A total of 293 non-overlapping nucleotides, excluding the primer regions, were analyzed using the genetic loci targeted by the influenza A primers. This corresponds to 2.15% of the influenza A virus genome. Out of 174 human samples analyzed from the 2005-2006 season, only two showed evidence for mixed viral populations at one of the six loci, corresponding to 1.1% of the samples. Thus, assuming the same mutation rate for the broader viral genome as for the region analyzed by PCR/ESI-MS, about 50% of the human H3N2 virus samples would have a mixed population of viruses.