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Crowdsourcing against coronavirus: Seattle biologists work on DIY test kit

With the lack of accessible testing still a hurdle in fighting the deadly virus, a data scientist is co-leading an effort to increase availability.

Zach Mueller, cofounder of SoundBioLab in Seattle, is a leader in a community effort to produce cheap, accessible coronavirus tests. (Dorothy Edwards/Crosscut)

Zach Mueller, co-founder of SoundBioLab in Seattle, is a leader in a community effort to produce cheap, accessible coronavirus tests. (Dorothy Edwards/Crosscut)

Since Washington state became the U.S. epicenter of a COVID-19 outbreak on Jan. 21, the lack of accessible viral testing kits has loomed as a major hurdle in curbing a disease responsible for infecting over 94,000 people globally and killing roughly 3,000. Eleven of those deaths have been in the Seattle area. But only the Centers for Disease Control and Prevention was allowed to perform tests early on, and the initial batch of tests distributed to states didn’t work

It’s only been in the past few days that some state and academic labs have received a green light to provide testing, and there’s still broad confusion over who can get tested, and where. 

“I'm hearing from families who are unable to get tested and, therefore, they don't know whether to stay home with their family or go to work,” Sen. Patty Murray, D-Washington, said Wednesday. “Unless we know how many [people] are impacted, and how this is spreading, we can't make those critical decisions for families and communities and businesses.”

The Washington State Department of Health says that as of March 4, the state was testing about 100 people per day. "We recognize the need to increase our ability to test people in WA state, due to the increase in community spread," a representative shared via Twitter. "We’re bringing other partners online to help," like the University of Washington, which newly has the capacity to test 1,000 samples per day

In the midst of concern over the apparent lack of rapid, accessible testing, some Seattleites are exploring ways to empower their neighbors to take health into their own hands. DIY biologists are helping to develop an internationally crowdsourced coronavirus test that would be produced by professional labs or even used by people with basic lab knowledge.

If they are successful, it could help the fight to contain Washington’s outbreak by making testing more available.

“From what I’ve seen, expanding the capabilities of detecting where it is will help us better understand who to quarantine at the right time and all of that sort of thing," says Zach Mueller, a software developer and co-founder of Seattle’s only community biology lab, SoundBio. "I think it’ll help us have a much better understanding of how it’s spreading … assuming it works of course.”

“It’s clear we're not nearly up to speed on [testing],” says Dr. Peter Hotez, a professor and dean of the National School of Tropical Medicine at Baylor College of Medicine. “I think unfortunately for Seattle's case, it's been an important case study in what could go wrong and what we need to do to fix this and our U.S. health care system."

Making coronavirus testing a team sport

Mueller is the co-leader of a new initiative started on Sunday to begin researching ways a crowdsourced test might come about. Biologist Dr. Thomas Landrain, who started France’s first community biology lab La Paillasse, also leads the international effort. Community biology labs function as resource and training hubs where people interested in do-it-yourself biology can safely gain lab skills and experience with common tools and equipment. 

“[The DIY biology] community has probably one mission today with regard to the coronavirus, [and] it's to produce an accessible alternative [test] that’s open source, because it needs to be easily shareable anywhere in the world … and as simple as possible, so that it only needs one person, who's not necessarily an expert, to perform the test,” says Landrain via video chat.

All of this is very much inchoate and rapidly evolving, with a lot left to clarify — from the exact test they’d use, to how’d they’d ensure test safety, to exactly who’s involved and how. But their intention is distinct: They’re driven by concerns over testing accessibility in their home countries of the U.S. and France, as well as worldwide. 

Landrain says it’s hard to get testing in France, “where we have a very modern health care system,” and “at some point you just realize, OK, what happens in Africa? What happens in Iran? ... The idea is, if it's not only the affordability but just the availability of these tests that is in question, can we design one that could be done in a nonoptimal environment, where you don't have a very good health care system?”

In addition to solving an urgent problem, Mueller says he hopes to prove that community-driven processes can develop these tests quickly and safely. “In the future, we'll probably have similar things happen. And so having something we can learn from and build stuff upon for future iterations [would] be great,” he says. 

The goal of the project, Mueller says, isn’t necessarily to equip people to safely test themselves, although that is a possible outcome. More important, he says, is developing an open-source protocol that people in appropriately certified labs around the world can use to easily produce test kits for their communities. 

Likely outcomes include a test that still needs to be produced by a commercial or institutional lab with more professional resources, he says, but their open-source test design would allow scientists to avoid dealing with patents that may be inherent in commercially designed tests. Mueller says commercial labs often have intellectual property rights to certain procedures and mixtures of reagents, and even if they don’t have patents, “they could just not share how it was developed and what the final mix of ingredients were.” 

“We can say, ‘Hey, you can produce this for your local community. Just start pumping these out; here’s the process and procedure and how to do [quality assurance]’ and all these things to ensure they’re able to produce more of the detection kits,” Mueller says. “The test could still need a medical professional to help administer it.” 

Another potential outcome, though, is developing a simple test people can use themselves. “It could potentially be like a set of simple instructions that theoretically, almost anybody could follow,” Mueller says.

Regardless, Mueller and Landrain are intent on finding ways to make the protocol cheap and accessible. The idea is not, Landrain says, to make a test that just anyone can perform on others, because that might spread disease and “because that would be a drama,” he says.

“The intent of this project is not to actually run tests on actual viral RNA in our labs. We’ll partner with professional labs… if we get to that stage,” Mueller says. 

Mueller and Landrain are recruiting people from around the world to join their project on Landrain’s collaborative online platform, Just One Giant Lab (JOGL). Landrain says community labs, which often have only a few dozen participants each, may not have the knowledge or bandwidth to develop and scale bigger projects with extra complexity. Combined, they have a better chance. 

“JOGL is a good platform for connecting more people,” Mueller says. “We could do it in a more ad hoc manner of just finding people randomly on the internet, and that’s what a lot of community projects that happen internationally have done. It starts up in one community lab first and then over time they build up some online presence that other people get attracted to … but JOGL, I think, is a good platform that could make the process of recruiting more people to your project much easier and faster and also make it easier to publicize the progress using one central location.” 

About two dozen people have signed up for the coronavirus project.

Many of those contributing to DIY testing efforts through community labs and elsewhere are high school students: Mueller, who has an informal synthetic biology education, has advised a number of high school community biology teams in an international synthetic biology competition known as iGEM

“This one seems also a bit ambitious … [but] it's probably more achievable than a lot of the other [projects] that we've done [in iGEM] in a way that's feasible, in the sense of creating something that has a measurable and immediately useful impact,” Mueller says. 

“[Mueller] reached out to me … and I joined because the project sounds very interesting and very useful for our current situation,” says Sophie Liu, 18, a senior at Newport High School in Bellevue, who was previously an iGEM team member and past SoundBio intern.

(While Mueller co-founded SoundBio lab, he says he’s “pretty hands off at this point,” and is no longer on the board or involved in running the lab.) 

While Liu is researching ways to adapt test kits for the project, she remains concerned about contracting the disease herself. “I'm currently not attending school, even though the Bellevue School District hasn't released any statement,” she says. “ I'm extremely concerned about the risk of going to school and going to a public space.” 

Liu says she’d need permission from her parents to participate in any lab-based testing. “They're quite concerned about just being in public in general, and testing just straight up with coronavirus would be even more concerning,” she says. 

The team has already gotten some good expert guidance from people like biologist Dr. Ellen Jorgensen, Mueller says, on things like which aspects of the viral genome to target in a test. They’re collecting resources on JOGL of viral sequences, and are talking about which proteins and plasmids they might use.

“The hardest part will definitely be testing it out and making sure that it gives at least reasonably useful results, and making sure we’re keeping all of the process safe,” Mueller says. His goal is to have a design selected and start partnering with places that can get real tests on real virus points in one month, “not necessarily something that we could share with people to start using right away. But if things are kind of aligned really well and we get all the extra advice really quickly, and the protocols and methods make sense, we'll see.” 

Beyond some review of existing tests, JOGL’s work has so far been limited to reaching out to experts for outside guidance, recruitment and an initial videoconference Wednesday for group members to meet each other and discuss possible paths forward. 

Neither Mueller nor Landrain are aware of community biology projects labs that have created viral test kits before, but there have been similar projects. They’re confident that they’ll be able to produce something viable. 

“We’re just ambitious people I guess,” Mueller says. “Just because something hasn’t been done before doesn’t mean we shouldn’t try it, and the way we’re trying to structure this project is we don’t want to release something that would potentially have a net negative on society, so we’re going to be very careful about what we actually share.” 

Community biology labs have produced detection kits for less contentious things before, and Mueller says there are examples of crowdsourced efforts to produce medically ambitious products. He points to the Open Insulin Project started in the Bay Area, an open-source project to produce insulin to circumvent companies raising the price on insulin medication for diabetics. 

How a DIY coronavirus test might work

Labs today detect the virus on throat and nose swabs using what’s known as a reverse transcriptase polymerase chain reaction (RT-PCR). This reaction helps scientists create billions or trillions of copies of small swabbed samples so that they have enough material to analyze. In this particular reaction, scientists convert RNA, the virus' genetic material, into DNA, which they copy and analyze for specific markers that indicate the virus.

Even professional labs certified to handle human samples run into hurdles with these tests, says Dr. Wesley Van Voorhis, director of the Center for Emerging and Re-emerging Infectious Diseases at UW. Van Voorhis’ lab is researching COVID-19, and also assisting local efforts around vaccines, drugs and diagnostics. At UW, researchers are using a test based on one developed by the World Health Organization. “The hardest part of the test [initially] was … you couldn't find anybody that had the disease” to take samples from to test your methods against, if you weren’t in the CDC, he says. “We could take synthetic RNA that we could make in a test tube to show that the test worked with synthetic RNA, but really knowing it would work in patient samples was tricky.” 

Mueller’s ideal test involves little more than dipping a sample swab in a tube with pre-prepared reagent material. “You’d keep it at a steady temperature for like an hour, and then the result would be either it gets cloudy or stays clear,” Mueller says. 

That kind of test would require a lot of care to design, they say, so that there’s very low room for errors like false positives or contamination that could cause problems. 

But experts expressed some skepticism about a DIY coronavirus test.

“At first I went, ‘Great, what a wonderful idea,’ ” Van Voorhis says at the idea of DIY biologists developing their own coronavirus test. “But the problem is with a really sensitive test like PCR, we have really strict ways to make sure that we don't have false positives and false negatives, and that we have access to real samples that can be tested periodically to make sure they're really working. I'm a little bit worried that somebody in their garage might not be able to do all that stuff.” 

Mueller says they wouldn’t intend for tests using human samples to be done at undercertified lab spaces. “Maria Chavez [of California’s BioCurious community lab] made the good point that essentially once you have a positive sample come back to a lab … then the whole lab would need to be quarantined and thoroughly cleaned, so that’s not a good idea to have the test be something that depends on your lab unless you're in a lab that's already well-equipped … where you’re allowed to have those disease-causing [specimens],” Mueller says. 

Even if a community lab were open to a project, it would have to make sure its biosafey level (BSL) rating allows it to engage with the project. SoundBio’s BSL-1 biosafety safety rating means it can work only with low-risk materials. 

Van Voorhis says biologists shouldn't handle patient samples for diagnosis in any lab with less than a BSL-2 environment, or "they’ll probably all come down with viruses and possibly bacterial illnesses.”

Human samples, Mueller says, might only be handled by people testing themselves while quarantined because they “can’t further contaminate themselves or anyone else,” but most likely it would be professional labs doing testing.

Community labs may still come into play, Mueller says. “The stuff we would be doing [there] for testing is testing either DNA or things that are not the actual virus, but things that give us clues to whether the test is trending in the right direction. But real virus material needs to be handled with professional labs, so we’ll need to connect with labs around the world that have that level of biosafety in their space.” 

Landrain says that in addition to protocol safety reviews, he’s only considering using parts of the virus in testing that can’t be transmitted.

“Arguably the nucleic acid or the RNA is nonviable if you treat it with something that decontaminates it, and you can still do PCR on it, but it's, yeah, that sounds a little scary,” Van Voorhis says. 

“The goal is really to show that an open community could actually produce [something] with the same standards as what you can find in institutions like the [World Health Organization], for example,” Landrain says. 

The board of Seattle’s SoundBio community lab just recently learned about the project and has expressed some caution.

“While we have not yet received a COVID-19 project proposal, if we do, it will be carefully reviewed like all our projects to ensure it is safe and adheres to our BSL-1 facility requirements,” the board members wrote in a statement. They encourage anyone with questions or concerns about COVID-19 “to contact their local health authorities.”

Yoshi Goto, SoundBio director of operations, says that he can’t speak for the lab but that his own response to the project is that it sounds "awesome." However, his biggest worries as a scientist are how testing would work and how biosafety would be ensured.

Goto wonders about the optics of a project involving the coronavirus and whether the public will think it's irresponsible for community labs to be involved.

Nevertheless, he believes the project encourages a positive interest in science. “Even the fact that we're [talking about] this and they’re starting a public discussion and a public awareness that you can do this is in itself a victory of this community project,” Goto says. “Seriously contemplating on these things… creates a good and safe opportunity to lower the chaos and empower citizens with more ownership and knowledge.”

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