The COVID-19 virus has spread across the globe with breathtaking speed. But all along, an international team of computational biologists has been close behind.
The researchers behind Nextstrain.org, which was co-created by scientists at Fred Hutchinson Cancer Research Center and University of Basel, are using genetic clues to track the virus’ spread and evolution in near real-time. Their work is helping countries and policymakers develop strategies to monitor and control outbreaks to save lives.
But as fast as the science — and the virus — are moving, the financial resources needed to expand that global sequencing work have lagged.
“The epidemic doesn’t stop and wait for money to come in,” said Dr. Emma Hodcroft, an epidemiologist at University of Basel and co-developer of Nextstrain.org. “But the way science works, it can be difficult if not impossible to take your existing research funds and use them for something new, no matter how important.”
Hodcroft said that labs with the equipment and expertise to perform whole-genome sequencing have reached out to the Nextstrain team, saying they want to contribute to this urgent effort — but they need funds for supplies.
That’s why Fred Hutch and Nextstrain.org are teaming up to raise $300,000 to bridge the gaps and expand the community of researchers sequencing COVID-19. The information gained from sequencing more samples of the virus won’t just strengthen Nextstrain, Hodcroft said; it will empower researchers everywhere to find creative ways to prevent the virus from spreading right now. And it will help scientists develop novel treatments over time.
“Making sure we have a global sequencing network is incredibly important,” Hodcroft said. “The more diverse samples we have, the better the picture of where the virus is, how it’s moving and how we can stop it.”
Hodcroft says the Nextstrain team is fortunate. Funding from Fred Hutch and the University of Basel has allowed them to develop the Nextstrain software over the last few years, so they could quickly pivot to track new viruses. On Jan. 12, as the first genetic sequences of the COVID-19 virus appeared out of China, they decided to shift their focus exclusively to the new coronavirus.
Today, the sun doesn’t set on the Nextstrain network: a small global team keeps crunching data 24/7. When Hodcroft and her colleagues in Basel, Switzerland, clock out, Dr. Trevor Bedford and Fred Hutch colleagues are at work in Seattle. When they sleep, Dr. James Hadfield in New Zealand takes over, and so on.
But their work depends on researchers worldwide. The genetic sequences they crunch are pulled from GISAID, an online repository where labs from all over the world post new genomic data.
While that has been a remarkable success story for open science and collaboration, not everyone who wants to contribute can. The breaking point for Hodcroft came in early March. She saw a Twitter thread by scientists she knew and respected who said they were ready to pitch in. They had samples from patients. They had the tools and technologies to sequence those samples.
But they didn’t have the funding to do it.
“I thought there must be a better way to do things,” Hodcroft said.
She and her colleagues partnered with Fred Hutch to launch a donation portal to support sequencing capacity in labs worldwide. Hodcroft plans to post an application form for researchers soon.
The Nextstrain team is eager to incorporate more data and more samples to build better maps of COVID-19’s movements.
“How it moved in the past is a good indication of how it will move in the future,” Hodcroft said. “As we start to lift social distancing measures, knowing those likely routes of transmission will help us monitor and respond if it flares back up. And it could also be relevant to future pandemics.”
Hodcroft says the work highlights the importance of supporting science. Just a few years ago, researchers struggled to get funding to study coronaviruses, she noted. They didn’t seem important or relevant.
“Imagine what we could have known if people had been studying coronaviruses and how they interact with the immune system,” she said. “We have to maintain funding for research on these viruses in between pandemics, because when they happen, we can’t do it fast enough.”
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