Investigating the early spread of the HIV epidemic

HIV jumped to humans multiple times through zoonotic events in Central and Western Africa, but all epidemic lineages emerged in the early 20th century. In a long-standing collaboration with Joao Sousa and Annemie Vandamme (KU Leuven) we used stochastic agent-based computer simulations to investigate how the transition from traditional tribal societies to colonial settlements created a permissive time window for the origin and initial spread of epidemic HIV strains and also how the introduction of drugs against bacterial sexually transmitted infections—which increase HIV transmission through genital ulcers—by the 1950’s contributed to closing this window. Our subsequent work developed this theory further, examining the enhanced heterosexual transmission of HIV due to various factors in the early 20th century. Key findings included the observation that the epicenters of HIV-2 emergence in Western Africa aligned with regions where male circumcision rates were lower compared to neighboring territories, and the identification of a peak of bacterial sexually transmitted infections coinciding with the early epicenter of pandemic HIV-1. We also summarized evidence on the dramatic impact of genital ulcers on HIV transmission.

After its initial spread in African epicenters, HIV-1 expanded to all continents, establishing a global phylogeographic pattern characterized by strong founder effects, where local epidemics arose from the expansion of a single viral lineage. We investigated the factors that hinder the mixing of similarly transmissible lineages and have contributed to the formation of this distinct phylogeographic pattern.

COVID-19 analyses

The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus. We contributed to a study quantifying the relative contribution of mobility restrictions, and that of behavioral changes that occurred already before the lockdowns, on the reduction of transmission during lockdowns in Western countries in early 2020. Additionally, we conducted a comprehensive literature review to provide a collection of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes.