COLA Clinical Laboratory Workforce Summit in Fort Worth, Texas, Engages Stakeholders in Effort to Train More Medical Laboratory Scientists

Representatives from almost 50 different clinical laboratories, professional associations, and societies came together this week to align efforts to expand the supply and retention of qualified laboratory scientists

FORT WORTH, TEXAS—Last week, representatives from a broad cross section of clinical laboratories, lab and pathology associations, public health laboratories, and lab regulatory bodies gathered specifically to identify ways to expand the number of skilled lab professionals.

COLA organized the “Workforce Action Alliance Summit,” a one-day gathering of key clinical laboratory stakeholders who share a common interest in developing initiatives that would directly increase the number of individuals choosing to pursue a career in laboratory medicine.

This is not a new problem, as the lack of trained laboratory scientists across all scientific disciplines has been acute for many years.

COLA Graphic
The logo above was developed by COLA to support the Workforce Action Alliance Summit. This year’s first work session took place last week in Fort Worth, Texas. Participants came from such organizations as the CDC Division of Laboratory Systems (DLS), American Society for Clinical Laboratory Science (ASCLS), American Society for Clinical Pathology (ASCP), Association of Public Health Laboratories (APHL), and American Association for Clinical Chemistry (AACC), along with a number of clinical laboratories. The goal of this initiative is to pull together wide-ranging interests within the profession of laboratory medicine and align specific efforts with projects that directly increase the recruitment, training, and retention of skilled laboratory scientists. (Graphic copyright: COLA.)

Call to Action

In a communication sent to invited participants, COLA’s CEO, Nancy Stratton, and COO, Kathy Nucifora, described the objective of the summit, writing:

“Clearly a call to collective action is required if we are to address the impending clinical laboratory workforce shortage. The past three years have demonstrated the significance of a resilient laboratory infrastructure, not only for the daily care of millions of Americans, but also during the global pandemic. The numerous efforts currently underway to resolve the shortage are unquestionably a component of the solution. Many, however, believe that these efforts are insufficient to close the gap between the projected number of new entrants into the profession, the rate at which those currently in the profession are departing, and the future demand for laboratory testing.”

Robert L. Michel, Editor-in-Chief of Dark Daily’s sister publication The Dark Report was a participant at COLA’S workforce summit. The Dark Report regularly profiles clinical laboratory organizations that have developed innovative and productive initiatives designed to increase the number of students choosing to train as medical technologists (MTs), clinical laboratory scientists (CLSs), medical laboratory technologists (MLTs) and other skilled lab positions.

In materials distributed at the summit, the ongoing gap between demand for skilled lab professionals and the supply was illustrated thusly:

“The US Department of Labor estimates 320,000 bachelors and associates degreed laboratory professionals are working in the United States. If each of those professionals worked a standard 40-year career, the natural annual attrition of 2.5% would require 8,000 new professionals to maintain their current numbers. This exceeds the current output of accredited educational programs by more than 1,000 annually.” 

Case Studies of Success

Over the course of the day, participants at the summit heard about the successes of certain laboratory organizations designed to get more students into training programs, supported by the educational courses required for them to become certified in their chosen area of laboratory medicine. These case studies centered around several themes:

  • Obtaining funding specifically to establish an MT/CLS training program to increase the number of candidates in a region. One example involved ARUP Laboratories and its success at working with a local Congressional representative to get a $3 million federal grant funded as part of a larger legislative package.
  • The medical laboratory scientist (MLS) program at Saint Louis University (SLU) worked with Quest Diagnostics to launch an accelerated bachelor’s degree program. The 16-month program combines online academic courses with intensive hands-on learning and clinical experiences in Quest’s Lenexa, Kansas, laboratory. The first students in this accelerated degree program began their studies in the spring semester of 2023.
  • By rethinking the structure of its existing didactic and experiential learning structure, NorthShore University HealthSystem’s MLS program, located at Evanston Hospital north of Chicago, doubled its enrollment capacity.

During the afternoon, working groups addressed ways that lab organizations can collaborate to increase recruitment and retention of laboratory scientists across all disciplines of lab medicine. This input was synthesized into action planning for the three priorities that can lead to expanding the lab workforce.

By day’s end, several working groups were organized with specific next steps. COLA is taking the lead in managing this initiative and giving it momentum. All clinical laboratory professionals and pathologists are welcome to participate in the Workforce Action Alliance (WAA). Anyone wishing to learn more can contact COLA by clicking here, calling 800-981-9883, or by visiting https://education.cola.org/contact-us-page.

Robert L. Michel

Related Information:

COLA Workforce Action Alliance Summit

Building the Capacity and Resiliency of the Laboratory Workforce

Industry Execs Will Convene to Address the Lab Workforce Shortage

Executives Convene to Address the Laboratory Workforce Shortage

Medical Laboratories Respond to Monkeypox Outbreak Using CDC-Developed Diagnostic Test

The federal agency shipped tests to five commercial clinical laboratory companies, augmenting efforts by public health labs

Medical laboratories in the US are ramping up their efforts to respond to an outbreak of monkeypox that has been spreading around the globe. Microbiologists and clinical laboratory scientists will be interested to learn that this infectious agent—which is new to the US—may be establishing itself in the wild rodent population in this country. If proved to be true, it means Americans would be at risk of infection from contact with rodents as well as other people.

The Centers for Disease Control and Prevention (CDC) announced on May 18 that it had identified the infection in a Massachusetts resident who had recently traveled to Canada. As of August 3, the federal agency was reporting 6,617 confirmed cases in the US.

Soon after the CDC’s initial announcement, public health labs belonging to the CDC’s Laboratory Response Network (LRN) were testing for the infection, according to an Association of Public Health Laboratories (APHL) press release. The LRN uses a CDC-developed test designed to detect Orthopoxviruses, the family that includes the monkeypox virus.

“Because there are no other non-variola orthopoxviruses circulating in the US, a positive test result is presumed to be monkeypox,” states the APHL press release.

Chris Mangal
“As we focus on the US response, we keep a close watch on the global outbreak. Infectious diseases don’t respect borders, as we know,” said Chris Mangal (above), director of public health preparedness and response, APHL, in a press release. “I am proud of how LRN member laboratories have rapidly and effectively responded to this emergency. This is precisely what the LRN was intended to do. Should this outbreak continue to grow, preparing for expanded testing and increasing capacity beyond LRN laboratories is important to ensuring we are ready for a surge in testing.” (Photo copyright: Association of Public Health Laboratories.)
 

 

Commercial Labs Get Involved

Seeking to bolster testing capacity, the federal Department of Health and Human Services (HHS) announced on June 22 that the CDC had begun shipping Orthopoxvirus PCR tests to five commercial lab companies. They include:

“By dramatically expanding the number of testing locations throughout the country, we are making it possible for anyone who needs to be tested to do so,” said HHS Secretary Xavier Becerra in an HHS press release.

Labcorp was first out of the gate, announcing on July 6 that it was offering the CDC-developed test for its customers, as well as accepting overflow from public labs. “We will initially perform all monkeypox testing in our main North Carolina lab and have the capacity to expand to other locations nationwide should the need arise,” said Labcorp chief medical officer and president Brian Caveney, MD, in a press release.

Mayo Clinic Laboratories followed suit on July 11, announcing that the clinic’s Department of Laboratory Medicine and Pathology would perform the testing at its main facility in Rochester, Minnesota.

“Patients can access testing through Mayo Clinic healthcare professionals and will soon be able to access testing through healthcare professionals who use Mayo Clinic Laboratories as their reference laboratory,” Mayo stated in a press release.

Then, Quest Diagnostics announced on July 13 that it was testing for the virus with an internally developed PCR test, with plans to offer the CDC test in the first half of August.

The lab-developed test “was validated under CLIA federal regulations and is now performed at the company’s advanced laboratory in San Juan Capistrano, Calif.,” Quest stated in a press release.

Public Health Emergency?

Meanwhile, the CDC announced on June 28 that it had established an Emergency Operations Center to respond to the outbreak. A few weeks later, on July 23, World Health Organization (WHO) Secretary-General Tedros Adhanom Ghebreyesus, PhD, declared that the outbreak represented “a public health emergency of international concern.”

He noted that international health regulations required him to consider five elements to make such a declaration.

“WHO’s assessment is that the risk of monkeypox is moderate globally and in all regions, except in the European region where we assess the risk as high,” he said in a WHO news release. “There is also a clear risk of further international spread, although the risk of interference with international traffic remains low for the moment. So, in short, we have an outbreak that has spread around the world rapidly, through new modes of transmission, about which we understand too little, and which meets the criteria in the International Health Regulations.”

Still, public health authorities have made it clear that this is not a repeat of the COVID-19 outbreak.

“Monkeypox virus is a completely different virus than the viruses that cause COVID-19 or measles,” the CDC stated in a June 9 advisory. “It is not known to linger in the air and is not transmitted during short periods of shared airspace. Monkeypox spreads through direct contact with body fluids or sores on the body of someone who has monkeypox, or with direct contact with materials that have touched body fluids or sores, such as clothing or linens. It may also spread through respiratory secretions when people have close, face-to-face contact.”

The New York Times reported that some experts disagreed with the CDC’s assessment that the virus “is not known to linger in the air.” But Professor of Environmental Health Donald Milton, MD, DrPH, of the University of Maryland, told The Times it is still “not nearly as contagious as the coronavirus.”

The Massachusetts resident who tested positive in May was not the first known case of monkeypox in the US, however, previous cases involved travel from countries where the disease is more common. Two cases in 2021—one in Texas and one in Maryland—involved US residents who had recently returned from Nigeria, the CDC reported. And a 2003 outbreak in the Midwest was linked to rodents and other small mammals imported to Texas from Ghana in West Africa.

Testing Procedures

The CDC has issued information for healthcare professionals, including guidelines for specimen collection, along with information for laboratory personnel who may be testing the specimens.

CNN reported on Aug. 4 that phlebotomists who work for Quest and Labcorp have refused to draw blood from suspected monkeypox patients.

“Labcorp and Quest don’t dispute that in many cases, their phlebotomists are not taking blood from possible monkeypox patients,” according to CNN. “What remains unclear, after company statements and follow-ups from CNN, is whether the phlebotomists are refusing on their own to take blood or if it is the company policy that prevents them. The two testing giants say they’re reviewing their safety policies and procedures for their employees.”

One symptom of monkeypox, the CDC states, is a rash resembling pimples or blisters. Clinicians are advised that two swabs should be collected from each skin lesion, though “procedures and materials used for collecting specimens may vary depending on the phase of the rash.”

“Effective communication and precautionary measures between specimen collection teams and laboratory staff are essential to maximizing safety when manipulating specimens suspected to contain monkeypox virus,” the CDC notes. “This is especially relevant in hospital settings, where laboratories routinely process specimens from patients with a variety of infectious and/or noninfectious conditions.” 

Perhaps the negative reaction to the CDC’s initial response to the COVID-19 outbreak in the US is driving the federal agency’s swift response to this new viral threat. Regardless, clinical laboratories and pathology groups will play a key role in the government’s plan to combat monkeypox in America.

Stephen Beale

Related Information:

CDC: Monkeypox

CDC and Health Partners Responding to Monkeypox Case in the US

CDC Activates Emergency Operations Center for Monkeypox Response

HHS Expanding Monkeypox Testing Capacity to Five Commercial Laboratory Companies

Labcorp to Begin Monkeypox Testing Today, Doubling Nationwide Testing Capacity

Labcorp First National Laboratory to Offer Monkeypox Test

Monkeypox (Orthopoxvirus), DNA, PCR Test

Mayo Clinic Laboratories to Begin Monkeypox Testing Today, Increasing Nationwide Testing Capacity

Mayo Clinic Laboratories Launches Monkeypox Test to Increase Access, Availability

Quest Now Offers a Test to Detect Monkeypox Virus DNA, Delivering Faster Answers for You and Your Patients

Quest Diagnostics to Begin Monkeypox Testing Today, Increasing Nationwide Testing Capacity

Quest Diagnostics Launches Monkeypox Virus Testing

APHL Supports Public Health Response to Monkeypox, Phased Expansion of Testing

World Health Organization: Monkeypox

Second Meeting of the International Health Regulations (2005) (IHR) Emergency Committee regarding the Multi-Country Outbreak of Monkeypox

WHO Director-General’s Statement at the Press Conference Following IHR Emergency Committee Regarding the Multi-Country Outbreak of Monkeypox

CDC Dismisses Airborne Transmission of Monkeypox. Some Experts Disagree.

We Let Monkeypox Spread for Too Long. If It Infects Our Pets, There’s No Getting Rid of It

FEMA Paid a Just-Formed Company Millions of Dollars for COVID-19 Specimen Collection Tubes That Were Unusable for Clinical Laboratory Testing

The fledgling test-kit company sent plastic preforms that were intended for use in the manufacturing of soda bottles, not clinical laboratory specimen tubes

When is a specimen tube not a specimen tube? When it is a plastic tube made for creating soda bottles. And that may be exactly what the Federal Emergency Management Agency (FEMA) received after paying $7.3 million to a fledgling Florida-based company that won a multi-million-dollar no-bid contract from the federal government for COVID-19 clinical laboratory testing supplies, which FEMA then shipped nationwide to states that had requested the supplies.

FEMA signed the deal with Fillakit, LLC, on May 7, 2020, “just six days after the company was formed,” reported ProPublica, which went on to state that the shipment of unusable Fillakit specimen tubes contributed to delays in rolling out widespread COVID-19 testing in the US.

According to ProPublica, Fillakit supplied “preforms” that are designed to be expanded with heat and pressure into 2-liter soda bottles, not laboratory specimen tubes.

Michelle Forman, a spokesperson for the Association of Public Health Laboratories, told ProPublica one major flaw of the Fillakit tubes is their size. “They are an unusual shape, so they don’t fit racks,” she said, “and we are getting lots of pushback about how difficult it is to work with them from our clinical partners.”

Fillakit image shows the preform tube that is intended to be die-molded into a large soda bottle
The photo of the preform sent by Fillakit above is taken from a Fox23 news report that stated “FEMA sent the Washington State Department of Health nearly 300,000 plastic tubes. They thought they were getting test tubes for coronavirus testing, but instead, they received tiny plastic preforms that can be made into 2-liter soda bottles.” This photograph shows the preform tube that is intended to be die-molded into a large soda bottle. That is why the cap on the tube is appropriate for the tubes intended purpose as a soda bottle.  (Photo copyright: Alison Grande, KIRO7/Fox23.)

Fillakit Employees Describe ‘Unsanitary’ Working Conditions

Ex-employees of Fillakit told the Wall Street Journal (WSJ) the specimen tubes were being handled in unsanitary open-air conditions in a warehouse outside of Houston where the test kits were being assembled.

“There were up to 250 workers crowded in a small warehouse room, shoulder to shoulder … working off of fold-up tables with supplies placed on the floor and handled without gloves,” Teresa Bosworth Green told Community Impact (CI), which reported that Green worked at Fillakit from May 11-20.

“We were told that we would be filling and capping tubes that would be used for COVID testing,” Green told CI.

However, according to CI, Green “expressed concern about the lack of cleanliness and facemasks. Green brought her own mask, but workers were not initially provided any.”

Green told CI, “People were breathing and coughing right over the solution.”

In a letter to FEMA and the Department of Health and Human Services (HHS) after Michigan received more than 322,000 tubes of transport media manufactured by Fillakit, Democrat Senators Debbie Stabenow and Gary Peters wrote, “Even if the tubes themselves were not unsuitable for testing purposes, the contamination risks inherent in such careless handling would cause serious concerns about the reliability of any tests conducted using these materials.”

On July 7, 2020, the Wall Street Journal reported that Fillakit had notified the Florida Secretary of State on June 26 that the company had been dissolved.

Kira Doyle, JD, owner/attorney at Kira Doyle Law in St. Petersburg, FL
Kira Doyle, JD (above), owner/attorney at Kira Doyle Law in St. Petersburg, Fla., who multiple media outlets listed as Fillakit’s manager, told the Tampa Bay Times that media portraits of the company have been unfair. In a series of emails, she said Fillakit was attempting to fill a void in the medical supply chain. “If you are interested in writing an article about empowered female business owners or entrepreneurs creating jobs and helping this great country during an unprecedented pandemic, Fillakit LLC, fits that profile,” Doyle wrote. (Photo copyright: Kira Doyle Law.)

Under Pressure, Feds Award Contracts for COVID-19 Test Supplies to Inexperienced Suppliers

Fillakit as just one example out of “more than 250 companies that got contracts worth more than $1 million without going through a fully competitive bidding process,” NPR reported.

“Government procurement experts say federal officials were trying to move quickly to deliver desperately needed personal protective equipment,” NPR continued. “But they question the need to turn to contractors who have never worked with the government before and lacked experience making or delivering the protective gear.”

Among those receiving contracts were companies with little to no experience in manufacturing clinical laboratory testing supplies, personal protective equipment (PPE), as well as others that had never worked in the medical field. One company imported vodka, while another was a school security consultant. Many of the contractors served as middlemen, securing PPE from Chinese manufacturers, which meant they often were “competing with federal agencies, state governments, and local health systems,” all of which were attempting to buy the same equipment in the global marketplace, NPR reported.

“Giving business to people who don’t have experience is something you don’t want to do in an emergency,” Joshua Schwartz, JD, a professor of Government Contracts Law and co-director of the Government Procurement Law Program at George Washington University School of Law, told NPR.

FEMA Defends Its Contracting Process

A ProPublica analysis of coronavirus contracts found that about 13% of total federal government pandemic spending went to first-time vendors. And in a follow-up article, ProPublica claimed, “many of the new contractors have no experience acquiring medical products.”

FEMA, however, maintains it pays for purchases only after they have been delivered to minimize potential for waste of taxpayer dollars. “FEMA does not enter into contracts unless it has reason to believe they will be successfully executed,” the agency told ProPublica.

The US’ lack of preparedness for the COVID-19 pandemic has resulted in missteps and misspending as federal agencies struggle to provide hospitals, clinical laboratories, and healthcare providers with personal protective gear and test supplies, and to ramp up COVID-19 testing nationwide.

This is yet another instance where federal agencies appear to lack the competencies required to fulfill healthcare requirements with proven products that meet critical specifications. Meanwhile, in every community throughout the United States, independent medical laboratories and hospital-based laboratories are clamoring for adequate supplies of everything from collect swabs and viral transport media to reagents and cuvettes.

—Andrea Downing Peck

Related Information:

The Trump Administration Paid Millions for Test Tubes and Got Unusable Mini Soda Bottles

Conroe-Based Company Made Unusable COVID-19 Test Supplies Using $10-Million FEMA Grant

Covid-19 Test-Tube Firm Awarded U.S. Contract, Is Accused of Unsanitary Workplace

Coronavirus Test-Kit Maker Dissolves Amid Probes

Senators Stabenow and Peters Press Trump Administration for Answers on Rewarding an Unreliable Company to Produce Testing Supplies

How a St. Petersburg Company with No History in Medical Supplies Won a $10 million Coronavirus Contract

A Closer Look at Federal COVID Contractors Reveals Inexperience, Fraud Accusations and a Weapons Dealer Operating Out of Someone’s House

Tracking Federal Purchases to Fight the Coronavirus: Search Contract Descriptions, Companies and Agencies

Feds Spend Billions on COVID-19 Contracts, Often without Fully Competitive Bidding

FEMA: Federal Support to Expand National Testing Capabilities

Instead of Coronavirus Testing Supplies, FEMA Sent 300K Tiny Soda Bottles to Washington

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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