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Project

Molecular epidemiology of HIV and hepaciviruses

Combating pathogen spread and its associated disease burden is a tremendous challenge requiring sustained research effort and decided public health measures. The availability of genomic data provides a major asset in characterizing viral emergence and the interplay between viral evolution and host ecological dynamics, including the determination of the key factors for interspecies transmissions and successful epidemic spread in the human population.

In this project, we will investigate the evolutionary origins and epidemic emergence of two important human viruses: hepatitis C virus (HCV) and human immunodeficiency virus (HIV). While the zoonotic origins of HIV-1 have been clearly established, an animal population that might have transmitted HCV to humans has not been identified yet. Inspired by recent findings of divergent hepaciviruses in rodents, we will perform a comprehensive investigation of hepacivirus diversity in various African rodent species to provide insights into the evolutionary origins of HCV. To this purpose, we will generate sequence data from a large set of African rodent samples and perform in-depth phylogenetic and phylogeographic analyses. 

While phylogenetic studies have contributed to our understanding of early epidemic onset in the Democratic Republic of Congo (DRC), historical estimates remain inherently uncertain. Motivated by the demonstrated possibility to inform such analyses with HIV-1 sequences recovered from archival specimens that date back decades ago (and thus are equivalent to molecular fossils), we propose as a second part of this project to scrutinize a unique, comprehensive library of archival samples from the putative heart of the pandemic in Central Africa we have collected over the years. We will complement these efforts by extending state-of-the-art phylogenetic reconstruction methodology to further refine time-estimates for the origin of HIV-1 group M, and to reconstruct the dynamics in viral population size and spatial expansion over time. The project will integrate experimental and computational work, and for both objectives, we build on existing collaborations with world leaders in the respective fields.

Date:1 Jun 2015 →  22 Jan 2021
Keywords:HIV-1, hepacivirus, molecular epidemiology
Disciplines:Microbiology, Systems biology, Laboratory medicine
Project type:PhD project