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Labs take stock of surprising flu season

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Amy Carpenter Aquino

March 2018—In a severe flu season that started early, laboratories faced unprecedented test volumes, used new testing platforms, and negotiated vendor supply shortages.

When laboratory staff at Arkansas Children’s Hospital in Little Rock began seeing a rising number of requests for respiratory tests, and five positive flu results, in September 2017, they suspected they were in for a record flu season, says Sherry Childress, BSMT(ASCP), technical chief, molecular diagnostics and immunology.

Sherry Childress (left) and Dr. Gail Woods with Dr. José Romero at Arkansas Children’s. “I think everyone around the country has been surprised by the number of cases we’re seeing,” Dr. Romero says.

Sherry Childress (left) and Dr. Gail Woods with Dr. José Romero at Arkansas Children’s. “I think everyone around the country has been surprised by the number of cases we’re seeing,” Dr. Romero says.

By the end of January, the laboratory had performed triple the number of flu tests compared with the previous flu season. The percent of samples testing positive through the end of January, for nucleic acid amplification and direct antigen testing combined, was 27.2. For the same period in 2016–17, it was 3.3.

“I think everyone around the country has been surprised by the number of cases we’re seeing,” says José Romero, MD, director, pediatric infectious diseases section, Arkansas Children’s Hospital. “We’re doing approximately 300 percent more,” he says of the hospital’s test volume.

Gail L. Woods, MD, who recently retired as chief of pediatric pathology at the hospital, says the laboratory uses the BioFire FilmArray res­piratory panel throughout the year and the CLIA-waived Quidel Sofia Influenza A+B fluorescent immunoassay only during flu season.

“When you’re in season,” Dr. Romero says, “the risk of having a false-positive goes down, so we prefer to use the rapid antigen. Certainly, PCR has a place if the patient is in the intensive care unit or one of the heme-onc units. I think the doctors are using it appropriately in-house.”

The laboratory switches to rapid antigen testing for flu when the number of positive results by PCR rises by 10 percent, which Dr. Romero says usually occurs no earlier than late December.

“In the 2016–2017 season,” Childress says, “we started rapid testing in mid-January. This year, we started it in November.” The laboratory has had a 40 percent positivity rate on the rapid antigen tests alone from Dec. 1 to Jan. 31.

Despite the flu season’s early start, the laboratory felt prepared, Childress says, because staff had the resources needed to provide rapid flu and comprehensive respiratory testing. “What we weren’t prepared for was vendor supply stocks that weren’t able to meet demand for a period of time in December,” she says. “It made us change the way we do business here in PCR testing.”

When it ran short of kits, the laboratory triaged testing through the infectious disease department to preserve its stock of Bio­Fire Film­Array respiratory panels. Patients who needed primarily flu or respiratory syncytial virus testing had a rapid antigen test, while physicians were required to get authorization from an infectious disease physician to order PCR testing for patients who needed the comprehensive panel. “And we’re still doing that,” Dr. Romero says, “though we’re not adhering to it as strictly as we were before.”

BioFire resolved the assay shortage quickly, Childress says. “They worked very hard with us because we were a pediatric hospital and they wanted to make sure we had what we needed.”

FilmArray respiratory panel testing at Arkansas Children’s shows that rhinovirus/enterovirus represents the largest percentage of positive pathogens (31 percent) among patients so far this year, followed by RSV at 17 percent, Childress says. The laboratory has seen a significant number of coronavirus OC43 and adenovirus cases.

Among positive flu cases, the laboratory saw 78 percent flu A and 22 percent flu B, which is different from last year, which saw 97 percent flu A, Dr. Woods says. The percentages of rhinovirus, enterovirus, and RSV cases were about the same for both years.

For next year’s flu season, Dr. Romero, who is also the Horace C. Cabe endowed chair in infectious diseases, University of Arkansas for Medical Sciences, would like to see a plan for handling an assay reagent shortage for both the antigen test and PCR panel. Though the triaging of testing worked well this year, he says, “we got caught unaware and had to make things up on the fly.” Childress is looking forward to completing verifications on the laboratory’s additional Sofia analyzer and training staff on a new BioFire Torch for the FilmArray respiratory panels, with the goal of providing PCR test results around the clock.

“For the lab’s part, I think it’s been fabulous to have a good rapid assay and the option of performing a comprehensive PCR panel,” Childress says. “We are getting really good, quick turnaround times, accurate data, efficiently reported. That’s very important to have, especially in a pediatric hospital.”

Interesting in several ways” is how Kevin Homer, MD, describes the 2017–18 flu season at Texas Health Huguley Hospital in Fort Worth. This flu season began the first week of December, six to eight weeks earlier than usual for the area.

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