When the COVID-19 pandemic first surged in spring 2020, hospital emergency rooms and intensive care units weren’t the only medical facilities that were overloaded. Clinical laboratories across the U.S. ramped up to purchase additional diagnostic testing equipment and adjust staff schedules to operate longer hours. Now, as SARS-CoV-2 testing demand is declining, laboratory directors in some areas of the nation have a little breathing room—and a chance to think about how they can repurpose their extra platforms going forward.
During the first wave, just as hospitals faced shortages of personal protective equipment, ventilators, and other necessary supplies, laboratories found themselves scrambling for reagents, pipette tips, and other testing equipment, in addition to having to juggle their short staffs to match their clients’ increased demands.
Elizabeth Palavecino, MD, director of clinical microbiology at Wake Forest Baptist Medical Center, in Winston-Salem, North Carolina, says she was lucky to have already had several different testing systems available, and just had to purchase one new one.
“If you didn’t have those instruments at the beginning [of the pandemic], it was almost impossible to get new instruments to start testing or increase your capacity,” she said.
Her lab started testing with its existing equipment, at one point using five different platforms from different vendors—a bit of a nightmare for competency testing and quality control. “We usually have one platform for one particular test, like flu, but in this case, because we couldn’t get enough reagent from any one vendor, we had to have different ones,” she said.
Then, one major company couldn’t keep up with the demand for pipettes specific to its high-throughput testing platform, forcing Palavecino and colleagues to start sending their samples out to a reference lab because they didn’t have the capacity to do all the testing that they needed in-house. “That was a big letdown,” she said.
The Children’s Hospital of Philadelphia, which performs a large amount of laboratory-developed, real-time polymerase chain reaction (PCR) testing, purchased an extra thermal cycler on top of the four they owned to keep up with testing volumes, said Rebecca Harris, MD, director of the infectious disease diagnostics laboratory. They also acquired an expansion for their rapid molecular testing platform to double its capacity, and one high-throughput automated PCR instrument to double capacity for that type of testing.
“We were better off than a lot of labs, because we were mainly relying on lab-developed tests as our main testing options, but we definitely had to restrict use of the rapid molecular test for most of the initial portion of the pandemic,” she said. “We have a lot better capacity for that now.”
Peter Perrotta, MD, chair of pathology services at West Virginia University (WVU) and director of pathology services for the WVU Health System, in Morgantown, helped establish and is CLIA director of the WVU Rapid Development Laboratory. The state-supported effort is a collaboration between his clinical laboratory team, WVU virologists and engineers, and Marshall University bioinformaticists. For this lab, the group purchased open platforms that would enable the development of COVID-19-related tests—both those that are molecular and PCR-based, and those that are protein- or enzyme-linked immunosorbent assay-based for antibody testing. During the COVID-19 peak, the lab hired three new people as well and staggered work shifts to adjust to the 24/7 schedule.
Shifting to Other Pathogens
Now, in the U.S. at least, it appears there’s light at the end of the tunnel. From mid-January to early March, SARS-CoV-2 testing declined about 26% nationwide, from an average of more than 2 million tests per day to about 1.5 million tests per day, according to data from The COVID Tracking Project, a volunteer effort launched by The Atlantic. (The project stopped collecting new data as of March 7.)
“The instrumentation and additional testing capacity we had to have was and remains an insurance policy” to handle high volumes of SARS-CoV-2 testing, Harris said. “But we are definitely thinking about ways we could put the additional testing capacity that we’ve already purchased to our advantage in the future.”
A clear-cut use in her laboratory could be maintaining some type of targeted viral respiratory panel, such as for influenza A and B, respiratory syncytial virus (RSV), and SARS-CoV-2, on an automated platform, she said. “Before the pandemic, our capacity for rapid molecular testing was really quite limited, and rapid flu testing in the lab was restricted to the emergency department,” said Harris. They also performed laboratory-developed flu/RSV tests with a 12-hour turnaround time, which was “pretty logistically challenging” to maintain in prepandemic times. Now, they could decrease turnaround times to 2 to 5 hours, she said.
Her laboratory also will assess if there is any high-volume testing they could convert to molecular methods with the extra equipment. “In our lab, that might be something like our MRSA, VRE, or group B strep screenings that we currently do by culture alone,” Harris said. “There might be other lab-developed molecular tests that we want to move to an automated platform if we think there’s a real clinical benefit in the improvement in turnaround time. And we will be looking at our send-out menu to see if there is anything that would be easy for us to now bring in-house, if there’s an FDA-approved method on a platform we have in the lab that would reduce costs, as well as if there is any other outreach testing that we should pursue now that we have this capacity.”
COVID-19 testing needs should continue to drop as more people become vaccinated, Palavecino said. Prior to the pandemic, her group had been thinking about purchasing equipment to do testing for group A Streptococcus to rule out pharyngitis in children. The automated real-time reverse transcription PCR system used by her lab could be repurposed to process additional tests like these. “If we get to a point where we have instruments available to do the testing, we may start using those instruments for other pathogens,” she said. Her lab had already previously used its antigen testing equipment for flu and RSV, so that, too, can resume more as COVID-19 recedes, she said.
Tackling Emerging Pandemic-Related Needs
Some laboratory equipment already is being repurposed. One piece of equipment Perrotta’s group purchased for molecular testing has been adapted for library preparation for SARS-CoV-2 sequencing. They’re now sequencing 200 to 400 samples a week to help epidemiologists track the entry and spread of SARS-CoV-2 variants across the state of West Virginia. They also are developing other molecular- and protein-based assays that are variant-specific. In addition, his team has developed quantitative and neutralization tests to characterize antibody responses.
“Our idea now is that we are going to be in emerging infections, a laboratory that will augment our state’s capability to respond to infectious diseases and other public health emergencies,” Perrotta said. Researchers are using equipment for some vaccine trials and other projects, many of which are coordinated by the WVU Clinical and Translational Science Institute, he added.
Overpreparing for the Future
Repurposing could happen for larger-scale laboratories, too. Quest Diagnostics performed and reported approximately 40 million molecular SARS-CoV-2 tests since March 2020, requiring the purchase of significant additional molecular equipment, said Barbara Feringa, MPH, executive director for the company’s women’s and reproductive health division.
Now, the company is planning to repurpose these upgraded platforms for women’s healthcare testing, such as for human papillomavirus, chlamydia, and gonorrhea and trichomonas, among other sexually transmitted infections. They also are considering consolidating additional molecular testing for other infectious diseases onto molecular platforms used for SARS-CoV-2 testing, Feringa said. Additional platforms used for viral load testing can be redeployed across regional labs to reduce turnaround times on tests for HIV and hepatitis C, said Jim Davis, the company’s executive vice president of general diagnostics.
The way things are going, laboratorians should have at least through 2021 to determine their future plans, our interviewees said.
“I think we’re going to have a certain level of COVID-19 testing that goes on for at least a year, through the next fall and winter, but hopefully we don’t see another spike,” Perrotta said.
Harris added, “I really stopped believing that I could accurately predict what’s going to happen during the pandemic, but I try to err on the side of being overprepared. I’m setting my own expectation that the lab may need to maintain high-volume testing into 2022. If it dies down sooner than that, I will be pleasantly surprised.”
Karen Blum is a freelance medical and science writer who lives in Owings Mills, Maryland. +Email: [email protected]