Genetic analysis of the coronavirus gives scientists clues about how it’s spreading
As the coronavirus spreads around the globe, it has mutated in tiny, subtle ways. Those mutations aren’t cause for concern, and so far, don’t appear to be making the virus any more or less dangerous. But scientists can use those slight changes to track the virus from person to person, and location to location.
“If we identify a new outbreak cluster in one state, and there’s a question of whether it’s related to a previous cluster or not, the small mutational changes can help you figure out if they’re connected,” says Patrick Boyle, a synthetic biologist at Ginkgo Bioworks.
The coronavirus is made up of around 29,000 building blocks of genetic material called nucleotides. Like other biotechnology companies and labs, Ginkgo has the technology to take a sample of the virus and read out the full sequence of those nucleotides. For the most part, the sequence will be the same in each sample. But the virus makes copies of itself within a human host, and sometimes, it can make mistakes — switching one or two nucleotides out for another. The version of the virus with those changes can then be passed on when that person infects someone else.
Ginkgo is repurposing its systems, which normally don’t sequence viruses, to analyze as many samples of the coronavirus as possible. The goal is to help build out the maps that show how the virus jumped from one person to the next. They’re hoping to scale up to be able to publish the full genetic sequence of 10,000 virus samples a day.
This is awesome. I know groups that currently have samples in need of sequencing. I’ll let them know about @Ginkgo‘s offer.
— Trevor Bedford (@trvrb) March 24, 2020
Despite the skyrocketing numbers of COVID-19 cases in the US, only a limited number of virus samples collected in the country have been sequenced in full. Scientists have more sequences from Washington state than other places. Consequently, they know more about the trajectory of the outbreak in Washington than they know about outbreaks in other states.
Some of that genetic data is how Trevor Bedford, a virologist at the Fred Hutchinson Cancer Research Center, was able to link a case of COVID-19 diagnosed on February 27 in Washington to a case that was diagnosed in late January in the state — indicating that the virus had been circulating locally, and undetected, for that entire time. It also showed that the January case sparked a cluster of illnesses that spread through the community.
Other states are starting to do the same kind of detective work, using genetic sequences to help clarify their outbreaks. An analysis of nine virus samples collected in Connecticut showed that the some were related to viruses found in Washington state, which suggests that the coronavirus was spreading domestically, not being repeatedly brought in from other countries. The analysis has not yet been peer-reviewed or published. Other preliminary research examined virus samples from northern California, and found that the coronavirus was introduced to the area at multiple points.
One challenge in expanding the number of virus sequences available, Boyle says, is obtaining patient samples to analyze. Labs in the US and other countries that are running tests for the virus receive hundreds or thousands of patient samples each day. But the focus of those labs is checking a sample to see if the coronavirus is there — and the patient has COVID-19 — or if it isn’t. The emphasis on testing and diagnosing patients is critical to track the pandemic, Boyle says.
“The problem is, it only gives you a positive or negative answer,” he says. Tests don’t provide any extra information about the particular virus in each patient. Ginkgo plans to partner with testing labs, so that they can take a closer look at the virus in a patient sample after the testing is done. Other labs and groups worldwide are embarking on similar projects: a research consortium in the United Kingdom, for example, has over $20 million in funding to sequence samples. Boyle says that Gingko is coordinating with some other labs interested in this work.
They’re also making sure that they can access the chemicals and other supplies they need to run the genetic analysis, Boyle says. “We want to make sure that our supply stream is not competing with the supply stream that keeps the testing running.”
Expanding the number of coronavirus sequences available will give scientists a picture of the outbreak, in the US and around the world. Along with testing, it’s one way scientists can keep track of the virus’s movements — and help to rein it in.
As the coronavirus spreads around the globe, it has mutated in tiny, subtle ways. Those mutations aren’t cause for concern, and so far, don’t appear to be making the virus any more or less dangerous. But scientists can use those slight changes to track the virus from person to person,…
