Table 2.
Genotype assignments of porcine influenza viruses from swine holdings in Northwest Germany, 2009 to 2011
| Isolate | Genotype assignmenta |
Genogroupb | |||||||
|---|---|---|---|---|---|---|---|---|---|
| HA | NA | PB1 | PB2 | PA | NP | M | NSc | ||
| R248/2009 | 1av | 1av | G1 | F1 | I1 | F1 | F1 | 1E-1 | 1.1 |
| WS336/2009 | 1av | 1av | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R778/2009 | 1av | 1av | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R819/2010 | 1av | 1av | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R369/2009 | 1av | 2hu | G2 | ? | I2 | F2 | F2 | 1E-2 | 2.1 |
| R1931/2010 | 1av | 2hu | G2 | ? | I2 | F2 | F2 | ? | 2 |
| R299/2009 | 1hu | 2hu | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R3394/09 | 1hu | 1av | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R757/2010 | 1hu | 2hu | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R856/2010 | 1hu | 2hu | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R1421/10 | 1hu | 2hu | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R75/11 | 1pdm | 2hu | D | C | E | ND | ND | 1A | 3 |
| R2035/11 | 1pdm | 2hu | D | C | ND | A | F3 | 1A | 3 |
| R495/2012 | 1pdm | 2hu | D | C | E | A | F3 | 1A | 3 |
| R325/2009 | 3 | 2 | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R494/2010 | 3 | 2 | G1 | F1 | I1 | F1 | ND | 1E-2 | 1 |
| R2807/2009 | 3 | 2 | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
| R83/2011 | 3 | 2 | G1 | F1 | I1 | F1 | F1 | 1E-2 | 1 |
a
Genotypes were assigned according to the results obtained with the FluGenome genotyping tool and a series of PhyML analyses of the complete open reading frame of each of the internal genome segments (see Fig. S2A to F in the supplemental material). Numbers 1 and 2 specifying some of the genotypes refer to different sister clades within the genotype, as shown in the figures in the supplemental material. ND, no data available; ?, no unambiguous classification is possible by use of the FluGenome genotyping tool (25).
b
Summary of the genotype constellation of the internal segments.
c
All NS sequences clustered with allele A.