Homologous recombination within each gene segment among Indonesian H5N1 isolates was extensively searched using Recombination Detection Program version 2 (RDP2) [59] , and the datasets are found to be free of homologous recombination. Putative reassortant viruses were preliminarily identified by their topological incongruity across the phylogenies of different gene segments. This was further investigated using a smaller set of Indonesian H5N1 virus isolates with full genome sequences, which included sequences of early viruses (n = 2), group 1-3 lineages (n = 12) and putative reassortant viruses (n = 10). The eight gene segment alignments were manually concatenated in the order of their length to generate a single alignment of complete genome sequences, and was further analyzed using 1) similarity plots and 2) bootscan analyses [60] implemented in SIMPLOT version 3.5.1 [61] , and 3) GARD [62] available via the Datamonkey website [63] . The hypothesis of reassortment was supported if the recombinant breakpoints were detected near the junctions where the genome segments were manually concatenated.