During the 2014–2015 influenza season, a decreased sensitivity for the detection of influenza A(H3N2)/3C.2a using a commercially available multiplex assay was encountered.
Gene sequencing of the influenza A matrix protein showed a point mutation (C163T) leading to a mismatch with the assay probes.
The known risk of false-negative results in molecular assays due to genomic variation is emphasized, especially in microorganisms subject to great variation such as influenza A.
Intensive monitoring of incidence, epidemiological data, and clinical context can give a first indication of missed influenza A strains.