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Washington Post Investigation into CDC’s Failed Rollout of COVID-19 Tests Shows Federal Government’s Missteps and Miscalculations, Part One of Two

Previously unreported email messages and documents paint vivid picture of public health laboratory officials’ dismay and frustration over testing delays

Between late January and early March, Clinical laboratory leaders watched with dismay as federal government missteps crippled the Centers for Disease Control and Prevention’s (CDC) rollout of its COVID-19 diagnostic testing in the early days of the pandemic. The resulting lack of testing capacity enabled the novel coronavirus’ spread across the United States.

This first part of Dark Daily’s two-part e-briefing covers how investigators at the Washington Post (WP) have produced a timeline describing the CDC initial failure to produce a reliable laboratory test for COVID-19 and the regulatory hurdles that blocked medical laboratories from developing their own tests for the virus. The WP’s report is based on previously unreleased email messages and other documents reviewed by the WP, as well as the newspaper’s exclusive interviews with medical laboratory scientists and officials involved.

A New York Times report on the federal government’s initial review of the testing kit failure pinned the blame on sloppy practices at CDC laboratories in Atlanta and a lack of expertise in commercial manufacturing. However, the WP reported that COVID-19 testing kits were delayed due to a “glaring scientific breakdown” at the central lab, created when the CDC facilities that assembled the kits “violated sound manufacturing practices” that resulted in cross contamination of testing compounds.

A US Department of Health and Human Services (HHS) investigation into the COVID-19 testing crisis is under way, however the HHS is not expected to release its report until 2021.

How Did We Get Here?

The US and other countries have criticized China for a lack of transparency about the virus’ emergence, which came to light on December 31, 2019, when China reported a cluster of pneumonia cases in Wuhan, according to a World Health Organization (WHO) timeline. A week later, Chinese authorities identified the pneumonia-like illness as being caused by a new novel coronavirus.

In the US, the first case of COVID-19 was found January 21 in a Washington State man who had traveled to Wuhan. But in the weeks that followed, the US government’s inability to establish a systematic testing policy became the catalyst for the virus’ ultimate spread to more than two million people, notes the CDC website.

ProPublica, which conducted its own investigation into the early stages of the government’s coronavirus response, blamed the failures on “chaos” at the CDC and “an antiquated public health system trying to adapt on the fly.”

The CDC’s first mistake may have been underestimating the danger COVID-19 posed to public health in this country. During a January 15 conference call, CDC scientists assured state and county public health officials that the agency was developing a COVID-19 diagnostic test which soon would be available, but which may not be needed “unless the scope gets much larger than we anticipate right now,” reported the WP.

A week later, an interview with CNBC, President Trump said, “We have it under control. It’s going to be just fine.”

CDC scientists designed their test in seven days, which, according to the WP investigators, is “a stunningly short period of time for a healthcare system built around the principles of medical quality and patient safety, not speed.” But when those initial CDC-made tests arrived at a New York City public health laboratory on February 8, lab technicians discovered the COVID-19 assays often indicated the presence of the coronavirus in samples that the lab’s scientists knew did not contain the virus.

When the scientists informed Lab Director Jennifer Rakeman, PhD, Assistant Commissioner, New York City Department of Health and Mental Hygiene, her response, according to the WP, was “Oh, s—. What are we going to do now?”

That night, Director Jill Taylor, PhD, Director of New York State’s Wadsworth Center public health reference laboratory, emailed state health officials, stating, “There is a technical problem in one of the reagents which invalidates the assay and will not allow us to perform the assay,” reported the WP. “I’m sorry not to have better news.”

Scott Becker (above), Executive Director of the Association of Public Health Laboratories (APHL), voiced his concerns about the CDC’s flawed COVID-19 test kits in an email to a CDC official, reported the WP. “The states and their governors are going to come unglued,” Becker wrote, adding, “If the CDC doesn’t get ahead of this, it will be a disaster.” (Photo copyright: Bill O’Leary/The Washington Post.)

‘The Silence from CDC is Deafening’

On February 10, Joanne Bartkus, PhD, then-Lab Director of the Minnesota Health of Department, wrote to APHL Executive Director Scott Becker: “The silence from CDC … is deafening. What is going on?” reported the WP.

By the end of February, the Associated Press (AP) reported that only 472 patients had been tested for COVID-19 nationwide. By comparison, South Korea, which identified its first case of COVID-19 on the same day as the US, was testing 1,000 people per day.

A WHO spokesperson told the WP that, “… no discussions occurred between WHO and CDC (or other US government agencies) about WHO providing COVID-19 tests to the US.” When the CDC’s original COVID-19 test kit failed, there may not have been a Plan B. This may explain why the opportunity to contain COVID-19 through surveillance testing was lost during the weeks it took to design a fix for the CDC test and loosen regulations so clinical laboratories could develop their own tests.

As medical laboratory scientists and clinical laboratory leaders know, the lack of early COVID-19 testing was a public health failure and painted a false picture of the virus’ spread. Nearly five months after the first case of the virus was confirmed in the US, testing capacity may only now be outpacing demand.

Click here to read part two of our coverage of the Washington Post’s investigation.

—Andrea Downing Peck

Related Information:

Inside the Coronavirus Testing Failure: Alarm and Dismay among the Scientists who Sought to Help

Contamination at CDC Lab Delayed Rollout of Coronavirus Tests

CDC Labs Were Contaminated, Delaying Coronavirus Testing, Officials Say

Audit of HHS’s Production and Distribution of COVID-19 Lab Test Kits

Internal Emails Show How Chaos at the CDC Slowed the Early Response to Coronavirus

Trump Says He Trusts China Xi on Coronavirus and the US Has it ‘Totally under Control’

Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies

Scientist described the speed at which SARS-CoV-2’s full sequence of genetic material was made public as ‘unprecedented’ and medical labs are rushing to validate tests for this new disease

In the United States, headlines scream about the lack of testing for the novel Coronavirus disease 2019 (COVID-19). News reporters ask daily why it is taking so long for the US healthcare system to begin testing large numbers of patients for SARS-CoV-2, the virus that causes COVID-19. Yet, pathologists and clinical laboratory scientists know that new technologies for gene sequencing and diagnostic testing are helping public health laboratories bring up tests for a previously unknown new disease faster than at any time in the past.

At the center of the effort to develop accurate new assays to detect SARS-CoV-2 and help diagnose cases of the COVID-19 disease are medical laboratory scientists working in public health laboratories, in academic medical centers, and in research labs across the United States. Their collective efforts are producing results on a faster timeline than in any previous discovery of a new infectious disease.

For example, during the severe acute respiratory syndrome (SARS) outbreak in 2003, five months passed between the first recognized case of the disease in China and when a team of Canadian scientists cracked the genetic code of the virus, which was needed to definitively diagnose SARS patients, ABC News reported. 

In contrast, Chinese scientists sequenced this year’s coronavirus (originally named 2019-nCoV) and made it available on Jan. 10, 2020, just weeks after public health officials in Wuhan, China, reported the first case of pneumonia from the unknown virus to the World Health Organization (WHO), STAT reported.

Increases in sequencing speed enabled biotechnology companies to quickly create synthetic copies of the virus needed for research. Roughly two weeks later, scientists completed sequencing nearly two dozen more samples from different patients diagnosed with COVID-19.

Molecular biologist Kristian Andersen, PhD (above right, with graduate students who helped sequence the Zika virus), an Associate Professor in the Department of Immunology and Microbiology at Scripps Research in California and Director of Infectious Disease Genomics at Scripps’ Translational Research Institute, worked on the team that sequenced the Ebola genome during the 2014 outbreak. He told STAT that the pace of sequencing of the SARS-CoV-2 coronavirus is “unprecedented.”  (Photo copyright: Scripps Research.)

Lower Sequencing Costs Speed COVID-19 Diagnostics Research

Additionally, a significant decline in the cost of genetic synthesis is playing an equally important role in helping scientists slow the spread of COVID-19. In its coverage of the SARS-CoV-2 outbreak, The Verge noted that two decades ago “it cost $10 to create a synthetic copy of one single nucleotide, the building block of genetic material. Now, it’s under 10 cents.” Since the coronavirus gene is about 30,000 nucleotides long, that price reduction is significant.

Faster sequencing and cheaper access to synthetic copies is contributing to the development of diagnostic tests for COVID-19, an important step in slowing the disease.

On Feb. 4, 2020, the US Food and Drug Administration (FDA) issued its first emergency use authorization (EUA) for a diagnostic test for the coronavirus called 2019-nCoV Real-Time RT-PCR Diagnostic Panel. The test was developed by the US Centers for Disease Control and Prevention (CDC).

“This continues to be an evolving situation and the ability to distribute this diagnostic test to qualified medical laboratories is a critical step forward in protecting the public health,” FDA Commissioner Stephen M. Hahn, MD, said in an FDA statement.

However, the Washington Post soon reported that the government-created coronavirus test kits contained a “faulty component,” which as of February 25 had limited testing in the US to only 426 people, not including passengers who returned to the US on evacuation flights. The Post noted that the nation’s public health laboratories took “the unusual step of appealing to the FDA for permission to develop and use their own [laboratory-developed] tests” for the coronavirus.

“This is an extraordinary request, but this is an extraordinary time,” Scott Becker,

Chief Executive of the Association of Public Health Laboratories (APHL), told the Post.

Parallel efforts to develop and validate tests for COVID-19 are happening at the clinical laboratories of academic medical centers and in a number of commercial laboratory companies. As these labs show their tests meet FDA criteria, they become available for use by physicians and other healthcare providers.

Dark Daily’s sister publication, The Dark Report just published an intelligence briefing about the urgent effort at the clinical laboratory of Northwell Health to develop both a manual COVID-19 assay and a test that can be run on the automated analyzers already in use in the labs at Northwell Health’s 23 hospitals. (See TDR, “Northwell Lab Team Validates COVID-19 Test on Fast Timeline,” March 9, 2020.)

Following the FDA’s March 13 EUA for the Thermo Fisher test, Hahn said, “We have been engaging with test developers and encouraging them to come to the FDA and work with us. Since the beginning of this outbreak, more than 80 test developers have sought our assistance with development and validation of tests they plan to bring through the Emergency Use Authorization process. Additionally,” he continued, “more than 30 laboratories have notified us they are testing or intend to begin testing soon under our new policy for laboratory-developed tests for this emergency. The number of products in the pipeline reflects the significant role diagnostics play in this outbreak and the large number of organizations we are working with to bring tests to market.”

So far, the FDA has issued a total of seven EUAs:

Pharma Company Uses Sequencing Data to Develop Vaccine in Record Time

Even as clinical laboratories work to develop and validate diagnostic tests for COVID-19, drug manufacturers are moving rapidly to develop a COVID-19 vaccine. In February, Massachusetts-based biotechnology company Moderna Therapeutics (NASDAQ:MRNA) announced it had shipped the first vials of its potential coronavirus vaccine (mRNA-1273) to the National Institute of Allergy and Infectious Disease (NIAID) for use in a Phase One clinical trial.

“The collaboration across Moderna, with NIAID, and with CEPI [Coalition for Epidemic Preparedness Innovations] has allowed us to deliver a clinical batch in 42 days from sequence identification,” Juan Andres, Chief Technical Operations and Quality Officer at Moderna, stated in a news release.

The Wall Street Journal (WSJ) reported that NIAID expects to start a clinical trial of about 20 to 25 healthy volunteers by the end of April, with results available as early as July or August.

“Going into a Phase One trial within three months of getting the sequence is unquestionably the world indoor record,” NIAID Director Anthony Fauci, MD, told the WSJ. “Nothing has ever gone that fast.”

There are no guarantees that Moderna’s coronavirus vaccine will work. Furthermore, it will require further studies and regulatory clearances that could delay widespread distribution until next year.

Nonetheless, Fauci told the WSJ, “The only way you can completely suppress an emerging infectious disease is with a vaccine. If you want to really get it quickly, you’re using technologies that are not as time-honored as the standard, what I call antiquated, way of doing it.”

In many ways, the news media has overlooked all the important differences in how fast useful diagnostic and therapeutic solutions for COVID-19 are moving from research settings into clinical use, when compared to early episodes of the emergence of a new infectious disease, such as SARS in 2003.

The story the American public has yet to learn is how new genetic sequencing technologies, improved diagnostic methods, and enhanced informatics capabilities are being used by researchers, pathologists, and clinical laboratory professionals to understand this new disease and give healthcare professionals the tools they need to diagnose, treat, and monitor patients with COVID-19.

—Andrea Downing Peck

Related Information:

To Fight the Coronavirus, Labs Are Printing Its Genome

DNA Sleuths Read the Coronavirus Genome, Tracing Its Origins and Looking for Dangerous Mutations

FDA Takes Significant Step in Coronavirus Response Efforts, Issues Emergency Use Authorization for the First 2019 Novel Coronavirus Diagnostic

Coronavirus (COVID-19) Update: FDA Issues Emergency Use Authorization to Thermo Fisher

A Faulty CDC Coronavirus Test Delays Monitoring of Disease’s Spread

Moderna Ships mRNA Vaccine Against Novel Coronavirus (mRNA-1273) for Phase 1 Study

Drugmaker Moderna Delivers First Experimental Coronavirus Vaccine for Human Testing

China Detects Large Quantity of Novel Coronavirus at Wuhan Seafood Market

Scientists Claim SARS Breakthrough

Discovery of ‘Hidden’ Outbreak Hints That Zika Virus Can Spread Silently

Research Use Only Real-Time RT-PCR Protocol for Identification of 2019-nCoV

Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19)

Roche’s Cobas SARS-Cov-2 Test to Detect Novel Coronavirus Receives FDA Emergency Use Authorization and Is Available in Markets Accepting the CE Mark

Hologic’s Molecular Test for the Novel Coronavirus, SARS-CoV-2, Receives FDA Emergency Use Authorization

Emergency Use Authorization (EUA) Information and List of All Current EUAs

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