The coronavirus epidemic this week reached Beadle County, South Dakota. A single case tied to travel has exploded into 14 infections and counting, with no way to know how many were exposed while supply shortages forced the entire state to briefly suspend testing.

Confirmed cases in New York City, where hospitals have fallen into chaos as resources run thin, on Thursday surpassed Beadle’s entire population of 18,500. With too few tests for too many cases, doctors there already had been told it no longer made sense to test most ill patients.

From its biggest cities to its smallest towns, America’s chance to contain the coronavirus crisis came and went in the seven weeks since U.S. health officials botched the testing rollout and then misled scientists in state laboratories about this critical early failure. Federal regulators failed to recognize the spiraling disaster and were slow to relax the rules that prevented labs and major hospitals from advancing a backup.

Scientists around the country found themselves shackled as the disease spread.

“We were watching a tsunami and standing there frozen,” said Dr. Debra Wadford, director of the public viral disease laboratory in California, where some of the country's earliest patients were identified.

The nation’s public health pillars — the Centers for Disease Control and Prevention and the Food and Drug Administration — shirked their responsibility to protect Americans in an emergency like this new coronavirus, USA TODAY found in interviews with dozens of scientists, public health experts and community leaders, as well as email communications between laboratories and hospitals across the country.

The result was a cascading series of failures now costing lives.

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MAP:Tracking the coronavirus outbreak

CDC leaders not only bungled their role in developing the first coronavirus test permitted in the country, they also misrepresented the efficacy of early solutions to state health authorities.

Then, public and private lab directors felt rebuffed by the FDA when they first offered to help troubleshoot the problem by developing their own tests. The agency, through its emergency authority, had placed restrictions on labs that can apply in emergencies but not in normal circumstances.

In a statement to USA Today, FDA spokeswoman Stephanie Caccomo said validating outside tests is essential in a crisis when "false results can lead to significant adverse public health consequences."

A reliable, accessible test was key to averting today’s disaster. Countries such as South Korea had already shown how such diagnostics — developed and scaled up with the help of the private sector at the onset — could be used to identify people with early infections before they spread the virus widely.

In late February, the CDC's deputy director of infectious disease projected calm in a conference call with state laboratories. The labs were told they could now send samples to the CDC and receive results within 24 hours.

“That was a bald-faced lie,” said Wadford. At that point, she was waiting four to five days on test results for samples she had sent to the CDC.

“The most disappointing part was that they couldn’t just be frank and straight with us,” said Wadford, who took detailed notes of the conference call that she dictated to USA TODAY. “Tell us the situation. Don’t sugarcoat it and lie. But to mislead us is just not right.”

The following week, President Trump tweeted: “The Coronavirus is very much under control in the USA. We are in contact with everyone and all relevant countries. CDC & World Health have been working hard and very smart. Stock Market starting to look very good to me!”

Since then, the U.S. went from 51 confirmed cases to more than 100,000, from zero deaths to over 1,900 as of Friday, while the economic toll of shuttering wide swaths of the country has cost millions their jobs and pummeled the stock market.

Brett Murphy and Letitia Stein are reporters on the USA TODAY national investigations team. Contact Brett at brett.murphy@usatoday.com or Letitia at lstein@usatoday.com.

Caccomo denied that the FDA was overly restrictive at the onset of the outbreak and then slow to adapt to the "unprecedented public health emergency.” The agency worked with outside labs as early as Jan. 22, she said, before opening up the emergency authorization process at the end of February.

"As the emergency evolved," Caccomo added, "FDA determined that the benefits of increased testing capacity outweighed the risks associated with use of additional tests."

The time lost in February was critical to containing the outbreak and helping hospitals prepare, experts say. With each delay, the virus spread undetected as people likely unaware of an infection attended conferences and weddings, frequented bars and restaurants and took long-planned cruise vacations.

America is now paying the price. More than half of the country’s population has been ordered to stay home to slow the spread. Doctors are rationing supplies. Like New York City, communities have limited testing because the outbreak has grown so large that hospitals must instead target the most vulnerable.

READ:Coronavirus lockdowns: These states are ordering residents to stay home or shelter in place

From Texas to New York –– the epicenter of the U.S. outbreak –– medical facilities burned through protective supplies, including masks, almost immediately, in part because doctors did not have widespread access to tests a month ago, forcing them to take extensive precautions with all patients showing symptoms.

New York City health officials now recommend against testing patients who do not require hospitalization, even if they have symptoms such as fever, to preserve limited resources. In viral social media posts, doctors describe hospitals overrun with the sick and dying. Patients with symptoms wait in clinic lines for up to 11 hours to get tested.

Dr. Alan Bigman, who runs a multi-speciality medical practice there, has agonized over an impossible position: pull patients away from jobs and out of the community without a diagnosis or risk running out of testing supplies for the next person who walks into the clinic.

“They have kids, and they have neighbors,” he said. “I need to know if they are positive or not.”

Healthcare workers:Tell us your coronavirus story

The crisis may soon be just as dire in rural communities. As of mid-March, Dr. April Abbott, the microbiology lab director at the largest hospital chain in southern Indiana, said she could not get equipment to run her own tests, in part because the federal government does not consider her area a priority like New York or California.

Hotspots could be hiding across the country. Smart thermometer company, Kinsa, recently noted an unusually high volume of fevers in east Texas and northern New Mexico, for instance, places where reported infections – and tests – remain low.

“We're not able to get testing supplies because we can't prove we need them,” Abbott said, “And we can't prove we need them because we can't perform the tests.”

Abbott initially looked into sending her Deaconess Hospital patients’ samples to other labs. But the state-run lab told her they were too overwhelmed by a bottleneck of demand to take them. Increasingly alarmed, she sent emails to private companies pleading for them to loan her equipment to run tests.

“Below Indianapolis, our state has virtually no functional testing capability,” Abbott wrote to a diagnostics company on March 16. “I cannot overemphasize the lack of testing available in our region.”

Eventually she found labs in other states to take her samples, but results took almost two weeks.

“The infrastructure has failed us,” Abbott said in an interview. As of mid-week, Indiana had confirmed just 645 cases of coronavirus.

Similar concerns were raised in South Dakota, where the resource-strapped state lab has lagged far behind others. Fewer than 2,200 test results were reported by the state as of Thursday, with 46 confirmed positive.

Health officials there had to suspend testing briefly just as its cases started to rise because the government's lab — then the only in-state option — ran out of testing supplies.

“I am absolutely appalled at what is going on,” said Ashley Kingdon-Reese, a home health care operator in Huron, South Dakota, who knows about a patient with likely exposure who continued to visit with family.

She fears the community was broadly exposed by these kinds of comings and goings while tests were backlogged.

People who could be spreading the virus, she said, “have been in the public the whole time.”

Federal testing push falls behind

Since early January, a virus raging in China had the attention of public health experts. A coronavirus, it was the newest member of a large family of viruses whose evils include the common cold. The name refers to how it looks under a microscope, with crown-like spikes on its surface.

U.S. intelligence communities soon began warning of a global pandemic, which The Washington Post reported last week was downplayed by the Trump administration.

After the first American case turned up in Seattle in late January, an infectious disease expert there began asking state and federal officials to let her repurpose nasal swab flu tests for the new coronavirus. The answer, the New York Times reported: no.

Twenty-plus years of public health preparedness drills dictated what the government should have done next: mobilize state, hospital and commercial laboratories to develop testing to isolate the sick and buy time for hospitals to activate plans for handling a surge.

“When you see a disaster coming, you want to go big and go now,” said Dr. Tara O’Toole, who helped develop pandemic response plans in the Department of Homeland Security under former President Barack Obama.

But for weeks, the federal testing push fell further and further behind.

On Jan. 31, after Americans began returning stateside from the outbreak’s origin in Wuhan, China, Health and Human Services Secretary Alex Azar declared a public health emergency, but called the threat to this country “low.”

Shortly after, the FDA gave the CDC authority through an emergency use authorization to begin rolling out a diagnostic test kit for the state public health labs.

If any scientists at universities, the public labs or private facilities wanted to develop their own tests — which they sometimes call “home brew” — or adopt the World Health Organization’s, they would need to submit separate applications with 28 pages of guidelines.

Labs found the process more burdensome than any other regulation they deal with.

Under normal circumstances, scientists can run various tests without special FDA approval. But emergency orders shift the regulatory landscape, imposing restrictions. Experts say the agency moved far too slowly to lift them, given the magnitude of the building crisis.

Instead, the FDA stuck with one of the most restrictive approaches possible, according to Dr. Josh Sharfstein, a former deputy commissioner at FDA.

“The response has been backwards,” said Sharfstein, now vice dean for public health practice and community engagement at Johns Hopkins University, who advocates for more regulation during non-emergencies and less in urgent situations like this one.

The FDA, an arm of the Department of Health and Human Services, regulates according to laws passed by Congress and guidance laid out by the administration. Yet Trump has blamed the initial approach on the prior administration, which he said created barriers that made it difficult to rapidly ramp up testing.

“I don’t take responsibility at all,” he said at a news conference two weeks ago.

The White House did not respond to requests for comment and directed USA TODAY to the health department, which also did not respond.

Dr. Margaret Hamburg, who served as commissioner of the FDA under former president Barack Obama and helped oversee the agency’s response to the H1N1 flu outbreak, said there was nothing stopping the administration from acting sooner.

“I’ve been confused by those characterizations of the FDA’s inability to move swiftly in a crisis,” Hamburg said.

Flawed test, then flawed response

The federal emergency declaration allowed the CDC to begin distributing test kits to state health department labs across the nation in early February.

Right away, a problem surfaced. California received its kits on a Friday. Scientists worked through the weekend, discovering that some components of the CDC’s test were flawed and produced inconclusive results.

The issue centered on one of the three testing components, or reagents, used to detect the new virus, COVID-19.

READ:'Not gone as smoothly as we would have liked': CDC fixes coronavirus testing kit glitch

On Sunday, Wadford, one of the directors of the California public health lab, frantically messaged colleagues at the Association of Public Health Laboratories. She wanted to know if other labs had encountered the same problem.

“We are hearing of it from at least one state lab,” an official from the laboratory association wrote back in an email. “Seems like it might be real.”

The CDC promised to quickly fix the test. But for two weeks, the agency offered temporary solutions — such as creating a new “surge” lab and offering to receive samples at CDC headquarters in Atlanta.

Those patches themselves were so flawed that results that took days were often inconclusive, too, according to Wadford. At one point, the surge lab also failed to immediately notify the state labs of positive cases by phone, as they had done earlier in crises.

The CDC has acknowledged problems with its testing development.

"This has not gone as smoothly as we would have liked," Dr. Nancy Messonnier, director of its National Center for Immunization and Respiratory Diseases, told reporters in late February.

Noting that the U.S. had few cases at the time, she added: "To date, our strategies have been largely successful."

The agency did not respond to a request for additional comment under deadline.

By the third week of February, still with no permanent solution in place, the FDA was well aware of the problem.

On Feb. 24 — the same day Trump tweeted “the Coronavirus is very much under control” — Scott Becker, executive director of the Association of Public Health Laboratories, sent a letter to the FDA begging the agency to scale back its original strategy and lift the home-brew restrictions preventing them from making their own tests.

Around the same time, more than 100 scientists in private labs and universities penned a similar letter to Congress.

“They are first responders with lab coats and they couldn’t actually gown up,” Becker said in an interview, calling the situation at that stage desperate.

On Feb. 29, the administration changed course and began rolling back the restrictions. The new strategy allowed both private and public labs to use a modified version of the CDC test and start developing their own.

In the coming days and weeks, the FDA continued to ease restrictions to make it easier for others to come online with tests, including commercial laboratories.

Experts criticize the agency, however, for moving slowly given the magnitude of the health epidemic unfolding.

“CDC tests were never supposed to meet the entire need for the U.S.,” said Dr. Tom Frieden, a former CDC director, noting that commercial labs and hospitals play critical roles in reaching the scale required in a major epidemic such as the new coronavirus.

During these lost weeks in February, federal officials missed their chance to contain the outbreak before it swept across the country, unseen.

As testing ramped up, states found themselves behind

At Texas Children’s Hospital, doctors lament the weeks that passed without an in-house test to show in hours, not days, what they were dealing with.

Dr. Jim Dunn, director of medical microbiology and virology at the hospital, had developed lab tests for the Zika virus for weeks before the FDA stepped in. He said the restrictions this time prevented Texas Children’s from getting out in front of COVID-19.

“They pulled the plug before we even had a chance to get going,” said Dunn, noting that the hospital expended resources in the early days when doctors didn’t know who did and didn’t have the virus. “It could have affected how the masks were allocated.”

South Dakota, initially appearing largely untouched by the epidemic, nonetheless rallied its emergency planners.

In Beadle County, the Huron Regional Medical Center rolled out a testing protocol that leaders now acknowledge was aggressive to the point of overuse.

Clinicians burned through supplies, using four nasal swabs to run testing for COVID-19 and other respiratory concerns. The protocol was eventually scaled back to one swab per nostril, then one per patient.

As the state lab backlogged, with limited supplies to process the tests, people with suspected cases were urged to self-quarantine.

“When we started out, there was no shortage of supplies,” said Dr. Jake Redden, the hospital’s vice president of quality, who coordinated with state health officials.

Testing hit a snag just as an early cluster of travel-related cases surfaced in the county of 18,500 people within a state whose entire population is less than 900,000.

Lacking a crucial chemical used to process the test, in short supply nationally, South Dakota’s public testing lab posted a notice online last Wednesday that it had temporarily suspended testing.

“It was alarming,” said Dr. Robert Summerer, president of the South Dakota State Medical Association.

The lack of test data presented a challenge for members of the association, who were trying to draft guidelines for the governor on closing restaurants and cancelling elective surgeries. No one knew whether the state really had few cases or was clueless for lack of test results.

Other states had commercial and hospital-based labs running, but South Dakota still lacked an in-state backup.

The day after the state halted testing, Republican governor Kristi Noem told the White House on a conference call that it had been juggling shortage issues for two weeks.

She described how the CDC kept directing the state to private suppliers, which would cancel orders for the chemical reagent at the last minute. After getting “a little pushy,” she said enough supplies had come in for her state to resume processing tests.

“I need to understand how you’re triaging supplies,” she told the White House, according to a transcript of the call. “I just don’t want to not be a priority area, because we’re a smaller state or less populated.”

“It will never happen to your state,” Trump responded.

With limited supplies, however, the state lab focused on processing cases identified as higher priority. As of early this week, authorities were awaiting results from 700 tests sent out of state to be processed by labs with four- to five-day turnaround times.

Beadle County’s cases already had multiplied as test results came back.

The day before the governor’s White House call, Beadle County had a single case.

On the day that Noem spoke with Trump, the count rose to four.

By Sunday, when city and county officials voted in an emergency session to shut down restaurants, gyms and movie theaters, there were 10.

READ:Gov. Kristi Noem confirms more coronavirus cases in state

Testing has ramped up within the state this week. So has fear.

The mayor of Beadle’s county seat, Huron, issued a news release to combat rumors circulating on social media that the virus had arrived in their community via its significant population of Karen immigrants from Myanmar. He noted the cases reported to that point all were white residents.

“If we’d have had better testing supplies,” Huron Mayor Paul Aylward told USA TODAY, “we could have been ahead of this curve.”

Data reporter Kevin Crowe contributed to this report.

Brett Murphy and Letitia Stein are reporters on the USA TODAY national investigations team. Contact Brett at brett.murphy@usatoday.com or @brettMmurphy or Letitia at lstein@usatoday.com, @LetitiaStein, by phone or Signal at 813-524-0673.