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 |
| Patterna | [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 H3N2d | |||||||
| 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.