0002-7090-8757
authors.initials: D
authors.lastname: Champredon
authors.affiliation: Department of Biology, McMaster University, Hamilton, Canada L8S 4L8.
authors.forename: Jonathan
authors.identifier: 0000-0003-0506-4794
authors.initials: J
authors.lastname: Dushoff
mesh_terms: D003141:Communicable Diseases / Q000453:epidemiology / Q000635:transmission*; D016358:Contact Tracing; D004196:Disease Outbreaks; D004812:Epidemiologic Methods; D006801:Humans; D008954:Models, Biological
keywords: contact-tracing; epidemiological model; generation interval; reproductive number