Researchers Launch SPRTA to Revolutionize Virus Evolution Tracking

Researchers at the European Molecular Biology Laboratory (EMBL) and the Australian National University have introduced a groundbreaking tool called SPRTA (SPR-based Tree Assessment) to improve the evaluation of phylogenetic trees during viral outbreaks. This innovative method addresses the challenges posed by the vast amounts of genomic data generated during pandemics, enabling scientists to better understand virus evolution and transmission.

Enhancing Phylogenetic Analysis

Phylogenetic trees are essential for tracking the evolution and spread of viruses, such as SARS-CoV-2, which caused the global COVID-19 pandemic. Traditional methods, particularly the bootstrap method developed by Felsenstein in 1985, have long been used to measure confidence in these trees. However, this approach is inefficient when dealing with the millions of genomes sequenced during a pandemic.

The newly published paper in the journal Nature outlines how SPRTA provides a scalable, efficient alternative for evaluating the reliability of phylogenetic trees. It allows researchers to quickly identify the most trustworthy aspects of evolutionary relationships, significantly improving decision-making during outbreaks.

“For nearly 40 years, scientists have relied on the same method to measure confidence in evolutionary trees,” said Nick Goldman, Group Leader at EMBL-EBI. “But when faced with the scale of data we saw during the COVID-19 pandemic, the old method simply couldn’t cope.”

Innovative Approach to Reliability

Unlike traditional techniques that focus solely on the strength of sample groups, SPRTA evaluates the probability of a virus strain descending from a specific ancestor while considering alternative evolutionary paths. The tool tests various scenarios by virtually rearranging tree branches and assessing how well each configuration fits the available data.

SPRTA then assigns probability scores, providing a clear view of which relationships among strains are solid and where caution is warranted. “With SPRTA, we’re not just making phylogenetic tree-building faster, we’re making it smarter,” commented Nicola De Maio, Senior Scientist at EMBL-EBI.

This method has proven effective with over two million SARS-CoV-2 genomes, allowing researchers to highlight reliable areas within the phylogenetic tree, identify uncertain placements due to incomplete data, and propose credible alternative origins for certain branches.

SPRTA is integrated into MAPLE, a tool developed by EMBL-EBI for efficiently constructing large phylogenetic trees. It is also available in IQ-TREE, one of the most widely used software packages in phylogenetic analysis. This accessibility ensures that researchers worldwide can utilize SPRTA for outbreak tracking, genomic surveillance, and evolutionary studies.

In conclusion, the development of SPRTA represents a significant advancement in the ability to assess phylogenetic confidence at a pandemic scale. This tool not only enhances the speed and reliability of evolutionary analysis but also equips scientists with the necessary resources to respond effectively to future health crises.