Flu Season in the Time of COVID-19

Between the usual respiratory disease season and the COVID-19 pandemic, we can expect more than 20 different pathogens to circulate in the northern hemisphere over the coming months. Combating these diseases and protecting our patients will require creative thinking, focused effort, and a sensitive, specific testing strategy based on proven technology. One approach is to utilize the FDA Emergency Use Authorized BioFire Respiratory 2.1 (RP2.1) Panel (EUA). It is an available test that offers rapid turnaround times, an efficient workflow, and the potential to detect not only SARS-CoV-2, but also co-infections. To learn more about this tool, we spoke with Amanda Harrington, Associate Professor of Pathology and Laboratory Medicine and Director of the Clinical Microbiology Laboratory at Loyola University Medical Center in Illinois.

How has the pandemic changed your work?
As a clinical microbiologist, I’ve worked in hospital laboratory medicine for more than a decade. Over the course of the pandemic, I’ve served as Director of Microbiology at Loyola University Medical Center, which is part of a three-hospital system of Loyola Medicine. Outside of point-of-care testing, our laboratory performs a majority of the COVID testing for our hospital system. My colleagues and I have been neck-deep in this virus – and its effects – ever since it began.

There are no routine days anymore, and the pace of our work has escalated significantly. We’ve had to focus on COVID-19 testing here in the laboratory and, for better or for worse, we’ve been doing a lot more logistics and supply chain management than is typical for clinical microbiology. We’re trying to make sure we have the right collection devices and test kits available at all times. Do we ever need to validate an alternate collection device or other testing component, like a different swab? It seems like almost daily – and that hasn’t changed since the onset of the pandemic.

Although our COVID-19 testing is operational, it has impacted areas of the laboratory one might not expect. We need alternative strategies not only for COVID-19, but also for routine testing. A lot goes on behind the scenes to keep clinical diagnostics running, and it’s all in response to COVID-19.

How has COVID-19 testing changed since the start of the pandemic?
Fortunately, new tools have come to market and more are on the way. Some aspects of the supply chain have stabilized; for example, we have more access to swabs than we did before. We’ve started to evaluate other specimen sources. What has yet to change is the overall fragmentation of the supply chain, so we’re never sure which test is available. It’s a daily challenge.

As a result, almost every lab I know has diversified its testing strategy. Offering more than one option is the biggest key to surviving, so many run four to eight different COVID-19 tests. When they can’t get supplies for one, they quickly pivot to another or adapt their strategy to compensate.

Initially, we were testing only symptomatic patients. Now, we’re beginning to test different populations for surgical procedures as more people return to hospitals for care. The demand for testing has increased – and, now that our students are going back to schools and universities, it will likely increase again.

How do you see the collaboration between labs and vendors playing out?
I applaud our commercial vendors because not every laboratory can produce in-house tests. Many, including ours, rely on industry partnerships and industry-developed tests. The tests that have come to market recently are fantastic.

We have good relationships with our industry partners, so they keep us informed about where they think they’re going. Every vendor I’ve spoken with is doing their best to increase manufacturing capacity. It’s difficult because you can’t just throw up a building and double your manufacturing capacity overnight. Across the industry, we’re trying to strategically manage capacity based on both existing and expected needs.

When did you begin using the BioFire Respiratory 2.1 Panel (EUA) for COVID-19 testing – and how has it helped you overcome the challenges you’ve faced?
The BioFire panel is different than many other tests because it’s a full, syndromic panel with random access and rapid turnaround. We validated the panel and started using it almost as soon as it was available. We use it in two ways — for situations where a rapid COVID-19 test is needed and for immunocompromised patients. For urgent situations, the fact that I can get test results in just over an hour is a benefit. This test also helps with patient placement in the hospital and care management for our transplant and pediatric groups, who are some of our most vulnerable patients in our hospital. Having a syndromic approach for those patients is a valuable tool, and having COVID-19 on that panel is key.

Over the summer, we were fortunate to have to focus only on single-target testing strategies. But, as the seasonal risk of respiratory disease goes up, we are looking to take advantage of the benefits of a respiratory panel. Without it, we won’t know if patients are presenting with symptoms of influenza, metapneumovirus, COVID-19, or some combination of communicable respiratory diseases we confront every year in the colder months. Having one comprehensive diagnostic test to provide those answers is very efficient.

Could you provide more detail on the accuracy, turnaround times, andworkflow of the panel?
The short turnaround time and the fact that it’s not a batch-based test makes the workflow efficient. Test results are rapid. In terms of accuracy, the panel has performed very well in laboratory comparisons with our other COVID-19 tests – and equally so when testing for other respiratory viruses.

Another feature we take advantage of in our laboratory is that our instrument interfaces directly with our laboratory information system. It saves time and effort because the results transfer seamlessly (eliminating delays from entry). It’s very easy to set up and the automatic transfer simplifies our workflow.

Why is it so important to detect co-infections?
That’s a significant issue for specific patient populations and one example is our pediatric group. They group their patients into cohorts based on the presence of different viruses to prevent co-infections. We’re not sure what co-infection will look like in the USA. Studies from China and elsewhere – including one from Chicago at the onset of the pandemic – have indicated variable prevalence, but we don’t know how that will play out as we move through respiratory illness season. The BioFire panel helps us detect sources of potential co-infection, and that’s something we’re concerned about right now as respiratory season approaches. One of our Master’s program medical laboratory scientists will be looking at this as her capstone project this flu season, so we’ll see what the data show.

In a traditional flu season, we do see co-infections, but it’s impossible to say what this year’s respiratory illness season will be like. We’ve been watching the data out of Australia and haven’t seen a lot of flu circulating. Is that the result of social determinants like mask-wearing and social distancing? Will those interventions suppress the circulation of other respiratory viruses or will we see a more traditional respiratory season again? Without the kind of data this panel provides, we really cannot predict that. As an additional benefit, BioFire aggregates submitted data to show what’s circulating across the regions; that will be really interesting.

How exactly will the panel be used through the winter flu season?
In past flu seasons, we’ve offered the BioFire Respiratory Panel to our emergency department and to our hospitalized patients. This year, based on demand due to COVID-19, we’re restricting it to our intensive care patients, our pediatric population, and our immunosuppressed population. We have to be strategic about utilization so we can keep up with demand throughout the season.

COVID-19 has taught me that predicting the future is impossible and you need the right tools. All we can do is assemble our tools and a game plan – and then three or four backup plans. This virus has forced us to think outside the box, to be more adaptable, and to use all of our tools, sometimes in unconventional ways. We’re happy to have access to BioFire’s panel as one of the tools to help diagnose COVID-19 and other respiratory illnesses, because such tools allow us flexibility and provide information that is necessary to help us improve patient care – and that’s why we’re here.

Dr. Harrington’s statements are not an endorsement of BioFire products. She was not compensated for participating in this interview.