Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study
Author(s)
Ratmann, O
Donker, G
Meijer, A
Fraser, C
Koelle, K
Type
Journal Article
Abstract
A key priority in infectious disease research is to understand the ecological and evolutionary drivers of viral diseases from data on disease incidence as well as viral genetic and antigenic variation. We propose using a simulation-based, Bayesian method known as Approximate Bayesian Computation (ABC) to fit and assess phylodynamic models that simulate pathogen evolution and ecology against summaries of these data. We illustrate the versatility of the method by analyzing two spatial models describing the phylodynamics of interpandemic human influenza virus subtype A(H3N2). The first model captures antigenic drift phenomenologically with continuously waning immunity, and the second epochal evolution model describes the replacement of major, relatively long-lived antigenic clusters. Combining features of long-term surveillance data from the Netherlands with features of influenza A (H3N2) hemagglutinin gene sequences sampled in northern Europe, key phylodynamic parameters can be estimated with ABC. Goodness-of-fit analyses reveal that the irregularity in interannual incidence and H3N2's ladder-like hemagglutinin phylogeny are quantitatively only reproduced under the epochal evolution model within a spatial context. However, the concomitant incidence dynamics result in a very large reproductive number and are not consistent with empirical estimates of H3N2's population level attack rate. These results demonstrate that the interactions between the evolutionary and ecological processes impose multiple quantitative constraints on the phylodynamic trajectories of influenza A(H3N2), so that sequence and surveillance data can be used synergistically. ABC, one of several data synthesis approaches, can easily interface a broad class of phylodynamic models with various types of data but requires careful calibration of the summaries and tolerance parameters.
Date Issued
2012-12-27
Date Acceptance
2012-10-19
Citation
PLoS Computational Biology, 2012, 8 (12)
ISSN
1553-7358
Publisher
Public Library of Science
Journal / Book Title
PLoS Computational Biology
Volume
8
Issue
12
Copyright Statement
© 2012 Ratmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
License URL
Sponsor
Medical Research Council (MRC)
Medical Research Council (MRC)
Medical Research Council (MRC)
Grant Number
G0600719B
G0800596
MR/K010174/1B
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Mathematical & Computational Biology
Biochemistry & Molecular Biology
BIOCHEMICAL RESEARCH METHODS
MATHEMATICAL & COMPUTATIONAL BIOLOGY
EVOLUTIONARY DYNAMICS
A H3N2
POPULATION-DYNAMICS
INFECTIOUS-DISEASE
EPOCHAL EVOLUTION
IMPACT
VIRUS
EPIDEMIOLOGY
DETERMINANTS
TRANSMISSION
Publication Status
Published
Article Number
e1002835