Precise Detection of Influenza A (H3N2) Subclade K

Reliable, Confident Diagnosis with BioCode® Respiratory Pathogen Panel

Introduction

Influenza A (Clade H3N2) subclade K (formerly J.2.4.1) has rapidly emerged with significant HA gene diversity due to antigenic drift. First identified in 2025 in Australia and New Zealand, it has since spread globally, accounting for most influenza cases in the UK and US, with reports of up to 90% in the US by January 2026^1,2,3. 

Applied BioCode® RPP Panel

• Detects of 17 common respiratory viral and bacterial pathogens, including Influenza A (matrix gene target)
• Differentiates between HA subtypes using three targets: classical H1, H1 2009 pandemic (pdm09), and H3
• Reports Influenza A positive result from either Flu A matrix gene detection or Flu A HA detection. 

Applied BioCode Flu A Surveillance Program

The Applied BioCode® Research and Product Development Department has an ongoing surveillance program to ensure patient testing percentages reflect the current epidemiological trends of Flu A targets. For example, the 2024-2025 influenza season report identified a mutation in the Flu A matrix gene of H1pdm09 strain which allowed us to ensure the assay is still able to detect H1pdm09 positives despite the mutation in the Flu A H1pdm09 MA gene. The surveillance program for the 2025-2026 season has noted the emergence of a new Flu A strain, H3N2 subclade K. Applied BioCode confirms that 95.6% of Flu A patient testing is now positive for the H3N2 subclade K target, consistent with the current diagnostic trends noted in the US³.  

In Silico Evaluation of Influenza, A Subclade K

1,112 sequences for MA and HA genes from Influenza A subclade K were obtained from GISAID and analyzed using DNA Software, Inc. 

In silico analysis showed:

• Strong, consistent binding for the FLUA (MA) target.  
• Genetic variation in the FLUA H3 (HA) binding region:
  
  1. 95% of analyzed sequences matched the FLUA H3 (HA) binding region by 95%
  2. 5% of analyzed sequences matched the FLUA H3 (HA) binding region by 92-95%. 
  3. Overall, genetic variation in subclade K HA should not impact assay performance.

In Vitro Evaluation of Influenza A Subclade K

Five gene fragments representative of Influenza A subclade K FLUA H3 HA variants and one control were tested to confirm the observed genetic variation will not impact FLUA H3 HA subtype performance. All variants were detectable by PCR, with one, which represents 2.5% of the Influenza A subclade K sequences analyzed in silico, showing variable detection at 5 copies per reaction. Overall, assay performance was not impacted by subclade K mutations.

Conclusions:

A rapidly spreading Influenza A (H3N2) Subclade K variant discovered in 2025 is causing most global flu cases. Despite mutations, the Applied BioCode respiratory panel accurately detects both Flu A MA and HA genes in new strains, underscoring the need for ongoing surveillance.

References

1. Dapat C, et al. Extended influenza seasons in Australia and New Zealand in 2025 due to the emergence of influenza A (H3N2) subclade K viruses. Eurosurveillance (2025). DOI: https://doi.org/10.2807/1560-7917.ES.2025.30.49.2500894
2. Centers for Disease Control and Prevention. (2026, January 10). Weekly US influenza surveillance report: Key updates for week 1, ending January 10, 2026. FluView. https://www.cdc.gov/flu/weekly
3. UK Health Security Agency. (2025, December 18). National flu and COVID19 surveillance report: 18 December 2025 (week 51). GOV.UK. https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2025-to-2026-season