In the fight against COVID-19, U.S. hospitals, test manufacturers and labs have found themselves careening from one crisis to the next.

First, as the number of those infected with the novel coronavirus mushroomed, tests in many places were so scarce that only the sickest could be tested.

Production of new and better test kits has increased, but the pipeline now is besieged by new hurdles. Supplies such as swabs to collect samples and chemicals to process them are running short. Labs that don’t have the equipment or capacity to do enough testing are forced to send them to the big commercial players, which in turn face bottlenecks that can delay results for as long as two weeks.

Susan Butler-Wu’s community hospital lab in Los Angeles initially had to send tests to commercial labs, which took as many as 12 days to process. After waiting weeks for a COVID-19 test to become available for her lab's machines, just over a week ago the hospital ran its first test.

“It’s very much an emotional rollercoaster for lab directors,” she said.

Once a test is approved, she said, “then it’s like the Hunger Games to try and see if you can get access to the product.”

Still, Butler-Wu says her lab is better off than most, because it can now do its own testing.

“This isn’t unique to just California. This is everywhere,” said Butler-Wu. “The midwest, East Coast, everywhere.”

In the U.S., diagnostic testing for the novel coronavirus has become a massive logistical failure that has made it impossible to realize how much the virus has truly spread and how many it has sickened. More than 12,000 have died and 374,000 people have tested positive.

Testing will become even more important as states attempt to lift restrictive rules that have shut down businesses and asked people to stay home for weeks, crushing the U.S. economy. A loosening of those rules, public health experts have said, will need to come with widespread testing that includes those who exhibit no symptoms, which can be followed up by more targeted quarantines while other people get back to work.

It is a picture that starkly differs from the one promoted by the White House in which anybody who wants can be tested for COVID-19.

A randomized survey of 323 hospitals conducted by the U.S. Department of Health and Human Services Office of the Inspector General and published Friday found that many faced severe shortages of testing supplies and frequently waited a week or longer for results. Those issues, the survey found, further strained already scarce resources like hospital beds and personal protective equipment.

More than a million Americans have now been tested for the novel coronavirus, but access varies widely from state to state and often even between hospitals in the same region. New York State has tested more than 340,000 people, while California, with double the population, had tested just 143,800 as of Monday. That’s nearly five times as many tests when counted per capita.

And that’s just tests performed. With many facilities relying on third parties to process tests, that step in the testing process often becomes another bottleneck resulting in lengthy delays. After aggressive efforts to cut down a backlog of more than 59,000 tests, the state of California was still waiting Monday for results on more than 14,000 tests.

In New Jersey, results have frequently been delayed by up to two weeks. That’s led Governor Phil Murphy to caution that each day’s numbers include stale data.

“We are getting only a very fuzzy picture of the scope of the problem, and it is very slow to develop,” said Eric Blank, the chief program officer for the Association of Public Health Laboratories. “There are all of these questions about the virus that have been swirling around, and we are only starting to get some sense of the issue.”

The FDA has cleared a slew of products from companies like Roche Holding AG, Abbott Laboratories, Becton, Dickinson & Company and Qiagen NV for emergency COVID-19 testing, which can often be performed on machines that already are employed by many laboratories across the U.S. for other kinds of tests. 

But producing and deploying tests takes time, and the limited supply that’s already available is doled out based on need to the hardest-hit areas. 

Roche's high-speed testing machines, which can process more than 4,000 results daily, are being deployed for COVID-19 testing “where they are needed most and can be most effective,” including at large national reference labs and “limited deployment to regional hospitals in the most highly impacted areas,” said Patrick Barth, a Roche spokesman. More than 60 individual labs now have COVID-19 testing enabled on Roche machines, Barth said.

Diagnostics firm BioMérieux got FDA clearance on March 24 for a COVID-19 test that can deliver results on site in about 45 minutes. However it’s only shipped to the Department of Defense because it’s still working to increase production, said Global Medical Affairs Vice President Christine Ginocchio. 

The situation, coupled with shortages of key supplies to process results has put pressure on commercial labs. Quest Diagnostics Inc., which had a massive backlog in outstanding test samples awaiting processing, said Monday that it’s slashed that in half to about 80,000. It’s now able to do more than 35,000 COVID-19 tests a day at its 12 labs, it said.  

In late March, when there were still 160,000 tests awaiting processing, results could take up to five days, a Quest spokesman said at the time, though reports from providers suggest at times it took much longer. Quest says now tests can be run, on average, in a day for priority patients and two to three days for others. Hotspot areas like New York and New Jersey, Chicago and Miami may take longer — three days or more — due to high demand, according to Quest.

In Delaware, Senator Chris Coons said Thursday that the state hospital and medical lab couldn’t process coronavirus tests because of a shortage of chemicals. So swabs were being sent to LabCore and Quest despite their backlogs of more than a week, Coons said.

The state had ordered $300,000 worth of the chemicals, but after a month waiting on backorder, the supplies were further held up by a miscommunication between the Food and Drug Administration and shipper DHL, Coons said.

"The shipment still hasn't moved," Coons said on Thursday, pulling up the order's tracking number. "It's been sitting in a warehouse for an entire week. We just want the chance to use the state of their state-of-the-art machinery." 

The shipment was scheduled to finally arrive on Saturday, but Coons' office hasn’t been able to confirm whether it had.

The shortage of kits to extract and run samples is one of the biggest issues facing public and private labs alike, APHL’s Blank said. Several public health labs, he said, have come within a day of running out, forcing them to prioritize processing only the most urgent tests.

German diagnostics firm Qiagen makes the extraction kits used in many tests. It’s doing everything it can to accelerate production in the face of “extraordinary demand,” spokesman Thomas Theuringer said.

“This demand has been challenging our capacity,” he said. “No company alone can meet the demand.”

Since Becton, Dickinson’s BD Max system was cleared by the FDA for COVID-19 testing, the company has also confronted “exceptionally high” demand, said Nikos Pavlidis, vice president of molecular diagnostics and women’s health and cancer. 

Like many other companies, the team has been prioritizing hotspots, working with local governments, health insurers and hospitals systems to allocate what’s provided, he said. 

“It’s not an easy process,” Pavlidis said. “And everybody that calls in needs the test tomorrow.”

According to the HHS OIG report, hospitals have also reported delays due to infrequent collection of samples, mailing delays, and restrictive lab hours.

As access to rapid testing grows, it could help ease the burden on this strapped supply chain. Receiving results more quickly also allows hospitals to better ration resources like staff and dwindling stocks of personal protective equipment, which have to be used while waiting for results, assuming anyone tested may be positive. In California, for example, of the 143,800 tested and the 129,693 that have been processed, just 14,336 came back positive.

The FDA recently approved a portable, five-minute test from Abbott Laboratories. That means a hospital could run tests on-site and quickly receive results, rather than sending them out to overrun labs. 

While President Donald Trump called the test “a whole new ballgame,” California Governor Gavin Newsom was more tempered at a press briefing later that day.

“It's an insignificant total number of tests that we can produce in 5 to 15 minutes in California,” he said. “The state of California received only 100 cassettes, 15 different labs, so do the math.”

Public-health labs are only expected to get 5,500 of those tests, according to a document circulated among HHS and Federal Emergency Management Agency employees that was publicized by Kaiser Health News. An Abbott spokesperson said that in addition to those tests, it had shipped more than 190,000 tests to 21 states as of Friday, prioritizing outbreak hotspots.

Concerns about shortages have prompted labs like Butler-Wu’s to build their own workarounds, including securing additional platforms from different diagnostics companies, to ensure they can keep testing no matter what.

The clinical virology laboratory at Stanford Health Care, which has performed more than 10,000 of California’s tests with a current turnaround time of less than 24 hours, has set up multiple different workflows with different sets of instruments and suppliers “so we don’t have to rely on any single one manufacturer,” said Benjamin Pinsky, the lab’s medical director. 

Swab shortages, though, have still proven to be an issue. 

“We’re not out of them yet. But we like to have a larger stockpile,” he said. “I don’t know when the D-Day is for them to run out.”

At University of California San Francisco, the lab has begun using more abundant research-grade reagents to process tests rather than those typically used in diagnostic labs. It has also begun using a different type of swab. 

In Indiana, Aria Diagnostics has been doing COVID-19 testing for first responders, health-care workers and patients in the state, but the private lab has struggled with shortages of swabs and the viral transport media that’s used to preserve patient specimens. 

To solve for the latter, it found unused pharmacy space in Carmel, Indiana, where it could assemble its own transport media and put it into small vials.

“What we’re doing is replicable, and we need to replicate this and teach everybody,” cofounder Zak Khan said. “People are hunting for those. Without it, you can’t take a specimen.”

The HHS report described hospitals splitting the media that preserves samples in testing kits in half to increase testing capacity, or using transfer media intended for flu and strep kits. On a call with reporters on Tuesday, Kim Hanson of the Infectious Diseases Society of America noted some labs are even attempting to validate Q-tips in place of swabs.

Delaware’s Coons said the state has approached Roche for "an emergency license” to formulate its own reagent.

The delays have frustrated Adam Vascellaro, chief medical officer of the Potawatomi Indian nation outside of Shawnee, Oklahoma. As of last week, they had tested 90 people, with four positive cases. Results, he said, take as long as two weeks to come back; they were still awaiting 33.

Such delays, he said, have meant artificially low numbers of reported cases. "We need real-time testing to understand what is going on and make real-time decisions," he said. "How do you treat a patient when you don't get lab results back for 14 days?"

Yet many Americans are still clamoring to be tested — and they don’t always take the news well when they don’t fit the criteria, said JD Zipkin, associate medical director for Northwell Health-GoHealth Urgent Care. Patients have screamed in the lobby, refusing to leave without a test, and even trashed its waiting rooms — to the point that security guards have been brought at some sites, he said. 

“I’ve personally called the police more in the last two to three weeks than I have in the entire rest of my career in urgent care combined,” Zipkin said.