Inferring HIV Transmission Patterns from Viral Deep-Sequence Data via Latent Typed Point Processes

TL;DR

This paper introduces a Bayesian spatial Poisson process model that infers HIV transmission patterns from deep-sequencing data, capturing transmission flow and statuses without pre-classification, and demonstrating high-resolution insights in a Uganda case study.

Contribution

The paper presents a novel latent typed point process framework that jointly infers transmission statuses and flow patterns directly from continuous covariate data, improving computational efficiency and resolution.

Findings

Successfully captures age-related transmission structures.

Provides high-resolution insights into HIV transmission flow.

Demonstrates computational advantages over discretization methods.

Abstract

Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious disease transmission. To more fully utilize these rich data and account for the uncertainties in phylogenetic analysis outcomes, we propose a spatial Poisson process model to uncover HIV transmission flow patterns at the population level. We represent pairings of two individuals with viral sequence data as typed points, with coordinates representing covariates such as gender and age, and the point type representing the unobserved transmission statuses (linkage and direction). Points are associated with observed scores on the strength of evidence for each transmission status that are obtained through standard deep-sequenece phylogenetic analysis. Our method is able to jointly infer the latent transmission statuses for all pairings and the transmission flow surface on the source-recipient covariate space. In contrast to existing methods, our framework does not require pre-classification of the transmission statuses of data points, instead learning them probabilistically through a fully Bayesian inference scheme. By directly modeling continuous spatial processes with smooth densities, our method enjoys significant computational advantages compared to previous methods that rely on discretization of the covariate space. We demonstrate that our framework can capture age structures in HIV transmission at high resolution, and bring valuable insights in a case study on viral deep-sequencing data from Southern Uganda.