Beyond Pango: The future of virus lineage classification

Keeping pace with ever-changing viruses is a challenge. This study unveils an automated system for classifying viral lineages based on genetics, offering a faster and more objective approach

Tracking and categorizing viruses like SARS-CoV-2 effectively is crucial for scientific research and public health initiatives. Traditionally, scientists used naming conventions based on geographical locations or specific characteristics to identify variants. However, given the rapid mutations in viruses, even a single mutation can create a new lineage, complicating classification. Additionally, the vast amount of genomic data associated with viruses like SARS-CoV-2 presents challenges for existing classification methods, which often involve manual curation and crowd-sourced proposals, leading to time-consuming processes and potential biases.

To overcome these challenges, we introduce Autolin, an automated system that utilizes genetic data to classify viral lineages. This approach proves to be efficient even with extensive datasets, offering a much quicker and more objective method compared to manual curation. The prospect of analyzing and classifying rapidly evolving viruses in real-time represents a significant advancement in our ability to monitor and comprehend these pathogens.

Autolin provides several benefits over current methods. Its speed allows researchers to keep up with the fast-paced evolution of viruses, while its reliance on genetic data helps eliminate biases inherent in manual curation or crowd-sourced approaches. This objectivity is crucial for ensuring clear and consistent communication regarding viral threats. Moreover, Autolin is highly scalable and can be applied to any virus, not just SARS-CoV-2, making it invaluable for addressing future public health challenges. Additionally, Autolin offers flexibility by allowing users to integrate information about the significance of specific mutations, leading to classifications that are more relevant from an epidemiological perspective.

Although Autolin is not without limitations and requires continuous updates as new data emerges, it represents a significant advancement in our ability to monitor and understand viruses. As genomic sequencing becomes more widespread globally, automated tools like Autolin will be indispensable for effectively managing future public health crises. With faster, more impartial, and scalable virus classification, researchers and public health officials will be better equipped to confront emerging pathogens and protect public health.


A framework for automated scalable designation of viral pathogen lineages from genomic data
Jakob McBroome, Adriano de Bernardi Schneider, Cornelius Roemer, Michael T. Wolfinger, Angie S. Hinrichs, Aine N. O’Toole, Chris Ruis, Yatish Turakhia, Andrew Rambaut, and Russell Corbett-Detig
Nature Microbiol. 9:550–560 (2024) | doi:10.1038/s41564-023-01587-5 | PDF