Researchers Unveil SPRTA Tool to Enhance Virus Evolution Analysis

Researchers at the **European Molecular Biology Laboratory** (EMBL) and the **Australian National University** have developed a groundbreaking tool called **SPRTA** (SPR-based Tree Assessment) to improve the analysis of viral evolution. Launched on **November 5, 2025**, SPRTA addresses the challenges faced during the COVID-19 pandemic when scientists struggled to accurately assess the reliability of phylogenetic trees due to the overwhelming number of viral genomes.

Phylogenetic trees are essential for understanding the relationships between virus strains and tracking their evolution. Traditional methods, such as **Felsenstein’s bootstrap**, have been the standard for nearly four decades. However, these approaches proved inadequate when analyzing millions of genomes, as they require extensive computational time and resources.

Revolutionizing Phylogenetic Analysis

The new tool, detailed in a paper published in the journal **Nature**, offers a scalable and efficient way to evaluate the confidence of each branch in a phylogenetic tree. SPRTA allows researchers to quickly identify which parts of the tree are reliable while also flagging areas of uncertainty. This capability is crucial during outbreaks, as it informs public health decisions and enhances pandemic preparedness.

Nick Goldman, Group Leader at EMBL-EBI, stated, “For nearly 40 years, scientists have relied on the same method to measure confidence in evolutionary trees, but when faced with the scale of data we saw during the COVID-19 pandemic, the old method simply couldn’t cope.” He emphasized that SPRTA provides a fast, reliable way to understand which aspects of the phylogenetic trees can be trusted.

SPRTA operates by analyzing the likelihood that a virus strain descends from a particular ancestor. It tests numerous potential scenarios by virtually rearranging the tree’s branches and evaluating how well each configuration fits the data, ultimately assigning a probability score for each connection.

Enhancing Pandemic Preparedness

Utilizing data from over **two million SARS-CoV-2 genomes**, SPRTA has demonstrated remarkable capabilities. It can highlight reliable sections of phylogenetic trees, identify uncertain sample placements due to incomplete data, and reveal credible alternative origins for specific branches.

This innovative tool is integrated into **MAPLE**, a platform developed at EMBL-EBI for building large phylogenetic trees efficiently. Furthermore, SPRTA is available in **IQ-TREE**, one of the most widely adopted phylogenetic software packages. By making SPRTA accessible through established tools, the research community worldwide can leverage its capabilities for outbreak tracking, genomic surveillance, and evolutionary studies.

Nicola De Maio, Senior Scientist at EMBL-EBI, noted, “With SPRTA, we’re not just making phylogenetic tree-building faster; we’re making it smarter.” This development represents a significant step forward in the field of evolutionary biology, providing researchers with the means to analyze large datasets effectively and respond to future pandemics with greater agility.

For more detailed findings, refer to the article by Nicola De Maio, “Assessing phylogenetic confidence at pandemic scales,” published in **Nature**. The study can be accessed via DOI: **10.1038/s41586-025-09567-x**.