Pathogen Evolution

Prof Dr Sébastien Calvignac-Spencer

The Department of Pathogen Evolution studies both current and historical samples and uses them to make targeted predictions about the potential spread of important pathogens, thus providing important contributions to public health.

Our Research

Ecological interactions that underpin human life are highly dynamic, and changes in complex ecosystems can have far-reaching consequences on human health. Therefore, One Health also has a very strong evolutionary component. Over the last decades, evolutionary biology concepts have provided a major contribution towards unveiling the short- and long-term dynamics of pathogen emergence and spread. The importance of evolutionary approaches has become particularly evident during the COVID-19 pandemic. Both the initial emergence event and the later spread and evolution of SARS-CoV-2 have been investigated using evolutionary genomics – with the rise of variants of concern (VOC) being pointed out in the first place by observational data and inferential statistics.

From a One Health perspective, evolutionary approaches complement ecological approaches in multiple ways. Firstly, they allow reconstructing the course of major emergence events. Genomic variation can be used to trace back the origin of a pathogen, providing essential insights regarding the original ecosystems that should be scrutinized through ecological approaches in order to understand the circumstances that favored the pathogen’s spread or its transition from animals to humans. Secondly, studying the very distant past of host-virus associations using contemporary genomic variation and statistical inference can inform us on the relative frequencies of host jumps over the long-term, highlighting pathogen groups of higher concern and allowing us to identify processes of general scope. Finally, evolutionary approaches offer the possibility to identify the forces which have shaped the evolution of a pathogen at the molecular level. For example, they can point at sites, which have been subjected to positive selection in a pathogen genome and correlate those to relevant phenotypic changes, e.g. mutations of concern in the spike protein of SARS-CoV-2. In doing so, they offer predictive power as to what should be monitored closely at the genomic level and which genomic variation should be accounted for when designing therapeutics or prophylaxis. The Department Pathogen Evolution can thus make important contributions to public health.