Facing a backlog, the state’s public health laboratory turned to the medical laboratory at Dartmouth Hitchcock Medical Center

Much of the attention surrounding the COVID-19 outbreak—the illness caused by the SARS-CoV-2 coronavirus—has focused on large urban areas such as New York City and Los Angeles. However, the virus is impacting many rural areas as well. This is true in New Hampshire, where the diagnostic response required close cooperation between the state’s public health laboratory and the clinical laboratory at its lone academic medical center. Their experience offers lessons for medical laboratory leaders nationwide.

“When these things happen and you surge beyond what you could imagine, it’s the relationships with people that matter more than anything,” said Christine L. Bean, PhD, Administrator of New Hampshire Public Health Laboratory Division of Public Health Services , Concord, N.H., during a recent Dark Daily webinar, titled, “What Hospital and Health System Labs Need to Know About Operational Support and Logistics During the COVID-19 Outbreak.”

As Bean explained, during the earliest stages of the pandemic the “CDC was doing the testing” and the state lab’s role was limited to submitting samples from patients deemed as “presumptive positives.” Then, on Feb. 4, the FDA granted an emergency use authorization (EUA) allowing use of the CDC-developed real-time reverse transcriptase PCR (RT-PCR) assay by designated labs.

The New Hampshire Public Health Laboratory (NHPHL) received its first test kit on Feb. 10, Bean said. But the kits were recalled due to validation problems with one of the reagents. On Feb. 26, the CDC issued revised test instructions allowing use of the test without the N3 primer and probe set that had caused the early validation issues. The NHPHL verified the test under the new guidelines and went live on March 2, she said.

However, with a capacity of 150 to 200 tests per day, the lab wasn’t equipped to handle a large volume. “Much of what we do is really population-based,” she said. “Most of the time we’re not doing patient diagnostic testing.”

Christine L. Bean, PhD (left), Administrator of the New Hampshire Public Health Laboratory, and Joel Lefferts, PhD (right), Assistant Professor of Pathology and Laboratory Medicine, and Assistant Director of the Molecular Pathology, at Dartmouth’s Geisel School of Medicine, spoke with Dark Daily’s Editor-in-Chief Robert Michel during a webinar on what hospital and health system labs need to know about operational support and logistics during the COVID-19 outbreak. The webinar can be freely downloaded by clicking here. (Photo copyright: Dark Daily.)

NHPHL Turns to the Medical Laboratory at DHMC-CGHT for Help

By April 1, the public health lab had received 3,500 samples for testing, “which is a lot for us,” said Bean. To help with the backlog, they turned to the Laboratory for Clinical Genomics and Advanced Technology at Dartmouth Hitchcock Medical Center (DHMC-CGHT) in Lebanon, N.H.

The DHMC-CGHT lab began having its own discussions about testing in the first week of February, said Joel A. Lefferts, PhD, HCLD, DABCC, Assistant Professor of Pathology and Laboratory Medicine and Assistant Director of Molecular Pathology at Dartmouth’s Geisel School of Medicine. They were unsure of how much need there would be, but “throughout the month of February, we started exploring different testing options,” he said during the Dark Daily webinar.

The Dartmouth-Hitchcock lab team began with the CDC test. However, Lefferts noted that the initial FDA guidance was “somewhat restrictive” and required specific RNA extraction kits and real-time PCR instruments. “If our lab didn’t have the capability to perform everything exactly as indicated, we would be running it off-label and would have to possibly submit our own EUA submission to the FDA,” he explained.

Later, though, the FDA and CDC loosened those restrictions and the lab began testing with the CDC assay on March 18, using a Thermo Fisher ABI 7500Dx instrument, Lefferts said. According to Thermo Fisher’s website, the ABI 7500Dx “is a real-time nucleic acid amplification and five-color fluorescence detection system available for in vitro diagnostic use.”

However, Lefferts continued, “we only had one of these 7500Dx instruments, and it was a relatively manual and labor-intensive process.” It allowed a maximum of 29 samples per run, he said, and took about five hours to produce results.

Then, the FDA granted an EUA for Abbott’s m2000 assay, which runs on the company’s m2000rt real-time PCR instrument. “We were really excited, because we happened to have two of these systems in our lab,” he said. “We quickly got on the phone and ordered some of these kits.”

The DHMC-CGHT lab went live with the new system on March 23. It can handle up to 94 samples per run, said Lefferts, and with two instruments running from 6 a.m. to 9 p.m., “there’s a potential to do as many as 10 runs per day.”

This was the system they used to help New Hampshire’s Public Health Lab with its backlog. “It was unbelievable to see that our backlog could be really wiped out,” said Bean.

Challenges for Medical Labs

Gearing up for testing in a public health emergency poses many challenges, Lefferts advised. “You need to look at what instrumentation you have in your laboratory, what the experience level of your lab team is, how much space you have, your expected batch size, and your needed turnaround time.”

The two labs also had to deal with regulatory uncertainty. “This EUA process is something for which we don’t have much experience,” he said. “Trying to juggle CLIA, CAP, the FDA, and possibly state regulations is a bit challenging. You definitely need to do your research and talk to other clinical laboratories that are doing this testing to get advice.”

Lefferts explained that the most significant challenges to develop and validate a molecular assay for COVID-19 included:

  • Availability of validation materials. Obtaining “positive [viral] samples may be a challenge, depending on where you are and what you have access to,” said Lefferts. However, he credits the FDA for being “very proactive” in suggesting alternative sources for “viral isolates or genomic RNA that’s been extracted from some of these viral isolates.”
  • Availability of collection kits. “We can do a lot more testing now,” he said, but one bottleneck is the limited availability of supplies such as nasopharyngeal swabs and viral transport media. “We’re looking at alternative collection options,” he said, such as 3D-printed swabs or even Q-tips [household cotton swabs], though “hopefully it won’t come to that.” The DHMC-CGHT lab also considered producing its own transport media.
  • Turnaround times. “Our lab wants to get those results out as soon as possible,” Lefferts said. “So, we’re looking at alternative methods to get that testing out sooner.” For example, “do we just do the SARS-CoV-2 testing on a patient, or do we need to do other influenza and other viral pathogens,” while also keeping up with other routine testing during the pandemic?
  • Staffing issues. “Fatigue is a big issue with members of our labs who put in lots of extra hours,” he said. The DHMC-CGHT lab has developed contingency plans in case lab personnel get sick.

The Bean-Lefferts 60-minute webinar was hosted by Dark Daily’s Editor-in-Chief Robert Michel on April 1. It is freely downloadable by clicking here, or by placing this URL in your web browser: https://www.darkdaily.com/webinar/what-hospital-and-health-system-labs-need-to-know-about-operational-support-and-logistics-during-the-covid-19-outbreak/.

This critical information will be highly useful for Laboratory Directors and Managers, Laboratory Supervisors and Team Leaders, Integrated Health System Leaders, Hospital Group Leaders, Physicians and Physician Group Leaders, Phlebotomy Managers, Courier and Logistics Managers, and Safety and Compliance Managers.

—Stephen Beale

Related Information:

What Hospital and Health System Labs Need to Know About Operational Support and Logistics During the COVID-19 Outbreak