Viral phylodynamics and the search for an ‘effective number of infections’

Author:

Frost Simon D. W.1,Volz Erik M.2

Affiliation:

1. Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK

2. Department of Epidemiology, University of Michigan – Ann Arbor, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA

Abstract

Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.

Publisher

The Royal Society

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology

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