In this work we describe a novel method that employs some of the best properties of each of the discussed techniques, and also supplies additional valuable information not provided by those techniques. For example, our method may identify mixed Black font: types determined through sequence analysis; blue font: experimentally determined base composition types; red font: experimentally determined base composition types for season 2005-06. Ten rare sequence types (,1.5%) were not uniquely discernable by the base composition analysis of the eight amplicons used in this analysis, as more than one subtype produced the same BC-type. These BC-types are indicated by asterisks. doi:10.1371/journal.pone.0000489.g003 populations of viruses, either as viral quasispecies as previously illustrated (i.e., development of ''drift'' strains) or co-infections with circulating strains (i.e., potential for development of ''shift'' strains). Recent advances in ESI-MS using bench-top mass spectrometers have enabled analysis of PCR amplicons with sufficient mass accuracy that the nucleotide base composition (the A, G, C, and T count) of the PCR amplicon can be unambiguously determined [23] . The approach outlined here provides two important advantages for surveillance. First, broad-range primers targeted to highly-conserved sites within the influenza virus family that flank highly variable, information-rich regions can be used to amplify sequences from highly diverse viruses in the same assay. The measured base compositions allow identification of the viral species with a high degree of resolution. For this approach, we selected primer pairs targeting the core gene segments (PB1, PB2, PA, M, NS, and NP) that have conserved regions spanning all known influenza viruses and used the resultant base compositions to infer the influenza virus H/N types. In silico analysis of influenza virus sequences from the GenBank database showed that this approach would detect all known influenza viruses and distinguish .90% of all species and types. This overcomes the limitations of directly targeting the H and N segments, which requires specific primer pairs for each known H/N type. Further, since the H/N segments evolve rapidly, newly emerging strains might not be readily detected by the traditional approach.