News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
Sign In

February COVID-19 Superspreader Event in Boston Confirmed by Use of Genetic Sequencing as Next-Gen Sequencing Is Put to Novel Uses, including in Clinical Laboratories

Gene sequencing is enabling disease tracking in new ways that include retesting laboratory specimens from before the SARS-CoV-2 outbreak to determine when it arrived in the US

On February 26 of this year, nearly 200 executives and employees of neuroscience-biotechnology company Biogen gathered at the Boston Marriott Long Wharf hotel for their annual leadership conference. Unbeknownst to the attendees, by the end of the following day, dozens of them had been exposed to and become infected by SARS-CoV-2, the coronavirus that causes the COVID-19 illness.

Researchers now have hard evidence that attendees at this meeting returned to their communities and spread the infection. The findings of this study will be relevant to pathologists and clinical laboratory managers who are cooperating with health authorities in their communities to identify infected individuals and track the spread of the novel coronavirus.

This “superspreader” event has been closely investigated and has led to intriguing conclusions concerning the use of genetic sequencing to revealed vital information about the COVID-19 pandemic. Recent improvements in gene sequencing technology is giving scientists new ways to trace the spread of COVID-19 and other diseases, as well as a method for monitoring mutations and speeding research into various treatments and vaccines. 

Genetic Sequencing Traces an Outbreak

“With genetic data, a record of our poor decisions is being captured in a whole new way,” Bronwyn MacInnis, PhD, Director of Pathogen Genomic Surveillance at the Broad Institute of MIT and Harvard, told The Washington Post (WaPo) during its analysis of the COVID-19 superspreading event. MacInnis is one of many Broad Institute, Harvard, MIT, and state of Massachusetts scientists who co-authored a study that detailed the coronavirus’ spread across Boston, including from the Biogen conference.

Titled, “Phylogenetic Analysis of SARS-CoV-2 in the Boston Area Highlights the Role of Recurrent Importation and Superspreading Events,” the paper explains how the researchers “sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region” in order to investigate how the virus was introduced and spread through the area. They traced a specific mutation in the virus—“a simple switch of two letters in the virus’ 30,000-character genetic code,” WaPo reported.

What they discovered is both surprising and enlightening. According to WaPo’s report, at least 35 new cases of the virus were linked directly to the Biogen conference, and the same strain was discovered in outbreaks in two homeless shelters in Boston, where 122 people were infected. The variant tracked by the Boston researchers was found in roughly 30% of the cases that have been sequenced in the state, as well as in Alaska, Senegal, and Luxembourg.

“The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission,” the researchers noted in their study abstract.

“The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into [Massachusetts] early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data,” they concluded.

Anthony Fauci, MD
Some experts think humankind may be entering a period of increased pandemics. In their report published in Cell, titled, “Emerging Pandemic Diseases: How We Got to COVID-19,” Anthony Fauci, MD (above) Director of the National Institute of Allergy and Infectious Diseases (NIAID), and David Morens, MD, a senior associate professor at Johns Hopkins School of Public Health and Senior Advisor to Fauci, wrote, “One can conclude from this recent experience that we have entered a pandemic era. The causes of this new and dangerous situation are multifaceted, complex, and deserving of serious examination.” (Photo copyright: NIAID.)

Genetic Sequencing and Mutation Tracking

The use of genetic sequencing to trace the virus could inform measures to control the spread in new ways, but currently, only about 0.33% of cases in the United States are being sequenced, MacInnis told WaPo, and that not sequencing samples is “throwing away the crown jewels of what you really want to know.”

Another role that genetic sequencing is playing in this pandemic is in tracking viral mutations. One of the ways that pandemics worsen is when viruses mutate to become deadlier or more easily spread. Scientists are using genetic sequencing to monitor SARS-CoV-2 for such mutations.

A group of scientists at Texas A&M University led by Yue Xing, PhD, published a paper titled, “MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences,” which explains that “Although most mutations are expected to be selectively neural, it is important to monitor if SARS-CoV-2 will eventually evolve to be a stronger or weaker infectious agent as time goes on. Therefore, it is vital to track mutations from newly sequenced SARS-CoV-2 genome.”

Another group of researchers have identified such a mutation. “A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal,” Bette Korber, PhD and her colleagues wrote in “Tracking Changes in SARS-CoV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 Virus,” published in Cell. Korber is a Laboratory Fellow at Los Alamos National Laboratory and visiting faculty at Santa Fe Institute.

Korber’s findings are important because the mutation the scientists identified appears to have a fitness advantage. “Our data show that, over the course of one month, the variant carrying the D614G Spike mutation became the globally dominant form of SARS-CoV-2,” they wrote. Additionally, the study noted, people infected with the mutated variant appear to have a higher viral load in their upper respiratory tracts.

Genetic Sequencing, the Race for Treatments, Vaccines, and Managing Future Pandemics

A vaccine is the best hope for stopping a pandemic, but short of a vaccine, an effective clinical laboratory treatment is the next best thing. And as Dark Daily reported in “Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies,” genetic sequencing is quickly becoming a critical tool to develop both.

If, as Fauci and Morens predict, future pandemics are likely, improvements in gene sequencing and analysis will become even more important for tracing, monitoring, and suppressing outbreaks. Clinical laboratory managers will want to watch this closely, as medical labs that process genetic sequencing will, no doubt, be part of that operation.

—Dava Stewart

Related Information:

Genetic Data Show How a Single Superspreading Event Sent Coronavirus Across Massachusetts and the Nation

How the Biogen Leadership Conference in Boston Spread the Coronavirus

How a Premier U.S. Drug Company Became a Virus ‘Super Spreader’

This Cambridge Drug Company Inadvertently Spread the Coronavirus. Now, It’s Creating A ‘Biobank’ To Hopefully Treat the Disease

Phylogenetic Analysis of SARS-CoV-2 in the Boston Area Highlights the Role of Recurrent Importation and Superspreading Events

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences

Tracking Changes in SARS-CoV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 Virus

The D614G Mutation in the SARS-CoV-2 Spike Protein Reduces S1 Shedding and Increases Infectivity

Emerging Pandemic Diseases: How We Got to COVID-19 Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies

UCSF and Stanford Researchers Investigate Why Some Infected with COVID-19 Are Asymptomatic, While Others Become Severely Ill or Die

Might clinical laboratories soon be called on to conduct mass testing to find people who show little or no symptoms even though they are infected with the coronavirus?    

Clinical laboratory managers understand that as demand for COVID-19 testing exceeds supplies, what testing is done is generally performed on symptomatic patients. And yet, it is the asymptomatic individuals—those who are shown to be infected with the SARS-CoV-2 coronavirus, but who experience no symptoms of the illness—who may hold the key to creating effective treatments and vaccinations.

So, as the COVID-19 pandemic persists, scientists are asking why some people who are infected remain asymptomatic, while others die. Why do some patients get severely ill and others do not? Researchers at the University of California San Francisco (UCSF) and Stanford University School of Medicine (Stanford Medicine) are attempting to answer these questions as they investigate viral transmission, masking, immunity, and more.

And pressure is increasing on researchers to find the answer. According to Monica Gandhi, MD, MPH, an infectious disease specialist and Professor of Medicine at UCSF, millions of people may be asymptomatic and unknowingly spreading the virus. Gandhi is also Associate Division Chief (Clinical Operations/Education) of the Division of HIV, Infectious Diseases, and Global Medicine at UCSF’s Zuckerberg San Francisco General Hospital and Trauma Center.

“If we did a mass testing campaign on 300 million Americans right now, I think the rate of asymptomatic infection would be somewhere between 50% and 80% of cases,” she told UCSF Magazine.

On a smaller scale, her statement was borne out. In a study conducted in San Francisco’s Mission District during the first six weeks of the city’s shelter-in-place order, UCSF researchers conducted SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing on 3,000 people. Approximately 53% tested positive for COVID-19 but had no symptoms such as fever, cough, and muscle aches, according to data reported by Carina Marquez, MD, UCSF Assistant Professor of Medicine and co-author of the study, in The Mercury News.

While their study undergoes peer-review, the researchers published their findings on the preprint server medRxiv, titled, “SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco.”

Pandemic Control’s Biggest Challenge: Asymptomatic People

In an editorial in the New England Journal of Medicine (NEJM), Gandhi wrote that transmission of the virus by asymptomatic people is the “Achilles heel of COVID-19 pandemic control.”

In her article, Gandhi compared SARS-CoV-2, the coronavirus that causes COVID-19, to SARS-CoV-1, the coronavirus that caused the 2003 SARS epidemic. One difference lies in how the virus sheds. In the case of SARS-CoV-2, that takes place in the upper respiratory tract, but with SARS-CoV-1, it takes place in the lower tract. In the latter, symptoms are more likely to be detected, Gandhi explained. Thus, asymptomatic carriers of the coronavirus may go undetected.

Viral loads with SARS-CoV-1, which are associated with symptom onset, peak a median of five days later than viral loads with SARS-CoV-2, which makes symptom-based detection of infection more effective in the case of SARS-CoV-1,” Gandhi wrote. “With influenza, persons with asymptomatic disease generally have lower quantitative viral loads in secretions from the upper respiratory tract than from the lower respiratory tract and a shorter duration of viral shedding than persons with symptoms, which decreases the risk of transmission from paucisymptomatic persons.”

Rick Wright of Redwood City, CA
Rick Wright (above), an insurance broker in Redwood City, Calif., was infected with the COVID-19 coronavirus while aboard a Diamond Princess Cruise. He underwent 40 days of isolation, and though he consistently tested positive for the coronavirus, he experienced no symptoms of the illness. “I never felt sick. Not a cough, wheezing, headache. Absolutely nothing,” he told Mercury News. (Photo copyright: The Mercury News.)

Stanford Studies Immune Responses in COVID-19 Patients

Meanwhile, scientists at the Stanford University School of Medicine were on their own quest to find out why COVID-19 causes severe disease in some people and mild symptoms in others.

“One of the great mysteries of COVID-19 infections has been that some people develop severe disease, while others seem to recover quickly. Now, we have some insight into why that happens,” Bali Pulendran, PhD, Stanford Professor of Pathology, Microbiology, and Immunology and Senior Author of the study in a Stanford Medicine news release.

The study, published in Science, titled, “Systems Biological Assessment of Immunity to Mild Versus Severe COVID-19 Infection in Humans,” was based on analysis of 76 patients with COVID-19 and 69 healthy people from Hong Kong and Atlanta. The researchers pointed to flailing immune systems and “three molecular suspects” in the blood of COVID-19 patients they studied.

The Stanford research suggested that three molecules—EN-RAGE, TNFSF14, and oncostatin-M—“correlated with disease and increased bacterial products in human plasma” of COVID-19 patients. 

“Our multiplex analysis of plasma cytokines revealed enhanced levels of several proinflammatory cytokines and a strong association of the inflammatory mediators EN-RAGE, TNFSF14, and OSM with clinical severity of the disease,” the scientists wrote in Science.

Pulendran hypothesized that the molecules originated in patients’ lungs, which was the infection site. 

“These findings reveal how the immune system goes awry during coronavirus infections, leading to severe disease and point to potential therapeutic targets,” Pulendran said in the news release, adding, “These three molecules and their receptors could represent attractive therapeutic targets in combating COVID-19.”

Clinical Laboratories May Do More Testing of Asymptomatic People

The research continues. In a televised news conference, President Trump said COVID-19 testing plays an important role in “preventing transmission of the virus.” Clearly this is true and learning why some people who are infected experience little or no symptoms may be key to defeating COVID-19.

Thus, as the nation reopens, clinical laboratories may want to find ways to offer COVID-19 testing beyond hospitalized symptomatic patients and people who show up at independent labs with doctors’ orders. As supplies permit, laboratory managers may want to partner with providers in their communities to identify people who are asymptomatic and appear to be well, but who may be transmitting the coronavirus. 

—Donna Marie Pocius

Related Information:

We Thought It Was Just a Respiratory Virus—We Were Wrong

Coronavirus: Why Don’t People Get Sick Despite Being Infected?

Asymptomatic Transmission, the Achilles’ Heel of Current Strategies to Control COVID-19

Study Reveals Immune System-Deviations in Severe COVID-19 Cases, a Stanford Study Shows

Why Do Some Get Sick and Others Don’t? Study May Unravel Mystery

Systems Biological Assessment of Immunity to Mild Versus Severe COVID-19 Infection in Humans

New Research Suggests Clinical Laboratory Blood Tests Could Fill A Void in Alzheimer’s Disease Diagnoses

Studies presented at the Alzheimer’s Association International Conference point to the p-tau217 protein as an especially useful biomarker

Researchers disclosed a potentially useful biomarker for Alzheimer’s Disease at a major conference this summer. The good news for clinical laboratories is that the biomarker is found in blood. If further research confirms these early findings, medical laboratories could one day have a diagnostic test for this condition.

That possibility emerged from the Alzheimer’s Association International Conference (AAIC), which was held online July 27-31. Researchers presented findings from multiple studies that suggested blood/plasma levels of a protein known as phospho-tau217 (p-tau217) can indicate brain anomalies associated with Alzheimer’s.“Changes in brain proteins amyloid and tau, and their formation into clumps known as plaques and tangles, respectively, are defining physical features of Alzheimer’s disease in the brain,” states an AAIC press release. “Buildup of tau tangles is thought to correlate closely with cognitive decline. In these newly reported results, blood/plasma levels of p-tau217, one of the forms of tau found in tangles, also seem to correlate closely with buildup of amyloid.”

At present, “there is no single diagnostic test that can determine if a person has Alzheimer’s disease,” the association states on its website. Clinicians will typically review a patient’s medical history and conduct tests to evaluate memory and other everyday thinking skills. That may help determine that an individual has dementia, but not necessarily that Alzheimer’s is the cause.

“Currently, the brain changes that occur before Alzheimer’s dementia symptoms appear can only be reliably assessed by positron-emission tomography (PET) scans, and from measuring amyloid and tau proteins in [cerebrospinal] fluid (CSF),” the association states. “These methods are expensive and invasive. And, too often, they are unavailable because they are not covered by insurance or difficult to access, or both.”

In the AAIC press release, Alzheimer’s Association Chief Science Officer Maria C. Carrillo, PhD, said that a clinical laboratory blood test “would fill an urgent need for simple, inexpensive, non-invasive and easily available diagnostic tools for Alzheimer’s.

“New testing technologies could also support drug development in many ways,” she added. “For example, by helping identify the right people for clinical trials, and by tracking the impact of therapies being tested. The possibility of early detection and being able to intervene with a treatment before significant damage to the brain from Alzheimer’s disease would be game changing for individuals, families, and our healthcare system.”

However, she cautioned, “these are early results, and we do not yet know how long it will be until these tests are available for clinical use. They need to be tested in long-term, large-scale studies, such as Alzheimer’s clinical trials.”

Eli Lilly Clinical Laboratory Alzheimer’s Test

In one study presented at the conference, titled, “Discriminative Accuracy of Plasma Phospho-tau217 for Alzheimer Disease vs Other Neurodegenerative Disorders,” researchers evaluated an experimental p-tau217 medical laboratory test developed by Eli Lilly. They published their research in JAMA Network.

The study, led by Oskar Hansson, MD, of Lund University in Sweden, included 1,402 participants. About half of these were enrolled in BioFINDER-2, an ongoing dementia study in Sweden. In this group, researchers were most interested in the test’s ability to distinguish Alzheimer’s from other neurodegenerative disorders that cause dementia.

Diagnostic accuracy was between 89% and 98%, the researchers reported, which was similar to the performance of PET imaging and CSF tests. P-tau217 was more accurate than magnetic resonance imaging (MRI) as well as other biomarkers, such as p-tau181.

Oskar-Hansson-PhD-Lund-University-400w@72ppi
“Today the majority of individuals with Alzheimer’s disease around the world do not get a timely diagnosis, which results in suboptimal symptomatic treatment and care,” Oskar Hansson, MD, said in an Eli Lilly news release. “With rising prevalence of Alzheimer’s disease, more patients will be evaluated in primary care and other clinics where CSF and PET biomarkers are not available. Blood-based biomarkers, like plasma p-tau217, together with digital tools for checking memory performance, such as smartphone-based apps, can considerably improve the diagnostic work-up of Alzheimer’s disease patients in such clinics.” (Photo copyright: Alzheimer’s Fund.)

Another cohort consisted of 81 participants in the Brain and Body Donation Program at Banner Sun Health Research Institute in Sun City, Ariz. In this program, elderly volunteers submit to periodic clinical assessments and agree to donate their organs and tissue for study after they die.

Here, the researchers’ primary goal was to determine the test’s ability to distinguish between individuals with and without Alzheimer’s. Researchers ran the p-tau217 test on plasma samples collected within 2.9 years of death and compared the results to postmortem examinations of the brain tissue. Accuracy was 89% in individuals with amyloid plaques and tangles, and 98% in individuals with plaques and more extensive tangles.

The third cohort consisted of 622 members of a large extended family in Colombia whose members share a genetic mutation that makes them susceptible to early-onset Alzheimer’s, The New York Times reported. Among the members, 365 were carriers of the mutation. In this group, levels of plasma p-tau217 increased by age, and “a significant difference from noncarriers was seen at age 24.9 years,” the researchers wrote in Jama Network. That’s about 20 years before the median age when mild cognitive impairment typically begins to appear in carriers.

Other Alzheimer Biomarker Studies Presented at AAIC

Suzanne Schindler, MD, PhD, a neurologist and instructor in the Department of Neurology at the Washington University School of Medicine (WUSM) in St. Louis, presented results of an Alzheimer’s Disease (AD) study that used mass spectrometry to analyze amyloid and p-tau variants in blood samples collected from participants. The researchers compared these with CSF and PET results and found that some of the of p-tau isoforms, especially p-tau217, had a strong concordance.

“These findings indicate that blood plasma Aβ and p-tau measures are highly precise biomarkers of brain amyloidosis, tauopathy, and can identify stages of clinical and preclinical AD,” stated an AAIC press release on the studies.

The WUSM researches launched the effort to develop and validate Alzheimer’s blood biomarkers called the Study to Evaluate Amyloid in Blood and Imaging Related to Dementia (SEABIRD) in April 2019. It runs through August 2023 and will seek to enroll more than 1,100 participants in the St. Louis area.

Another study presented at the conference compared the performance of p-tau217 and p-tau181 in distinguishing between Alzheimer’s and Frontotemporal Lobar Degeneration (FTLD), another condition that causes dementia. Study author Elisabeth Thijssen, MSc, of the UC San Francisco Memory and Aging Center reported that both biomarkers could be useful in differential diagnosis, but that p-tau217 was “potentially superior” for predicting a tau positive PET scan result.

For decades, physicians have wanted a diagnostic test for Alzheimer’s Disease that could identify this condition early in its development. This would allow the patient and the family to make important decisions before the onset of severe symptoms. Such a clinical laboratory test would be ordered frequently and thus would be a new source of revenue for medical laboratories.

—Stephen Beale

Related Information:

How is Alzheimer’s Disease Diagnosed?

Alzheimer’s Diagnosis and Treatment

Diagnosing Alzheimer’s: How Alzheimer’s is Diagnosed

New Alzheimer’s Disease Blood Test Could Enable Early Diagnosis and Advance Understanding of How Disease Impacts Those Living with It

Lilly’s p-tau217 Blood Test Shows High Accuracy in Diagnosis of Alzheimer’s Disease in Data Published in JAMA

P-Tau217 May Detect Alzheimer Disease, Brain Amyloidosis, Tauopathy

New Blood Test Shows Great Promise in The Diagnosis of Alzheimer’s Disease

‘Amazing, Isn’t It?’ Long-Sought Blood Test for Alzheimer’s in Reach

Scientists Get Closer to Blood Test for Alzheimer’s Disease

Discriminative Accuracy of Plasma Phospho-tau217 for Alzheimer Disease vs Other Neurodegenerative Disorders

US Government Purchases 150 Million COVID-19 Antigen Tests from Abbott Laboratories for $760 Million; Only CLIA-Certified Clinical Laboratories Can Do Testing

Abbott sends the SARS-CoV-2 test results directly to patients’ smartphones, which can be displayed to gain entrance into areas requiring proof of COVID-19 testing

There is no greater example that COVID-19 is a major force for change in the clinical laboratory industry than the fact that—though the US federal government pays 50% of the nation’s total annual healthcare spend of $3.5 trillion—it recently spent $760 million to purchase 150 million COVID-19 tests from Abbott Laboratories (NYSE:ABT), an American multinational medical devices and healthcare company headquartered in Abbott Park, Ill., “to expand strategic, evidence-based testing in the United States,” according to the company’s website.

In August, the federal Food and Drug Administration (FDA) granted an emergency use authorization (EUA) to Abbott for its BinaxNOW portable rapid-response COVID-19 antigen (Ag) test. The credit-card sized test costs $5 and can return clinical laboratory test results in minutes, rather than hours, days, or in some cases, weeks, the Wall Street Journal (WSJ) reported.

The test includes a free smartphone app called NAVICA, which enables those tested to receive their test results directly on their mobile devices—bypassing the patient’s primary care physicians.

According to Abbott’s website, the app “allows people who test negative to get an encrypted temporary digital NAVICA Pass, similar to an airline boarding pass. NAVICA-enabled organizations will be able to verify an individual’s negative COVID-19 test results by scanning the individual’s digital NAVICA Pass to facilitate entry into facilities.”

This feature of Abbott’s new COVID-19 test is a good example of how quickly innovation in the medical laboratory testing profession is bringing new features and new capabilities to the marketplace. By marrying the SARS-CoV-2 test with the NAVICA Pass feature, Abbott hopes to deliver increased value—not just to physicians and their patients—but also to employers with employee screening programs and federal government programs designed to screen federal employees, as well as being used for screening travelers at airports and other transportation hubs.

Abbott appears to be banking that in the future such identification will be required to “enter organizations and other places where people gather,” as the company’s website states.

Testing Limited to CLIA-Certified Clinical Laboratories

An HHS news release announcing the government’s planned distribution of the BinaxNOW tests stated that “Testing will be potentially deployed to schools and to assist with serving other special needs populations.”

In the news release, Alex Azar, HHS Secretary, said, “By strategically distributing 150 million of these tests to where they’re needed most, we can track the virus like never before and protect millions of Americans at risk in especially vulnerable situations.”

The EUA adds that “Testing of nasal swab specimens using [BinaxNOW] … is limited to laboratories certified under CLIA that meet the requirements to perform high, moderate, or waived complexity tests. This test is authorized for use at the [point of care], i.e., in patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation.”

The FDA’s EUA describes the BinaxNOW portable rapid-response COVID-19 antigen test (above) as “a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2 in direct nasal swabs from individuals suspected of COVID-19 by their healthcare provider within the first seven days of symptom onset.” The test costs $5 and Abbott sends results directly to the patient’s smartphone using the free NAVICA app included with the test. (Photo copyright: Abbott Laboratories.)

IVD Companies See Boom in COVID-19 Test Sales

Demand for COVID-19 testing has created opportunities for in vitro diagnostics (IVD) companies that can develop and bring tests to market quickly. 

Recent issues of Dark Daily’s sister print publication—The Dark Report (TDR)—covered IVD companies’ second quarter (Q2) boom in sales of COVID-19 instruments and tests, while also noting a fall-off in routine clinical laboratory testing during the COVID-19 pandemic. 

Abbott Laboratories saw molecular diagnostics sales increase 241% in Q2 driven by $283 million in sales of COVID-19 testing, while rapid diagnostic COVID-19 testing rose 11% on $180 million in sales in Q2, TDR reported, based on Abbott data.

“There is huge economic incentive for diagnostic companies to develop technologies that can be used to create rapid tests that are cheap to perform,” said Robert Michel, Publisher and Editor-in-Chief of TDR and Dark Daily. “In this sense, COVID is a major force for change.”

“This new COVID-19 antigen test is an important addition to available tests because the results can be read in minutes, right off the testing card,” said Jeff Shuren, MD, JD (above), Director of the FDA’s Center for Devices and Radiological Health (CDRH), in an FDA news release announcing the federal government’s $760 million purchase of 150 million Abbott BinaxNOW rapid-response antigen COVID-19 tests. “This means people will know if they have the virus in almost real-time. Due to its simpler design and the large number of tests the company anticipates making in the coming months, this new antigen test is an important advancement in our fight against the pandemic.” (Photo copyright: The New York Times.)

Abbott Invests in Proving BinaxNOW’s Capabilities

Abbott has a lot riding on the BinaxNOW test. Its portable, rapid molecular ID NOW COVID-19 test was touted by President Trump during a White House press briefing in March as “a whole new ballgame.” But then, researchers at New York University (NYU) published study data that questioned the accuracy and reliability of the test, which Dark Daily covered in “Abbott Labs’ ID NOW COVID-19 Rapid Molecular Test Continues to Face Scrutiny Over False Negatives.”

Thus, Abbott is determined to ensure this product launch is successful and that the test works as promised. According to a news release, “In data submitted to the FDA from a clinical study conducted by Abbott with several leading US research universities, the BinaxNOW COVID-19 Ag Card demonstrated sensitivity of 97.1% (positive percent agreement) and specificity of 98.5% (negative percent agreement) in patients suspected of COVID-19 by their healthcare provider within the first seven days of symptom onset.”

“The massive scale of this test and app will allow tens of millions of people to have access to rapid and reliable testing,” said Joseph Petrosino, PhD, professor and chairman, Molecular Virology and Microbiology, Baylor College of Medicine, in the Abbott news release. “With lab-based tests, you get excellent sensitivity but might have to wait days or longer to get the results. With a rapid antigen test, you get a result right away, getting infectious people off the streets and into quarantine so they don’t spread the virus.”

Abbott has invested hundreds of millions of dollars in two manufacturing facilities where the tests will be made, John Hackett Jr, PhD, an immunologist and Abbott’s Divisional Vice President Applied Research and Technology, and lead scientist on the BinaxNOW project, told The Atlantic.

“Our nation’s frontline healthcare workers and clinical laboratory personnel have been under siege since the onset of this pandemic,” said Charles Chiu, MD, PhD, professor of Laboratory Medicine at University of California, San Francisco, in the Abbott news release. “The availability of rapid testing for COVID-19 will help support overburdened laboratories, accelerate turnaround times, and greatly expand access to people who need it.”

However, other experts are not so sure. In the Atlantic article, Michael Mina MD, PhD, Assistant Professor Epidemiology at Harvard’s T.H. Chan School of Public Health, voiced the need to test both asymptomatic and pre-symptomatic people. “This is the type of [COVID-19] test we have been waiting for—but may not be the test.”

Nevertheless, the federal government’s investment is significant. Abbott plans to start shipping tens of millions of tests in September and produce 50 million tests per month starting in October, Forbes reported.

Shifting Clinical Laboratory Paradigms

BinaxNOW will be performed without doctors’ orders, in a variety of locations, and results go directly to patients’ smartphone—without a pathologist’s interpretation and medical laboratory report. This is new ground and the impact on non-CLIA labs, and on healthcare in general, is yet to be seen.

Clinical laboratory managers will want to monitor the rise of rapid-response tests that can be easily accessed, conducted, and reported on without physician input. 

—Donna Marie Pocius

Related Information:

Trump Administration Will Deploy 150 Million Rapid Tests in 2020

In Vitro Diagnostics Firms Report Boom in Sales of COVID-19 Instruments, Tests

FDA Authorizes First Diagnostic Test Where Results Can Be Read Directly from Testing Card

Abbott’s Fast, $5, 15-Minute Easy-to-Use COVID-19 Antigen Test Receives FDA Emergency Use Authorization; Mobile App Displays Test Results to Help Our Return to Daily Life; Ramping Production to 50 Million Tests a Month

Performance of the Rapid Nucleic Acid Amplification by Abbott ID NOW COVID-19 in Nasopharyngeal Swabs Transported in Viral Media and Dry Nasal Swabs, in a New York City Academic Institution

Trump to Announce Deal with Abbott Laboratories for 150 Million Rapid COVID-19 Tests

Abbott Labs’ ID NOW COVID-19 Rapid Molecular Test Continues to Face Scrutiny Over False Negatives

Abbott Provides Update on ID NOW

A New Era of Coronavirus Testing is About to Begin

U.S. Approves Abbott Labs’ $5 Mass-Scale COVID-19 Test

‘There’s an App for That’ is Becoming the Norm in Healthcare as Smartphones Provide Access to Patient Medical Records and Clinical Laboratory Test Results

Amazon’s app-based employee healthcare service could be first step toward retailer becoming a disruptive force in healthcare; federal VA develops its own mHealth apps

More consumers are using smartphone applications (apps) to manage different aspects of their healthcare. That fact should put clinical laboratories and anatomic pathology groups on the alert, because a passive “wait and see” strategy for making relevant services and lab test information available via mobile apps could cause patients to choose other labs that do offer such services.

Patient use of apps to manage healthcare is an important trend. In January, Dark Daily covered online retail giant Amazon’s move to position itself as a leader in smartphone app-based healthcare with its launch of Amazon Care, a virtual medical clinic and homecare services program. At that time, the program was being piloted for Seattle-based employees and their families only. Since then, it has been expanded to include eligible Amazon employees throughout Washington State.

Mobile health (mHealth) apps are giving healthcare providers rapid access to patient information. And healthcare consumers are increasingly turning to their mobile devices for 24/7 access to medical records, clinical laboratory test results, management of chronic conditions, and quick appointment scheduling and prescription refills.

Thus, hearing ‘There’s an app for that’ has become part of patients’ expectations for access to quality, affordable healthcare.

For clinical laboratory managers, this steady shift toward mHealth-based care means accommodating patients who want to use mobile apps to access lab test results and on-demand lab data to monitor their health or gain advice from providers about symptoms and health issues.

Amazon, VA, and EMS Develop Their Own mHealth Apps

The Amazon Care app can be freely downloaded from Apple’s App Store and Google Play. With it, eligible employees and family members can:

  • Communicate with an advice nurse;
  • Launch an in-app video visit with a doctor or nurse practitioner for advice, diagnoses, treatment, or referrals;
  • Request a mobile care nurse for in-home or in-office visits;
  • Receive prescriptions through courier delivery.

The combination telehealth, in-person care program, mobile medical service includes dispatching nurses to homes or workplaces who can provide “physical assessments, vaccines or common [clinical laboratory] tests.”

Glen Tullman, Executive Chairman of Livongo
“Amazon is a company that is experimenting a lot with a variety of opportunities in healthcare,” Glen Tullman (above), Executive Chairman of Livongo, a healthcare company specializing in treating diabetes, and an Amazon partner company, told CNBC. “It’s one to watch.” (Photo copyright: CNBC.)

However, the US federal Department of Veterans Affairs (VA) also is becoming a major player in the mHealth space with the development of its own mobile app—VA Launchpad—which serves as a portal to a range of medical services.

Veterans can access five categories of apps that allow them to manage their health, communicate with their healthcare team, share health information, and use mental health and personal improvement tools.

Neil C. Evans, MD, Chief Officer in the VA Office of Connected Care
“The VA was an early adopter of digital health tools and remains a leader within US healthcare in leveraging technology to enhance patient engagement,” Neil C. Evans, MD (above), Chief Officer in the VA Office of Connected Care, told Healthcare IT News. “These digital tools are allowing veterans to more actively understand their health data, to better communicate with VA clinical teams, and to engage more productively as they navigate their individual health journeys,” Evans added. (Photo copyright: Department of Veterans’ Affairs.)

mHealthIntelligence reported that mobile health tools also are enabling first responders to improve emergency patient care. At King’s Daughters Medical Center in Brookhaven, Miss., emergency medical technicians (EMTs) are using a group of mHealth apps from DrFirst called Backline to gain real-time access to patients’ HIPAA-compliant medication histories, share clinical data, and gain critical information about patients prior to arriving on the scene.

Using Backline, EMTs can scan the barcode on a patient’s driver’s license to access six months’ worth of medication history.

“In the past, we could only get information from [patients] who are awake or are willing to give us that information,” Lee Robbins, Director of Emergency Medical Services at King’s Daughters Medical Center in Brookhaven, Miss., told mHealthIntelligence. “Knowing this information gives us a much better chance at a good outcome.”

Smartphone App Detects Opioid Overdose

The opioid crisis remains one of the US’ greatest health challenges. The federal Centers for Disease Control and Prevention (CDC) reported 47,600 opioid-related deaths in 2017, and the problem has only gotten worse since then.

To curtail these tragic deaths, University of Washington (UW) researchers developed a smartphone app called Second Chance, that they believe can save lives by quickly diagnosing when an opioid overdose has occurred.

The app uses sonar to monitor an opioid user’s breathing rate and, according to a UW press release, can detect overdose-related symptoms about 90% of the time from up to three feet away. The app then contacts the user’s healthcare provider or emergency services.

The UW researchers are applying for US Food and Drug Administration (FDA) clearance. They published their findings in the journal Science Translational Medicine.

While Demand for mHealth Apps Grows, Concern over Privacy and Security also Increases  

According to mobile data and analytics company App Annie, global downloads of medical apps grew to more than 400 million in 2018, up 15% from two years earlier.

“As with mobile banking, consumers are showing they trust mobile apps with their most sensitive information and are willing to leverage them to replace tasks traditionally fulfilled in-person, such as going into a bank branch or, in the case of medical apps, to a doctor’s office,” App Annie’s website states.

However, the proliferation of mHealth apps has raised privacy and safety concerns as well. While the FDA does regulate some mobile health software functions, it does not ensure an mHealth app’s accuracy or reliability.

In his article, “Dangers of Defective Mobile Health Apps and Devices,” published on the Verywell Health website, Kevin Hwang, MD, MPH, physician, researcher, and Medical Director of UT Physicians General Internal Medicine Center in the Texas Medical Center at the University of Texas Medical School at Houston, points out that “most mHealth apps have not been tested in a rigorous manner.”

Fierce Healthcarereported that federal lawmakers are worried veterans who use the VA’s 47 mHealth apps could find their sensitive healthcare information shared or sold by third-party companies. In fiscal year 2018, veterans participated in more than one million video telehealth visits, a VA press release reported.

US Rep. Susie Lee, D-Nevada, Chairperson of the House Veterans’ Affairs Subcommittee on Technology Modernization, told Fierce Healthcare, “As we assess the data landscape at the VA and the larger health IT space, we need to look at where protections exist or don’t exist and whether we need more guardrails.”

What does all this mean for clinical laboratories? Well, lab managers will want to keep an eye on the growing demand from consumers who want direct access to laboratory test data and appointment scheduling through mHealth apps. And, also be aware of HIPAA regulations concerning the sharing of that information.

—Andrea Downing Peck

Related Information:

How Amazon is Using IoT to Care for Its Employees

Amazon Launches Amazon Care, a Virtual Medical Clinic for Employees

VA Seeing Substantial Growth in Telehealth, Key Patient Engagement Tools

VA Releases Launchpad App to Streamline Healthcare Access for Veterans and Caregivers

Drug Overdose Deaths

Smartphone App Can Detect Opioid Overdoes Using Sonar

VA Exceeds More than One Million Video Telehealth Visits in FY2018

Medical Apps Transform How Patients Receive Medical Care

Dangers of Defective Mobile Health Apps and Devices

mHealth Tools Help Providers Access Data When They Most Need it

Here’s How Amazon Employees Get Health Care Through a New App—A Glimpse of the Future of Medicine

VA Launches New mHealth App to Consolidate Vets’ Access to Resources

The VA Recommends Apps for PTSD and Pain Management. It’s Led to New Veteran Privacy Concerns

Researchers Use Nanopore Sequencing Technology to Complete First Gapless End-to-End Assembly of Human X Chromosome

Ability to produce unbroken DNA sequencing could eventually be used by medical laboratories to identify gene sequences that play significant roles in a variety of diseases and health conditions

While near 24/7 coronavirus coverage occupies much of the media, it is refreshing to report on important breakthroughs in clinical laboratory medicine and diagnostics that are unrelated to the COVID-19 pandemic. It wasn’t long ago that the top stories in advanced medicine revolved around whole-genome sequencing, so it’s nice to return to the topic, if just for a little while.

Using nanopore sequencing technology from multiple companies, researchers at the University of California Santa Cruz Genomics Institute (UCSC Genomics Institute) have produced what they say is the first telomere-to-telomere or end-to-end map of the human X chromosome. This could prove to be a major milestone for genomics research and help scientists gain a better understanding of certain genetic conditions.

The completely gapless DNA sequencing was produced by using new sequencing technologies that enable much longer reads of strings of DNA base pairs. In the past, most sequencing technologies produced relatively short reads of each sequence, which then had to be painstakingly pieced together to assemble the complete genome.

“With nanopore sequencing we get ultra-long reads of hundreds of thousands of base pairs that can span an entire repeat region, so that bypasses some of the challenges,” said Karen Miga, PhD, a post-doctoral research scientist at the UCSC Genomics Institute and lead author of the study, in a UCSC news release.

The UCSC researchers published their paper, titled, “Telomere-to-Telomere Assembly of a Complete Human X Chromosome,” in the multidisciplinary scientific journal Nature.

UCSC Researchers Find ‘Rich’ Information in the ‘Gaps’ in Reference Sequences

Nanopore sequencing technology from Oxford Nanopore Technologies was combined with sequencing technologies from Pacific Biosciences (PacBio) and Illumina, as well as with optical maps from Bionano, to produce the results of the research. The combination of these technologies allowed the UCSC team to produce a whole-genome sequence assembly with no gaps and with a previously unforeseen level of accuracy.

“These repeat-rich sequences were once deemed intractable, but now we’ve made leaps and bounds in sequencing technology,” Miga said.

According to the Oxford Nanopore Technologies website, “Nanopore sequencing is a unique, scalable technology that enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.”

By filling in gaps in the human genome, the UCSC researchers opened up new possibilities to finding clues and answers regarding important questions about our genes and how they may contribute to illnesses.

Karen Miga, PhD post-doctoral researcher at the UCSC Genomics Institute speaking at a podium

“We’re starting to find that some of these regions where there were gaps in the reference sequence are actually among the richest for variation in human populations, so we’ve been missing a lot of information that could be important to understanding human biology and disease,” said Karen Miga, PhD (above), post-doctoral researcher at the UCSC Genomics Institute and lead author of the study, in the UCSC news release. (Photo copyright: UCSC Genomics Institute.)

During their research, the team had to manually resolve several gaps in the sequence and identify variants within the repeat sequence to serve as markers. They were then able to align the long reads and connect them together to span the centromere of the X chromosome. The centromere is a difficult region of repetitive DNA that is found in every chromosome. It encompasses an area of very repetitive DNA that spans 3.1 million base pairs.

“For me, the idea that we can put together a 3-megabase-size [3-million base pairs] tandem repeat is just mind-blowing. We can now reach these repeat regions covering millions of bases that were previously thought intractable,” Miga said.

The researchers also had to employ a polishing strategy using data obtained from different sequencing technologies to ensure accuracy.

“We used an iterative process over three different sequencing platforms to polish the sequence and reach a high level of accuracy,” Miga explained. “The unique markers provide an anchoring system for the ultra-long reads, and once you anchor the reads, you can use multiple data sets to call each base.”

Linking Gene Variations to Specific Genetic Diseases

Besides the advantages of providing ultra-long reads, nanopore sequencing can also detect bases that have been modified by methylation, a biological process by which methyl groups are added to the DNA molecule. Methylation is an epigenetic change that can alter the activity of a DNA segment without changing the sequence, and can have important effects on the DNA structure and gene expression. When located in a gene promoter, DNA methylation typically acts to repress gene transcription.

The researchers were able to observe and map patterns of methylation on the X chromosome and found some interesting trends in methylation patterns within the centromere. By looking at this previously unmapped area of the genome, scientists may be able to search for potential links between these variations and genetic diseases.

“You could be turning a blind eye to some of the richest sequence diversity that exists in the human population, and some of that sequence diversity that you’re not looking at could be correlated with disease in a way we’ve never been able to study before,” Miga told OneZero.

The work performed by researchers at the UCSC Genomics Institute could provide genetic scientists with a road map for producing complete sequences in other human chromosomes. This may lead genomic researchers to identify gene sequences that play significant roles in a variety of diseases and health conditions. In turn, this would give clinical laboratories new biomarkers for diagnosing disease and other chronic conditions in patients.

—JP Schlingman

Related Information:

Telomere-to-Telomere Assembly of a Complete Human X Chromosome

Scientists Achieve First Complete Assembly of Human X Chromosome

Researchers Just Took a Major Step toward Decoding the Entire Human Genome

Oxford Nanopore Technologies Raises $180 Million to Expand Development of Its Revolutionary Hand-held DNA Sequencer; Might Medical Labs Get a POCT Solution?

;