Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

TL;DR

This paper introduces a phylodynamic method combining epidemiological modeling with viral phylogenetics to jointly estimate disease dynamics and evolutionary history from viral sequences, aiding outbreak control strategies.

Contribution

The authors develop the Birth-Death SIR (BDSIR) method, integrating a compartmental SIR model with phylogenetic analysis to infer epidemiological parameters and history simultaneously.

Findings

Estimated HIV-1 R0 ranged from 1.9 to 3.2.

HCV epidemic in Cruz del Eje started around 1906.

Detected decline in HIV epidemic growth in the late 1990s.

Abstract

The evolution of RNA viruses such as HIV, Hepatitis C and Influenza virus occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible-infected-removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our Birth-Death SIR method (BDSIR) to two viral data sets. First, five human immunodeficiency virus type 1 clusters sampled in the United Kingdom between 1999 and 2003 are analyzed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 90's. The analysis of a hepatitis C virus (HCV) genotype 2c data set shows that the local epidemic in the C\'ordoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880--1920. The estimated time of epidemic peak is around 1970.