To further investigate the putative reassortant human and cat viruses, a selected dataset (n = 24) of manually concatenated full genomes (Figure 2A ; see Methods) of Indonesian H5N1 HPAI viruses were analyzed using more sophisticated analysis methods, including similarity plots, bootscan analyses and GARD analyses (genetic algorithm for recombination detection). In the similarity and bootscan plots ( Figure 2B and 2C), the putative reassortants (represented by a consensus sequence) showed a high degree of sequence similarity and phylogenetic clustering with the group 3 strain A/Indonesia/6/05 in the MP and PB1 segments, but not in other genomic regions, where they were more similar to the consensus sequence of group 2 viruses ( Figure 2B and 2C). Moreover, GARD detected two well-supported breakpoints near the boundaries of MP and PB1 segments in the concatenated genomes ( Figure 2D ), suggesting that the phylogenetic incongruence was significant between the three regions. In summary, all three analyses agreed that the newly reassortant strains had arisen from acquiring PB1 and MP genome segments from the group 3 lineage and the remaining segments from the group 2 lineage.