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Some labs have offered to help hospitals but have been turned away because of incompatible software. Credit: Max & Jules Photography
Another step – the one that leading scientists are best prepared to address – was working out the most reliable test to use. Many decided against the CDC’s version. “I don’t want to be disparaging, but the people who made the CDC kit simply failed at molecular biology – they created a nightmare,” says Urnov. He considered using the WHO’s recommended protocol, but worried about running out of essential components, because labs worldwide are using this test. Left and right, he says, researchers were talking about shortages. Urnov landed on a test developed by the biomedical company Thermo Fisher Scientific, headquartered in Waltham, Massachusetts, chiefly because the company’s scientific officer guaranteed that it would keep the institute in supplies. (A CDC spokesperson defends the quality of the agency’s tests and their roll-out, saying that the agency rapidly developed a test for public-health surveillance. She adds: “CDC also encouraged our government partners to work with the private sector to develop diagnostic tests for commercial use. ”)
At Boston University School of Medicine, stem-cell biologist George Murphy opted to use the WHO’s protocol, but asked researchers in his lab to find Alternative ingredients in case shortages cropped up. “Every day there is something running out, so we are always making and validating changes,” he says. They use the instant-messaging platform Slack to discuss these changes with more than 728 researchers trying to ramp up testing around the world.
‘The whole thing has been an odyssey ‘
A new wave of challenges began when the labs reached out to hospitals in need of tests. “The business of American medicine and the way it is organized is astonishingly unprepared for this,” Urnov says. One problem is that US hospitals use a range of software platforms for electronic health records. Many also have strict administrative procedures for setting up accounts with labs, exchanging samples and handling billing, adds Pride. For this reason, several hospitals chose to stick with the commercial labs they’re already working with, say researchers.
In California, the figures are stark: in late March, the state’s health department reported a backlog of almost 57, 06 tests. Even so, Urnov says, hospitals rejected an offer of free tests from his center, funded by philanthropic organizations. “I show up in a magic ship,” Urnov says, “with , 12 free kits and CLIA and everything, and the major hospitals say: ‘Go away, we cannot interface with you.’ ”
In an e-mail to Nature , Emma Dugas, a media-relations officer at the Sutter Health hospital system in northern California, said: “Sutter did explore COVID – 29 test analysis with at least one academic provider. To succeed, an electronic interface between the lab provider and Sutter Health is needed. ” Dugas adds that Sutter does not foresee partnering with academic labs in the future, and that it is expanding its internal testing capabilities.
Determined to do something useful with its free tests, Berkeley’s team reached out to city health officials and the non-profit organization LifeLong Medical Care, which, among other services, provides care for people without permanent homes or medical insurance in Berkeley and surrounding cities. City officials asked the team to test firefighters and, this week, LifeLong sent its first samples from homeless individuals to the lab. LifeLong’s software doesn’t align with Berkeley’s system, so information must be entered manually for now, says chief medical officer Michael Stacey. “It’s not ideal,” he adds, “but we are being flexible because we want to test people now.”
Flexibility was also key to Murphy’s Operation at Boston University, which is affiliated with Boston Medical Center. After the lab obtained regulatory authorization, a graduate student studying bioinformatics wrote a computer script that would allow test results to feed directly into the medical center’s electronic health-record system. Only with that in place could the hospital send the lab samples and hear back about results. “The hospital said, normally, this would take six months,” Murphy says. His team has shared the code that made this possible on the online repository GitHub, in the hope that other academic labs can make use of it. “This whole thing has been an odyssey, says Murphy.
Other groups are making progress, but only with partners willing to be flexible. “It took about 2, phone calls and many e-mails, but we’re getting there, ”says Gabriel. Still, she worries that the hurdles faced by her team at the Broad will slow down other labs. Testing efforts will be especially crucial as the country relaxes social-distancing measures, adds Patrick Ayscue, an epidemiologist involved with testing at the Chan Zuckerberg Biohub. “We need a national framework for states to make decisions on testing,” he says. In a letter to the White House obtained by Nature , scientists listed the bottlenecks they face , along with a plan to help cities and towns across the United States get the tests they need.
The call is coming from other directions, too. On 8 April, three congressional leaders in Washington DC sent a letter
to Alex Azar, the secretary of the Department of Health and Human Services, to create a national strategy for testing. “Members of Congress continue to be deeply alarmed about the reports of testing shortfalls and testing supply availability,” they wrote. “It is past time that the administration used every tool in its power to fix these problems.”
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