Table 1. Criteria used for clade designation.

No.	Criteria
1	Maintain previously designated clade numbers where possible (i.e., clade 2.2 remains 2.2 and clade 1 remains 1)
2	New clade designations based on phylogenetic tree topology derived from all available sequences (the large tree)
	H5N1 progenitors (closest to Gs/Guangdong/1/96) re-designated as clade 0
	Subsequent clades numbered starting from clade 3 (i.e., clades 3–9)
	Clades designated by presence of a distinct common node shared by at least 4 isolates (in a monophyletic group)
	Additional branches designated as a single clade evolves into more than one distinct lineage (i.e., clade 2.2 or clade 2.3.1; based on sharing of a common node and monophyletic grouping)
3	Average percentage pairwise distances between and within clades (using Kimura 2-parameter)
	Distinct clades should have >1.5% average distances between other clades
	Distinct clades should have <1.5% average distances within the clade (may be slightly higher in clades with highly evolved outliers; i.e., Ck/Shanxi/2/2006 in clade 7)
4	Bootstrap (based on 1,000 neighbor-joining bootstrap replicates) >60% bootstrap value at clade-defining node