TABLE 3.

Gene sequences analyzed and probes designed for each of the eight segments and the HA and NA subtypes of influenza A virus genome

Gene	No. of sequencesa	No. of cladesb	Min identity within the clades (%)c	No. of probes selectedd
PB2	926	3	84	54
PB1	897	4	85	40
PA	910	5	84	57
H1	206	4	85	21
H2	41	2	85	10
H3	379	5	86	24
H4	18	4	87	14
H5	189	2	87	11
H6	45	3	87	12
H7	77	4	89	15
H8	5	1	>90	4
H9	61	3	87	18
H10	8	2	>90	7
H11	9	2	>90	6
H12	8	2	>90	6
H13	3	2	>90	6
H14	2	1	>90	4
H15	7	1	>90	4
H16	8	4	>90	12
NP	906	5	85	66
N1	360	4	85	28
N2	351	2	82	27
N3	40	3	87	13
N4	10	3	89	10
N5	14	2	>90	6
N6	19	2	87	7
N7	28	3	87	10
N8	207	4	86	16
N9	14	2	>90	6
M	1,001	2	86	13
NS	1,146	2	81	17

^aFull-gene sequences available in GenBank before July 2010 or reported in reference 9.

^bMonophyletic groups in each constructed phylogenetic tree.

^cNucleotide sequence identity among the gene sequences comprising each clade.

^dNumber of probes that recognize all sequences within a clade at least three times.