Influenza is associated with rapid evolution due to lack of RNA polymerase proofreading, immunogenic selection and frequent rearrangement of gene segments. Evolutionary changes affecting the performance of diagnostic testing have long been recognized. Hence, it is not surprising that such challenges apply to nucleic acid amplification tests, even though they are designed to target highly conserved regions. Initially, case reports involved single isolates of A(H1N1)pdm09. Over the past four years, subtype H3N2 viruses evolved to viral clades with mutations in the WHO recommended target region, such that almost all isolates worldwide have significantly reduced sensitivities with many commercial PCR tests.