The CDC’s failed race to roll out an early virus test
breaks caused by nature or biological terrorism, said the CDC’s approach was simply too narrow.
It would have been prudent, he said, “to use the WHO test that was already available. At the same time, get a better understanding of the performance of that test — see if you could improve on it with a second-generation test, as opposed to trying to develop your own test, independent of what’s out there.”
Without tests to identify the early cases, health authorities nationwide were unable to isolate the infected and trace the rapid spread among their close contacts. Those who were asymptomatic, yet contagious, went undetected.
CDC Director Robert Redfield, an appointee of President Donald Trump, took a hands-off approach while the in-house manufacturing efforts foundered and agency scientists clashed over whether to alter the design of the problemplagued test, according to CDC and other federal officials.
James Le Duc, who as the director of the Galveston National Laboratory in Texas oversees development of diagnostics for rare pathogens, said he is perplexed by the CDC’s decision-making.
“The test that the WHO used early on was quite successful,” said Le Duc, a former senior CDC official who still serves as an adviser to the agency. “I frankly don’t know why CDC didn’t accept it.”
Redfield and other CDC leaders declined to be interviewed or to respond to written questions about the agency’s handling of the test.
“Appreciate the opportunity, but we are going to pass,” said CDC spokesman Benjamin N. Haynes.
The struggles with the test kits had far-reaching consequences.
“If we would have put [tests] out there quicker, could we have saved lives? Well sure,’’ said Peter C. Iwen, director of the Nebraska Public Health Laboratory in Omaha. “If we would have diagnosed quicker, we would have saved people.”
Anew virus was exploding in Wuhan, a Chinese city with 11 million people connected by its airport to destinations around the world. In the United States, doctors and hospitals were waiting for the federal Centers for
Disease Control and Prevention to develop a test to detect the threat.
On Jan. 13, the World
Health Organization had made public a recipe for how to configure such a test, and several countries wasted no time getting started: Within hours, scientists in Thailand used the instructions to deploy a new test.
The CDC would not roll out one that worked for 46 more days.
Inside the 15-acre campus of the CDC in northeast
Atlanta, the senior scientists developing the coronavirus test were fighting and losing the battle against time.
The agency squandered weeks as it pursued a test design far more complicated than the WHO version and as its scientists wrestled with failures that regulators would later trace to a contaminated lab.
The Washington Post reviewed internal documents and interviewed more than 30 government scientists and others with knowledge of the events to understand more fully the missteps in those early weeks as the coronavirus began to spread unchecked across the nation. Most spoke anonymously because they were not authorized to do so publicly.
This account reveals new details about how an overly ambitious test design and laboratory contamination caused the CDC’s delay, and describes previously unreported challenges that confronted the agency scientists assigned to carry out the work.
CDC leaders underestimated the threat posed by the new virus — and overestimated the agency’s ability to design and rapidly manufacture a test. Qualitycontrol measures failed to prevent the shipping of compromised kits to dozens of state and local public health labs.
The CDC’s response to what became the nation’s Since its founding in 1946, deadliest pandemic in a the CDC has grown from a century marked a low point regional bulwark against in its 74-year history. More malaria in the southern than 329,000 Americans United States to a world have died of the virus. In an leader in fighting diseases of agency long known for its all kinds. competence, hubris became Nowhere has the CDC’s the nemesis that could not be presence abroad been larger overcome. than in Thailand, where the
The CDC has quietly agency maintains offices and removed or shifted to other a staff of about 170 epidemiduties several scientists who ologists, laboratory specialwere involved in developing ists and others. In 1980, the the coronavirus test, accordCDC established its first ing to those familiar with the overseas epidemiology promatter. Those displaced gram in a suburb of Bangincluded a longtime division kok, training a new cadre of director, a supervising disease detectives. branch chief and a respiratoIn early January, Thai ry virus specialist who led doctors in Bangkok were the design of the test. worried by the outbreak in
The problems with the Wuhan, less than seven CDC’s test kits are the subhours away by airliner. They ject of ongoing inquiries by strategized at length about the Department of Health the threat with their local and Human Services’ inCDC counterparts. They also spector general and the U.S. learned from scientists Government Accountability enough about the genetic Office. makeup of the new coronavi
“We missed the game,” a rus to begin developing a senior CDC disease-transmolecular test for in-hospital missionuse.specialistsaidinan interview. “Many people That initial test would use here wish we had done real-time polymerase chain things differently.” reaction, or RT-PCR, to
Nearly all of those in examine sputum samples in charge at the highest levels search of unique genetic of the CDC lacked hands-on material from the virus. lab expertise and for weeks On Jan. 12, using their new deferred to subordinates - test, the Thais became the scientists who were logging first country to confirm a grueling, high-pressure coronavirus case outside hours on the highly techChina, a sickened traveler nical work. from Wuhan.
Stephen A. Morse, a reThe same day, the Chinese tired agency microbiologist posted on the Internet what who had helped establish a public health authorities formal affiliation with the worldwide had been waiting public health labs to ensure for: the complete genetic rapid responses to out- sequence of this previously
Agency grew into world leader
unseen strain of the coronavirus, the cause of the disease soon to be named covid-19.
Another breakthrough came the next day, Jan. 13, when the WHO publicly shared a protocol, essentially a recipe, specifying the materials needed to build a molecular test.
The Thais used that protocol to make a second test to detect the virus. This redundancy would eventually become the model for developing a vaccine against the virus.
“Multiple shots on goal,” as Anthony Fauci, the U.S. infectious-disease expert, often said of the approach. That way, said Fauci, if one attempt stalled or failed, another might score.
The approach paid off immediately for the Thais.
“We have not relied only on one testing technique from one laboratory,” Krit Pongpirul, a researcher and clinical epidemiologist at Bangkok’s Bumrungrad International Hospital, said in an email exchange with The Post.
Using their version of the WHO test, Thai health officials within days found other cases, including a taxi driver. He had not been to Wuhan, but Pongpirul and a colleague suspected he had become infected by Chinese travelers. Thai officials traced and tested close contacts of the cabbie and others who were found to be infected. The contacts were persuaded to isolate themselves to prevent the virus from spreading.
One of the infected, the Thais found, was asymptomatic - an early warning that the coronavirus was being spread by those not overtly sick.
“Patient 4 had detectable [virus] for 4 consecutive days, but we were only able to follow her for 7 days before she returned to China,” the Thai doctors and others wrote in a subsequent scientific journal article. “Her case is an example of a person without reported symptoms but with radiologic evidence of disease and detectable virus over several days.”
By the end of January, the Thais had diagnosed 11 patients with covid-19, according to Pongpirul, who described the details in the email correspondence and in the journal Emerging Infectious Diseases, published by the CDC.
Four of Pongpirul’s 11 co-authors were CDC specialists - three of them based in Bangkok and the other in Atlanta.
“The early availability of the RT-PCR testing definitely helped to reduce transmission and save lives,” Pongpirul told The Post by email.
The Thai scientists shared their success and insights in a Jan. 13 conference call that included CDC personnel in Bangkok and at headquarters in Atlanta.
“This was the first indication of international spread,” said an Atlantabased official who described the call as riveting. “‘Why Thailand?’ We found out there was a direct flight from Wuhan.’’
John R. MacArthur, a physician who had led the CDC’s Thailand operations since 2013, said that when PCR testing confirmed the first case there, “I immediately contacted CDC leadership in Atlanta to let them know what was happening.”
“Seeing the first case outside of China, I thought, was a big moment,’’ MacArthur said in a phone interview.
MacArthur, one of the co-authors of the journal article, said the CDC’s lab training in Thailand gave officials there “the tools that they needed to respond very quickly and effectively.’’
At CDC headquarters,
officials did not adopt the strategy that proved successful in Thailand.
Instead, the agency planned to design and manufacture its own test inhouse and ship 300 of those kits to 120 public health labs throughout the United States.
At the time, CDC officials in Atlanta expected that the strain emanating from Wuhan, while worrisome, would be no worse than two earlier coronaviruses that spurred dread before fizzling out, those familiar with the matter said.
One of those viruses, severe acute respiratory syndrome, or SARS, originated in China in late 2002 and killed 774 people worldwide, but none in the United States. Middle East respiratory syndrome, or MERS, emerged in 2012 and over the next seven years killed 866 people, but resulted in only two U.S. infections and no deaths.
Neither SARS nor MERS was known to be widely spread by people who had no symptoms.
“It was being treated as a MERS situation or a SARS situation,” said a CDC scientist who had helped confront the new threat in January and who declined to speak on the record because he was not authorized to do so. “At that point we thought it was going to be a limited activity.”
‘Can you make this happen?’
In the first week of January, Nancy Messonnier, a physician and director of the CDC’s National Center for Immunization and Respiratory Diseases at the Atlanta campus, spoke to Stephen Lindstrom, an accomplished respiratory virus specialist. She wanted to know if, and how soon, he could get a coronavirus test up and running.
“Can you make this happen?” she asked, according to a person familiar with the exchange.
Lindstrom, co-inventor of seven earlier CDC tests for strains of the flu, had transitioned in 2018 to lead a respiratory virus lab that focused on diseases other than influenza.
Before saying yes to Messonnier, Lindstrom had an ask that she would promptly grant: He needed to pull in at least 20 people to supplement his staff of eight lab specialists.
On Jan. 9, Lindstrom outlined his plans to Messonnier, as well as the director of the viral diseases division, Mark A. Pallansch, and the respiratory viruses branch chief, Susan Gerber, among others. In a conference room near Messonnier’s eighthfloor office, Lindstrom narrated a slide show that spelled out how the test manufacturing and other tasks would be divided up.
That same week, Lindstrom recruited Julie M. Villanueva, who was also a PhD scientist and with whom he had collaborated on anti-flu efforts over the previous decade. In 2016, she had led the CDC’s Emergency Operations Center during an outbreak of the Zika virus.
Over the next few days, Lindstrom, who had not previously designed a coronavirus test, set about researching what materials were necessary as well as a recipe for combining them to detect the virus with PCR.
All of the CDC scientists and officials involved with the test’s development and named in this report - including Messonnier, Lindstrom, Pallansch, Gerber and Villanueva - declined to comment or referred questions to the agency’s public affairs office.
Invented in 1983, PCR is a multi-step test to detect infectious agents, including viruses in humans, using a sample of sputum or other genetic material. A machine extracts nucleic acids from the sample, placing them into a small tube with various chemical reagents, including an enzyme that converts viral RNA, which is present in coronaviruses, into DNA.
Some of the solution is then transferred to tiny plastic wells containing additional reagents to help detect whether the virus is present. The wells are placed into a PCR machine, resembling a midsize office photocopier.
The process seeks to copy and amplify targeted regions of the coronavirus genome. If the virus is present in the original sample, a detectable, fluorescent dye is released.
Two components that Lindstrom designed for the CDC’s test, called N1 and N2, focused on separate regions of the virus’s genome, a conventional approach.
But Lindstrom, aided by a lab colleague with coronavirus experience, Xiaoyan Lu, chose to add a third component that distinguished the CDC’s test design from others: This component would identify a wider family of coronaviruses, including SARS and bat-carried strains not known to have infected humans. They called it N3, and Lindstrom told colleagues it would help detect the novel coronavirus if it began to mutate, according to interviews with those familiar with the matter.
Villanueva’s chief role was to ensure that each step of development and production was properly documented and communicated to the public health labs and to regulators at the Food and Drug Administration. CDC officials expected the FDA to expedite emergency authorization of the test, and scientists said Lindstrom and Villanueva worked so seamlessly that colleagues took to calling them what sounded like one name, “Steve-andJulie.”
On Jan. 17, just days after the Chinese made public the virus’s genetic sequence, Messonnier announced at a news briefing that health authorities in Thailand and Japan had already used molecular testing to detect coronavirus cases. Testing was beginning as well in South Korea and Taiwan.
“We at the CDC also have the ability to do that today, but we are working on a more specific diagnostic,” Messonnier said, indicating that the agency was seeking a more sophisticated test.