Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates

TL;DR

This paper introduces Bayesian mixture models that incorporate phylogenetic data and infection time estimates to improve population-level source attribution of infectious diseases, especially for rapidly evolving viruses.

Contribution

The study develops a novel Bayesian mixture modeling approach combining evolutionary clock data and covariates for better transmission source inference.

Findings

Population-level source attribution improves with infection time data.

Phylogenetic data alone cannot reliably identify individual transmission sources.

Application to HIV data in Amsterdam demonstrates method's effectiveness.

Abstract

In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time passing since divergence of pathogen variants in individuals, which is problematic in viruses with high within-host evolutionary rates. This prompted us to consider possible transmission pairs in terms of phylogenetic data and additional estimates of time since infection derived from clinical biomarkers. We develop Bayesian mixture models with an evolutionary clock as signal component and additional mixed effects or covariate random functions describing the mixing weights to classify potential pairs into likely and unlikely transmission pairs. We demonstrate that although sources cannot be identified at the individual level with certainty, even with the additional data on time elapsed, inferences into the population-level sources of transmission are possible, and more accurate than using only phylogenetic data without time since infection estimates. We apply the approach to estimate age-specific sources of HIV infection in Amsterdam MSM transmission networks between 2010-2021. This study demonstrates that infection time estimates provide informative data to characterize transmission sources, and shows how phylogenetic source attribution can then be done with multi-dimensional mixture models.