Detecting transmission and reassortment events for influenza A viruses with genotype profile method

Table 1 Genotype profiles for human, swine and avian influenza A viruses

Hosts	Human		Swine			Avian
Group	Classic human	2009 S-OIV	Classic swine	Eurasian avian-like	Triple reassortant	Waterfowl	Domestic poultry
Pattern^a	[A, ?, A/B, 4, A, 6, B, 1A]	[C, D, E, 1A, A, 1F, F, 1A]	[B, A, C, 1A, A, 1B, A, 1A]	[F, G, I, 4, F, 6, F, 1E]	[C, D, E, 4, A, 6, A, 1A]	[C, F, E/H, 4, H, 6, E, 1D/2B]	[K/G, G, D/E, 4, F, 6, F, 1E/1F/2A]
H1N1	[A, A, A, 1B, A, 1A, B, 1A]^c	[C, D, E, 1A, A, 1F, F, 1A]	[B, A, C, 1A, A, 1B, A, 1A]	[F, G, I, 1C, F, 1F, F, 1E]	[C, D, E, 1A, A, 1B, A, 1A]	[C, F, E/H, 1D, H, 1E, E, 1D/2B]
	[A, A, B, 1B, A, 1A, B, 1A]^c
H1N2				[F, G, I, 1B, F, 2A, F, 1E]	[C, D, E, 1A/1B, A, 2A, A, 1A]
H2N2	[A, E, B, 2A, A, 2A, B, 1A]
H3N2	[A, D, B, 3A, A, 2A, B, 1A]			[F, G, I, 3A, F, 2A, F, 1E]	[C, D, E, 3A, A, 2A, A, 1A]	[C, F, H, 3C, H, 2D/2G, E, 1D]
	Swine H3N2^d
Other subtypes						[C, F, E/H, 4, H, 6, E, 1D/2B]^e	[K/G, G, D/E, 4, F, 6, F, 1E/1F/2A]^e
1 (PB2)^b	A	C	B	F	C	C	K/G
2 (PB1)	A/D/E	D	A	G	D	F	G
3 (PA)	A/B	E	C	I	E	E/H	D/E
4 (HA)	1B/2A/3A	1A	1A	1B/1C/3A	1A/1B/3A
5 (NP)	A	A	A	F	A	H	F
6 (NA)	1A/2A	1F	1B	1F/2A	1B/2A
7 (MP)	B	F	A	F	A	E	F
8 (NS)	1A	1A	1A	1E	1A	1D/2B	1E/1F/2A

^aPattern: the patterns for the lineages of the gene segments. '?': the pattern in the gene segment is ambiguous; 4/6: similar as the symbol '?' and refers to fourth (HA)/sixth (NA) segment; 'A/B': both A and B are conserved in the gene segment.
^b1~8: gene segments ordered from PB2 to NS. Characters are conserved lineages in the segments while first three lineages underlined are defined as 'genetic codes'.
^c[A, A, A, 1B, A, 1A, B, 1A] is the genotype for H1N1 subtype dominated in 1930s and 1940s while [A, A, B, 1B, A, 1A, B, 1A] dominated from 1947, reappeared in 1977 and was present up to date.
^dThe genotype of swine subtype H3N2 is listed here due to its entirely transmitting from human H3N2.
^eAvian have various different subtypes that are listed in Additional file 1, Table S1.

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