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University of Vermont Microbiology Laboratory Identifies Inefficiencies When Performing Pooled Testing for COVID-19

The key to success with pooled testing, says the lab’s director, is having the right personnel and equipment, and an LIS that supports the added steps

Experts believe pooled testing for COVID-19 could reduce the number of standard tests for SARS-CoV-2 by conserving testing resources and cutting lab spending on tests and testing supplies. However, some clinical laboratories have found pooled testing causes inefficiencies due to the lab’s lack of staff, limitations of existing equipment, and biosafety hood space, as well as not having a laboratory information system (LIS) that can manage the large volume of specimens and retesting involved in pooled testing.

One such example is the microbiology lab at 562-bed University of Vermont Medical Center (UVMC) in Burlington, Vt. After evaluating the pooled-testing method, Christina M. Wojewoda, MD, pathologist, Director of Clinical Microbiology at UVMC and an Associate Professor at the Larner College of Medicine at University of Vermont, decided last summer not to do pooled testing, due to the manual steps that the process requires.

The manual steps include having clinical laboratory scientists work under protective hoods to limit the virus’ spread, and both hood space and med techs are in short supply at UVMC, she explained during an exclusive interview with The Dark Report, Dark Daily’s sister publication.

“Our evaluation then is the same as it is now,” she commented. “The barriers to pooling still hold true. Instead of pooling, we keep up with the volume of COVID-19 samples by balancing in-house SARS-CoV-2 testing and send-out testing.”

Low Viral Load a Problem in Pooled Testing for SARS-CoV-2

Another problem, Wojewoda added, is when one patient’s sample in a pool of specimens has a low viral load of SARS-CoV-2. Clinical labs in some states have found that when the prevalence of the novel coronavirus in the population is below 5%, then pooled testing could be an effective testing strategy. However, although Vermont has a relatively low presence of the COVID-19 virus in the population, Wojewoda remains concerned about the viral load in a pooled sample.

“For us, it is less of an issue with prevalence in the population than an issue with low viral load in one patient sample, and that can happen with any prevalence level,” she said. “If there is a low level of virus in one sample, and that sample is combined with samples from four other patients to create the pool, you could dilute the virus below the assay’s level of detection. That means you could miss low-level positive patients.

“When we first considered pooling, we worried about missing those patients, but since then we’ve learned more about the SARS-CoV-2 virus,” she continued. “Now, we now know that patients start producing high levels of virus quickly and that low virus levels often occur toward the end of their infection, after they’ve probably been tested or identified.

“That means we’re less concerned with low levels of virus now than we were initially, at least when pooling five specimens in one tube. But it’s still something to watch for,” she noted.

What About Too Much Virus?

The opposite of this problem also is a concern. If the incidence of infection is too high in a population, then pooled testing could produce too many positive results. The required retesting then makes the process inefficient.

Wojewoda has heard similar concerns from her colleagues at other medical laboratories. They said they were not doing pooled SARS-CoV-2 testing for some of the same reasons.

“When we looked into pooled testing, a number of complications made it impractical,” she said. “Instead, we have been testing each patient individually.”

Since the spring, UVMC’s microbiology lab has run 200 to 500 molecular COVID-19 tests per day on two Hologic Panther instruments and has run a laboratory-developed test (LDT) from the federal Centers for Disease Control and Prevention (CDC) on the ABI 7500 from Applied Biosystems of Waltham, Mass., a Thermo Fisher Scientific (NYSE:TMO) company.

When patient COVID-19 samples exceed 500 in a day, UVMC sends those specimens to the Broad Institute in Cambridge, Mass., for testing.

During the summer, the rate of COVID-19 infections in Vermont was at about 1%, Wojewoda noted. In the last week of December, the Vermont Department of Health reported the seven-day average percentage of positive tests was 2.2%.

Laboratory Information System Challenges When Doing Pooled Testing

In addition to her concerns about the level of detection, UVMC’s laboratory information system (LIS) was another worry. “Clinical laboratories are designed to test one sample and get one result, and that one result goes into one patient’s chart,” she explained. “But when the lab makes a pool of, say, five patients’ samples, those five results need to go into five patients’ charts.

Wojewoda estimates that manual data entry for each of those results takes a solid minute per sample. “That’s not a lot, but it adds up over time, and it’s not something we do normally.”

Normally, lab test results get filed automatically into the patient’s chart, and then those results are available to patients online, she noted.

“There may be multiple fixes for this problem of accurately and efficiently getting pooled test results into the LIS, then reported to each individual patient, but for us the current state of our computer system requires that we enter each result into each patient’s chart manually. We try not to do that as much as possible because of the potential for errors from manual entry,” she said.

When Automation Falls Short

In addition, Wojewoda said that pooled testing cannot be automated the way most standard clinical laboratory tests are run.

“With routine testing, we put a sample on the instrument and let the test run,” she explained. “When we get the result, it goes into the patient’s chart. But, for pooled testing, we have to collect five samples and then pause to manually put a little bit of each of those five samples into one tube. Then, we put that tube on the instrument.

“After we get the results, we manually report the negative results into each patient’s chart,” she continued. “But if they’re positive, then lab staff must find the five tubes and test each one individually. Therefore, we’re doubling the time it normally takes to produce and report a positive result for SARS-CoV-2.”

Any positive results in a pooled sample, she explained, are held up at the instrument so that the lab staff can pull those five samples from the pool and test each one individually. “Then those individual results go into each patient’s chart, because potentially only one of the five might be positive. We don’t want all five of those patients to be labeled as positive if only one is positive,” she added.

UVMC lab Director Christina M. Wojewoda, MD
Pooled testing for COVID-19 adds a layer of complexity that the UVMC lab does not normally do, noted the lab’s Director Christina M. Wojewoda, MD (above), a pathologist and Director of Clinical Microbiology at the University of Vermont Medical Center (UVMC) in Burlington, in an interview with The Dark Report. She added that the lab’s staff is already stretched thin and doing as much as possible. “In all these ways, pooled testing is different from how we usually run clinical lab tests. It’s clear that the idea behind pooled testing is to improve efficiency, and yet the need for manual data entry and pulling pooled samples apart create inefficiencies,” she commented. (Photo copyright: University of Vermont.)

Shortage of Lab Techs and Hood Space Compound Inefficiencies of Pooled Testing

Another problem is the requirement to pipette each specimen, she noted. “All infectious samples require hood space and a lab technician to do the work under the hood. But both hood space and lab techs are in short supply.”

Wojewoda explained that some tests being run at the UVMC lab are not being tested from the primary tube.

“There’s often a step where we take some of the primary sample and put it into a tube or cartridge for the test. Then, we put multiple samples together, and we have to pipette each one into the tube without cross contaminating the other samples,” she explained.

“At the same time, we have to track the five patient samples so that we can find the original specimen for testing if we need to do so later. All those steps take more staff time.

“So, while pooled testing saves reagents, it also takes more staff time for pipetting and data entry and the need to record which samples are in which tubes,” she noted. “That might require a spreadsheet or other electronic means to track which samples come from which patients.

“An automated way to do the pipetting would be helpful and would increase staff safety,” she added. “I worry when we’re working with something as infectious as SARS-CoV-2, because the lab techs must dig swabs out of liquid media before discarding them, while being careful not to contaminate anything around them.”

Pooled testing for COVID-19 clearly has potential. But, as Wojewoda explained, it brings complications that can cause inefficiencies. Clinical laboratory managers will want to evaluate existing instrumentation, automation, staffing, and laboratory informatics capabilities to determine if and how their labs would experience similar inefficiencies before a final decision to begin a program of pooled testing for COVID-19.

—Joe Burns

Related Information:

Is COVID-19 Pooled Testing Good for Labs, Bad for IVDs?

Officials Differ on Value of COVID-19 Pooled Testing

Memphis Path Lab Pivots to COVID, Pooled Testing

NY Hospital Lab Succeeds with Pooled COVID-19 Testing

Critical Shortages of Supplies and Qualified Personnel During the COVID-19 Pandemic is Taking a Toll on the Nation’s Clinical Laboratories says CAP

As demand for SARS-CoV-2 coronavirus testing increases, leaders of the College of American Pathologists meet online to brainstorm possible solutions to the crisis

In September, the College of American Pathologists (CAP) began its series of “virtual media briefings” given by leading pathologists and physicians at the forefront of COVID-19 testing which are designed to “offer insights and straight talk” on the crisis confronting today’s clinical laboratories.

During the third virtual meeting on December 9, presenters discussed how the ever-increasing demand for COVID-19 testing has placed an enormous amount of stress on clinical laboratories, medical technologists (MTs), and clinical laboratory scientists (CLSs) responsible for processing the high volume of SARS-CoV-2 tests, and on the supply chains medical laboratories depend on to receive and maintain adequate supplies of testing materials.

The CAP virtual meetings, collectively titled, “The Rapidly Changing COVID-19 Testing Landscape: Where We Are/Where We Are Going,” are available for viewing on YouTube and Facebook.

Critical Supply Chain Deficiencies Hamstring Nation’s Clinical Laboratories

“As soon as we get one set of supplies, then it’s another set of supplies that we can’t get our hands on,” said Christine Wojewoda, MD, Clinical Pathologist and Associate Professor at the University of Vermont Medical Center, during the third CAP virtual briefing. “Right now, we’re very concerned that our lab can’t get pipette tips that have a certain filter in them to transfer patient samples into the tubes that we need, or the plates that we need to do the testing. If we can’t get the patient sample into where it needs to go, safely, without contaminating other patient samples, that’s a big issue.” 

Other members of the CAP panel concurred with Wojewoda and indicated that their clinical labs also are encountering supply chain challenges.

“It’s a daily battle,” said Amy Karger, MD, PhD, Clinical Pathologist and Associate Professor at University of Minnesota Physicians. “One of our managers spends hours a day making sure our lab has enough supplies, plastics, and chemicals to do the testing that we want to do. And he is often having to look for alternative solutions for COVID-19 testing, making phone calls, trying to find alternative products, and so we have a consistent worry about that.”

A June survey of CAP-accredited laboratories for COVID-19 testing found that more than 60% of lab directors reported difficulties in procuring critical supplies needed to conduct COVID-19 testing. The respondents indicated they encountered substantial barriers to obtaining equipment needed for SARS-CoV-2 testing—particularly test kits (69%), swabs (66%), and transport media (62%).

Staff Burnout and Shortages at Many Medical Laboratories

Karger also indicated that she is concerned about staff burnout and the toll the workload is taking on medical technologists at her laboratory. 

“Lab staff have been working full throttle since March. I think that is often lost on people. They kind of assumed that when cases were low with COVID-19, that maybe the lab staff got a break. Well, that wasn’t the case,” she stated, adding, “They [the medical technologists] were planning for this surge that we’re experiencing now and have been working often seven days a week, double shifts to get us to this point of high testing capacity [to respond to the demand for COVID-19 testing].” 

Another member of the CAP panel echoed Karger’s concerns.

“We worry about that as well,” said Patrick Godbey, MD, Founder and Laboratory Director at Southeastern Pathology Associates and current CAP President. “This demand for COVID-19 testing has made an already bad situation worse because there’s an absolute shortage of medical laboratory personnel and the increased demands on clinical labs have made this shortage even more acute.” 

Almost all of the surveyed CAP-accredited laboratories reported losses in revenue and financial stress since the pandemic started. But few had applied for any of the available funds offered through federal assistance programs. The survey found that the top issues among pathologists reported by laboratory directors were:

  • reduced work hours (72%),
  • reductions in pay (41%),
  • increased burnout (21%), and
  • increased work hours (20%).

According to the survey, the top stresses affecting non-pathologist professionals working in clinical labs were:

  • reduced work hours (69%),
  • reduced staff capacity (36%),
  • temporary furloughs (34%), and
  • increased burnout (31%).

‘An Overwhelming Sense of Doom’

Of course, clinical laboratory managers have been dealing with dwindling availability of qualified personnel for years, as one medical technologist training program after another closed and the supply of MTs and CLSs tightened. Dark Daily’s sister publication The Dark Report covered this trend as far back as 2012. (See, “GHSU Graduates Med Techs Using Distance Training: Medical Laboratory Scientist training program helps laboratories to recruit and to train MLSs.)

The diminishing labor pool trained for COVID-19 testing—coupled with high stress/burnout among existing staff—is a major impediment to ongoing expansion in the daily number of molecular COVID-19 tests that can be performed by the nation’s labs.

Also, the already-tight supply of med techs means many metropolitan area labs—particularly hospital labs—are operating with just 75% of the number of staff they are authorized to hire, because there are no techs available. Thus, existing staff are working lots of overtime, and vacant FTE positions are being temporarily filled by MTs placed by employment agencies.

A New York Times (NYT) article in December, titled, “‘Nobody Sees Us’: Testing-Lab Workers Strain Under Demand,” revealed that testing teams across the country are dealing with “burnout, repetitive-stress injuries, and an overwhelming sense of doom.” The article reported on the shortages of supplies needed to perform testing and states there is a “dearth of human power” in the field of pathology as well.

The supply of MTs and CLSs, molecular PhDs, clinical pathologists, MLTs, and other laboratory scientists available to work in the nation’s labs is finite and training programs take years to produce qualified workers to perform laboratory testing. 

Karissa Culbreath, PhD, Scientific Director, Infectious Diseases at TriCore Reference Laboratories
In the NYT article, microbiologist Karissa Culbreath, PhD (above), Scientific Director, Infectious Diseases at TriCore Reference Laboratories, and Assistant Professor of Pathology at the University of New Mexico, said that when shortages arise, “there are workarounds for almost everything else, but people are irreplaceable.” In addition to the large volume of COVID-19 tests that labs are expected to perform, they also must keep up with the other tests that are sent to them for analysis. Some facilities are even transitioning to 24/7 testing to keep up with the demand. “Labs are trying to maintain our standard of operation with everything else, with a pandemic on top of it,” said Culbreath. (Photo copyright: KOB 4/NBC.)

Should Clinical Lab Workers Be First to Receive the COVID-19 Vaccine?

In the third CAP virtual media briefing, the panel suggested that medical laboratory workers should be among the first to receive the COVID-19 vaccine.

“They are encountering and handling thousands of samples that have active live virus in them,” Karger said. “We are getting 10,000 samples a day [for SARS-CoV-2 testing]. That’s a lot of handling of infectious specimens and we do want them to be prioritized for vaccination.”

She added, “From an operational standpoint, we need to keep our lab up and running. We don’t want to have staff out such that we would have to decrease our SARS-CoV-2 testing capacity, which would have widespread impact on our health system and our state.”

Since the pandemic began nearly a year ago, there have been more than 18 million cases of COVID-19 confirmed in the US and more than 300,000 people have died from the virus, according to data from the federal Centers for Disease Control and Prevention (CDC).

And, as we move into flu season, the number of new COVID-19 cases is reportedly increasing, which adds more stress to clinical laboratories and their supply chains. As this is unlikely to end anytime soon, clinical lab managers must find new ways to do more with less.  

—JP Schlingman

Related Information:

The Rapidly Changing COVID-19 Testing Landscape: Where We Are/Where We Are Going

‘Nobody Sees Us’: Testing-Lab Workers Strain Under Demand

Clinical Laboratory COVID-19 Response Call

Pathologists Explore COVID-19 Testing Challenges, Breakthroughs

Labs Brace for Impact of Infection, COVID-19 Testing Surge as Thanksgiving Looms

Help Wanted at COVID-19 Testing Labs

Pathologists Want First Crack at COVID Vaccines

Clinical Laboratories Need Creative Staffing Strategies to Keep and Attract Hard-to-Find Medical Technologists, as Demand for COVID-19 Testing Increases

Three Federal Agencies Warn Healthcare Providers of Pending Ransomware Attacks; Clinical Laboratories Advised to Assess Their Cyberdefenses

Sophisticated cyberattacks have already hit hospitals and healthcare networks in Oregon, California, New York, Vermont, and other states

Attention medical laboratory managers and pathology group administrators: It’s time to ramp up your cyberdefenses. The FBI, the federal Department of Health and Human Services (HHS), and the federal Cybersecurity and Infrastructure Security Agency (CISA) issued a joint advisory (AA20-302A) warning US hospitals, clinical laboratories, and other healthcare providers to prepare for impending ransomware attacks, in which cybercriminals use malware, known as ransomware, to encrypt files on victims’ computers and demand payment to restore access.

The joint advisory, titled, “Ransomware Activity Targeting the Healthcare and Public Health Sector,” states, “CISA, FBI, and HHS have credible information of an increased and imminent cybercrime threat to US hospitals and healthcare providers.” It includes technical details about the threat—which uses a type of ransomware known as Ryuk—and suggests best practices for preventing and handling attacks.

In his KrebsOnSecurity blog post, titled, “FBI, DHS, HHS Warn of Imminent, Credible Ransomware Threat Against U.S. Hospitals,” former Washington Post reporter, Brian Krebs, wrote, “On Monday, Oct. 26, KrebsOnSecurity began following up on a tip from a reliable source that an aggressive Russian cybercriminal gang known for deploying ransomware was preparing to disrupt information technology systems at hundreds of hospitals, clinics, and medical care facilities across the United States. Today, officials from the FBI and the US Department of Homeland Security hastily assembled a conference call with healthcare industry executives warning about an ‘imminent cybercrime threat to US hospitals and healthcare providers.’”

Krebs went on to reported that the threat is linked to a notorious cybercriminal gang known as UNC1878, which planned to launch the attacks against 400 healthcare facilities.

Clinical Labs, Pathology Groups at Risk Because of the Patient Data They Keep

Hackers initially gain access to organizations’ computer systems through phishing campaigns, in which users receive emails “that contain either links to malicious websites that host the malware or attachments with the malware,” the advisory states. Krebs noted that the attacks are “often unique to each victim, including everything from the Microsoft Windows executable files that get dropped on the infected hosts to the so-called ‘command and control’ servers used to transmit data between and among compromised systems.”

Charles Carmakal, SVP and Chief Technology Officer of cybersecurity firm Mandiant told Reuters, “UNC1878 is one of the most brazen, heartless, and disruptive threat actors I’ve observed over my career,” adding, “Multiple hospitals have already been significantly impacted by Ryuk ransomware and their networks have been taken offline.”

John Riggi (above), senior cybersecurity adviser to the American Hospital Association (AHA), told the AP, “We are most concerned with ransomware attacks which have the potential to disrupt patient care operations and risk patient safety. We believe any cyberattack against any hospital or health system is a threat-to-life crime and should be responded to and pursued as such by the government.” Hospital-based medical laboratories and independent clinical laboratories that interface with hospital networks should be assess their vulnerability to cyberattacks and take appropriate steps to protect their patients’ data. (Photo copyright: American Hospital Association.)

Multiple Healthcare Provider Networks Under Attack

Hospitals in Oregon, California, and New York have already been hit by the attacks, Reuters reported. “We can still watch vitals and getting imaging done, but all results are being communicated via paper only,” a doctor at one facility told Reuters, which reported that “staff could see historic records but not update those files.”

Some of the hospitals that have reportedly experienced cyberattacks include:

In October, the Associated Press (AP) reported that a recent cyberattack disrupted computer systems at six hospitals in the University of Vermont (UVM) Health Network. The FBI would not comment on whether that attack involved ransomware, however, it forced the UVM Medical Center to shut down its computer system and reschedule elective procedures.

Threat intelligence analyst Allan Liska of US cybersecurity firm Recorded Future told Reuters, “This appears to have been a coordinated attack designed to disrupt hospitals specifically all around the country.”

He added, “While multiple ransomware attacks against healthcare providers each week have been commonplace, this is the first time we have seen six hospitals targeted in the same day by the same ransomware actor.”

An earlier ransomware attack in September targeted 250 healthcare facilities operated by Universal Health Services Inc. (UHS). A clinician at one facility reported “a high-anxiety scramble” where “medical staff could not easily see clinical laboratory results, imaging scans, medication lists, and other critical pieces of information doctors rely on to make decisions,” AP reported.

Outside of the US, a similar ransomware attack in October at a hospital in Düsseldorf, Germany, prompted a homicide investigation by German authorities after the death of a patient being transferred to another facility was linked to the attack, the BBC reported.

CISA, FBI, HHS, Advise Against Paying Ransoms

To deal with the ransomware attacks, CISA, FBI, and HHS advise against paying ransoms. “Payment does not guarantee files will be recovered,” the advisory states. “It may also embolden adversaries to target additional organizations, encourage other criminal actors to engage in the distribution of ransomware, and/or fund illicit activities.” The federal agencies advise organizations to take preventive measures and adopt plans for coping with attacks.

The advisory suggests:

  • Training programs for employees, including raising awareness about ransomware and phishing scams. Organizations should “ensure that employees know who to contact when they see suspicious activity or when they believe they have been a victim of a cyberattack.”
  • Regular backups of data and software. These should be “maintained offline or in separated networks as many ransomware variants attempt to find and delete any accessible backups.” Personnel should also test the backups.
  • Continuity plans in case information systems are not accessible. For example, organizations should maintain “hard copies of digital information that would be required for critical patient healthcare.”

Evaluating Continuity and Capability

The federal agencies also advise healthcare facilities to join cybersecurity organizations, such as the Health Information Sharing and Analysis Center (H-ISAC).

“Without planning, provision, and implementation of continuity principles, organizations may be unable to continue operations,” the advisory states. “Evaluating continuity and capability will help identify continuity gaps. Through identifying and addressing these gaps, organizations can establish a viable continuity program that will help keep them functioning during cyberattacks or other emergencies.”

Dark Daily Publisher and Editor-in-Chief, Robert Michel, suggests that clinical laboratories and anatomic pathology groups should have their cyberdefenses assessed by security experts. “This is particularly true because the technologies and methods used by hackers change rapidly,” he said, “and if their laboratory information systems have not been assessed in the past year, then this proactive assessment could be the best insurance against an expensive ransomware attack a lab can purchase.”

—Stephen Beale

Related Information:

Ransomware Activity Targeting the Healthcare and Public Health Sector

FBI, DHS, HHS Warn of Imminent, Credible Ransomware Threat Against U.S. Hospitals

Hackers Hit Hospitals in Disruptive Ransomware Attack

Several Hospitals Targeted in New Wave of Ransomware Attacks

Hospitals Hit with Ransomware Attacks as FBI Warns of Escalating Threat to Healthcare

Ransomware Attacks on Hospitals Could Soon Surge, FBI Warns

Building Wave of Ransomware Attacks Strike U.S. Hospitals

Oregon Hospital Shuts Down Computer System After Ransomware Attack

Three St. Lawrence County Hospitals Hit by Ransomware

‘Unusual Network Activity’ at Ridgeview Medical Center

Brooklyn and Vermont Hospitals Are Latest Ryuk Ransomware Victims