Pooling test samples is a common way to improve laboratory productivity and reduce the consumption of reagents and other supplies. Unfortunately, early hopes that test pooling could help labs during the COVID-19 pandemic quickly waned. Skyrocketing positivity rates, inflexible laboratory infrastructures and labor constraints dissuaded most labs from adopting the practice. COVIDLiMS from LabLynx, Inc. is a laboratory information management system that’s optimized for COVID-19 testing and can enable test pooling in as little as a week.
The Promise of Pooling COVID-19 Tests
The US Food and Drug Administration has authorized test pooling in a wide range of healthcare settings. Pharmaceutical and medical device companies can use test pooling when conducting pyrogen and endotoxin tests. Blood collection services can use test pooling to screen donated blood and blood components for HIV and hepatitis C. Following the pandemic of 2016, the FDA authorized pooled testing of blood donations for the Zika virus.
When conducting a pooled test, lab employees extract partial aliquots from ten, twenty or one hundred individual samples and combine them into a single sample. Labs then test this pooled sample. If the test returns a negative result, then all contributing patients are considered negative. If the test returns a positive result, then each contributing sample must be tested separately to determine which ones are positive.
What makes sample pooling an attractive option for clinical testing labs? When positivity rates are low and the presence of the test target is rare, pooled tests make labs more efficient. They replace as many as one hundred separate tests with a single pooled test. This reduces both labor and materials costs and lets labs improve both throughput and turn-around times.
Many in the testing community recognized that widespread, frequent testing would be needed to monitor and control the growing COVID-19 pandemic. They hoped that pooled testing would help labs increase their testing capacity and alleviate the shortage of reagents and other supplies.
In mid-2020, for example, the FDA granted an Emergency Use Authorization (EUA) to Quest Diagnostics allowing the laboratory to pool samples with Quest’s in-house molecular testing. “Pooled specimen testing is a proven technique that will help us to optimize testing capacity at this critical time for our country,” CEO and President Steve Rusckowski said.
Schools and other institutions are relying on test pooling to handle high-volume screening programs. Princeton University’s COVID-19 response team recently adopted sample pooling in its campus screening program.
The Reality of COVID-19 Test Pooling
Over the past year, however, many laboratories set aside their plans for sample pooling. For both intrinsic and extrinsic reasons, the presence of the SARS-CoV-2 virus became too prevalent. Labs get the most benefit from sample pooling when few pooled samples test positive. Princeton’s campus positivity rate, for example, hovered around 0.3% in January and dropped below 0.1% in February. In those conditions, the pooled sample can draw from many contributing samples and will require few retests. But SARS-CoV-2 positivity rates during the latest surge soared above 10% which required much smaller pools and more frequent retests.
Without the benefit of large pools, the extra labor that pooled testing requires becomes a factor. Somebody has to pipette the partial aliquots from each contributing sample into the pooled sample. Labor costs grow as sample pool sizes shrink and the number of pooled tests rises. An automated pipetting system could handle the job — if a lab already had one. Many labs don’t. And making large investments for a short-term use case is hard to justify.
The infrastructure laboratories do have is also a limiting factor. In an interview with Minnesota Public Radio’s Marketplace, Northwell Health’s medical director Jordan Laser said, “In the background of a pandemic, when everyone is using every single resource 24/7 to meet the demand of testing, there was no room, no time, no personnel to invest in creating those systems to do pooling.”
Pooled testing requires a level of sample tracking above and beyond normal testing. Each patient sample and each pooled sample must be accessioned, stored and tracked. What complicates things is the crucial need to track the relationship between the pooled samples and their contributing samples accurately. Labs that did not already conduct test pooling quickly found that their information infrastructure could not adapt to the new approach without expensive and time-consuming development effort.
COVIDLIMS Lets Labs Start Test Pooling Quickly
Even though the reality of COVID-19 test pooling never lived up to its promise, the potential benefits remain. In the short-term, campus and workplace screening programs can tap into those benefits since they are testing populations with low positivity rates. In the long-term, vaccination programs and other efforts will reduce positivity rates in the broader population. Yet laboratory infrastructure remains a challenge.
LabLynx, Inc. adapted its innovative laboratory information management systems to serve the unique needs of COVID-19 testing laboratories. COVIDLIMS comes pre-populated with the assays and workflows for molecular and rapid PCR testing. In addition, COVIDLIMS has the sample tracking features needed for pooled testing, currently in use by LabLynx COVID-19 diagnostics lab clients, who are experiencing significant benefits. Barcoded labels and relationship tracking ensure that results from pooled tests link to individual patients. Integration with laboratory instruments automates quality control so the right sample gets the right tests – and results. And included reporting tool and optional web portals let labs communicate results automatically to healthcare providers as well as patients – in fully secure HIPAA compliance.
Laboratories can deploy COVIDLIMS in as little as a week to improve the throughput and turn-around times of their COVID-19 testing services with immediate impact. And as new or revised assays are adopted, COVIDLIMS is easily user-configured to the new processes. And since COVIDLIMS includes all of the features of LabLynx’s enterprise ELab laboratory LIMS/LIS, labs can extend the benefits of COVIDLIMS to other non-COVID testing services.
If your lab needs the productivity gains from pooled COVID-19 testing as well as the benefits of a flexible, scalable laboratory informatics solution optimized for COVID-19, then contact LabLynx today. Visit covidlims.com, contact LabLynx at firstname.lastname@example.org, or at 866-LABLYNX (522-5969).
“COVID test pooling hampered by high positivity rates and logistical hurdles”, Modern Healthcare.
“Guidance for Industry Pyrogen and Endotoxins Testing: Questions and Answers”, US Food and Drug Administration.
“Use of Nucleic Acid Tests on Pooled and Individual Samples from Donors of Whole Blood and Blood Components (including Source Plasma and Source Leukocytes) to Adequately and Appropriately Reduce the Risk of Transmission of HIV-1 and HCV”, US Food and Drug Administration.
“FDA announces revised guidance on the testing of donated blood and blood components for Zika virus”, US Food and Drug Administration.
“Princeton’s COVID-19 lab approved to begin “pooling” samples”, The Daily Princetonian.