Nextstrain virus-tracking platform moves into new phase

Nextstrain (originally Nextflu) was co-created in 2015 by genomic epidemiologist Trevor Bedford, PhD, now an affiliate investigator at Fred Hutch, and University of Basel computational biologist Richard Neher, PhD.

“Viruses mutate as they transmit between people. By reconstructing viral family trees, we can understand something about that transmission process,” McCrone said. “It used to be that in order to stay current, scientists had to either run their own analyses or read papers as they came out — but scientific publication is much slower than virus transmission. Nextstrain revolutionized that process by making up-to-date analyses widely available on the web.”

Now, Nextstrain’s core team monitors the evolution and spread of 22 pathogens, including influenza, SARS-CoV-2, Ebola, hantavirus and tuberculosis. The platform enables academic and public health research groups to share analyses and makes genomic epidemiology more accessible, particularly in areas with fewer resources.

“JT very much has the experience for this role,” said Bedford, who is a scientific advisor on the new award. “He has a lot of experience in these large datasets on both the technical side and application side. He’ll do an excellent job.”

What’s next for Nextstrain?

Over the past decade, “there’s been continual change towards more public health capacity and more local capacity, and less reliance on bespoke academic collaborators,” Bedford said. The Nextstrain platform now supports routine, automated surveillance. McCrone will lead efforts to further improve the ability of users, particularly those in public health, who may not have training in genomic epidemiology, bioinformatics or coding to track the evolution of local and global outbreaks.

The new Gates Foundation funding will support four primary goals:

• Enhance user-driven analysis and sharing: The Nextstrain team will introduce simple, ready-to-use workflows and allow users to customize analyses without resorting to complex coding. To better support global users, Nextstrain will expand language options for documentation and enable offline use.
  
  
• Strengthen Pathogen Genomic Initiative surveillance networks: To strengthen genomic surveillance in Africa and Asia, the Nextstrain team will provide training to build local expertise and collaborate with researchers on the ground.
  
  
• Scale to large, complex genomic datasets: Nextstrain will adapt its analytical methods and visualization techniques to handle larger and more complex genomic datasets.
  
  
• Evaluate large language model (LLM) interpretations of outputs: To see if AI can give non-expert users a boost, the team will assess how well LLMs interpret Nextstrain outputs and develop guidance on how to effectively use AI for genomic data analysis.

McCrone brings expertise in bioinformatics and fast-evolving viruses

McCrone, who joined Fred Hutch in 2023, is a microbiologist and immunologist who studies rapidly mutating viruses.

“A lot of research looks at how viruses evolve and transmit at the country level, city level, global level,” McCrone said. “We're interested in how viral diversity arises within individuals and at the moments when the virus is transmitted. Since coming to Fred Hutch I have tried to straddle those two realms of scale. The goal is to create models that link what's going on in individuals with what we're seeing at the population level.”

His multidisciplinary approach leverages large datasets to uncover how processes within infected hosts and across continents shape pathogen diversity and impact human health. The viruses he and his team have investigated include SARS-CoV-2, influenza and Ebola.  McCrone also worked closely with Nextstrain scientists during the COVID-19 pandemic.

“It’s been great having JT as a sibling lab,” Bedford said. “He’s already very involved with Nextstrain, so this transition is quite natural.”