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Clinical Laboratories and Pathology Groups

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New Artificial Intelligence Algorithm Uses Routine Clinical Laboratory Tests to Identify Patients Likely Infected with COVID-19

At hospitals where results of molecular COVID-19 testing can take up to several days to return, this new method for identifying potentially infected patients could improve triage

Frustrated by shortages of essential COVID-19 tests and supplies—as well by lengthy coronavirus test turn-around times—researchers at Weill Cornell Medicine have created an Artificial Intelligence (AI) algorithm that can use routine clinical laboratory test data to determine if a patient is infected with SARS-CoV-2, the coronavirus that causes the COVID-19 disease.

This is an important development because the turn-around-time (TAT) for common lab tests is generally much shorter than COVID-19 molecular diagnostics—such as real-time reverse transcription polymerase chain reaction (RT-PCR), currently the most popular coronavirus test—and certainly serological (antibody) diagnostics, which require an infection incubation time of as much as 10-14 days before testing.

Some RT-PCR diagnostic tests for COVID-19, which detect viral RNA on nasopharyngeal swab specimens, can take up to several days to return depending on the test and on the lab’s location. But routine medical laboratory tests generally return much sooner, often within minutes or hours, making this a potential game-changer for triaging infected patients.

Machine Learning Brings AI to COVID-19 Diagnostics

Advances in the use of AI in healthcare have led to the development of machine-learning algorithms that are being utilized as diagnostic tools for anatomic pathology, radiology, and for specific complex diseases, such as cancer. The Weill Cornell scientists wanted to see if alternative lab test results could be used by an algorithmic model to identify people infected with the SARS-CoV-2 coronavirus.

Sarina Yang, MD, PhD
“When patients come to the [emergency department] and the doctor orders several panels of routine lab [tests] and also the [SARS-CoV-2] RT-PCR test, generally the routine test results come back in a couple of hours,” Sarina Yang, MD, PhD (above), one of the authors of the study, told Modern Healthcare. “So, we thought it could be useful to use the routine labs to predict whether the RT-PCR results would be positive or negative to improve the triage process.” Yang is an assistant professor in the Department of Pathology and Laboratory Medicine, and Assistant Director of the central laboratory and Director of the toxicology laboratory at Weill Cornell Medicine. (Photo copyright: Weill Cornell Medicine.)

To perform the research, the team incorporated patients’ age, sex, and race, into a machine learning model that was based on results from 27 routine lab tests chosen from a total of 685 different tests ordered for the patients. The study included 3,356 patients who were tested for SARS-CoV-2 at New York-Presbyterian Hospital/Weill Cornell Medical Center between March 11 and April 29 of this year. The patients ranged in ages from 18 to 101 with the mean age being 56.4 years. Of those patients, 1,402 were RT-PCR positive and the remaining 1,954 were RT-PCR negative.  

Using a machine-learning technique known as a gradient-boosting decision tree, the algorithm identified SARS-CoV-2 infections with 76% sensitivity and 81% specificity. When looking at only emergency department (ED) patients, the model performed even better with 80% sensitivity and 83% specificity. ED patients comprised just over half (54%) of the patients used for the study. 

Weill Cornell Medicine Algorithm Could Lower False Negative Test Results

The algorithm also correctly identified patients who originally tested negative for COVID-19, but who tested positive for the coronavirus upon retesting within two days. According to the researchers, these results indicated their model could potentially decrease the amount of incorrect test results.

“We are thinking that those potentially false negative patients may demonstrate a different routine lab test profile that might be more similar to those that test positive,” Fei Wang, PhD, Assistant Professor of Healthcare Policy and Research at Weill Cornell Medicine and the study’s senior author, told Modern Healthcare. “So, it offers us a chance to capture those patients who are false negatives.”

The researchers validated their model by comparing the results with patients seen at New York Presbyterian Hospital/Lower Manhattan Hospital during the same time period. Among those patients, 496 were RT-PCR positive and 968 were negative and the algorithmic model performed with 74% specificity and 76% sensitivity. 

In their study, published in the Oxford Academic journal Clinical Chemistry, titled, “Routine Laboratory Blood Tests Predict SARS-CoV-2 Infection Using Machine Learning,” the Weill Cornell Medicine scientists concluded that their research illustrated the algorithm could:

  • preliminarily identify high-risk SARS-CoV-2 infected patients before RT-PCR results are available,
  • risk stratify patients in the ED,
  • select patients who need relatively urgent retesting if initial RT-PCR results are negative,
  • help isolate infected patients earlier, and
  • assist in the identification of SARS-CoV-2 infected patients in areas where RT-PCR testing is unavailable due to financial or supply constraints.

Early Results of Study Promising, But More Research is Needed

Wang noted that more research is needed on the algorithm and that he and his colleagues are currently working on ways to improve the model. They are hoping to test it with different conditions and geographies.

“Our model in the paper was built on data from when New York was at its COVID peak,” he told Modern Healthcare. “At that time, we were not doing wide PCR testing, and the patients who were getting tested were pretty sick.”

At the time of the study, the positivity rate for COVID-19 at New York-Presbyterian Hospital was in the 40% to 50% range. That was substantially higher than the current positivity rate, which is in the 2% to 3% range, Modern Healthcare reported.

“This model we built in a population in New York in a certain time period, so we can’t guarantee that it will work well universally,” Wang told Modern Healthcare.

It’s exciting to think that advances in software algorithms may one day make it possible to combine routine clinical laboratory testing and create diagnostics that identify diseases in ways the individual tests were not originally designed to do.

This study is an example that researchers in AI and informatics are working to bring new tools and diagnostic capabilities to clinical laboratories. Also, this is a demonstration of how a patient’s results from multiple other types of lab tests can by analyzed using AI and similar analytical algorithms to diagnose a health condition unrelated to the original reasons for performing those tests.

If this can be demonstrated with other diseases and health conditions, it would open up one more way that pathologists and clinical laboratory scientists can contribute to more accurate diagnoses and improved selection of the most appropriate therapies for individual patients.

—JP Schlingman

Related Information:

Routine Lab Tests Could Help Identify COVID-19 Patients

Routine Laboratory Blood Tests Predict SARS-CoV-2 Infection Using Machine Learning

Mobile Device Software Companies Are Developing Smartphone Apps That Use Artificial Intelligence to Test for COVID-19, Potentially Bypassing the Clinical Laboratory Altogether

Florida Hospital Utilizes Machine Learning Artificial Intelligence Platform to Reduce Clinical Variation in Its Healthcare, with Implications for Medical Laboratories

Apple Updates Its Mobile Health Apps, While Microsoft Shifts Its Focus to Artificial Intelligence. Both Will Transform Healthcare, But Which Will Impact Clinical Laboratories the Most?

Clinical Laboratory Testing of USS Theodore Roosevelt’s Crew During COVID-19 Outbreak Offers Insights into the Coronavirus’ Impact on Young Healthy Adults

The CDC and US Navy study reveals common symptoms and suggests best protective measures to prevent spread in enclosed environments that clinical labs and pathology groups could use to protect their staff members

Results from a study conducted by the US Navy and the federal Centers for Disease Control and Prevention (CDC) of sailors onboard the USS Theodore Roosevelt during the recent COVID-19 outbreak aboard the ship may be useful for pathologists and clinical laboratory managers. The study also provides public health and infectious disease specialists with an opportunity to learn more about how the SARS-CoV-2 coronavirus spreads in enclosed environments.

The aircraft carrier garnered headlines in April due to a widespread outbreak of the coronavirus among its crew. The investigators asked crewmembers to complete a questionnaire and provide samples for a serological antibody test and molecular diagnostics test, reported the Navy’s Bureau of Medicine and Surgery (BUMED). The goal was to learn more about the disease and how it spreads in high-density environments. The COVID-19 tests were conducted April 20-24 while the ship was docked in Guam.

The CDC published the results on June 12 in its “Morbidity and Mortality Weekly Report.”

An Early Picture of Infection in Young People

“This study paints a picture of current and prior SARS-CoV-2 infection among young adults living in close quarters,” said the study’s lead author Dan Payne, PhD, an epidemiologist at the CDC, in the BUMED statement. “This data will contribute to understanding COVID-19 in the US military, as well as among young adults in other close communal environments.”

Participation in the study was voluntary. At the time of testing, a total of 1,417 service members were still on the ship or at the base in Guam, the researchers wrote in their study. Among them, 383 crewmembers agreed to complete the survey and provide a blood sample for an enzyme-linked immunosorbent assay (ELISA) antibody test. Out of that group, 267 also provided nasal swab samples for a reverse transcription polymerase chain reaction (RT-PCR) molecular diagnostic test.

aircraft carrier USS Theodore Roosevelt (CVN 71) during the investigation into the COVID-19 outbreak in April 2020
A clinical laboratory team from the Naval Hospital Guam and the Navy and Marine Corps Public Health Center are seen above collecting surveys, nasal swabs, and blood samples from sailors assigned to the aircraft carrier USS Theodore Roosevelt (CVN 71) during the investigation into the COVID-19 outbreak in April. The ship’s medical leaders established an emergency command center, initiated a roving and deep cleaning team, and continually educated the crew on social distancing and proper protective procedures and behaviors, to mitigate the spread of the SARS-CoV-2 coronavirus. (Photo copyright: US Navy.)

The questionnaire sought information about sailors’ demographic factors, health history, symptoms, and preventive behaviors, such as mask wearing and physical distancing. Crewmembers who tested positive for reactive antibodies received an additional test to detect presence of neutralizing antibodies that inhibit the virus.

The median age of participants was 30 years. About 75% were male. Only 28 (7.3%) reported comorbidities such as a history of asthma, diabetes, hypertension, or immunosuppression, which are considered risk factors for developing serious cases of the COVID-19 disease.

Key findings of the CDC/Navy’s study:

  • 228 participants (59.7%) tested positive for reactive antibodies. Of those, 135 (59.2%) tested positive for neutralizing antibodies.
  • 235 participants had previously tested positive in a SARS-CoV-2 diagnostic test. Of those, 212 (90.2%) tested positive for reactive antibodies.
  • A total of 238 participants had a previous or current SARS-CoV-2 infection. Of these, 18.5% reported no symptoms.
  • Of the 194 sailors who reported symptoms, 115 (59.3%) sought medical care, and two were hospitalized.
  • The most frequently reported symptoms were headache (66.5%), loss of taste or smell or both (61.3%); myalgia (56.2%); runny nose (55.7%); and fatigue (55.2%).
  • The most effective preventive measures were avoidance of common areas, increased physical distancing, and use of face coverings.

“What we saw was that most of the infections were actually mild, in addition to those that were asymptomatic,” Payne told reporters after the study was published, reported CNN. “And this is perhaps different from studies of older Americans, or maybe even those who were hospitalized already, and certainly much different from those with underlying health conditions.”

But with the high number of asymptomatic cases, “symptom-based surveillance might not detect all infections,” noted the researchers, who cautioned that “the analysis was conducted on a convenience sample of persons who might have had a higher likelihood of exposure, and all information was based on self-report, raising the possibility of selection and recall biases.”

In January, the crew of the Roosevelt totaled about 4,800 sailors, reported Defense One. However, after docking in Guam, many sailors were moved to hotel rooms for quarantine. As of May 5, at least 1,156 crewmembers had tested positive for infection, Stars and Stripes reported, and one had died.

Sailors aboard the USS Theodore Roosevelt were examined prior to re-boarding the ship
Sailors aboard the USS Theodore Roosevelt were examined prior to reboarding the ship following off-ship quarantine or isolation. Only those found to be negative for the coronavirus, were allowed to board the ship. (Photo copyright: US Navy.)

Impact of COVID-19 on the USS Theodore Roosevelt’s Crew

As of April 6, 172 crew members had tested positive for COVID-19, including the ship’s captain Brett Crozier. At that time, 61% of the crew had received clinical laboratory testing and 1,999 sailors had been moved off the ship into quarantine, reported Defense One. By the next day, 270 sailors tested positive, a 57% increase from the previous day.

By April 14, 589 crew members were diagnosed positive for COVID-19. With 92% of the crew tested, 3,922 were found to be negative for the infection. Nevertheless, 4,024 sailors—nearly 83% of the crew—were moved into isolation quarters off-ship to prevent spread of the coronavirus.

In their study, the Navy/CDC researchers concluded: “In this convenience sample of young, healthy US service members experiencing close contact aboard an aircraft carrier, those with previous or current SARS-CoV-2 infection experienced mild illness overall, and nearly 20% were asymptomatic. Approximately one third of participants reported fever, myalgia, and chills and had higher odds of SARS-CoV-2 infection than did persons who reported cough and shortness of breath. Participants reporting anosmia (loss of sense of smell) or ageusia (loss of sense of taste) had 10 times the odds of having infection, compared with those who did not.

“In this sample of intensely exposed subjects, assessed at a single point in time, results demonstrated that antibodies developed and that, at the time of specimen collection, many of these were neutralizing antibodies. … This is a promising indicator of immunity, and in several participants, neutralizing antibodies were still detectable >40 days after symptom onset. Ongoing studies assessing the humoral antibody response over time will aid the interpretation of serologic results in an outbreak investigation such as this.

“These results provide new indications of symptomatology of SARS-CoV-2 infections and serologic responses among a cohort of young US adults living in a congregate environment and contribute to a better understanding of COVID-19 epidemiology in the US military. The findings reinforce the importance of nonpharmaceutical interventions such as wearing a face covering, avoiding common areas, and observing social distancing to lower risk for infection in similar congregate living settings.”

Not all the specific lessons learned from this COVID-19 outbreak aboard a US Navy vessel will be applicable to clinical laboratories and anatomic pathology groups. Nevertheless, it is probable that the data gleaned from the CDC/Navy study aboard the USS Theodore Roosevelt will someday mean civilian Americans can count on improved responses to disease outbreaks from the nation’s testing laboratories.

—Stephen Beale

Related Information:

SARS-CoV-2 Infections and Serologic Responses from a Sample of U.S. Navy Service Members — USS Theodore Roosevelt, April 2020

Navy Investigation Finds 60 Percent of USS Theodore Roosevelt Volunteers Have COVID-19 Antibodies

New Study of USS Theodore Roosevelt Sailors Reveals How Coronavirus Affects Young, Healthy Adults

What the USS Roosevelt Can Teach Us about COVID-19 Spread

Sick Sailors Recovering on Guam Will Fly Home Rather than Rejoin USS Theodore Roosevelt

13 USS Roosevelt Sailors Test Positive for COVID-19, Again

CDC Study: Lower COVID-19 Infection Rate for TR Sailors Who Wore Face Coverings and Social Distanced

Findings from USS Theodore Roosevelt Public Health Investigation Support Force Health Protection

Theodore Roosevelt Sailors Volunteer to Support Public Health Outbreak Investigation

Outbreak Investigation Aboard US Aircraft Carrier May Contain Clues about COVID-19 Among the Young and Healthy

After Outbreak on Carrier Roosevelt, Many Have Antibodies

Navy Ship Outbreak Shows Most Young Aren’t Spared COVID Symptoms

We Still Don’t Fully Understand the Label ‘Asymptomatic’

Clinical and Immunological Assessment of Asymptomatic SARS-CoV-2 Infections

Multiple Studies Raise Questions About Reliability of Clinical Laboratory COVID-19 Diagnostic Tests

In the absence of a “gold standard,” researchers are finding a high frequency of false negatives among SARS-CoV-2 RT-PCR tests

Serology tests designed to detect antibodies to the SARS-CoV-2 coronavirus that causes the COVID-19 illness have been dogged by well-publicized questions about accuracy. However, researchers also are raising concerns about the accuracy of molecular diagnostics which claim to detect the actual presence of the coronavirus itself.

“Diagnostic tests, typically involving a nasopharyngeal swab, can be inaccurate in two ways,” said Steven Woloshin, MD, MS, in a news release announcing a new report that “examines challenges and implications of false-negative COVID-19 tests.” Woloshin is an internist, a professor at Dartmouth Institute, and co-director of the Geisel School of Medicine at Dartmouth.

“A false-positive result mistakenly labels a person infected, with consequences including unnecessary quarantine and contact tracing,” he stated in the news release. “False-negative results are far more consequential, because infected persons who might be asymptomatic may not be isolated and can infect others.”

Woloshin led a team of Dartmouth researchers who analyzed two studies from Wuhan, China, and a literature review by researchers in Europe and South America that indicated diagnostic tests for COVID-19 are frequently generating false negatives. The team published their results in the June 5 New England Journal of Medicine (NEJM).

For example, one research team in Wuhan collected samples from 213 hospitalized COVID-19 patients and found that an approved RT-PCR test produced false negatives in 11% of sputum samples, 27% of nasal samples, and 40% of throat samples. Their research was published on the medRxiv preprint server and has not been peer-reviewed.

The literature review Woloshin’s team studied was also published on medRxiv, titled, “False-Negative Results of Initial Rt-PCR Assays for COVID-19: A Systematic Review.” It indicated that the rate of false negatives could be as high as 29%. The authors of the review looked at five studies that had enrolled a total of 957 patients. “The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability,” they wrote. “Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection.”

Another literature review, published in the Annals of Internal Medicine, titled, “Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure,” estimated the probability of false negatives in RT-PCR tests at varying intervals from the time of exposure and symptom onset. For example, the authors found that the median false-negative rate was 38% if a test was performed on the day of symptom onset, versus 20% three days after onset. Their analysis was based on seven studies, five of which were peer-reviewed, with a total of 1330 test samples.

Doctors also are seeing anecdotal evidence of false negatives. For example, clinicians at UC San Diego Health medical center treated a patient with obvious symptoms of COVID-19, but two tests performed on throat samples were negative. However, a third test, using a sample from a bronchial wash, identified the virus, reported Medscape.

The lesson for clinicians is that they can’t rely solely on test results but must also consider their own observations of the patient, Joshua Metlay, MD, PhD, of Massachusetts General Hospital told Medscape.

Sensitivity and Specificity of COVID-19 Clinical Laboratory Tests

The key measures of test accuracy are sensitivity, which refers to the ability to detect the presence of the virus, and specificity, the ability to determine that the targeted pathogen is not present. “So, a sensitive test is less likely to provide a false-negative result and a specific test is less likely to provide a false-positive result,” wrote Kirsten Meek, PhD, medical writer and editor, in an article for ARUP Laboratories.

“Analytic” sensitivity and specificity “represent the accuracy of a test under ideal conditions in which specimens have been collected from patients with either high viral loads or a complete absence of exposure,” she wrote. However, “sensitivity and specificity under real-world conditions, in which patients are more variable and specimen collection may not be ideal, can often be lower than reported numbers.”

In a statement defending its ID Now molecular point-of-care test, which came under scrutiny during a study of COVID-19 molecular tests by NYU Langone Health, Northwell Health, and Cleveland Clinic, according to MedTech Dive, Abbott Laboratories blamed improper sample collection and handling for highly-publicized false negatives produced by its rapid test. An FDA issued alert about the test on May 14 noted that Abbott had agreed to conduct post-market studies to identify the cause of the false negatives and suggest remedial actions.

Issues with Emergency Use Authorizations

In their NEJM analysis, Woloshin et al point to issues with the FDA’s process for issuing Emergency Use Authorizations (EUAs). For example, they noted variations in how manufacturers are conducting clinical evaluations to determine test performance. “The FDA prefers the use of ‘natural clinical specimens’ but has permitted the use of ‘contrived specimens’ produced by adding viral RNA or inactivated virus to leftover clinical material,” they wrote.

When evaluating clinical performance, manufacturers ordinarily conduct an index test of patients and compare the results with reference-standard test, according to the Dartmouth researchers. For people showing symptoms, the reference standard should be a clinical diagnosis performed by an independent adjudication panel. However, they wrote, “it is unclear whether the sensitivity of any FDA-authorized commercial test has been assessed in this way.” Additionally, a reference standard for determining sensitivity in asymptomatic people “is an unsolved problem that needs urgent attention to increase confidence in test results for contact-tracing or screening purposes.”

Stephen Rawlings, MD, PhD
“To truly determine false negatives, you need a gold standard test, which is essentially as close to perfect as we can get,” Stephen Rawlings, MD, PhD, (above), a resident physician of internal medicine and infectious diseases fellow at UC San Diego’s Center for AIDS Research (CFAR), who has been working on SARS-CoV-2 test validation since March. “But there just isn’t one yet for coronavirus,” he told Medscape. (Photo copyright: University of California, San Diego.)

In a perspective for Mayo Clinic Proceedings, Colin P. West, MD, PhD; Victor M. Montori, MD, MSc; and Priya Sampathkumar, MD, offered four recommendations for addressing concerns about testing accuracy:

  • Continued adherence to current measures, such as physical distancing and surface disinfection.
  • Development of highly sensitive and specific tests or combinations of tests to minimize the risk of false-negative results and ongoing transmission based on a false sense of security.
  • Improved RT-PCR tests and serological assays.
  • Development and communication of clear risk-stratified protocols for management of negative COVID-19 test results.

“These protocols must evolve as diagnostic test, transmission, and outcome statistics become more available,” they wrote.

Meanwhile, clinical laboratories remain somewhat on their own at selecting which COVID-19 molecular and serology tests they want to purchase and run in their labs. Complicating such decisions is the fact that many of the nation’s most reputable in vitro diagnostics manufacturers cannot produce enough of their COVID-19 tests to meet demand.

Consequently, when looking to purchase tests for SARS-CoV-2, smaller medical laboratory organizations find themselves evaluating COVID-19 kits developed by little-known or even brand-new companies.

—Stephen Beale

Related Information:

New Report Examines Challenges and Implications of False-Negative COVID-19 Tests

Questions about COVID-19 Test Accuracy Raised Across the Testing Spectrum

COVID-19 Test Results: Don’t Discount Clinical Intuition

FDA Provides New Tool to Aid Development and Evaluation of Diagnostic Tests That Detect SARS-CoV-2 Infection

EUA Authorized Serology Test Performance

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

Coronavirus (COVID-19) Update: FDA Provides Promised Transparency for Antibody Tests

Understanding Medical Tests: Sensitivity, Specificity, and Positive Predictive Value

Webinar Part 1: Quality Issues Your Clinical Laboratory Should Know Before You Buy or Select COVID-19 Serology Tests

Webinar Part 2: Achieving High Confidence Levels in the Quality and Accuracy of Your Clinical Lab’s Chosen COVID-19 Serology Tests, featuring James Westgard, PhD

FDA Issues its First Emergency Use Authorization for an Antigen-based Diagnostic as Top IVD Manufacturers Race to Supply Medical Laboratories with COVID-19 Tests

Though experts say an antigen test is not as accurate as PCR tests, its low cost, ease of use, and widespread availability make it a boon for clinical labs performing COVID-19 testing

While COVID-19 exploded around the world, the US Food and Drug Administration (FDA) unleashed the nation’s in vitro diagnostics developers by issuing dozens of Emergency Use Authorizations for new coronavirus laboratory-developed tests (LDTs). Most of these EUAs are for Reverse Transcription-Polymerase Chain Reaction (RT-PCR) tests that detect the presence of SARS-CoV-2, the coronavirus that causes the COVID-19 illness, and for Enzyme-linked Immunosorbent Assay (ELISA) serological tests that detect antibodies present in the blood of people who have become infected with the coronavirus.

However, one LDT that received a lot of media attention was the Sofia 2 SARS Antigen FIA from Quidel (NASDAQ:QDEL), which received an EUA on May 8. The assay is designed to run on the company’s Sofia 2 Fluorescent Immunoassay Analyzer and is the first antigen test for which the FDA has issued an EUA.

As former FDA commissioner Scott Gottlieb, MD, explained on Face the Nation, “this kind of technology is a real game changer … it’s a very rapid test that could be used in a doctor’s office. Doctors now have about forty thousand of these Sofia machines already installed in their offices … you do a simple nasal swab and the test itself scans for the antigens that the virus produces.

“The test is about 85% sensitive. So, let’s say a hundred people come into a doctor’s office who have COVID-19, eighty-five of them are going to be able to be tested positive with this test very quickly. It’s a cheap test. It’ll probably be about five dollars a test and you can get a result within five minutes … you’re getting a very fast result and you can start to take action immediately.

“The company itself said that they’re going to be able to produce about two hundred thousand of these tests starting right away. But in several weeks, they’ll be able to produce up to 1.5 million a week. So, this dramatically expands our testing capacity as long as doctors are able to run these tests in their offices.”

Former FDA Commissioner Scott Gottlieb, MD
In an interview on CBS’ Face the Nation, former FDA Commissioner Scott Gottlieb, MD (above), said, “These antigen-based tests aren’t as reliable, meaning they’re not as sensitive. So, they’re going to miss some patients who have COVID. But in the hands of a doctor who already has a high index of suspicion that the patient may have the disease … they allow you to dramatically expand testing. And they’re very cheap. They’re very easy to perform. And again, most doctors have these machines already in their offices.” (Photo copyright: US Food and Drug Administration.)

Other LDTs That Have Received EUAs

Here’s a look at other laboratory-developed tests from major manufacturers that have received emergency-use authorizations from the FDA:

Abbott Laboratories

Test: Abbott RealTime SARS-CoV-2 assay
Type: Molecular (rRT-PCR)
EUA Issued: March 18, 2020

This test is designed for use with Abbott’s m2000 RealTime system, which is installed in about 200 US medical laboratories, the company says. It can run up to 470 patient samples in 24 hours. As of a May 11 statement, the company said it had shipped more than two million tests in the US.

Test: Alinity m SARS-CoV-2 assay
Type: Molecular (rRT-PCR)
EUA Issued: May 11, 2020

This test is designed for use with Abbott’s Alinity m system, which the company describes as its “most advanced laboratory molecular instrument,” with the ability to run up to 1,080 tests in 24 hours, according to a press release.

Test: ID NOW COVID-19
Type: Molecular
Instrument: ID Now
EUA Issued: March 27, 2020

This is a rapid test designed for use with the ID Now system, a compact portable instrument for point-of-care settings such as urgent care clinics. As of May 11, Abbott said it had shipped more than 1.7 million tests in the US, and that it planned to increase manufacturing capacity to two million tests per month.

However, the test has encountered some stumbling blocks. On May 14, the FDA issued an alert stating that the ID Now COVID-19 test could produce inaccurate negative results. This came after researchers at NYU Langone Health, Northwell Health, and Cleveland Clinic reported problems with the test, according to MedTech Dive. Abbott issued a statement suggesting that the problems were due to improper sample collection and handling, however, the FDA said that Abbott had agreed to conduct post-market studies to identify the cause of the false negatives and suggest remedial actions.

Test: SARS-CoV-2 IgG assay
Type: Chemiluminescent microparticle immunoassay (CMIA) antibody test
EUA Issued: April 26, 2020

This is a qualitative test designed to detect the presence of IgG antibodies following a SARS-CoV-2 infection. The FDA authorized use of the assay on Abbott’s Architect i2000SR system in April, and then followed up with a May 11 EUA for its use on the Alinity i system. In a statement, Abbott said it planned to ship 30 million tests globally starting in May.

Cepheid

Test: Xpert Xpress SARS-CoV-2
Type: Molecular (rRT-PCR)
EUA Issued: March 21, 2020

In a March statement, the FDA touted this as the first point-of-care COVID-19 test to receive an EUA. The company estimates the detection time as approximately 45 minutes. It is designed for use with Cepheid’s GeneXpert Dx diagnostic software and GeneXpert Infinity systems, which have nearly 5,000 US installations, according to a Cepheid statement.

Hologic, Inc.

Test: Aptima SARS-CoV-2 assay
Type: Molecular (Dual Kinetic Assay)
EUA Issued: May 14, 2020

This test runs on Hologic’s Panther system, which, according to a Hologic press release, can provide results in about three hours and run more than 1,000 tests per day. The company claims that more than 1,000 Panther systems are installed in US labs, and that it expects to produce an average of one million tests per week.

This was the second Hologic test to receive and EUA. On March 16, the FDA issued an EUA for the Panther Fusion SARS-CoV-2 assay, a PCR test that runs on the Panther Fusion system.

Ortho Clinical Diagnostics

Test: VITROS Total and IgG COVID-19 Antibody Test
Type: ELISA Antibody Test
EUA Issued: April 14, 2020

Ortho’s antibody test is designed for use with its VITROS XT 7600, 3600, 5600, and ECi/ECiQ immunodiagnostic systems, which, the company says are installed in more than 1,000 US labs. The Total Reagent Pack is a qualitative test that detects the presence of all antibodies against SARS-CoV-2.

On April 24, Ortho announced it had received another FDA EUA, this one for its Anti-SARS-CoV-2 IgG test, which detects the presence of IgG antibodies. In a statement, the company said it expects to produce “several million” IgG tests per month.

Roche Diagnostics

Test: cobas SARS-CoV-2
Type: Molecular (rRT-PCR)
EUA Issued: March 12, 2020

This test is designed for use with Roche’s cobas 6800 and 8800 systems. The 6800 can process up to 384 results in an eight-hour shift, Roche says, compared with 1,056 results for the 8800 model. The company says results are available in about 3.5 hours. In a statement, Roche said it planned to ship 400,000 tests per week.

Test: Elecsys Anti-SARS-CoV-2
Type: Electrochemiluminescence immunoassay (ECLIA) Antibody Test
EUA Issued: May 2, 2020

Roche describes this as a qualitative antibody test that can be used on cobas e series immunoassay analyzers. Testing time is 18 minutes. As of May 19, the test was live at more than 20 US labs, “with plans in the next several weeks to increase to more than 200 commercial and hospital lab sites with the ability to perform millions of tests per week,” the company stated in a press release.

It’s likely the FDA will continue to issue emergency-use authorizations as the agency receives more applications from IVD manufacturers.

—Stephen Beale

Related Information:

FDA Approves First Antigen Test for Detecting the Coronavirus

Ex-FDA Chief Calls New Covid-19 Antigen Test a ‘Game-Changer’

Serology-based Tests for COVID-19

Serology Testing Free Webinar

Molecular-based Tests for COVID-19

Current Molecular and Antigen Tests with FDA EUA Status

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

Sean Penn’s Foundation Partners with Healthcare Providers in Four States to Offer Drive-Thru COVID-19 Molecular and Serological Clinical Laboratory Specimen Collections

Goal of his foundation is to provide access to COVID-19 medical laboratory tests for first responders, as well as low-cost tests to the general public

Early in April, when many of the nation’s clinical laboratories were facing numerous challenges in their attempts to obtain adequate supplies for collecting, transporting, and testing for COVID-19, a Hollywood actor was funding his foundation and obtaining enough supplies for his foundation to offer access to COVID-19 testing to residents in his community of Malibu—as well as in other areas.

In many ways, local medical laboratories that offer COVID-19 tests are competing with actor/philanthropist Sean Penn’s Community Organized Relief Effort (CORE) foundation for the supplies they need to provide COVID-19 testing to the patients in their own communities. The non-profit organization says it is working with various healthcare providers to provide free coronavirus testing to first responders, and low-cost testing to the general public, in eleven cities and counties in California, Georgia, North Carolina, and Illinois.

In fact, the volume of COVID-19 testing CORE currently provides is large enough that The Hollywood Report published a story on June 3, titled, “How Sean Penn Made the Biggest COVID-19 Testing Site in U.S.” The article stated that, “In late May, Mayor Eric Garcetti announced the opening of a new COVID-19 testing site at Dodger Stadium in partnership with CORE, the Los Angeles Dodgers, Live Nation Entertainment, Red Rock Entertainment, and the Los Angeles Fire Department. Operated by CORE and LAFD, this site has capacity to test 6,000 residents a day free of charge––making it three times the size of any other location in L.A. County and said to be the largest testing site in the U.S.”

The Reporter did not make the distinction that the Dodger Stadium site is only collecting specimens. And, no news accounts of the CORE COVID-19 testing program names the clinical laboratories that CORE currently uses to perform the coronavirus tests for the specimens it collects.

CORE Partnered with Private Healthcare Provider Elevated Health

CORE first got underway in 2010 providing disaster relief following the catastrophic magnitude 7.0 earthquake in Haiti. It was known then as the Jenkins-Penn Haitian Relief Organization (J/P HRO). The foundation initiated its support of COVID-19 testing efforts in California in April, reported the Orange County Register (OCR). At that time, testing was much more limited than it is today and drive-thru testing in most areas in America was not available.

In Huntington Beach, Orange County, Calif., CORE partnered with Elevated Health to provide molecular polymerase chain reaction (PCR) tests and serological antibody tests for a fee at a drive-thru location in the city of Westminster, reported the OCR.

Elevated Health’s COVID Clinic website enables consumers to complete pre-test enrollment and payment before arriving at the drive-up testing site at the Westminster Mall. 

“Right now, hospitals have very strict guidelines on who can be tested. Public health departments are overwhelmed and possibly underfunded. That’s where I’m trying to bridge the gap,” Matthew Abinante, DO, a doctor of osteopathy and Elevated Health’s founder and CEO, told the OCR.

The coronavirus test kits Elevated Health uses are made in China and were purchased from Georgia-based HealthTrackRx. According to Abinante, they are “FDA authorized, but not FDA approved,” reported the OCR.

Clinical laboratory leaders may be intrigued to see consumers waiting their turn at drive-through testing lines as they take COVID-19 diagnosis into their own hands. Sites like the one above run by Elevated Health at the Westminster Mall demonstrate that people are willing to patronize providers that serve their needs directly. (Photo copyright: Orange County Register.)

CORE Aims to Be a Model for Partnering in Testing

Though CORE’s COVID-19 testing relief efforts are no longer limited to Los Angeles County, that is where it all began. Specimen collection at drive-through sites for COVID-19 tests initially prioritized first responders and essential workers. CORE funds provided for a staff of 70 people at four of the 35 drive-thru specimen collection sites in LA, reported CBS Los Angeles(CBSLA).

CORE-funded services also made it possible for Los Angeles city employees—who were running the drive-thru specimen collection sites—to return to their primary jobs as emergency first responders, reported the Associated Press (AP). 

“It’s something that we can adapt to very quickly with the training of the Los Angeles Fire Department initially. And we’re able to take all those firemen and put them back in to serve the people in the way that we need them to,” said Penn in the AP article.

At that time, city officials planned to perform 10,000 tests a day, Deputy Mayor Jeff Gorell, JD, told the LA Times. The City of Los Angeles purchased the tests and CORE covered the cost of staff, volunteers, and personal protective equipment (PPE), reported the LA Times.

“We have servers and people from the Peace Corps, actresses—a lot of people from the communities where the test site is. We’re trying to hire as much locally as possible,” Ann Lee, CORE’s Chief Executive Officer, told Business Insider.

CORE also partnered with the City of Malibu in western Los Angeles County to provide mobile COVID-19 testing services for the city’s 3,000 residents, first responders, and essential workers from April 6 to 17 at a testing site at Malibu City Hall.

“This is what I hope will be a model in terms of the government and community foundation partnerships that can be replicated not only in the city of Los Angeles and throughout California, but throughout the country,” Sean Penn (above at the COVID-19 drive-thru testing site in Malibu, Calif.), founder of CORE, told CBSLA. Since making that statement, CORE has gone on to partner with healthcare providers in three other states to provide coronavirus drive-thru specimen collection. (Photo copyright: Associated Press/ABC News.)

Should Drive-Through Testing Continue Post-Pandemic?

An April Dark Daily e-briefing reported on drive-thru COVID-19 specimen collection operations across 30 states. The e-briefing also noted that drive-thru collections protects medical laboratory professionals and emergency department staff from possible exposure to infectious agents.

It’s likely many industries—from education and retail to travel and restaurants—will be revamped as a result of the pandemic. Clinical laboratory leaders and pathologists will want to study the different approaches used to develop drive-through COVID-19 specimen collection; how some providers that ran them partnered with charitable organizations such as CORE; why drive-thru specimen collection appeals to consumers; and how it may improve phlebotomists’ safety and increase clinical laboratory business.

—Donna Marie Pocius

Related Information:

How Sean Penn Made the Biggest COVID-19 Testing Site in U.S.

Private Coronavirus Testing Sites Draw Crowds in Malibu and Westminster

Coronavirus: Mayor Garcetti and Sean Penn of CORE in Partnership

Sean Penn’s Non-Profit Helps Los Angeles, Malibu Expand Testing

Sean Penn Wants to “Save Lives” With Free COVID-19 Testing

Sean Penn’s Nonprofit Boosts COVID-19 Testing Efforts in Los Angeles  

Sean Penn Nonprofit, CORE, Provides Coronavirus Testing in Los Angeles

Drive-Through Coronavirus Testing Spreads Across 30 States Lowering Risk of Exposure to Phlebotomists and Clinical Laboratory Professionals

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