With new cases and clusters of the Covid-19 illness in the news every day, along with canceled events, closed workplaces, and shortages of hand sanitizer, it can feel like we’re already losing the fight against this outbreak. But in some ways, scientists are better equipped than ever before to follow and understand the new virus.
“We’re really at a very exciting time right now,” says Emma Hodcroft, a molecular epidemiologist at the University of Basel in Switzerland. Unlike traditional epidemiologists, who monitor when and where sick patients show up, molecular epidemiologists can track disease by monitoring the genes in the virus itself.
Hodcroft is part of the team behind Nextstrain, an open, online platform that detects how diseases are evolving in real time. The team has worked on viruses including influenza, Zika, and Ebola. In recent months, they’ve pivoted to studying the new coronavirus that causes Covid-19.
These scientists rely on the fact that viruses, like any living thing, pick up random mutations in their genes — sometimes as simple as a change in one letter of the genetic code — as they proliferate over generations. The new coronavirus carries its genetic code in RNA rather than DNA as humans and most other organisms do. RNA viruses mutate at an especially high rate, which makes them nimble at evolving and adapting. But that also helps scientific detectives track them.
From a swab of a Covid-19 patient’s nose, scientists can quickly sequence the entire 30,000-letter genome of the virus infecting that patient, according to Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Center in Seattle and one of Nexstrain’s developers. “We can use these sequences to reconstruct which infection is connected to which infection,” Bedford wrote in a blog post. By building a family tree of viruses, scientists can deduce what the disease has been doing behind the scenes.
For example, the first known Covid-19 patient in this country was a traveler who returned to Washington State from Wuhan, China, in mid-January. Tests for the virus weren’t widely available then. But at the end of February, scientists with the Seattle Flu Study began looking for the coronavirus in samples from people who’d been tested for influenza. They soon found it in a high school student who hadn’t been to China.
The genes of the student’s virus were nearly identical to the genes in the virus of the first Washington patient, with a few new mutations. That suggested the student’s infection was a direct descendant — like a viral grandchild — of that first patient’s. The most likely explanation, Bedford writes, is that the coronavirus had been quietly circulating in the Seattle area for the intervening five weeks and infecting hundreds of people.
Understanding how the disease is moving can help public health officials fight it strategically. For example, the genes of viruses in several other countries match samples from Italy, suggesting travelers to Italy are bringing the virus back home. Hodcroft says that’s true of most cases in Switzerland so far. It means the disease might be contained in Switzerland by isolating those people and their close contacts. But in Seattle, if the virus has been spreading in secret, it makes sense for the whole population to take preventive steps like avoiding large gatherings.
Recent technological advances have made this kind of rapid detective work possible. High-quality genetic sequencing has gotten faster, cheaper, and more readily available in recent years. Computing power has increased, too.
The other critical development, Hodcroft says, is not a technological advance but a cultural one. Instead of saving their data for future peer-reviewed publications, scientists are now freely sharing information with each other. Researchers worldwide are posting coronavirus genome sequences to GISAID, an open-access platform created for influenza. On a forum called Virological, scientists are sharing and discussing their own analyses of coronavirus genetic data. Researchers at Johns Hopkins University are pooling up-to-the-minute case numbers at a freely available online dashboard.
Hodcroft says this level of data sharing is like nothing that’s happened before. “We have never had, in any kind of outbreak, so much information at such a relatively early stage.” And that puts us humans in a unique position against our latest viral foe, she says. “We really have an unprecedented ability to harness all of this and use it in ways that we couldn’t have imagined a few years ago.”
Elizabeth Preston is a science writer in the Boston area.