Speaker
Description
Naming matters, especially when viruses evolve faster than our labels. Non-polio enteroviruses (NP-EVs) cause diseases ranging from mild infections to severe neurological illnesses in children. Yet their clade nomenclature often reflects chance sampling and outdated circulation patterns rather than current evolutionary understanding. Subjective naming systems complicate communication between researchers, clinicians, and public health authorities, especially when clades are associated with increased virulence or recombination.
To address the issue of inconsistent clade assignments, we developed an algorithmic nomenclature framework for NP-EVs. This framework replaces manual, non-scalable clade designation with reproducible, parameter-based phylogenetic criteria. The framework is designed to be transferable across enterovirus species, providing consistent clade definitions while remaining flexible to virus-specific evolutionary dynamics.
To ensure that this work goes beyond a purely conceptual nomenclature proposal, we embedded the framework directly into Nextclade, a practical, real-time viral surveillance tool. Originally developed for SARS-CoV-2, Nextclade offers quality control, phylogenetic placement, and clade assignment, all in one tool. We created the first Nextclade datasets for NP-EVs, focusing on four epidemiologically important viruses: Enterovirus D68, Enterovirus A71, Coxsackievirus A16, and Coxsackievirus A10. The new algorithmic nomenclature is provided alongside existing naming systems to enable direct comparison and gradual community adoption.
Building these datasets also revealed a lesser-discussed challenge. Many NP-EV reference sequences date back to the 1950s and they are poorly suited for modern phylogenetic inference, alignment, and mutation calling. Thus, we explored using inferred ancestral sequences as functional references to improve consistency and interpretability across analyses.
Our work emphasizes the importance of reproducible nomenclature, integrated analytical tools, and updated reference strategies. These elements are essential for conducting scalable evolutionary analyses and translating genomic data into real-time NP-EV surveillance.
| Expedited Notification | No thanks, I do not require Expedited Notification |
|---|
