Software rapidly tracks viral variants with high accuracy

Varilly, Sabeti and Fry saw an opportunity to accelerate the process, while making data accessible and easier to interpret. The result is Delphy, a new platform for rapid, interactive phylogenetic analysis. In a paper published in Nature, the researchers report how they rebuilt state-of-the-art phylogenetic tree models to make them faster, more efficient, and scalable, while maintaining the models’ accuracy. Because Delphy runs entirely within a web browser, anyone with a laptop can perform these analyses without specialized training, software, or computing infrastructure.  

The researchers demonstrated that Delphy could analyze 100,000 viral DNA sequences and create phylogenetic trees 100 to 1,000 times faster than existing methods, reducing a months-long task into one that takes hours. To use the platform, users input sequence data, click “run,” and then explore the resulting tree by moving across lineages, mutations, and time to see patterns of viral evolution. This makes complex outbreak analysis more accessible to public health teams working in real time.

Delphy.bio is now freely available to anyone who needs to map virus sequence data to understand the course of an outbreak.

“Doing large scale sequencing of viruses is now the norm, but the old tools don’t work as well with such large numbers of sequences to analyze,” said Varilly, first author of the new paper and a computational research scientist in the Sabeti lab. “Public health officials have a lot to juggle, so the goal of Delphy is to simplify and speed up the process as much as possible while maintaining accuracy. This project was driven by the idea that genomic sequencing can be used earlier and help contain outbreaks faster.”

“The challenge was not just displaying an enormous amount of data, but making it useful,” said Ben Fry, principal at Fathom Information Design. “Delphy gives people a way to move through the tree, ask questions of it, and learn about the tree by interacting with it.”

“To respond to outbreaks quickly, we need to empower frontline scientists and public health teams everywhere to carry out the most advanced analyses themselves,” said Sabeti, senior author of the study. “We are tremendously excited that Delphy can bring this capability directly to the front lines, allowing people anywhere to generate rigorous insights quickly and use them to guide faster, more effective outbreak response.”

Viral family tree

Viruses are constantly evolving and mutating, and oftentimes the more a virus circulates, the more likely the virus will acquire new mutations that can impact its ability to spread and infect people. Analyzing viral genomes to build phylogenetic trees allows scientists and public health officials to reconstruct outbreak timelines, visualize how and when one strain mutated from the next, and estimate how quickly the virus is changing and spreading. These insights can inform public health interventions, and the faster experts can make these decisions based on accurate and reliable data, the more likely they can contain outbreaks quickly. 

Creating phylogenetic trees from thousands of viral DNA sequences using previous methods can take weeks, even months. Varilly and his team simplified and streamlined Delphy’s statistical calculations to speed up the analysis. 

To test Delphy’s accuracy, the team reproduced analyses from recent outbreaks and epidemics, including Ebola, Zika, SARS-CoV-2, mpox, and H5N1. They report two to three orders of magnitude increase in the speed of analysis, showing that Delphy could create a phylogenetic tree from a dataset of 100,000 virus DNA sequences within a day. Delphy can also identify key viral lineages and mutations and the timing of their emergence with the same accuracy as other commonly used methods.

Importantly, Delphy runs all calculations locally on the user’s side, so sequence data never leaves the user’s computer. Once Delphy.bio loads, a user can do their analysis without an Internet connection.

Varilly says he hopes that the public health community will adopt Delphy to help with outbreak response.  “It’s exciting to be at the forefront developing new solutions that hopefully are not far away from being utilized everywhere,” he said.