It has been previously shown that the receptor binding specificity of hemagglutinin [34] and mutations in the viral polymerase (e.g., lysine at residue 627 of PB2) [35] [36] [37] can determine viral transmissibility and replication in different host species. None of the aforementioned HA mutations which confer recognition to human-type host cell receptors [34, 38] were found in the Indonesian reassortant viruses; however, our detection of positively selected sites in the PB2 gene of the reassortant viruses could potentially reflect adaptation to mammalian hosts, and requires further investigation. In particular, amino acid changes on two positively selected sites (threonine to methionine at reside 76, glutamic acid to glycine and alanine at reside 677) were found on the internal branches of the reassortant lineage, corresponding to molecular changes during sustainable transmissions. However, some of these positively selected changes may also result from the compensatory evolution as the mix of genome segments from different strains might alter their epistatic physiochemistry [39] . Although most of the human isolates in our datasets were epidemiologically unlinked, such linkage is theoretically possible if many asymptotic or mildly manifested human infections are not reported. Recently, some evidence of subclinical or asymptotic H5N1 infection in humans has been put forward [40, 41] ; however, the ability of the viruses to transmit from these infected individuals to other susceptible individuals remains unknown.