Sherrie Rice
May 2020—Christine C. Ginocchio, PhD, MT(ASCP), in an April 8 CAP TODAY webinar, reported findings on the analytical efficiencies and sensitivities of four of the original and most common of the SARS-CoV-2 assays.
Dr. Ginocchio, vice president of global medical affairs for BioMérieux/BioFire Diagnostics, also spoke about virological assessment, antibody tests, coinfections, and syndromic testing, in the webinar made possible by a special educational grant from BioFire. Watch the full webinar here.
The study she shared, by Vogels, et al., compared the quantitative reverse-transcription PCR assays of the China CDC, the U.S. CDC, the Berlin Institute of Virology, and Hong Kong University (Vogels CBF, et al. https://doi.org/10.1101/2020.03.30.20048108). “They used spike samples to do this evaluation,” she said. Nine primer-probe sets used in the assays were studied, and all can be used to detect SARS-CoV-2, “but there are clear differences in the ability to differentiate between true negatives and positives with low amounts of virus,” the authors write.
For one assay, the RdRp-SARSr set from the Berlin Institute, the Ct values were significantly higher than those of the others. “All have similar sensitivities among the primer-probe sets with the exception of this one primer set,” Dr. Ginocchio said. The RT-PCR amplification efficiencies were near or above 90 percent.
Many primer-probe sets, including the “N2” and “N3” sets issued by the U.S. CDC, have background amplification with SARS-CoV-2–negative nasopharyngeal swabs, which may lead to inconclusive results, according to the study. Similar results were found for one of the China CDC assays.
“We have to continue to evaluate these assays as we go through the pandemic,” Dr. Ginocchio said, and understand the assay targets. “And keep in mind that these are RNA viruses and they like to mutate, and this could affect everybody’s assay within a couple of months.”
Another study she reported on, by Wölfel, et al., looked at virological assessment of hospitalized patients with coronavirus (Wölfel R, et al. https://doi.org/10.1101/2020.03.05.20030502). “They found there were very high levels of virus emitted from both throat and nasopharyngeal swabs from the earliest points in the illness,” Dr. Ginocchio said, when people generally engage in their daily routine activities.
“What was interesting is that people were emitting greater than 1,000 times more virus than during the peak shedding of SARS-CoV-1,” and this may explain the rapid spread of SARS-CoV-2, she said.
In the study, viral shedding was found to drop after about five days, except in patients with pneumonia. “People with mild infections can still test positive days or weeks after illness,” but they’re likely no longer infectious by about 10 days after the start of symptoms.
Antibodies typically develop about six to 12 days in, “and the rapid rise of antibodies, they believe, may explain why about 80 percent of the people infected with the virus do not develop severe disease.”
It is known that the RT-PCR tests are generally positive by the time of symptom onset, Dr. Ginocchio said, and the viral titers tend to peak in the five- to seven-day range (Lippi G, et al. https://doi.org/10.1515/cclm-2020-0285). “They begin to come down, and after symptom relief is when we tend to find that the RT-PCR tests become PCR negative.”
Like others, she questions whether the sensitivity of the rapid antigen tests will be acceptable, but acknowledges they may provide a point-of-care rapid diagnostic option for settings in which RT-PCR assays are not available. Antibody tests will be important for epidemiologic purposes—“to take a look at the true transmission rates,” and to assess potential immunity in the population.
“Because I have a feeling,” she said, “that we’re not going to be done with this virus in one wave. This virus will come back in a second wave and in a third wave, and we need to know what is the risk and what are the levels of herd immunity.”
The molecular test options are rapid point-of-care single tests for SARS-CoV-2 only, high-throughput batch or random-access tests for SARS-CoV-2 only, or syndromic panels with SARS-CoV-2. “We know very little right now, unfortunately, about coinfections with SARS-CoV-2,” she said. In a study from China, of 316 patients with multiple respiratory pathogens, 104 were positive for CoV-2, and six of the 104 had coinfection with coronavirus (3/104), influenza A virus (2/104), rhinovirus (2/104), and influenza A H3N2 (1/104) (Wang M, et al. http://medrxiv.org/lookup/doi/10.1101/2020.02.12.20022327). “A lot of these patients who didn’t have SARS-CoV-2 had other viruses, so it was helpful to be able to make that alternative diagnosis,” Dr. Ginocchio said. Evaluating the role of both viral and bacterial coinfections in the severity of COVID-19 disease will be important, she added.
Mycoplasma coinfections have been seen with COVID-19, and Mycoplasma would require treatment, she noted. “And a preliminary analysis by Ian Brown, MD, at Stanford School of Medicine (Brown I, et al. Medium.com) found that about one in five people with COVID-19 are also infected with other respiratory viruses.”
Secondary bacterial infections are a risk, Dr. Ginocchio said, given the number of patients on ventilators for long periods, though here, too, the data are limited. “One study showed that four out of 13 patients in the ICU developed a secondary infection, but they didn’t give the causes of those infections” (Huang C, et al. Lancet. 2020; https://doi.org/10.1016/S0140-6736(20)30183-5). In another limited study, one of 99 patients had superinfection with Klebsiella pneumoniae, Acinetobacter, and Aspergillus spp. (Chen N, et al. Lancet. 2020;395:507–513). The BioFire Pneumonia Panel would be a “good complementary test” for those at risk for the secondary infections, she said, noting that such secondary bacterial infections could be highly multidrug resistant. Rapid identification of bacterial coinfections could drive the early administration of targeted antimicrobial therapy.
BioFire will soon seek emergency use authorization from the FDA for its FilmArray Respiratory Panel 2.1, which is its Respiratory Panel 2 (which tests for 21 respiratory pathogens) plus SARS-CoV-2, so 22 respiratory pathogens in all. EUA will be followed by 510(k) submission.
Sherrie Rice is editor of CAP TODAY.