Research team wins top prize for paper on virus evolution

Research team wins top prize for paper on virus evolution

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February 26, 2026
A smiling man seated at a desk in an office with three computer monitors displaying scientific or molecular diagrams and text. The individual is wearing a checkered shirt and sits beside a keyboard, mouse, and laptop on a wooden desk with overhead cabinets.
Chun Wu, Ph.D., is an associate professor in the Departments of Chemistry & Biochemistry and Biological & Biomedical Sciences in the College of Science & Mathematics.

A Rowan University research team led by Chun Wu, Ph.D., has received the 2025 Zuckerkandl Prize for the year’s best paper published in the Journal of Molecular Evolution, a leading journal in the field. The award recognizes exceptional scholarship in understanding how DNA, RNA and proteins change over time.

Wu, an associate professor in the Departments of Chemistry & Biochemistry and Biological & Biomedical Sciences in the College of Science & Mathematics, collaborated with Ph.D. students Nicholas J. Paradis and Khushi Jain, who conducted extensive research in his lab.

Their May 2025 paper, “Substitution-Mutation Rate Ratio (c/µ) as Molecular Adaptation Test Beyond Ka/Ks: A SARS‑CoV‑2 Case Study,” challenges a long‑standing method used to study how viruses evolve. For decades, researchers have relied on an approach called Ka/Ks, which assumes certain types of genetic changes—known as synonymous mutations—have no impact on a virus, and solely focuses on how protein changes impact virus evolution.

Wu’s team demonstrated that this assumption is often incorrect. By analyzing SARS‑CoV‑2, the virus that causes COVID‑19, they showed that synonymous mutations can influence viral behavior and that the Ka/Ks method can misclassify important evolutionary changes. To address this, they developed a new metric to more accurately detect meaningful adaptations across the entire viral genome including the region that does not code proteins.

This new approach could improve scientists’ ability to track emerging variants, inform vaccine and drug development, and deepen understanding of how viruses evolve.

The awards committee determined the team’s paper “has the potential to stimulate the development of new tools for comparative genomic data analysis and reveal previously hidden patterns of adaptive evolution in non-coding genomic regions such as untranslated regions, pseudogenes, and introns.”

The Zuckerkandl Prize is named for Emile Zuckerkandl, a founding editor of the Journal of Molecular Evolution and a pioneer in molecular evolutionary biology.