Table 1. Results of the evolutionary analysis of the hemagglutinin (HA) protein of the H1av and the H1pdm09 lineages obtained in the Danish swine influenza A virus (swIAV) surveillance 2011–2018, including division of the H1pdm09 sequences into the ones located in and outside the Sw-L cluster.
The best-fitting substitution model M1a and M2a indicates neutral/negative selection and positive selection, respectively. The global ω ratio indicates average dN/dS ratio of the sequences. The positions in which positive selection occurred are given, and the positions are numbered from the first methionine. The TempEst correlation coefficient indicates how well the sequences are accumulating nucleotide changes proportionally to elapsed time. The substitution rate was calculated based on the length of the HA gene (1701nts) and represents the number of substitutions for the entire gene per year.
| H1pdm n = 48 |
H1pdm09 Sw-L cluster n = 30 |
H1pdm09 outside the Sw-L cluster n = 18 |
H1av n = 78 |
|
|---|---|---|---|---|
| Probability of M1a/M2a (%) | 0.1/99.9 | 91/9 | 0.1/99.9 | 0.1/99.9 |
| Global ω ratio | 0.27 | 0.25 | 0.26 | 0.19 |
| Positions with positive selection (antigenic site/RBS) | 142K (Sa), 154P (Ca1/RBS), 172E (Sa), 174V (Sa), 200A (RBS), 202S, 204D (RBS), 206R (Sb/RBS), 207T (Sb/RBS) | - | 142K (Sa), 154P, 159K (Ca1/RBS), 160G, 172E (Sa), 178L (Sa), 179N (Sa), 200A (RBS), 202S, 203D (Sb/RBS), 204D (RBS), 206R (Sb/RBS), 207T (Sb/RBS), 338I, 391G | 142Q (Sa), 159K (Ca1/RBS), 172R (Sa), 173E (Sb) |
| TempEst correlation coefficient | 0.87 | 0.85 | 0.93 | 0.56 |
| Substitution rate | 4.9 × 10−3 per site per year = 8.3 nt substitutions per year |
4.6 × 10−3 per site per year = 7.8 nt substitutions per year |
6.1 × 10−3 per site per year = 10.4 nt substitutions per year |
4.6 × 10−3 per site per year = 7.8 nt substitutions per year |