COVID-19 variants and the flu season: How diagnostics providers are racing against unknowns

With the Northern Hemisphere heading for its second flu season since the onset of the COVID-19 pandemic, and the emergence of a new variant of SARS-CoV-2, diagnostics companies are rising to the challenge posed by the demand for rapid testing of respiratory pathogens. This challenge is compounded by last year’s remarkably light flu season, which has been attributed to the use of COVID-19 mitigation measures, such as national lockdowns, travel restrictions, mask mandates and social distancing, that have since been relaxed in many countries. With cases of both Delta and now Omicron variants of COVID-19 rising across Europe, and the potential for a resurgence in influenza, being both flexible and pragmatic are proving critical while diagnostic companies prepare to arm the healthcare industry with the right tools at a moment’s notice.

Providing an insider’s perspective, Dr. Tania Nolan, head of assay design and development at LGC, Biosearch Technologies, explores some of the complexities behind predicting the circulation of influenza and other seasonal respiratory viruses amidst the COVID-19 pandemic, and shares how diagnostic providers are adapting to frequent changes in testing demand. Nolan also examines the differences between running multiplex assays versus singular assays to detect multiple respiratory pathogens, and shares her thoughts on the role COVID-19/flu combination testing could play going forwards.

A flu season guessing game

The circulation of seasonal respiratory viruses has changed dramatically throughout the COVID-19 pandemic. In both Northern and Southern hemispheres, historically low levels of within-season influenza activity have been observed since April 2020, while the circulation of other viruses such as respiratory syncytial virus (RSV) has also substantially decreased^[1-3]. Interestingly, seasonal shifts in the activity of respiratory viruses have also been reported. Following a relative absence in winter, a large resurgence of RSV cases was observed in the 2020/2021 summer in Western Australia and has subsequently been matched in the US and Europe since mid-May 2021^[4-6]. “In the UK, RSV cases are now tailing off, but we have no idea what’s going to happen next,” says Nolan. “It’s a reasonable belief that we could see another peak, so I think complacency would be very unwise.”

This uncertainty is reiterated for influenza. While it is possible that the pattern of decreased circulation will endure through the current flu season, the relaxation of COVID-19 mitigation measures, particularly travel restrictions, could drive an increase in influenza transmission. At present, cases remain low in Europe^[7-8]. “So far, we’ve seen a handful of flu A and flu B in the UK,” says Nolan. “As we relax around COVID-19, it very much depends on whether those flu strains get into the population and where they're seeded from, and whether we go back to using infection control measures for COVID-19.”

Faced with these uncertainties, diagnostic companies are having to expend substantial effort and agility in preparing for all possible scenarios and are frequently changing their approach. “It's like doing science on quicksand,” Nolan remarks. “I’ve never seen quite as much change in such a short time.”

Along with the potential resurgence of influenza virus strains, there is also uncertainty as to the impact of the new Omicron variant, as well as the emergence of other novel variants of SARS-CoV-2. Omicron is the most heavily mutated coronavirus variant reported so far and has been designated as a Variant of Concern by the World Health Organization. However, much remains unknown about how its mutations influence the virus’ behaviour with regards to transmissibility, severity, and the effectiveness of existing vaccines. For diagnostics providers, preparing for multiple scenarios is therefore essential. “We’ve gone from having a clear focus on diagnostics for SARS-CoV-2 to then thinking about winter respiratory disorders, and now back to looking at variants,” Nolan explains. “This is the reality of trying to be prepared to quickly provide the right tests.”

Multiplex versus singular assays

In response to COVID-19 and flu season uncertainty, many diagnostics providers and testing labs are transitioning from single assays to multiplex tests that are able to simultaneously analyze samples for multiple pathogens. A number of these have recently been developed in order to detect and differentiate between SARS-CoV-2, influenza A viruses, influenza B viruses, and RSV, which bear similar signs and symptoms. For example, the U.S. Centers for Disease Control and Prevention (CDC) released an Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay, a PCR test that detects and differentiates RNA markers from SARS-CoV-2, influenza A, and influenza B. Correctly identifying these viruses is essential for patient treatment and has important infection control implications, including guidance on isolation and quarantine measures, as well as population-wide strategies for reducing COVID-19 transmission.

While noting the advantages multiplex molecular tests provide for throughput and sample efficiency, Nolan sees limitations in their application when dealing with multiple viral unknowns. “If you're on a solid foundation and you know the profile of the pathogens in a population, I see the utility in expending time, effort, and resources to optimize these multiplex tests,” she says. “However, if after running a certain number of samples, a pathogen not included in the assay begins to circulate, you’ve effectively got to start all over again.”

Mutations in the target sequence of pathogens included in these assays are also of concern, Nolan asserts. If the target sequence of an assay needs to be frequently revisited due to a high mutation rate, like we’re seeing in the SARS-CoV-2 S gene, a more conserved target region of the genome is preferred to avoid false negatives. This risk increases if the assay relies on only one assay per target. “Being restricted to one COVID-19 target makes me very nervous,” she adds.

In the current landscape, Nolan suggests that running multiple singular assays at high-throughput could provide better adaptability. “With individual assays, each one is optimized and you can respond very quickly to changes in your needs, because it's easier to adjust the workflow,” she says.

Though no-one can predict the intensity of this year’s flu season, the recent increase in cases of COVID-19 including its latest variant is cause for heightened preparedness in the diagnostics industry. With a portfolio of paired enzymes and master mixes, custom oligos, qPCR probes, and nucleic acid extraction/purification kits, Biosearch Technologies is well positioned to support partners through all stages of assay development, for both singular and multiplex diagnostics. To see a real-world example of the rapid implementation of a high-throughput COVID-19 testing and surveillance program, see the related article: Transition to molecular diagnostics: How agricultural expertise has helped to keep COVID-19 positive rates low

Want to know more on this topic?

• Hear from Prof. Jim Huggett on the need for reproducible and standardized metrics for SARS-CoV-2, and Daniel Evans on the importance of using accurate metrics for COVID-19 diagnosis.

• Join our expert speakers as they discuss why the choice of unit is important when quantifying virus in the panel discussion: A lesson from COVID-19 on the dangers of using Cq to quantify nucleic acids.

References
1. Adlhoch C, et al. Spotlight influenza: The 2019/20 influenza season and the impact of COVID-19 on influenza surveillance in the WHO European Region. Euro Surveill. 2021 Oct
2. Rodgers L. et al. Changes in Seasonal Respiratory Illnesses in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic. Clin Infect Dis. 2021 Jul
3. van Summeren J, et al. Low levels of respiratory syncytial virus activity in Europe during the 2020/21 season: what can we expect in the coming summer and autumn/winter? Euro Surveill. 2021 Jul
4. Foley DA, et al. The interseasonal resurgence of respiratory syncytial virus in Australian children following the reduction of coronavirus disease 2019–related public health measures. Clin Infect Dis. 2021 Feb
5. Olsen SJ, et al. Changes in Influenza and Other Respiratory Virus Activity During the COVID-19 Pandemic - United States, 2020-2021. MMWR Morb Mortal Wkly Rep. 2021 Jul
6. Williams TC, Sinha I, Barr IG, Zambon M. Transmission of paediatric respiratory syncytial virus and influenza in the wake of the COVID-19 pandemic. Euro Surveill. 2021 Jul
7. England PH. National flu and COVID-19 surveillance reports: 2021 to 2022 season. [Accessed: 18 Nov 2021]. Available from: https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
8. European Centre for Disease Prevention and Control (ECDC). Flu News Europe: weekly influenza updates. [Accessed: 18 Nov 2021]. Available from: https://flunewseurope.org/