Currently, rapid methods for influenza virus diagnosis rely on antigen-specific antibody probes [7] , or real-time reverse transcription PCR (RT-PCR) analysis of the matrix (M) gene for identification of the viral species [8, 9] followed by H and N subtype specific RT-PCR assays for determination of the viral subtypes [10, 11] . Since there are many H and N subtypes with significant intra-and inter-subtype sequence variations, these methods do not identify all H and N subtypes, nor are they likely to identify reassortants or newly emerging genetic variants. Further, none of the current surveillance methods provide information relevant to tracking antigenically novel strains that emerge each year or distinguish amongst multiple lineages of influenza viruses that can co-circulate and persist in a popula-tion [12] . Secondary genome sequence comparisons and phylogenetic analyses are necessary to fully understand the multiple lineages of viruses, recognize newly emergent influenza variants, and monitor global spread of these viruses [12, 13] . For instance, analysis of human influenza virus H3N2 sequences from 1999-2004 revealed that at least three major clades of influenza viruses were in circulation after the 2002-2003 influenza season [12] . The differences were due to multiple reassortment events though all shared a common H-gene lineage. Several similar wholegenome studies with avian influenza viruses have revealed the presence of multiple, region-specific sub-lineages of the HPAI H5N1 virus in Southeast Asia that are spreading to Europe and Africa [14] [15] [16] [17] [18] .