Seasonal average nAMPs were remarkably consistent between institutions within a given year. The differences in the matrix gene averages between H3N2 and H1N1 seasons were consistent with the number and location of mismatches in the molecular assay. Instrument manufacturers, laboratories and regulatory agencies should work out an approach to capture this type of data electronically on national and regional levels so that seasonal sequence drift affecting the performance of molecular assays can be monitored.