Researchers Launch SPRTA to Revolutionize Virus Evolution Analysis

Researchers at the European Molecular Biology Laboratory (EMBL) and the Australian National University have introduced a groundbreaking tool called SPRTA (SPR-based Tree Assessment) aimed at enhancing the accuracy of phylogenetic trees in tracking virus evolution. This innovative method addresses the shortcomings of traditional techniques, particularly in the context of large-scale genomic data generated during pandemics.

Addressing the Challenges of Phylogenetic Analysis

With the onset of the COVID-19 pandemic, scientists sought to build evolutionary family trees to understand the origins and relationships among new strains of the virus. However, analyzing millions of genomes posed significant challenges, making it difficult to assess the reliability of these trees. The traditional method, known as Felsenstein’s bootstrap, has been the standard for nearly 40 years but proved inadequate for the vast datasets encountered during the pandemic.

SPRTA, detailed in a paper published in the journal Nature, offers a scalable and efficient solution. The tool enables researchers to evaluate the reliability of each branch within a phylogenetic tree more rapidly, which is essential for effective outbreak tracking and pandemic preparedness. According to Nick Goldman, Group Leader at EMBL-EBI, “SPRTA gives us a fast, reliable way to understand which parts of these massive trees we can trust.” This capacity for rapid analysis is crucial for responding to future health crises.

How SPRTA Enhances Phylogenetic Assessment

The traditional bootstrap method relies on repetitive analyses that can take considerable time, rendering it ineffective for the swift demands of pandemic response. In contrast, SPRTA employs a novel approach by analyzing the likelihood of a virus strain descending from a specific ancestor, while also identifying alternative evolutionary paths. The tool virtually rearranges branches of the phylogenetic tree and assesses how well each scenario fits the data, ultimately assigning a probability score for each connection.

This advancement not only accelerates the process of phylogenetic tree construction but also improves the quality of evolutionary analysis. As stated by Nicola De Maio, Senior Scientist at EMBL-EBI, “With SPRTA, we’re not just making phylogenetic tree-building faster, we’re making it smarter.” This tool empowers researchers to discern robust relationships from uncertain ones even when working with extensive genomic datasets.

In their research, the teams utilized over two million SARS-CoV-2 genomes to demonstrate SPRTA’s capabilities. The results revealed that the tool could effectively highlight reliable sections of phylogenetic trees, identify uncertain sample placements due to incomplete or noisy data, and uncover credible alternative origins for specific branches.

SPRTA is integrated into MAPLE, a tool designed for efficient construction of large phylogenetic trees, and is also accessible through IQ-TREE, one of the most widely adopted phylogenetic software packages. This integration ensures that SPRTA is open and available for researchers globally, enhancing efforts in outbreak tracking, genomic surveillance, and evolutionary studies.

This new methodology marks a significant step forward in the field of evolutionary biology and showcases the importance of adapting analytical tools to meet the challenges posed by large-scale health crises. As global health organizations prepare for future pandemics, tools like SPRTA will be essential for making informed decisions based on reliable data.

For more details, refer to the study by Nicola De Maio titled “Assessing phylogenetic confidence at pandemic scales,” published in Nature on November 5, 2025 (DOI: 10.1038/s41586-025-09567-x).