Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees

DOI10.1214/17-STS637zbMATH Open1407.62402arXiv1609.09051MaRDI QIDQ667682FDOQ667682

Caroline Colijn, Yuanwei Xu, Diepreye Ayabina, Michelle Kendall, James Stimson

Publication date: 1 March 2019

Published in: Statistical Science (Search for Journal in Brave)

Abstract: Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data from pathogens. The logic behind such approaches is that isolates that are nearly genetically identical are more likely to have been recently transmitted than those that are very different. A number of methods have been developed to perform this inference. However, testing their convergence, examining posterior sets of transmission trees and comparing methods' performance are challenged by the fact that the object of inference - the transmission tree - is a complicated discrete structure. We introduce a metric on transmission trees to quantify distances between them. The metric can accommodate trees with unsampled individuals, and highlights differences in the source case and in the number of infections per infector. We illustrate its performance on simple simulated scenarios and on posterior transmission trees from a TB outbreak. We find that the metric reveals where the posterior is sensitive to the priors, and where collections of trees are composed of distinct clusters. We use the metric to define median trees summarising these clusters. Quantitative tools to compare transmission trees to each other will be required for assessing MCMC convergence, exploring posterior trees and benchmarking diverse methods as this field continues to mature.

Full work available at URL: https://arxiv.org/abs/1609.09051

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zbMATH Keywords

Bayesian inferencemodellingepidemiologygenomicsinfectious diseases

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Epidemiology (92D30)

Cites Work

• Geometry of the space of phylogenetic trees
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• Reconstructing transmission trees for communicable diseases using densely sampled genetic data
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Cited In (6)

• A statistical model for genetic mapping of viral infection by integrating epidemiological behavior
• Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times
• Design and analysis of infectious disease studies. Abstracts from the workshop held February 18--24, 2018
• Integrating genealogy and epidemiology: The ancestral infection and selection graph as a model for reconstructing host virus histories
• Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data
• Tajima's D and Site-Specific Nucleotide Frequency in a Population during an Infectious Disease Outbreak

Uses Software

• BEAST

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