VIBES: A Multi-Scale Modeling Approach Integrating Within-Host and Between-Hosts Dynamics in Epidemics

TL;DR

VIBES is a multi-scale modeling framework that combines within-host viral dynamics with population-level social contact networks to better understand and predict epidemic properties like transmission timing and the impact of interventions.

Contribution

This paper introduces VIBES, a novel multi-scale model integrating biological and social factors to analyze epidemic dynamics, specifically applied to SARS-CoV-2.

Findings

Shorter generation time with social contact modeling

Increased pre-symptomatic transmission due to social factors

Pathogen transmissibility influences epidemic timing metrics

Abstract

Infectious disease spread is a multi-scale process composed of within-host (biological) and between-host (social) drivers and disentangling them from each other is a central challenge in epidemiology. Here, we introduce VIBES, a multi-scale modeling framework that explicitly integrates viral dynamics based on patient-level data with population-level transmission on a data-driven network of social contacts. Using SARS-CoV-2 as a case study, we analyze three emergent epidemic properties, namely the generation time, serial interval, and pre-symptomatic transmission. First, we established a purely biological baseline, thus independent of the reproduction number (R), from the within-host model, estimating a generation time of 6.3 days for symptomatic individuals and 43.1% presymptomatic transmission. Then, using the full model incorporating social contacts, we found a shorter generation time (5.4 days at R=3.0) and an increase in pre-symptomatic transmission (52.8% at R=3.0), disentangling the impact of social drivers from a purely biological baseline. We further show that as pathogen transmissibility increases (R from 1.3 to 6), competition among infectious individuals shortens the generation time and serial interval by up to 21% and 13%, respectively. Conversely, a social intervention, like isolation, increases the proportion of pre-symptomatic transmission by about 30%. Our framework also estimates metrics that are challenging to obtain empirically, such as the generation time for asymptomatic individuals (5.6 days; 95%CI: 5.1-6.0 at R=1.3). Our findings establish multi-scale modeling as a powerful tool for mechanistically quantifying how pathogen biology and human social behavior shape epidemic dynamics as well as for assessing public health interventions.