It is important to recognize that our phylogenetic groupings (groups 1, 2, and 3) of Indonesian H5N1 viruses ( Figure 1 and Table S6 ) are slightly different to those by Smith and coworkers [10] who did not require the same level of clustering support for each group, leading to the inclusion of earlier viruses (predominantly 2003-2004) . We chose to be conservative, and did not include poorly supported branches (e.g., earlier viruses) in our viral group definition. Therefore, we did not define a group corresponding to the group B of Smith et al., because most of group B taxa are earlier viruses. Groups 1 and 2 in this study correspond to groups C and A defined by Smith et al. respectively, plus some more recent viruses. Smith did not report group 3, because the sequences were unavailable at that time.