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Clinical Laboratories and Pathology Groups

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In the Field, Clinical Laboratory Specimen Transportation is Being Complicated by the COVID-19 Pandemic

Lab leaders who adopt best practices in courier services will help ensure their lab’s supply chains remain secure

Hospital and health systems using courier services to transport patients’ biological specimens from doctors’ offices and other locations to clinical laboratories for testing and reporting are finding those services delayed or disrupted by the COVID-19 pandemic.  

Limited office hours, closed physician practices, and the need for drivers to take time for symptom checking on healthcare campuses are among the growing challenges faced by couriers transporting medical laboratory specimens during this pandemic, experts told Dark Daily.

All these developments require courier operations and logistics companies to think outside the box for solutions that address the unique challenges triggered by the SARS-CoV-2 pandemic that have disrupted the normal operations of physicians’ offices, hospitals, and other healthcare providers. For example, many clinical labs struggle to obtain enough specimen collection and specimen transport supplies to sustain both their nascent COVID-19 testing programs and their routine testing operations.

One national logistics company recognized that it could help labs with the disruption in the supply chain for laboratory supplies caused by the coronavirus outbreak. In the early weeks of the pandemic, West Haven, Conn.-based Lab Logistics and its sister company Path-Tec, took the initiative to develop collaborations and strategic partnerships with several established manufacturers of medical laboratory supplies. Now it could not only be a source of much-needed supplies for its clients, but its network of couriers could supply the increase in services for all the locations where such supplies were needed.

Meanwhile, the coronavirus outbreak caused widespread disruption to the daily activities of hospitals, health systems, physician’s offices, and other providers. According to Susan Uihlein, Senior Vice President Business Development-Hospital Couriers at Lab Logistics—a company that creates, implements, and manages courier models customized to medical laboratory, hospitals, and health systems—in response to the pandemic, there was an immediate need by one of the largest multi-regional Health Systems in New York to align courier and logistics services to meet the new realities of how its facilities would respond to patient needs. It was also necessary that logistics solutions be complementary with the health systems’ COVID-19 policies.

“This health system requested that Lab Logistics’ drivers access the hospital’s personnel tracking application upon arrival,” explained Uihlein. “The health system’s new COVID-19 policy required everyone wishing to enter the health system campus to complete a coronavirus screening process—including having a temperature reading taken—and then receive a status confirmation on a smartphone screen. This obviously impacted the couriers’ progress on their routes.”

“We have 2,600 medical-specific couriers throughout the United States, and although all couriers undergo extensive orientation regarding known infectious transport, this current situation has spotlighted how important (COVID-19) is to our clients,” Brian McArdle, President and Chief Executive Officer of Lab Logistics, told Dark Daily.

“The couriers represent us and our clients,” he continued. “They are out in the field, they are picking up, delivering, and rolling with the punches as far as what a healthcare system or a clinical laboratory needs from them—from photo IDs to wearing masks and gloves. The process keeps evolving. And we have evolved with it.”

 “Our operations team makes sure that we work with each client to flexibly react to changes in that day’s pickups and deliveries, as appropriate. There has been much optimization and on-the-fly changes,” said Uihlein.

In fact, the coronavirus pandemic resulted in a 26% increase in requests for specimen delivery, PPE, and COVID-19 related supply chain movement, according to data on the California, Louisiana, and New York City healthcare markets provided by Lab Logistics.

“Every day there have been changes to what is open and closed. We had to manage that through our proprietary healthcare dispatch system and with the couriers,” Susan Uihlein (above), Senior Vice President Business Development-Hospital Couriers at Lab Logistics, told Dark Daily. Lab Logistics transports medical specimens, supplies, and pharma for more than 350 US hospitals, healthcare systems, and clinical laboratories. (Photo copyright: LinkedIn.)

Clinical Laboratories Should Review Specimen Transport Procedures

Clearly, the COVID-19 pandemic is putting unique stresses on the logistics and transportation services operated by hospital systems, medical labs and anatomic pathology groups. That why it would be timely and appropriate for lab leaders to review/update best practices and necessary requirements that ensure efficient management of clinical laboratory specimens.

“The COVID-19 pandemic triggered heightened risks in security, custody, and transit tracking of specimens so as to maintain a heightened biosafety level, while at the same time, the pandemic dramatically reduced the daily volume of more routine lab samples,” notes a Special Edition White Paper Dark Daily produced in partnership with Lab Logistics, titled, “Specimen Management and Logistics Issues to Evaluate for Continuous Quality Improvement—3 High-Risk Medical Courier Support Services.”

Topics covered in this highly-informative white paper include:

  • Handling and tracking laboratory specimen samples;
  • Confirming medical security, chain of custody, and transit tracking;
  • Coordinating test kits, supplies, reagents, lab equipment, and instruments;
  • Approaching a medical courier service conversion.

“By utilizing a logistics system that includes a dedicated courier, medical laboratories and healthcare systems can manage all aspects of transportation specimen transport, including handling and tracking of specimens, medical security, chain of custody, tracking supply inventory, and delivery. Successfully executed, all of these functions can generate financial improvements,” notes the white paper.

Tracking Specimen Arrival and Predicting Which Tests Will Be Needed

One technology that lab and healthcare system leaders can use to control costs and staffing involves online real-time tracking of drivers to enhance test turnaround time and determine when tests will be performed.

Lab Logistics’ version of this technology uses barcode scanning, GPS (Global Positioning System) tracking, and an online portal that enables its clients to view the routes and stops a driver has made for the lab. Lab leaders can determine how many specimens are expected, and what type of tests will be required, before the specimens arrive.

“They can see the volume coming in and they can staff-up based on the information we are giving them and not over-staff. It’s really good information,” Uihlein said.

Lab Logistics’ platform also integrates with a hospital’s laboratory information system (LIS) through the lab’s barcode. “The integration makes it possible for labs to get faster information from the field into their systems and create accessioning,” Uihlein explained.

Specimen Management Improved through Route Tracking

Tracking their drivers has enabled some labs to find new routes with less stops. Mike Napolitano, former General Manager for Constitution Diagnostics Network, Sunrise Medical Laboratory, and Sonic Healthcare, discovered that modified routes enhanced his lab’s efficiency. 

“We found that some drivers were doing daily pickups and we were not getting any specimens. Some clients were on vacation, stopped using the laboratory altogether, or weren’t doing that type of laboratory work anymore,” Napolitano told the white paper researchers.

Driver tracking also enabled Ochsner Health System in Louisiana to avoid “hot shots”—one-time delivery pickups which could be 90 miles away from the lab, explained Lloyd Gravois, Assistant Vice President of Logistics-Supply Chain, in the white paper. 

Medical laboratory leaders who wish to enhance their lab’s specimen management and solve logistics issues during and after the COVID-19 pandemic are encouraged to download a copy of the Free Special Edition white paper by clicking here, or by placing this URL in their web browsers: https://www.darkdaily.com/free-special-edition-white-paper-specimen-management-and-logistics-issues-to-evaluate-for-continuous-quality-improvement-3-high-risk-medical-courier-support-services/.

—Donna Marie Pocius

Related Information:

Specimen Management and Logistics Issues to Evaluate for Continuous Quality Improvement: 3 High-Risk Medical Courier Support Services

Woman Who Can Smell Parkinson’s Disease in Patients Even Before Symptoms Appear May Help Researchers Develop New Clinical Laboratory Test

She worked with researchers at the University of Manchester in England to identify volatile biomarkers for Parkinson’s disease that may lead to first noninvasive screening

Clinical pathologists and medical laboratories are used to working with certain biological indicators that drive diagnostics and clinical laboratory testing. Mostly, those biomarkers are contained within various liquid samples, such as blood and urine. But what if a person’s odor could accurately predict risk for certain diseases as well?

Far-fetched? That’s what Parkinson’s researcher Tilo Kunath, PhD, first thought when he was contacted by a woman who claimed she could “smell” Parkinson’s disease coming from her husband. Kunath is Group Leader, Reader in Regenerative Neurobiology, at the Center for Regenerative Medicine at the University of Edinburgh, and head of the Tilo Kunath Research Group, which focuses on how the protein, alpha-synuclein, causes degeneration of neurons in Parkinson’s patients, as well as on producing a cell-based therapy for Parkinson’s disease.

Joy Milne, a retired nurse from Perth, Scotland, is the women whose heightened sense of smell enabled her to detect her husband’s Parkinson’s a decade before he was diagnosed with the disease.

Of course, Milne did not know at the time that what she was smelling was in fact a disease. She told NPR that she first noticed that her husband’s smell had changed from “his lovely male musk smell,” which she’d noticed when they first met, into “this overpowering sort of nasty yeast smell.”

Frequent washing did not remove the odor and as time went on the smell became stronger. When aspects of her husband’s personality and sleep habits also began to change, Joy convinced her husband, Les Milne, an anesthetist, to seek a diagnosis, thinking he had a brain tumor. Les was diagnosed with Parkinson’s disease.

It was 20 years later, when the Milnes attended a Parkinson’s disease support group, that Joy recognized the same distinctive smell she had noticed on Les on the other members of the group. That’s when the Milnes first realized Joy’s heightened sense of smell was something quite unique and possibly unprecedented.  

Retired nurse Joy Milne of Perth, Scotland
Retired nurse Joy Milne (above) of Perth, Scotland, has an uncanny ability to diagnose Parkinson’s disease based on her highly sensitive sense of smell. Before her husband was diagnosed with the disease, she noticed a change in his smell. When she later recognized the same distinct odor among participants in a Parkinson’s support group, the Milnes asked scientists to investigate. (Photo copyright: NPR.)

Dogs Can Do It, Why Not Humans?

The concept that a disease gives off an aroma that can be detected by humans or animals is not far-fetched. As far back as 2013, Dark Daily was writing about such research. For example, in “C. diff-sniffing Beagle Dog Could Lead to Better Infection Control Outcomes in Hospitals and Nursing Homes,” we wrote about one hospital’s innovative approach to early detection of Clostridium difficile (C. diff) infection using a two-year-old beagle named Cliff that was faster at detecting certain infections than standard clinical laboratory tests used daily in hospitals throughout the world.

And in, “Researchers Determine That Individuals’ ‘Breathprints’ Are Unique; May Have Potential for Clinical Laboratory Testing When Coupled with Mass Spectrometry Technology,” we reported on research that showed a person’s breathprint is as unique as a fingerprint and may be as effective as bodily fluids in diagnosing diseases. The research also showed it was feasible to combine breath specimens and mass spectrometry to accurately identify disease, possibly leading to new diagnostic assays.

Thus, when the Milnes approached Dr. Kunath about Joy’s ability to “smell” Parkinson’s, they were on solid ground. However, he was not convinced.

“It just didn’t seem possible,” Kunath told NPR. “Why should Parkinson’s have an odor? You wouldn’t think neurodegenerative conditions such as Parkinson’s, or Alzheimer’s, would have an odor.”

But Kunath reconsidered after learning of research presented during the Experimental Biology annual meeting in 2019, which showed canines can in fact effectively detect lung cancer biomarkers in blood serum.

He contacted Milne and devised an experiment in which a group of people who had Parkinson’s disease, and another group that did not, would take home t-shirts and wear them overnight. The next day the t-shirts were assigned randomized numbers and put in a box. Milne then smelled each of the 12 t-shirts and assigned each one a score.

Kunath told NPR that Milne was “incredibly accurate.” She had misidentified only one shirt worn by a person in the control group. She incorrectly diagnosed the person with Parkinson’s. However, three months later, that man was in fact diagnosed with Parkinson’s, meaning Joy’s accuracy was 12-for-12.

“She was telling us this individual had Parkinson’s before he knew, before anybody knew,” Kunath told the BBC Scotland.

In an ensuing study, “Discovery of Volatile Biomarkers of Parkinson’s Disease from Sebum,” published in 2019 in ACS Central Science, the researchers describes the “distinct volatiles-associated signature” of Parkinson’s disease, which includes “altered levels of perillic aldehyde and eicosane, the smell of which was then described as being highly similar to the scent of Parkinson’s disease by our ‘Super Smeller.’” Joy Milne co-authored the study.

The concept of the human body producing volatile chemicals that can serve as biomarkers for disease or illness is not new to clinical laboratory professionals. The urea breath test, for example, to detect the presence of active H. pylori bacteria in the stomach is a longstanding example of one such diagnostic test.

Inspired by Milne’s accuracy, Kunath enlisted the help of Perdita Barran, PhD, Director of the Michael Barber Center for Collaborative Mass Spectrometry at the University of Manchester in England, to identify the specific compounds that contributed to the smell Joy had detected on her husband and the other Parkinson’s patients.

Barran led a larger Manchester University study which was published on ChemRxiv, titled, “Sebum: A Window into Dysregulation of Mitochondrial Metabolism in Parkinson’s Disease,” which was funded by a Michael J. Fox research grant (12921). Barran and her research team, which included Milne, “found 10 compounds linked to Parkinson’s by using mass spectrometry and other techniques” on skin sebum samples, reported NPR.

“We really want to know what is behind this and what are the molecules. And then, [determine if] the molecules [can] be used as some sort of diagnostic test,” Kunath told NPR.

A Definitive, Noninvasive Test for Parkinson’s?

The UK researchers discovered in the skin sebum volatile biomarkers of Parkinson’s disease that may lead to development of the first definitive test for the disease.

Katherine Crawford, Scotland Director of Parkinson’s UK, aka the Parkinson’s Disease Society of the United Kingdom, said a noninvasive diagnostic test for Parkinson’s would be game changing.

“We still effectively diagnose it today the way that Dr. James Parkinson diagnosed it in 1817, which is by observing people and their symptoms,” Crawford told BBC Scotland. “A diagnostic test like this could cut through so much of that, enable people to go in and see a consultant, have a simple swab test and come out with a clear diagnosis of Parkinson’s.”

“It wouldn’t have happened without Joy,” Barran told BBC Scotland. “For all the serendipity, it was Joy and Les who were absolutely convinced that what she could smell would be something that could be used in a clinical context, and so now we are beginning to do that.”

A viable, working diagnostic test based on these new biomarkers may be years away. Nevertheless, clinical laboratory leaders will want to follow the ongoing efforts toward development of a noninvasive swab test for Parkinson’s disease. Such a breakthrough would revolutionize Parkinson’s testing and might never have come to light without the persistence of a woman with an extremely sensitive sense of smell.

—Andrea Downing Peck

Related Information:

Her Incredible Sense of Smell Is Helping Scientists Find New Ways to Diagnose Disease

Discovery of Volatile Biomarkers of Parkinson’s Disease from Sebum

Parkinson’s Smell Test Explained by Science

Scientists Sniff Out Parkinson’s Disease Smell

The Woman Who Can Smell Parkinson’s Disease

Sebum: A Window into Dysregulation of Mitochondrial Metabolism in Parkinson’s Disease

Accuracy of Canine Scent Detection of Lung Cancer in Blood Serum

C. diff-sniffing Beagle Dog Could Lead to Better Infection Control Outcomes in Hospitals and Nursing Homes

Researchers Determine That Individuals’ ‘Breathprints’ Are Unique; May Have Potential for Clinical Laboratory Testing When Coupled with Mass Spectrometry Technology

COVID-19 Pandemic Triggers Decline in Anatomic Pathology Testing and Shows How Digital Pathology, Remote Sign-Out Can Increase Pathology Services

Because of ‘shelter in place’ orders, many anatomic pathologists are reviewing digital images from home during the COVID-19 outbreak and demonstrating the value of whole slide imaging, digital pathology, and CMS’ recent amended remote sign-out policy

COVID-19 is already triggering many permanent changes in the way healthcare is organized and delivered in the United States. However, not until the SARS-CoV-2 pandemic eases will the full extent of these changes become visible. This will be particularly true for anatomic pathology and the profession’s expanded use of telepathology, digital pathology, and whole-slide imaging.

Since early March, specimen referrals and revenues have collapsed at anatomic pathology groups and laboratories across the nation. Dark Daily’s sister publication, The Dark Report (TDR), was first to quantify the magnitude of this collapse in tissue referrals to pathology groups. In an interview with The Dark Report, Kyle Fetter, Executive Vice President and General Manager of Diagnostic Services at XIFIN, Inc., explained that pathology clients using XIFIN’s revenue cycle management services were seeing an average 40% decrease in specimens. And, for certain pathology sub-specialties, the drop-off in specimen referrals was as much as 90%. (See TDR, “From Mid-March, Labs Saw Big Drop in Revenue,” April 20, 2020.)

The College of American Pathologists (CAP) appealed to the Centers for Medicare and Medicaid Services (CMS) to allow pathologists to work remotely. In response, CMS issued a memorandum which stated, “Due to the public health emergency posed by COVID-19 and the urgent need to expand laboratory capacity, CMS is exercising its enforcement discretion to adopt a temporary policy of relaxed enforcement in connection with laboratories located at temporary testing sites under the conditions outlined herein.”

Since then, many physicians, including pathologists, have quickly adapted to working remotely in some form.

Push for Remote Pathology Services Acknowledges Anatomic Pathologist Shortage

The CMS memorandum (QSO-20-21-CLIA), which the federal agency issued to laboratory surveyors on March 26, 2020, notes that CMS will exercise “enforcement discretion to ensure pathologists may review pathology slides remotely” if certain defined conditions are met.

CMS’ decision, which “is applicable only during the COVID-19 public health emergency,” is intended to increase capacity by allowing remote site review of clinical laboratory data, results, and pathology slides.

Ordinarily, CLIA regulations for cytology (a branch of study that focuses on the biological structure of cells) state that cytology slide preparations must be evaluated on the premises of a laboratory that is certified to conduct testing in the subspecialty of cytology. However, a fast-acting Congressional letter sent by 37 members of Congress to US Department of Health and Human Services (HHS) Secretary Alex Azar II, MD, states, “it is unwise and unnecessary to overburden the remaining pathologists with excess work due to staffing shortages, thereby increasing the risk of burnout, medical error, and further shortages in staffing due to exposure. The number of COVID-19 cases will increase and peak over the next two months and will stretch existing healthcare systems to their limits.”

In response to the CMS remote waiver, the CAP committee on Digital and Computational Pathology, and the Informatics committee, published additional guidance on the CAP website.

Decreasing Number of ‘Active Pathologists’ Drives Adoption of Telepathology, Digital Pathology, and Whole-slide Imaging

The current COVID-19 outbreak is just the latest factor in support of enabling remote review of anatomic pathology images and cases. The trend of using telepathology, whole-slide imaging (WSI), and digital pathology systems has been gathering momentum for several years. Powerful economic forces support this trend.

The Dark Report devoted its June 10, 2019, issue to a deep dive of the challenges currently facing the anatomic pathology profession. In particular, TDR noted a study published May 31, 2019, in the Journal of the American Medical Association (JAMA) Network Open, titled, “Trends in the US and Canadian Pathologist Workforces from 2007 to 2017.” The study’s authors—pathologists in the United States and Canada—reported that between 2007 and 2017 the number of active pathologists in the United States decreased from 15,568 to 12,839—a 17.53% decline.

TDR noted that these findings imply there are fewer pathologists in the United States today in active practice to handle the steady increase in the number of cases requiring diagnostic review. In turn, this situation could lead to delays in diagnoses detrimental to patient care.

In fact, the National Health Service (NHS) in the United Kingdom is dealing with exactly this situation. The Telegraph reported that one in four cancer patients in the UK have delays of as much as eight weeks in the diagnosis of their biopsy. It is generally recognized that the UK lacks the number of histopathologists it needs to substantially shorten time to diagnoses. To address this, the NHS is implementing a national digital pathology network featuring Amazon’s Alexa virtual assistant to deliver health advice to the UK’s citizens. (See Dark Daily, “UK’s NHS Will Use Amazon Alexa to Deliver Official Health Advice to Patients in the United Kingdom,” December 2, 2019.)

In the United States, the COVID-19 pandemic created an “immediate need for remote sign-outs, reviews, and consults,” said Mike Bonham, MD, PhD (above), Chief Medical Officer for Proscia, a digital pathology software developer, in an interview with Dark Daily. “In the context of highly relevant workflow and workforce challenges, it reinforces the opportunity for wider adoption of digital pathology.” Prior to the outbreak of COVID-19, several distinct forces were driving adoption and use of digital pathology in combination with traditional microscopy, he said. (Photo copyright: Proscia.)

Distinct Forces Beginning to Reshape Anatomic Pathology

In recent years, the anatomic pathology profession has faced growing financial pressure, a shrinking workforce, and a surge in the global demand for pathology—issues that come at a time when biopsies and cancer diagnostics require greater expertise.

As Dark Daily and The Dark Report previously reported, digital pathology gained momentum starting with the US Food and Drug Administration’s approval to market the Philips IntelliSite Pathology Solution (PIPS) whole-slide imaging (WSI) system in April 2017. The second WSI system cleared by the FDA was the Aperio AT2 DX System from Leica Biosystem Imaging.

When it comes to adopting a digital pathology system (DPS), it is important to realize that digital pathology testing has moved forward at a rapid pace outside the US, explains a new white paper from Dark Daily, titled, “Anatomic Pathology at the Tipping Point? The Economic Case for Adopting Digital Technology and AI Applications Now.”

Gaining knowledge and first-hand experience of digital pathology adoptions is vital to future business development in anatomic pathology services.

Emerging Cancer Diagnostics Using Digital Pathology and Computational Solutions

Digital pathology adoption can be seen in various specialties of cancer care—in particular skin, breast, and prostate. One example is the University of California San Francisco (UCSF) School of Medicine, which adopted digital pathology in February 2015.

The UCSF School of Medicine started with frozen slide sections and moved to the broader volume of pathology slides. Since 2015, UCSF’s School of Medicine has moved toward a fully digital pathology operation and has serialized the adoption by specialty, according to Zoltan Laszik, MD, PhD, attending physician at UCSF and Professor of Clinical Pathology in UCSF’s Departments of Pathology and Laboratory Medicine.

Laszik is among a handful of specialists and digital pathology early adopters who collaborated on the new Dark Daily white paper, which is available for free download.  

Through the adoption of digital pathology, glass slides are digitized using a whole-slide image scanner, then analyzed through image viewing software. Although the basic viewing functionality is not drastically different than that provided by a microscope, digitization does bring improvements in lab efficiency, diagnostic accuracy, image management, workflows, and revenue enhancements.

Additionally, artificial intelligence (AI)-based computational applications have emerged as an integral part of the digital pathology workflow in some settings, the white paper explains.

“These developments are important to anatomic pathologists because the traditional pathology business model continues to transform at a steady pace,” noted Robert L. Michel, Editor-in-Chief of The Dark Report.

Anthony Magliocco, MD, FRCPC, FCAP, President and CEO of Protean BioDiagnostics and former Professor and Chair of Pathology at Moffitt Cancer Center, is featured in the white paper as well. His new pathology service model provides routine pathology services, precision oncology, second opinions, liquid biopsies, genetics, and genomics to cancer centers from a Florida-based specialty laboratory.

In addition to the white paper, Magliocco will share his experience adopting digital pathology during a free webinar, titled, “Streamlined Operations, Increased Revenue, Higher Quality of Care: Conclusive Evidence on the Value of Adopting Digital Pathology in Your Lab.” The webinar takes place Wednesday, May 13, and is hosted by Dark Daily.

To register for this important learning opportunity, click here or place this URL in your web browser: https://www.darkdaily.com/webinar/streamlined-operations-increased-revenue-higher-quality-of-care-conclusive-evidence-on-the-value-of-adopting-digital-pathology-in-your-lab/.

These digital pathology technologies represent an innovative movement shaping the present and future of pathology services. Pathologists wanting to learn more are encouraged to sign up for the May 13 webinar, which will build on the body of evidence and commentary that is included in the new white paper, and which will be available for free on-demand download following the live broadcast.

—Liz Carey

Related Information

Free Download New White Paper: Anatomic Pathology at the Tipping Point? The Economic Case for Adopting Digital Technology and AI Applications Now

To Register for Free Webinar Taking Place on May 13, 1 pm Eastern

Clinical Laboratory Improvement Amendments (CLIA) Laboratory Guidance During COVID-19 Public Health Emergency

Trends in the US and Canadian Pathologist Workforces From 2007 to 2017

UK’s NHS Will Use Amazon Alexa to Deliver Official Health Advice to Patients in the United Kingdom

New Telemedicine Strategies Help Hospitals Address COVID-19

CMS Memorandum: QSO-20-21-CLIA, March 26, 2020

Rush, Carter Lead Successful Effort to Ensure Pathologists are Able to Address Critical Testing Needs During Pandemic

March 25, 2020, Congressional Letter to HHS Secretary Alex Azar II, MD

CAP Secures Remote Work Waiver for Pathologists

Recent Updates on COVID-19: Remote Sign-Out of Cases with Digital Pathology FAQs

Laboratory Staff Turnover: A College of American Pathologists Q-Probes Study of 23 Clinical Laboratories

Is the Profession of Anatomic Pathology Shrinking?

Expert Sees Pros, Cons in DP and WSI Systems

Live Event Update: Executive War College on Laboratory and Pathology Management

UC Berkeley Creates COVID-19 Robotic Testing Laboratory in Record Time by Reallocating Equipment and Training Researchers to Do Clinical Analysis

Medical laboratory leaders may be inspired by this rapid start-up and its outreach to students and the Bay area

In what could take a typical clinical laboratory months or even years to launch, the Innovative Genomics Institute (IGI) at the University of California, Berkeley managed to make a COVID-19 diagnostic testing laboratory operational in just a few weeks. 

Even more impressive is that the automated testing lab can reportedly process (with results in four hours) up to 3,000 patient samples daily for SARS-CoV-2, the coronavirus that causes the COVID-19 illness.

The IGI COVID-19 testing laboratory has high-throughput polymerase chain reaction (PCR) machines—some reallocated from idle university research labs—which can process the CDC 2019-novel coronavirus Real-Time (RT) PCR diagnostic panel, according to a Berkeley news release.

“All of our laboratories do PCR every day. But for this test we need to go above and beyond to ensure accurate detection,” said Jennifer Doudna, PhD, IGI Executive Director and UC Berkeley Professor of Molecular and Cell Biology, in an IGA news release.

“We put in place a robotic pipeline for doing thousands of tests per day,” she continued, “with a pipeline for managing the data and getting it back to clinicians. Imagine setting that up in a couple of weeks. It’s really extraordinary and something I’ve never seen in my career.”

In operation since April 6, the Berkeley COVID-19 testing lab’s main source for referrals is the University Health Services Tang Center. Testing services also are offered to medical centers across the East Bay area, San Francisco Business Times reported.

Robert Sanders, UC Berkeley’s Manager Science Communications, told Dark Daily the COVID-19 lab performs about 180 tests per day and has tested 1,000 people so far—80% of the samples came from the campus community. About 1.5% to 4% of the tests were found to be positive for the SARS-CoV-2 coronavirus among the groups tested.

“We hope other academic institutions will set up testing labs too,” he said.

How Did Berkeley Set Up a COVID-19 Diagnostic Lab So Fast?

To get up and running quickly, university officials drew from the campus and surrounding business community to equip and operate the laboratory, as well as, train researchers to do clinical analysis of patient samples.

Though the methodology to test for the coronavirus—isolating RNA from a biological sample and amplifying it with PCR—is standard fare in most research labs worldwide, including at UC Berkeley, the campus’ research labs were shuttered due to the spread of the coronavirus.

IGI reached out to the idle labs for their high-throughput PCR systems to start-up the lab. Through its partnership with University Health Services and local and national companies, IGI created an automated sample intake and processing workflow.

Additionally, several research scientists who were under government-mandated stay-at-home orders made themselves available. “My own research is shut down—and there’s not very much I can do other than stay in my home … finally I’m useful,” said PhD candidate Holly Gildea in a Berkeleyside article which noted that about 30 people—mostly doctoral students and postdoctoral researchers—are being trained to oversee the process and monitor the automated equipment.     

Postdoctoral fellows Jenny Hamilton (left) and Enrique Shao (right) with an automated liquid-handling robot (Hamilton Microlab STAR), which will be used to analyze swabs from patients to diagnose COVID-19. Hamilton and Shao volunteered to train to become CLIA certified so as to process patient samples. When analyzing real samples from patients, they would be wearing full personal protective equipment (PPE), including mask, face shield, gown and gloves. (Photo and caption copyright: Max and Jules Photography/UC Berkeley.)

Federal and State Authorities Remove Hurdles

In her article, “Blueprint for a Pop-up SARS-CoV-2 Testing Lab,” published on the medRxiv servers, Doudna summarized “three regulatory developments [that] allowed the IGI to rapidly transition its research laboratory space into a clinical testing facility.

  • “The first was the FDA’s March 16th Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency. This policy simplified the process for getting authorization for a testing method and workstream.
  • “The second was California Governor Newsom’s Executive Order N-25-20, which modified the requirements for clinical laboratory personnel running diagnostic tests for SARS-CoV-2 in a certified laboratory.
  • “The third was increased flexibility and expediency at the state and federal levels for certification and licensure requirements for clinical laboratory facilities under the Clinical Laboratory Improvement Amendments (CLIA) program. Under these emergency conditions, the California Department of Public Health (CDPH) was willing to temporarily extend—once the appropriate regulatory requirements have been fulfilled—an existing CLIA certificate for high-complexity testing to a non-contiguous building on our university campus.”

“These developments,” wrote Doudna, “enabled us to develop and validate a laboratory-developed test (LDT) for SARS-CoV-2, extend the UC Berkeley Student Health Center’s clinical laboratory license to our laboratory space, and begin testing patient samples.”

Lessons Learned Implementing a Pop-Up COVID-19 Testing Laboratory

“Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to others in setting up similar testing centers,” she wrote. 

Learned strategies Doudna says could aid other academic research labs transform to a “SARS-CoV-2 Diagnostic Testing Laboratory include:

  • Leveraging licenses from existing CLIA-certified labs;
  • Following FDA authorized testing procedures;
  • Using online HIPAA training;
  • Managing supply chain “bottlenecks” by using donated equipment;
  • Adopting in-house sample barcoding;
  • Adapting materials, such as sampling tubes, to work with donated equipment;
  • Reaching out for donations of personal protective equipment (PPE).

Cost of equipment and supplies (not including staff) was $550,000, with a per test cost of $24, Doudna noted.  

“As the COVID-19 pandemic continues, our intention is to provide both PCR-based diagnostic testing and to advance research on asymptomatic transmission, analyze virus sequence evolution, and provide benchmarking for new diagnostic technologies,” she added.

Medical laboratory leaders understand that the divide between clinical and research laboratories is not easy to surmount. Nevertheless, UC Berkley’s IGI pulled it off. The lab marshaled resources as it took on the novel coronavirus, quickly developed and validated a test workflow, and assembled and trained staff to analyze tests with fast TAT to providers, students, and area residents. There’s much that can be learned from UC Berkeley IGI’s accomplishments.

—Donna Marie Pocius

Related Information:

Berkeley Scientists Spin Up a Robotic COVID-19 Testing Lab

IGI Launches Major Automated COVID-19 Diagnostic Testing Initiative

Berkeley Lab Pivots from Editing DNA to Processing COVID-10 Tests

Governor Newsom Declares State of Emergency to Help State Prepare for Broader Spread of COVID-19

Governor Newsom Issues New Executive Order Further Enhancing State and Local Government’s Ability to Respond to COVID-19 Pandemic

Jennifer Doudna’s Berkeley Institute Launches COVID-19 Testing Lab

UC Berkeley to Test 5,000 Healthy People in Bay Area for Coronavirus

Blueprint for a Pop-up SARS-CoV-2 Testing Lab

CRISPR Pioneer Doudna Opens Lab to Run COVID-19 Tests

FDA Issues First Approval for At-Home COVID-19 Test to LabCorp’s Pixel; Other Clinical Laboratory-Developed At-Home Test Kits May Soon Be Available to General Public

Though the potential is high for false positives and false negatives, some experts believe at-home COVID-19 testing still holds promise for slowing the spread of the coronavirus

Laboratory Corporation of America (LabCorp) is the first diagnostic test developer to receive approval from the US Food and Drug Administration (FDA) to market an at-home specimen collection kit for COVID-19. In an April 21 FDA news release, the federal agency announced it had “re-issued the emergency use authorization (EUA) for the Laboratory Corporation of America COVID-19 RT-PCR Test to permit testing of samples self-collected by patients at home using LabCorp’s Pixel by LabCorp COVID-19 Test home collection kit.”

The kit includes a nasal swab for specimen collection and a shipping package for returning the sample to a designated medical laboratory. Pixel is designed to work with LabCorp’s COVID-19 RT-PCR test, a real-time reverse transcription polymerase chain reaction (rRT-PCR) test that determines if an active SARS-CoV-2 coronavirus is present. The Pixel specimen-collection kit can be purchased for $119 on LabCorp’s website.

Presently, the Pixel kit is only available to healthcare workers and first responders who are symptomatic or who believe they may have been exposed to the virus. However, in a news release LabCorp stated that it “intends to make COVID-19 self-collection kits available to consumers in the coming weeks.”

Though purchasers have to pay for the kit themselves, a notice on LabCorp’s website states that the company “will work with you to get your purchase reimbursed by your health plan,” and that LabCorp is “actively working on a more streamlined solution, so you don’t have to pay up front.” LabCorp created a COVID-19 microsite where customers can receive future updates on the Pixel at-home test kit.

Adam Schechter LabCorp and Donald Trump
In LabCorp’s news release, Adam Schechter (at podium), President and CEO, emphasized his company’s commitment to helping patients and healthcare providers fight the COVID-19 crisis through LabCorp’s “leading testing capabilities and deep scientific and research expertise,” adding, “Our at-home collection kits are designed to make it easier and safer to test healthcare workers and first responders during this important time.” (Photo copyright: Yahoo News/Chip Somodevilla.)

Though Finger-stick At-home Tests Prove Inaccurate, Optimism Remains

As COVID-19 wreaks havoc around the globe, in vitro diagnostic (IVD) developers, clinical laboratory companies, and healthcare professionals have scrambled to find an accurate, cost effective way to definitively test individuals for the coronavirus.

Complicating matters is the fact that many people are asymptomatic carriers who show no symptoms of the illness, but who can infect others.

Earlier this year, the UK government was optimistic that an at-home serological antibodies test would enable its citizens to collect their own blood specimens via finger sticks, and that the test would provide a way for individuals to test themselves for the coronavirus.

According to CNBC, the United Kingdom (UK) ordered millions of antibody tests, but after disappointing results, returned the kits and requested a refund.

The New York Times (NYT) reported that the British government paid $20 million upfront for two million untried antibody test kits from two Chinese companies: AllTest Biotech in Hangzhou and Wondfo Biotech in Guangzhou. Then, UK government officials announced the tests would be available to citizens within weeks, and Prime Minister Boris Johnson publicly declared the tests would be “simple as a pregnancy test.”

Neither of those predictions would come to pass. In April, British researchers announced that none of the coronavirus tests they had tried were accurate enough to be of any value.

“Sadly, the tests we have looked at to date have not performed well,” said Sir John Bell, Regius Professor of Medicine, University of Oxford, Medical Sciences Division, in a blog post titled, “Trouble in Testing Land.”

“We see many false negatives … and we also see false positives,” he wrote, adding that the UK “is now uniquely positioned to evaluate and find the optimal test for this disease, but no country has found a kit that is up to standard.” He also noted that locating such a test should be possible, but that it may take another month or more to find.

The Chinese companies defended their tests. In the Chinese newspaper Global Times, Wondfo stated its tests are “intended only as a supplement for patients who had already tested positive for the virus,” and on its website, AllTest stated its tests should “only [be] used by professionals,” not by patients at home, the New York Times reported.

Will At-home COVID-19 Testing Ever Work?

At-home testing kits for COVID-19 may seem like a great solution to the testing dilemma, but they could also prove to be problematic. “This may not be as good as it sounds,” Edo Paz, MD, a New York Presbyterian-trained cardiologist, Clinical Director at Heartbeat Health, and Vice President Medical, at K Health, a digital health company located in New York City, told CNET.

“Collecting a proper sample from the nose or mouth takes training and shipping delays of the specimen back to the lab could impact the quality of the sample,” he said, adding, “There could be a high false negative rate, leading people who are actually infected to believe they are not, potentially contributing to the crisis.”

Clinical pathologists have a unique understanding of the challenges that must be overcome for capillary blood to be of any use for testing, and of the potential for mishandling of specimens inherent in at-home test kits.

Nevertheless, with the SARS-CoV-2 coronavirus continuing to infect people around the world, the number and variety of tests will likely increase, which could create an upsurge in business for clinical laboratories and present new challenges for performing COVID-19 tests.

—JP Schlingman

Related Information:

Coronavirus (COVID-19) Update: FDA Authorizes First Test for Patient At-Home Sample Collection

LabCorp’s At-home COVID-19 Test Kit is the First to be Authorized by the FDA

LabCorp COVID-19 At-Home Test Kit Receives FDA Emergency Use Authorization

LabCorp COVID-19 RT-PCR Test EUA Summary

Pixel by LabCorp COVID-19 Test (At-Home Kit)

Trouble in Testing Land

U.K. Paid $20 Million for New Coronavirus Tests. They Didn’t Work

Hopes for At-home Finger-prick Coronavirus Test Dashed after Accuracy is Questioned

Can You use a Coronavirus Home Testing Kit? Not Yet, and Here’s Why

Antibody Tests Could be Key to Reopening the Country. Here’s How They Work.

Dozens of Coronavirus Antibody Tests on the Market Were Never Vetted by the FDA, Leading to Accuracy Concerns

Tech Companies Suggest Ways Location Tracking Could Help Health Authorities Fight the COVID-19 Coronavirus by Identifying People Who May Need Clinical Laboratory Testing

Privacy concerns have one tech giant suggesting alternatives to sharing potentially identifiable location tracking data

Expect an interesting debate on the use of location tracking as a way to manage this and future pandemics. It is a debate that has implications for clinical laboratories. After all, if location tracking identifies individuals who may have been exposed to an infectious disease, will health authorities want those individuals to be immediately tested?

Location tracking has been around for quite some time. Anyone who owns a smartphone knows that digital map and navigation software applications (apps) locate our position and track our movements. That’s how they work. Maps are good. But does collecting and sharing location tracking data violate personal privacy laws that some Silicon Valley tech giants want to use to help public health officials track disease? Maybe.

Google, Facebook, and other tech companies have been talking to the US federal government about ways to use location tracking data from smartphones and online software applications to combat the spread of SARS-CoV-2, the coronavirus that causes the COVID-19 illness, reported the Washington Post.

The tracking data could be used by public health officials to spot disease outbreaks in populations and predict how it might spread. Analyzing the data generated by smartphone tracking and reporting apps also could be used to identify individuals who may have been exposed to the coronavirus, and who should get clinical laboratory tests to determine if they need medical intervention.

However, Google is apparently resistant to using its collected location data to track and identify individuals. Instead, Google Health’s Head of Communications and Public Affairs, Johnny Luu, said Google was “exploring ways that aggregated anonymized location information could help in the fight against COVID-19. One example could be helping health authorities determine the impact of social distancing, similar to the way we show popular restaurant times and traffic patterns in Google Maps,” said Luu in a statement. He stressed, though, that any such arrangement “would not involve sharing data about any individual’s location, movement, or contacts,” reported the Washington Post.

Can Privacy be Maintained While Tracking Disease?

Google’s sister company, Verily, launched a screening website in March for people who believe they may have COVID-19. The pilot program is only available to some California residents. Users of the service complete a series of online questions to determine their coronavirus risk and whether or not they should seek medical attention.

To use the service, individuals must log into the site using a Google account and sign a consent authorization form which states data collected may be shared with public health officials, a move that has received criticism.

Jacob Snow, JD, a technology and civil liberties attorney with the American Civil Liberties Union (ACLU) of Northern California, expressed concerns about Verily’s program. “COVID-19 testing is a vital public necessity right now—a core imperative for slowing this disease,” he told CNET. “Access to critical testing should not depend on creating an account and sharing information with what is, essentially, an advertising company.

“This is how privacy invasions have the potential to disproportionately harm the vulnerable,” he continued. “Google should release this tool without those limits, so testing can proceed as quickly as possible.”

Facebook, on the other hand, has had a Disease Prevention Map program in place for about a year. This program provides location information provided by individuals who choose to participate to health organizations around the globe.

“Disease prevention maps have helped organizations respond to health emergencies for nearly a year and we’ve heard from a number of governments that they’re supportive of this work,” said Laura McGorman, Policy Lead, Data for Good at Facebook, in a statement, reported CNET. “In the coronavirus context, researchers and nonprofits can use the maps, which are built with aggregated and anonymized data that people opt in to share, to understand and help combat the spread of the virus.”

Researchers at Carnegie Mellon University worked with Facebook to create the COVID-19 Symptom Map (above), which is based on aggregated data drawn from self-reported symptoms Facebook. The map, which updates regularly, is viewable by day, counties, hospital referral regions, and COVID-19 symptoms. “This is work that social networks are well-situated to do. By distributing surveys to large numbers of people whose identities we know, we can quickly generate enough signal to correct for biases and ensure sampling is done properly,” wrote Mark Zuckerberg, Facebook founder and CEO, in a Washington Post op-ed about the Carnegie Mellon’s results, reported MobiHealthNews. (Graphic copyright: Facebook/Business Insider.)

Privacy Organizations Voice Concerns

Privacy and civil liberties issues regarding the collection and use of smartphone data to curtail the pandemic are of concern to some organizations. There may be legal and ethical implications present when using personal data in this manner.

Al Gidari, JD, Director of Privacy, Center for Internet and Society at Stanford University Law School, says the balance between privacy and pandemic policy is a delicate one, reported the Washington Post. “The problem here is that this is not a law school exam. Technology can save lives, but if the implementation unreasonably threatens privacy, more lives may be at risk,” he said.

In response to public privacy concerns following the Washington Post’s report, representatives for Google and Facebook said the companies have not shared any aggregated and anonymized data with the government regarding contact tracing and COVID-19, reported the Washington Post.

Google reiterated that any related projects are still in their early stages and that they are not sure what their participation level might look like. And, CEO Mark Zuckerberg stated that Facebook “isn’t prepared to turn over people’s location data en masse to any governments for tracking the coronavirus outbreak,” reported CNET.

“I don’t think it would make sense to share people’s data in a way where they didn’t have the opportunity to opt in to do that,” Zuckerberg said.

The potential use of location tracking data, when combined with other information, is one example of how technology can leverage non-medical information and match it with clinical data to watch population trends.

As of April 23, there were 2,637,911 confirmed cases of COVID-19 and 184,235 deaths from the coronavirus worldwide, according to www.worldometers.info/coronavirus. And, cases of coronavirus disease have been reported in 213 countries according to the World Health Organization (WHO).

As testing increases, more cases will be reported and it is unknown how long the virus will continue to spread, so advocates of location tracking and similar technologies that can be brought to bear to save lives during a disease outbreak may be worth some loss of privacy.

Pathologists and medical laboratory professionals may want to monitor the public debate over the appropriate use of location tracking. After all, at some future point, clinical laboratory test results of individuals might be added to location tracking programs to help public health authorities better monitor where disease outbreaks are occurring and how they are spreading.

—JP Schlingman

Related Information:

U.S. Government, Tech Industry Discussing Ways to Use Smartphone Location Data to Combat Coronavirus

Google, Facebook Could Help US Track Spread of Coronavirus with Phone Location Data

Google, Facebook, and Other Tech Companies Are Reportedly in Talks with the US Government to Use Your Location Data to Stop the Coronavirus—And to See If Social Distancing Is Really Working

Google Wary of Sharing User Location Data in Pandemic Fight

Google, Other Companies Get Your Data If You Use Verily’s Coronavirus Site

Zuckerberg: Facebook Isn’t Giving Governments Data to Track Coronavirus Spread

Coronavirus: Google Says It Hasn’t Shared Location Data in Virus Response

CDC: Coronavirus (COVID-19)

WHO: Coronavirus Disease (COVID-19) Outbreak Situation

Facebook Launches COVID-19 Symptom Maps

Facebook Just Released an Interactive COVID-19 Map That Shows How Many People Are Reporting Symptoms in Your Area

Facebook and Carnegie Mellon University COVID-19 Symptom Map

Facebook Rolls Out Three New COVID-19 Related Health Tracking Maps

Self-Reported Symptoms from Surveys Posted on Facebook, Google Outlets Correlate with Confirmed Tests, According to Carnegie Mellon

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