Experimental Evolution: New JKU Method Explores the Dynamics of Virus Mutations

JKU researchers have created a new method to better understand evolutionary dynamics.

Marta Pelizzola; Credit: privat
Marta Pelizzola; Credit: privat

Evolution - or more precisely, coronavirus mutations - is currently keeping the world on the edge of its seat. Understanding the mutation process dynamics will be key to keeping this pandemic, as well as keep any future pandemics at bay. Researchers at Johannes Kepler University Linz are proposing a new method to do just that.

The HIV virus, rather than the coronavirus, was the starting point. Prof. Andreas Futschik (Department of Data Analysis and Econometrics) explains: "This is because the HIV virus mutates much faster than the coronavirus." Together with Italian scientist Marta Pelizzola and colleagues in Göttingen (Germany) and Berkeley (USA), he has developed a new methodology at the JKU to reconstruct so-called haplotypes and their frequencies from sequenced genome data. Haplotypes are genetic patterns found on one and the same chromosome.

While it may sound complicated, in principle it is a statistical method designed to identify frequent mutation patterns and estimate their temporal and spatial dynamics, making it possible to trace developmental processes in a precise way. How does it work? Prof, Futschik added: "As HIV mutates so quickly, patients often have different mutations in their bodies." The researchers took samples at different points in time, enabling them to trace virus development in the bodies of those affected in a precise manner. "The method not only works in regard to viruses, but also for all rapidly reproducing organisms. This means the evolutionary process is more easily traceable."

Although this is base-knowledge research, specific applications can already be taken into consideration. For example, one potential application would be to study sewer samples in an effort to identify emerging viral strains. Prof. Futschik says that more importantly, "… the reconstructed haplotypes could help us better understand evolutionary dynamics. These could be infection dynamics caused by bacteria and viruses, but also – when it comes to higher organisms - adaptation processes to the environment."

The new method has already been tested on fruit flies, nematodes, and even mice. The researchers' paper titled "Multiple Haplotype Reconstruction from Allele Frequency Data" was recently published in the renowned journal Nature Computational Science.