COVID testing capacity falls short as flu season nears

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Despite these difficulties, McGonnagle and Dr. Abel say, capacity could be increased substantially within just four to five weeks, in part by laboratories bringing back their furloughed staff.

In addition, they say, new technologies have become available that could expand testing capacity, but they don’t expect them to become widely used in clinical laboratories.

Assays based on next-generation sequencing or mass spectrometry (PCR plus MALDI-TOF) technologies might make it possible to run thousands of samples at a time, but the underlying platforms tend to be expensive and the required preanalytical work is extensive, Dr. Abel said. For labs that already have high-end next-gen sequencers or MALDI-TOF mass spectrometry instruments up and running, though, these assays could be viable options for increasing capacity for SARS-CoV-2 testing. Next-generation sequencers, for instance, can run nearly 4,000 tests in a 12-hour shift, Dr. Abel said, pointing out that sequencer manufacturers might consider this application attractive enough to invest in placing their machines in clinical labs. “There will be some interest in the market for this,” he predicts.

McGonnagle said the nightmare scenario is that COVID-19 will be rampant when flu season hits: “If it becomes a severe flu season, the diagnostic dilemma is going to be just incredible.”

When the pandemic began in this country, Dr. Abel said, many laboratories were still running tests for the end of the last flu season. At the time, some were required to test first for influenza and to move on to COVID-19 testing only if the flu results were negative. As flu season wound down, that approach was abandoned. But for the upcoming flu season, laboratory teams will have to prepare to test for both pathogens, or establish an algorithm to determine the sequence of tests to use. If there is still a need for large-scale COVID-19 testing when flu season begins, a rapid multiplex test covering both influenza and SARS-CoV-2 would make sense for many labs, and these kinds of tests should be ready in time for flu season, Dr. Abel said. “The viable multiplex provider is going to be a big winner here,” McGonnagle added.

Dr. Abel considered some of the latest research in COVID-19 immunity for a look at what could become important for clinical testing in the future.

Recent studies suggest that testing for T cells, for instance, might offer insight into a patient’s immune response to SARS-CoV-2 infection. “T helper cells that recognize the SARS-CoV-2 spike protein can play a very important role in immunity,” Dr. Abel said. Studies published in Cell and Nature have demonstrated that some people have T cells able to recognize protein antigens from the new coronavirus despite their never having been exposed to SARS, MERS, or COVID-19. “This is probably due to cross-reactivity with proteins from common coronaviruses,” he said. “There might be a part of the population that has some preexisting immunity against COVID-19.” Spotting these T cells in a patient might be useful in diagnostics as well as in vaccine development.

“The problem is that this is really pure research at this point,” he said, adding, “There is a significant knowledge gap in our understanding of the T cell response.”

Meredith Salisbury is a writer in the New York City area.