Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times

DOI10.1515/SAGMB-2019-0026zbMATH Open1461.92115arXiv1801.07660OpenAlexW3094457295WikidataQ100757577 ScholiaQ100757577MaRDI QIDQ830652FDOQ830652

Authors: Hesam Montazeri, Susan Little, Mozhgan Mozaffarilegha, Niko Beerenwinkel, Victor G. DeGruttola 

Publication date: 7 May 2021

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Abstract: Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to evaluate them. Several methods have been proposed to infer transmission chains from sequence data; however, existing methods do not generally reliably reconstruct transmission trees because genetic sequence data or inferred phylogenetic trees from such data are insufficient for accurate inference regarding transmission chains. In this paper, we demonstrate the lack of a one-to-one relationship between phylogenies and transmission trees, and also show that information regarding infection times together with genetic sequences permit accurate reconstruction of transmission trees. We propose a Bayesian inference method for this purpose and demonstrate that precision of inference regarding these transmission trees depends on precision of the estimated times of infection. We also illustrate the use of these methods to study features of epidemic dynamics, such as the relationship between characteristics of nodes and average number of outbound edges or inbound edges-- signifying possible transmission events from and to nodes. We study the performance of the proposed method in simulation experiments and demonstrate its superiority in comparison to an alternative method. We apply them to a transmission cluster in San Diego and investigate the impact of biological, behavioral, and demographic factors.

Full work available at URL: https://arxiv.org/abs/1801.07660

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zbMATH Keywords

Monte Carlo Markov chainHIVEbolaphylogenetic analysistransmission trees

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Epidemiology (92D30) Genetics and epigenetics (92D10)

Cites Work

• Testing and interval estimation for two-sample survival comparisons with small sample sizes and unequal censoring
• Multiple imputation: current perspectives

Cited In (1)

• Integrating genealogy and epidemiology: The ancestral infection and selection graph as a model for reconstructing host virus histories

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