At 7.47 am. on the Sunday of Memorial Day weekend, Jay Butler pounded out a grim email to colleagues at the United States Centers for Disease Control and Prevention in Atlanta.

Butler, then the head of the agency’s coronavirus response, and his team had been trying to craft guidance to help Americans return safely to worship amid worries that two of its greatest comforts – the chanting of prayers and singing of hymns – could launch a deadly virus into the air with each breath.

The week before, the CDC had published its investigation of an outbreak at an Arkansas church that had resulted in four deaths. The agency’s scientific journal recently had detailed a superspreader event in which 52 of the 61 singers at a two-and-a-half-hour choir practice developed Covid-19. Two died.

Butler, an infectious disease specialist with more than three decades of experience, seemed the ideal person to lead the effort. Trained as one of the CDC’s elite disease detectives, he had helped the Federal Bureau of Investigation investigate the anthrax attacks, and he had led the distribution of vaccines during the H1N1 flu pandemic when demand far outstripped supply.

But days earlier, Butler and his team had suddenly found themselves on President Donald Trump’s front burner when the president began publicly agitating for churches to reopen. That Thursday, Trump had announced that the CDC would release safety guidelines for them “very soon”. He accused Democratic governors of disrespecting churches, and deemed houses of worship “essential services”.

Butler’s team rushed to finalise the guidance for churches, synagogues and mosques that Trump’s aides had shelved in April after battling the CDC over the language. In reviewing a raft of last-minute edits from the White House, Butler’s team rejected those that conflicted with CDC research, including a worrisome suggestion to delete a line that urged congregations to “consider suspending or at least decreasing” the use of choirs.

On Friday, Trump’s aides called the CDC repeatedly about the guidance, according to emails. “Why is it not up?” they demanded until it was posted on the CDC website that afternoon.

The next day, a furious call came from the office of the vice president: The White House suggestions were not optional. The CDC’s failure to use them was insubordinate, according to emails at the time.

Fifteen minutes later, one of Butler’s deputies had the agency’s text replaced with the White House version, the emails show. The danger of singing was not mentioned.

Early that Sunday morning, as Americans across the country prepared excitedly to return to houses of worship, Butler, a churchgoer himself, poured his anguish and anger into an email to a few colleagues.

“I am very troubled on this Sunday morning that there will be people who will get sick and perhaps die because of what we were forced to do,” he wrote.

When the next history of the CDC is written, 2020 will emerge as perhaps the darkest chapter in its 74 years, rivaled only by its involvement in the infamous Tuskegee experiment, in which federal doctors withheld medicine from poor Black men with syphilis, then tracked their descent into blindness, insanity and death.

A historic low

With more than 216,000 people dead this year, most Americans know the low points of the current chapter already. A vaunted agency that was once the global gold standard of public health has, with breathtaking speed, become a target of anger, scorn and even pity.

How could an agency that eradicated smallpox globally and wiped out polio in the United States have fallen so far?

ProPublica obtained hundreds of emails and other internal government documents and interviewed more than 30 CDC employees, contractors and Trump administration officials who witnessed or were involved in key moments of the crisis.

Although news organisations around the world have chronicled the CDC’s stumbles in real-time, ProPublica’s reporting affords the most comprehensive inside look at the escalating tensions, paranoia and pained discussions that unfolded behind the walls of CDC’s Atlanta headquarters. And it sheds new light on the botched Covid-19 tests, the unprecedented political interference in public health policy, and the capitulations of some of the world’s top public health leaders.

Senior CDC staff describe waging battles that are as much about protecting science from the White House as protecting the public from Covid-19. It is a war that they have, more often than not, lost.

Employees spoke openly about their “hill to die on” – the political interference that would prompt them to leave. Yet again and again, they surrendered and did as they were told. It was not just worries over paying mortgages or forfeiting the prestige of the job. Many feared that if they left and spoke out, the White House would stop consulting the CDC at all, and would push through even more dangerous policies.

To some veteran scientists, this acquiescence was the real sign that the CDC had lost its way. One scientist swore repeatedly in an interview and said, “The cowardice and the caving are disgusting to me.”

Collectively, the interviews and documents show an insular, rigorous agency colliding head-on with an administration desperate to preserve the impression that it had the pandemic under control.

Some of the key wounds were self-inflicted. Records obtained by ProPublica detail for the first time the cataclysmic chain of mistakes and disputes inside the CDC labs making the first US test for Covid-19. A respected lab scientist made a fateful decision to use a process that risked contamination, saw signs of trouble, but sent the tests to public health labs anyway. Many of those tests did not work, and the scramble to fix them had serious consequences.

Even when the CDC was not to blame, the Trump administration exploited events to take control of the agency’s messaging. As a historically lethal pandemic raged, the White House turned the CDC into a political bludgeon to advance Trump’s agenda, alternately blocking the agency’s leaders from using their quarantine powers or forcing them to assert those powers over the objections of CDC scientists.

Once seen as an apolitical bulwark, the CDC endured meddling on multiple fronts by officials with little or no public health experience, from Trump’s daughter Ivanka to Stephen Miller, the architect of the president’s immigration crackdown. A shifting and mysterious cast of political aides and private contractors – what one scientist described as young protégés of Trump’s son-in-law, Jared Kushner, “wearing blue suits with red ties and beards” – crowded into important meetings about key policy decisions.

Agency insiders lost faith that CDC director Robert Redfield, a Trump appointee who had been at the agency only two years, would, or could, hold the line on science. One division leader refused to sign what he viewed as an ill-conceived and xenophobic Trump administration order. Redfield ultimately signed it himself.

CDC director Robert Redfield. Photo credit: Andrew Caballero-Reynolds/ AFP

Veteran CDC specialists with global reputations were marginalised, silenced or reassigned – often for simply doing what had always been their job. Some of the agency’s most revered scientists vanished from public view after speaking candidly about the virus.

The Trump administration is “appropriating a public enterprise and making it into an agent of propaganda for a political regime”, one CDC scientist said in an interview as events unfolded. “It is mind-boggling in the totality of ambition to so deeply undermine what’s so vitally important to the public.”

The CDC repeatedly declined to make Butler, Redfield or any other employees mentioned in this story available for questions, and a CDC spokesperson declined to comment on behalf of the agency. The White House did not respond to an email seeking comment.

A spokesperson for the Department of Health and Human Services, which oversees the CDC, rejected accusations of political interference.

“Under President Trump, Health and Human Services has always provided public health information based on sound science,” the Health and Human Services spokesperson said. “Throughout the Covid-19 response, science and data have driven the decisions at Health and Human Services.”

People interviewed for this story asked to remain anonymous because they feared retaliation against themselves or their agency.

In interviews and internal correspondence, CDC employees recounted the stunning fall of the agency many of them had spent their careers building. Some had served on the front lines of the CDC’s most storied battles and had an earned confidence that they could swoop in and save the world from the latest plague, whether it was E coli on a fast-food burger or Ebola in a distant land.

Theirs was the model other nations copied. Their leaders were the public faces Americans turned to for the unvarnished truth. They had served happily under Democrats and Republicans.

‘Bankruptcy of trust’

Now, 10 months into the crisis, many fear the CDC has lost the most important currency of public health: trust, the confidence in experts that persuades people to wear masks for the public good, to refrain from close-packed gatherings, to take a vaccine.

Martin Cetron, the agency’s veteran director of global migration and quarantine, coined a phrase years ago for what can happen when people lose confidence in the government and denial and falsehoods spread faster than a disease. He called it the “bankruptcy of trust.”

He had seen it during the Ebola outbreak in Liberia in 2014, when soldiers cordoned off the frightened and angry residents of the West Point neighbourhood in Monrovia, the capital. Control of a pandemic depended not just on technical expertise, he told colleagues then, but on faith in public institutions.

Today, some CDC veterans worry that it could take a generation or longer to regain that trust.

“Most of us who saw this could be retired or dead by the time that’s fully fixed,” one CDC official said.

Anne Schuchat, the CDC’s top career scientist, was one of the first to notice a brief report about four cases of “unexplained pneumonia” in Wuhan, China, in an emerging diseases bulletin. It followed a warning about a “red blotch disease” in the grape industry.

As a disease detective in 2003, Schuchat had been dispatched to China to investigate the outbreak of SARS, a respiratory disease that killed about 800 people and shut down parts of Asia. Her role in that outbreak and in later epidemics inspired the virus hunter played by Kate Winslet in the movie Contagion.

Unflappable and regarded as brilliant, Schuchat eases the tension at meetings by singing ditties about the latest outbreak set to Broadway tunes. Nobody wants to disappoint her.

At 8.25 am on December 31, 2019, Schuchat emailed Butler and other colleagues asking if “any of your folks know more about the ‘unknown pneumonia’” in Wuhan.

Emails and calls bounced among the agency’s leaders, a handful of veterans with more than a century of experience among them. Dan Jernigan, the flu chief, and his boss, Nancy Messonnier, met at headquarters to plan. Within hours, they learned there were 27 cases – seven of them severe – with fever, difficulty breathing and a buildup of abnormal substances in the lungs. All the cases were believed to be connected to an outdoor seafood market. “Raises concern about SARS,” Messonnier wrote in an email.

Representational image. Photo credit: PTI

The news reached Cetron in New Hampshire. While celebrating the holidays at a beer-and-tacos pub across the river in Vermont, he told family and friends about a new virus in China that he worried could affect the whole world. “We should be bracing ourselves,” he said.

If the outbreak had been a movie, this would have been the scene where the heroine mobilises an all-star squad of specialists to save the planet. Schuchat’s team is seen as among the top infectious disease experts in the world. All of them had started out in the CDC’s Epidemic Intelligence Service, an elite corps of globetrotting disease fighters. They were a brain trust forged by decades of defending the country from outbreaks.

But in the 11 years since the H1N1 flu pandemic, the terrain had shifted. Politics and budget cuts had weakened the agency at home and abroad. Meanwhile, the regime in Beijing had grown increasingly aggressive and authoritarian. The Trump administration’s trade war had worsened tensions. And after a series of tough-minded leaders who were adept at protecting the agency and its mission, Trump’s first choice as director quit after Politico reported that she had purchased tobacco stocks while leading the CDC, which fights lung diseases.

Trump appointed Redfield in 2018. He was an HIV researcher who had treated AIDS patients since the earliest days of the disease. He’d wanted the CDC job for decades, and had been passed over for it twice. During his first all-hands meeting at the Atlanta campus, he had choked up describing the honour of leading the agency.

In the fierce chaos of Trump’s Washington, the CDC needed a streetfighter. Instead, it got “the nicest grandfather you can imagine,” a senior health official said. A former colleague described how Redfield, a devout Catholic, prayed with the ailing Elijah Cummings, a Democratic congressman from Baltimore, during a visit to the Capitol.

Redfield took over an agency that, despite its $8.3 billion budget, was feeling the chronic funding woes of the American public health system, which has been quietly gutted since the Great Recession. As the coronavirus began its march through the United States, years of federal and state cuts had left about 26,000 fewer employees at state, county and municipal health agencies since 2009, according to the nonpartisan Trust for America’s Health.

With a mission of protecting America from diseases, the CDC was stretched thin. Over the decades, its portfolio had expanded to include almost every malady, chronic or acute.

Failure of network in China

The CDC’s global presence was suffering too. An infusion of hundreds of millions of dollars at the time of the Ebola epidemic in 2014 allowed the agency to increase its presence to as many as 65 countries, but a large chunk of those funds ran out in 2019.

As funding expanded and contracted in recent years, the CDC had to cut over 300 posts overseas, including both Americans and foreigners. By the time Schuchat noticed the blurb about an outbreak in Wuhan, her agency no longer had an office inside the Chinese Center for Disease Control and Prevention, its counterpart in Beijing. While the US agency once had more than a dozen Americans in China, by January only three remained.

On January 3, Redfield phoned his agency’s closest ally in Beijing, George Gao, the director of China’s CDC, a microbiologist trained at Oxford and Harvard. Gao said his agency had sent a field investigation team to Wuhan. But during conversations in the next few days, many of Redfield’s questions about the mystery disease went unanswered. Gao, who was usually open and talkative, sounded guarded, according to several officials familiar with the conversations.

Nevertheless, Redfield assured federal health and national security officials that information was flowing from China thanks to his rapport with Gao, knowledgeable people said.

On January 6, Redfield sent Gao a carefully worded letter offering the help of CDC experts. Expecting the Chinese to accept “very soon”, CDC leaders began preparing a team to go to China, emails show.

To Redfield’s chagrin, however, the conversations with Gao came to a sudden halt. Ominous news accumulated: the first recorded death, January 9, the first case outside China, January 13. In the secure, high-tech room where the CDC brain trust met, the mood turned dark as the scientists began to fear they were confronting a pandemic.

“We were slowly convincing folks: It does not matter if you believe it or not, but this is the circumstantial evidence,” a senior lab official said. “And you have to prepare.”

Amid the scramble to find out what was happening in China, CDC officials began telling the public not to panic. But they conveyed the serious nature of the threat.

On January 17, for example, Messonnier said that the CDC was “especially concerned about a novel coronavirus” because related viruses – SARS and Middle East Respiratory Syndrome – were “difficult outbreaks with many people getting ill and deaths”.

It appeared that the illness had been spreading since at least early December, but data on cases provided by Chinese authorities was woefully incomplete, listing only the dates patients were hospitalised, not what symptoms they had or for how long, the senior lab official said.

“We knew they were good enough epidemiologists to get that data,” the official said. “Why are not they announcing the results?”

The lab official tried to contact a chief virologist at the China CDC who was usually helpful, but got no response. Neither did colleagues who reached out to Chinese scientists with whom they had collaborated for years. The Americans concluded that the regime in Beijing was telling them to keep quiet.

Gao had also run up against a cover-up by authorities in Wuhan, health and national security officials said. Gao’s field investigators were “told there was no evidence of human-to-human transmission,” said Ray Yip, a former country director for the CDC in China. “They did not show them all the cases. They had a couple of cases of hospital workers infected by then, and that’s obviously human-to-human, how else did they get it?”

During the SARS epidemic in 2003, Time magazine reported that Chinese authorities had hidden 31 infected health workers from the world by pulling them from their hospital, loading them into ambulances, and driving them around Beijing until a visiting delegation from the World Health Organization left the hospital.

Representational image. Photo credit: AFP

In January, the bond between the US and Chinese health agencies became a double-edged sword. Chinese leaders were wary about Gao’s relationship with the Americans, who heard rumblings that he would be made the scapegoat for the outbreak. Meanwhile, Redfield’s reputation suffered in Washington because he did not deliver.

“The China CDC and the US CDC were almost seen as one,” a senior US health official said. “Redfield contributed to this by talking about how much he talked to Gao, the information exchange they had going. There was a sentiment blaming Redfield for the inability to get more information.”

In reality, the blame went beyond Redfield and his agency. China was a hard target. Even the US spy agencies struggled to gather intelligence on the evolution of the disease. Still, at the moment of truth, the CDC’s decades of investment in building a network in China did not pay off. That failure created an early and significant schism between the agency and the Trump administration.

“What the f*** are we paying for people to be in China if they cannot go where there is an outbreak when there’s an outbreak,” Joe Grogan, then the head of the White House’s Domestic Policy Council, recalled saying repeatedly at the time.

Deputy National Security Advisor Matthew Pottinger was another influential critic of the CDC and one of the first senior White House officials to realise the magnitude of the coronavirus threat. Pottinger had served as a Marine intelligence officer and worked in China as a correspondent for The Wall Street Journal. His coverage of the SARS pandemic had helped shape his view of China as what he called “an expansionist totalitarian empire”.

Pottinger clashed with CDC officials when he pushed to limit travel from China. Many of the agency’s scientists held the traditional public health view that border closures interfere with the movement of medical personnel and goods. On January 31, Trump issued an order restricting most foreigners from entering the United States if they had been in China within the 14 days before their arrival.

The CDC deployed personnel to airports to screen incoming passengers for symptoms, a measure that leaders now admit was futile, given the high number of asymptomatic cases. (Of the 754,124 travellers screened at the US airports by mid-September, only 24 cases of Covid were confirmed, according to CDC records.)

The CDC had gone from being the world’s finest disease SWAT team to batting back claims from the administration that it was doing a lousy job.

Another blow came on February 25, after an ill-fated press conference about the steps Americans might need to take to protect themselves. Leading that briefing was Messonnier, the no-nonsense director of the CDC’s powerful immunization and respiratory diseases center, who had come to prominence during the 2001 anthrax attacks.

Asked by the media team to add a personal touch, Messonnier said she had told her children they needed to prepare for a significant disruption of their lives and had called their school to ask about plans for online learning. Afterward, she left to take her children to the dentist.

But her words had rocked Wall Street and the White House. Soon the staff in the Atlanta Emergency Operations Center saw a news alert with a photo of Messonnier pop up on their phones. A CDC veteran remembers thinking: “Oh, crap, the stock market dropped!”

The market’s fall infuriated the president. Trump had privately confessed to author Bob Woodward that he was publicly downplaying the virus to prevent panic. The CDC would pay the price for undercutting that narrative.

The next day, Trump put Vice President Mike Pence in charge of his coronavirus task force and assumed the role of communicator-in-chief. The CDC, which had been the public face of the government during every health crisis in memory, soon became nearly invisible. After a few more briefings, a Pence aide told the agency’s media staff that this was the president’s stage, not theirs.

Even when Redfield was allowed to speak publicly, his sleepy eyes and soft, droning tone anesthetised listeners. The agency had been effectively muzzled.

“When it mattered the most, they shut us up,” a senior CDC official said. “The threat is clear. If we want to ever be able to talk tomorrow or next week or next month – or whatever is being dangled in front of us, you stay inside the lines.”

A friend of one CDC scientist ribbed him: “We keep waiting for the CDC to show up on a milk carton as a missing child.”

In the months that followed, CDC scientists watching the president’s news conferences on a wall of screens in the agency’s Emergency Operations Center were dumbfounded as Trump countermanded science in a flurry of inaccuracies and dangerous advice, saying the virus would soon go away, theorising about injecting disinfectant as a treatment and dismissing recommendations about wearing a mask.

CDC scientists watching the president’s news conferences on a wall of screens in the agency’s Emergency Operations Center were dumbfounded as Trump countermanded science in a flurry of inaccuracies and dangerous advice. Photo credit: Reuters

Developing a test

As the agency stumbled in China and at home, a group of lab scientists was assigned a high-stakes mission: developing a test for the coronavirus.

Inside a small lab on the CDC’s Atlanta campus, microbiologist Stephen Lindstrom was put in charge. A Saskatchewan native who speaks at a breakneck clip, Lindstrom had studied in Tokyo and defended his PhD dissertation in Japanese. During the H1N1 flu pandemic, his team had invented a test, jumped through regulatory hurdles and shipped it around the world in just two weeks’ time.

“Frankly, he kind of lives for the pressure,” said one of his colleagues.

But this time around, just about everything that could go wrong did. Calculated decisions went sideways, and Lindstrom couldn’t find a quick way to right them. Mystifying contamination appeared at every turn, relegating tests to the trash heap. Precious weeks were lost.

The CDC declined to make Lindstrom available for questions. But lab records obtained by ProPublica and interviews reveal for the first time the mounting pressure and the cascading troubles inside the lab.

As soon as Lindstrom’s team received the genetic sequence from scientists in China in January, they got to work. By the time German researchers on January 13 announced the recipe for the test that would be adopted by the World Health Organization, Lindstrom’s team was almost done building its own.

Lindstrom had turned to the lab’s expert on coronaviruses to design the US test. They chose one that looked for three targets on the same coronavirus gene. While the first and second targets were unique to the new virus spreading in China, the third would identify a broader family of coronaviruses, useful if the virus circulating in China mutated as it infected Americans.

Such a test works like this: Imagine three different pieces of velcro, each custom-made to stick to one of those three genetic targets. If any of them finds a perfect match in a patient’s sample, the test will cause that snippet of genetic material to duplicate over and over until there’s enough to light up a signal, alerting a technician that there is a positive test result.

To make sure the tests work properly, microbiologists prefer to validate a test using actual virus samples taken from people. Lindstrom did not have that, but he could use lab-made pieces of the virus to do the same thing. He also needed to make the velcro-like testing ingredients that find matches in patient samples.

Making both the testing ingredients and the snippets of the virus in the same location, though, goes against best practices. Even in world-class labs, manufacturing pieces of a virus can leave microscopic traces in the environment and on equipment for months. Those can later contaminate tests so that even water would give a positive result. That kind of false-positive renders the tests useless.

Lindstrom’s lab did not have the equipment or expertise needed to make the raw materials for the test. But an underground corridor led to another CDC lab – the “core facility” – in a gleaming glass tower. Lindstrom had used it many times to quickly make testing materials. The facility could make what Lindstrom needed, but it was risky.

Hiring a private company to take on one of those tasks would add at least 10 days to production times, an eternity during an outbreak. So Lindstrom hedged his bets. He placed an order with a contractor for the genetic pieces he needed, but also asked the core facility to make those snippets along with the velcro-like ingredients.

“It is a pretty dangerous procedure to make that in the same facility” due to contamination, said one CDC scientist. “Trying to fast-track it this way was risky.”

Years ago, low-level contamination ruined some CDC tests for Middle East Respiratory Syndrome, even though the core facility made the viral pieces on a different floor from the velcro-like ingredients, according to a person familiar with the matter.

Initially, it looked as if Lindstrom had made a good call. The core facility cranked out the parts needed for the tests and they passed quality checks, suggesting that making all of them in the house was not a problem. On January 20, his lab was able to identify the first positive US case. Still, Lindstrom showed a rare flash of anxiety, telling colleagues: “This is going to either make me or break me.”

Soon specimens were pouring in. At that point, Lindstrom’s lab was the only one in the country able to test samples to confirm whether patients had Covid-19. At the same time, his team was racing to get authorisation from the Food and Drug Administration for test kits that could be distributed to state and local public health labs. Exhausted CDC scientists arrived at 7 am and left after 11 pm.

With that authorisation in the works, Lindstrom asked the core facility to begin mass-producing the ingredients that stick to the three genetic targets in a human sample. Then Lindstrom made a second risky decision. He had his team produce the stand-in for the virus that labs would use to check that a positive sample would trigger a positive result, lab records show.

The ingredients made by Lindstrom’s lab and the core facility passed the quality checks, records show, so Lindstrom sent them to another CDC lab to process and put in vials for the test kits.

Shortage of tests

The first sign of trouble appeared on February 3. Lindstrom’s team performed quality checks on two lots of tests. In one lot, the third target was showing up as present when testers were using only water – a false-positive result. The other lot was fine, records show. Though the flawed lot was set aside, this was a red flag. Contamination can be difficult to eliminate once it occurs, and the batch that failed had gone through the same lab spaces like the one that passed. Nevertheless, Lindstrom released the good lot of tests to be sent to public health labs.

While those tests were in transit, his team performed one last round of quality checks. This time, one of the test kits that they believed was fine also came back with a false positive, records show. Confoundingly, the next day that same kit performed as it should when Lindstrom’s lab checked it, according to a lab record.

Complaints poured in as soon as the tests arrived at the public health labs. Before screening any samples from patients, scientists checked to ensure the tests worked, using water for a negative and the stand-in for the virus for a positive. They found the same problem with the third target: It registered as positive when just testing water.

“There is likely a widespread issue that will need to be addressed immediately,” a California public health official said in an email to the CDC on February 8.

“Aw Shit!” Lindstrom muttered to his staff. His team rechecked bulk testing ingredients from that lot, and found no issues. Then they pulled a portion from the freezer that hadn’t been opened since they received it from the core facility. A few false positives turned up, records show. So Lindstrom’s lab ordered from the core facility a replacement for the ingredient that is supposed to stick to the third target. But he also had contractors make some too.

At first, it looked like the problem could be solved quickly. The core facility delivered test ingredients that passed quality checks on February 11. But subsequent checks – after they had been put in vials again – showed problems, records show.

Lindstrom told colleagues he was convinced there was contamination, but some CDC leaders insisted that the problem was actually a faulty design akin to a software bug – that Lindstrom had chosen genetic sequences that could cause a glitch and show a false positive, according to emails and interviews. While they debated, public health labs with the faulty kits couldn’t process samples, and the FDA still had not authorised any tests made by commercial labs. Instead of a network of labs around the country testing sick people, Lindstrom’s team remained one of the few that could do it, using kits they had made before the problem arose.

The air was filled with tension. At one point, a manager on the CDC coronavirus response team banged on the door to Lindstrom’s lab and demanded test results from his staff rather than waiting for them to be entered in the agency’s database, according to a scientist who was present. During a meeting, Lindstrom yelled at his colleagues for going around him and browbeating his people, according to an official who was present.

When it seemed things couldn’t get any worse, they did. Public health labs began reporting on February 12 that they also were having problems with the part of the test that was supposed to stick to the first target. Subsequent checks by Lindstrom’s lab found the same problem, records show. Lindstrom now had an issue with the ingredients that were supposed to match two of the three targets. And it was not clear whether there was contamination in his lab, the core facility or the separate facility that put the material into vials. Two weeks after the first complaint, the CDC still did not have a solution.

The FDA’s head of lab diagnostics showed up to troubleshoot and found Lindstrom’s lab in disarray. The Wall Street Journal later reported that the FDA official’s boss told CDC leaders that if it had been any other lab, they would have shut it down.

Public health labs were clamouring for tests, and Lindstrom was running out of options. The replacement material that was supposed to stick to the third target was made incorrectly and had to be scrapped, records show. The test kits he had ordered from contractors had not arrived yet.

It seemed like the virus’ fingerprints were everywhere. So when the core facility sent some test ingredients that passed quality checks, Lindstrom hired a contractor to put them in vials. Even those tests came back with problems, a lab record shows.

With the FDA’s blessing, Lindstrom cobbled together test ingredients from different batches that had all passed quality checks, and they dropped the troublesome third target.

By the end of February, three weeks after public health labs first reported problems, the CDC started to send new test kits.

In the aftermath, an investigation by Health and Human Services lawyers pointed to Lindstrom’s lab as a likely source of contamination and praised the core facility for following “extreme precautionary measures” that minimised risk. Lindstrom fumed to colleagues that the Health and Human Services report was inaccurate. He was adamant that evidence showed the contamination originated in the core facility, not his own lab, records show.

The CDC did its own review but never released it. Separately, the Health and Human Services inspector general has been investigating. And some CDC scientists remain convinced that the problem wasn’t contamination but faulty design.

Anger and mistrust caused by the shortage of tests fell on the CDC – even if the FDA shared the blame for sticking to a cumbersome regulatory process that delayed the rollout of more tests. The combination of delays and missteps by the nation’s two top health agencies put the United States dangerously behind in assessing the spread of the virus. In contrast, South Korean officials gave near-instantaneous approval to commercial labs, and they quickly began testing 10,000 people a day.

In a written statement, FDA spokeswoman Lauren-Jei McCarthy said her agency “has demonstrated unprecedented regulatory flexibility in order to speed development and quickly authorise tests”. The FDA, she said, streamlined its process to allow “diagnostic tests to be developed, validated, and deployed within weeks rather than several months to over a year, as traditionally required.”

In July, the acting director of Lindstrom’s division summoned him. He was reassigned to a new job with no official title and few responsibilities.

The following month, a CDC journal published a study that showed that Lindstrom had not been the only one struggling with faulty tests. Commercial labs in Europe had similar problems that delayed testing in at least nine countries.

By then, though, the damage had been done. To the public and within the federal government, the CDC had failed catastrophically at a critical juncture.

This article first appeared on ProPublica.