Test Might Determine What Ails You: COVID-19 or Influenza

A multiplex PCR assay may be capable of simultaneously detecting and differentiating influenza viruses, respiratory syncytial virus (RSV), and SARS-CoV-2.

The coming flu season may be like no other. True, as Lynnette Brammer, who heads the domestic influenza surveillance team at the Centers for Disease Control and Prevention, recently told Infection Control Today®: Flu can cause lots of problems every fall. We say all the time—and I know people get tired of hearing it, but I think right now it’s truer than ever—flu is incredibly unpredictable.”

Still, there’s the little matter of us reemerging from the COVID-19 pandemic. Last year, infection preventionists feared that hospital emergency rooms would be filled with patients suffering from respiratory diseases and providers would have to difficulty determining whether to treat for COVID-19 or some other problem, like the flu. That didn’t happen. The mitigation efforts used to combat COVID-19—hand hygiene, social distancing, masking—stopped the flu in its tracks and the U.S. had the lowest flu rates on record.

This year, COVID-19 mitigation efforts won’t be in general use and that could cause problems. Brammer told ICT® that last year “the diagnosis was a lot easier, because almost all the respiratory illness was due to one thing…. We expect flu will come back.” However, she added that COVID-19 greatly enhanced flu surveillance in the United States and the rest of the world.

Also, testing for respiratory illnesses have improved dramatically, and innovation continues.

For instance, findings presented this week at the American Society of Microbiology (ASM) 2021 World Microbe Forum demonstrated that a multiplex PCR assay may be capable of simultaneously detecting and differentiating influenza viruses, respiratory syncytial virus (RSV), and SARS-CoV-2.

The real-time assay was still able to detect low abundances of SARS-CoV-2 in human clinical samples with high concentrations of influenza and/or RSV—meaning patients with previous SARS-CoV-2 infection and current respiratory viral infection can be defined.

Led by Benjamin M. Liu, of the Department of Pathology at the University of Utah School of Medicine in Salt Lake City, investigators sought to contribute to the “urgent need” for differential and definitive diagnoses of viral infections and co-infections after the COVID-19 pandemic—and especially during major respiratory infection seasons.

The ChromaCode HDPCR Respiratory Virus 6 (RV6) qPCR assay used probe-limited chemistry and calibrators that allow for multiplexing and end-point fluorescence detection and differentiation of SARS-CoV-2, influenza A and B viruses (IAV; IBV), and RSV.

“Common respiratory viruses, e.g. RSV, IAV, and IBV mimic SARS-CoV-2 in clinical presentations but have different clinical courses, therapies and outcomes,” Liu and colleagues wrote. “Some commercially available single-well multiplex assays…allow for large scale screening in the context of the pandemic, but lack the ability to distinguish IAV and IBV.”

The team sought to evaluate the analytical and clinical performance of the RV6 assay through a limit of detection (LOD) study through all 4 viruses, with LOD defined as the lowest dilutions with a detection rate of 100%.

They evaluated the assay through 77 nasophrayngeal specimens previously assessed via the multiplex assay from TaqPath, as well as discrepant samples being tested by the orthogonal Panther Fusion Flu/A/B/RSV assay.

Through the 77 samples, the RV6 assay detected 2 more single positives for IBV or RSV than the TaqPath assay; both samples tested negative by the Panther assay as well. All but 1 of 29 “flu” positive samples identified by the TaqPath assay were differentiated by the RV6 assay as either IAV (n = 15) or IBV (n = 14). The remainder sample returned as IAV+IBV.

“The RV6 assay demonstrated high analytical sensitivity and specificity in simultaneous detection/differentiation of IAV, IBV, RSV and SARS-CoV-2 in human clinical specimens and warrants further clinical validation,” investigators concluded.

This article originally appeared inContagion®.