TABLE 4.
Amino acid differences, within each influenza A virus protein, between swine and cat H1N1pdm strains isolated in France and reference strain A/California/04/2009
| H1N1pdm strain | % aa differences with A/California/04/2009 in each viral protein (absolute no. of aa differences)a
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PB2 (759 aa) | PB1 (757 aa) | PA (716 aa) | PA-X (232 aa) | HA (564 aa) | NP (498 aa) | NA (469 aa) | M1 (252 aa) | M2 (97 aa) | NS1 (219 aa) | NS2 (121 aa) | All (4,684 aa) | |
| A/Sw/France/72-160174/2016 | 1.05 (8) | 0.4 (3) | 0.56 (4) | 1.72 (4) | 3.01 (17) | 0.8 (4) | 3.2 (15) | 1.59 (4) | 2.06 (2) | 3.2 (7) | 4.13 (5) | 1.56 (73) |
| A/Sw/France/12-160129/2016 | 1.05 (8) | 0.4 (3) | 0.70 (5) | 1.72 (4) | 2.84 (16) | 0.8 (4) | 3.2 (15) | 1.59 (4) | 1.03 (1) | 3.2 (7) | 4.13 (5) | 1.54 (72) |
| A/Sw/France/35-160233/2016 | 1.19 (9) | 0.4 (3) | 0.84 (6) | 1.72 (4) | 3.01 (17) | 1 (5) | 2.99 (14) | 1.59 (4) | 1.03 (1) | 3.65 (8) | 4.13 (5) | 1.62 (76) |
| A/Sw/France/40-160098/2016 | 0.92 (7) | 1.32 (10) | 0.98 (7) | 0.86 (2) | 3.72 (21) | 0.4 (2) | 2.56 (12) | 0.4 (1) | 2.06 (2) | 3.2 (7) | 1.65 (2) | 1.56 (73) |
| A/Sw/France/65-160089/2016 | 1.05 (8) | 1.32 (10) | 0.98 (7) | 0.86 (2) | 3.55 (20) | 0.6 (3) | 2.56 (12) | 0.4 (1) | 2.06 (2) | 3.2 (7) | 1.65 (2) | 1.58 (74) |
| A/Sw/France/40-160120/2016 | 0.53 (4) | 1.72 (13) | 0.84 (6) | 0.86 (2) | 3.37 (19) | 0.6 (3) | 2.56 (12) | 0.79 (2) | 4.12 (4) | 4.57 (10) | 2.48 (3) | 1.67 (78) |
| A/Sw/France/01-150203/2015 | 1.19 (9) | 1.19 (9) | 0.98 (7) | 0.86 (2) | 3.72 (21) | 0.4 (2) | 2.56 (12) | 0.4 (1) | 1.03 (1) | 3.2 (7) | 1.65 (2) | 1.56 (73) |
| A/Sw/France/64-150052/2015 | 0.79 (6) | 0.92 (7) | 0.70 (5) | 1.29 (3) | 3.37 (19) | 1.2 (6) | 1.92 (9) | 0.4 (1) | 2.06 (2) | 1.83 (4) | 2.48 (3) | 1.39 (65) |
| A/Sw/France/57-140136/2014 | 1.05 (8) | 0.53 (4) | 0.84 (6) | 1.29 (3) | 2.48 (14) | 0.6 (3) | 1.71 (8) | 1.19 (3) | 3.09 (3) | 2.74 (6) | 1.65 (2) | 1.28 (60) |
| A/Sw/France/35-140382/2014 | 1.05 (8) | 0.79 (6) | 0.70 (5) | 0.43 (1) | 2.30 (13) | 1.2 (6) | 1.92 (9) | 1.19 (3) | 2.06 (2) | 2.74 (6) | 1.65 (2) | 1.30 (61) |
| A/Sw/France/71-130116/2013 | 0.53 (4) | 0.53 (4) | 0.84 (6) | 1.29 (3) | 1.95 (11) | 0.6 (3) | 1.28 (6) | 1.59 (4) | 1.03 (1) | 1.83 (4) | 0.83 (1) | 1.00 (47) |
| A/Sw/France/18-120333/2012 | 0.92 (7) | 0.79 (6) | 1.12 (8) | 0.86 (2) | 3.37 (19) | 0.6 (3) | 1.28 (6) | 1.19 (3) | 3.09 (3) | 1.37 (3) | 0 (0) | 1.28 (60) |
| A/Sw/France/18-120158/2012 | 0.79 (6) | 0.79 (6) | 0.98 (7) | 0.86 (2) | 3.01 (17) | 0.6 (3) | 1.28 (6) | 1.19 (3) | 2.06 (2) | 1.37 (3) | 0 (0) | 1.17 (55) |
| A/Sw/Haute-Loire/0578/2011 | 0.53 (4) | 0.4 (3) | 0.14 (1) | 0 (0) | 2.48 (14) | 0.6 (3) | 1.71 (8) | 0.79 (2) | 0 (0) | 1.37 (3) | 0.83 (1) | 0.83 (39) |
| A/Sw/Sarthe/0255/2010 | 0.4 (3) | 0.13 (1) | 0.56 (4) | 1.29 (3) | 1.60 (9) | 0.4 (2) | 1.71 (8) | 0 (0) | 0 (0) | 0.91 (2) | 0.83 (1) | 0.70 (33) |
| A/Sw/Sarthe/0262/2010 | 0.53 (4) | 0.13 (1) | 0.42 (3) | 1.29 (3) | 1.60 (9) | 0.6 (3) | 1.71 (8) | 0 (0) | 0 (0) | 0.91 (2) | 0.83 (1) | 0.73 (34) |
| A/Sw/Cote d’Armor/110466/2010 | 0 (0) | 0.53 (4) | 0.42 (3) | 0.43 (1) | 1.06 (6) | 0 (0) | 0.43 (2) | 0 (0) | 2.06 (2) | 0.46 (1) | 0 (0) | 0.41 (19) |
| A/Cat/France/0514/2009 | 0 (0) | 0.13 (1) | 0.28 (2) | 0.43 (1) | 1.06 (6) | 0 (0) | 0.21 (1) | 0.4 (1) | 0 (0) | 1.84 (4) | 0 (0) | 0.34 (16) |
| dN/dS ratiob | 0.0779 | 0.0545 | 0.0577 | 0.0948 | 0.1494 | 0.0421 | 0.1876 | 0.1328 | 0.2171 | 0.1859 | 0.3890 | |
a
The numbers in parentheses are the absolute numbers of amino acid differences in each protein. The two proteins (or three in the case of equality) in which the most mutations were found for each strain are indicated in boldface type.
b
The dN/dS ratio, the ratio between the number of nonsynonymous substitutions (dN) and the number of synonymous substitutions (dS), was measured from averages of pairwise comparisons of all sequences selected to build the phylogenetic trees with SNAP v2.1.1.