Table 1. Distribution of 222 polymorphisms in 10 paired upper and lower respiratory tract samples and 3 lower respiratory samples analyzed with Sanger and next generation sequencing (NGS).
| # | Strain | Sample | FluA load (copies/ml) | No. reads | 222 polymorphisms | No. variants | |
|---|---|---|---|---|---|---|---|
| NGS (%) | Sanger | ||||||
| 1 | A/Pavia/11/2015 | NS | negative | NA | - | - | - |
| BAL | 3.8x107 | 7566 | D (34.59), N (38.53), G (26.88) | D/N/G | 30 | ||
| 2 | A/Pavia/15/2015 | NS | 5.9x104 | 3264 | D (100) | D | 7 |
| BAL | 1.9x105 | 4725 | D (100) | D | 17 | ||
| 3 | A/Pavia/42/2015 | NS | 1.8x102 | ND LVL | - | - | - |
| BAL | 1.2x108 | 5593 | D (38.98), N (58.1) A (2.91) | D/N | 12 | ||
| 4 | A/Pavia/171/2015 | NS | 5.2x105 | 6493 | D (100) | D | 8 |
| BAL | 6.4x108 | 5993 | D (100) | D | 16 | ||
| 5 | A/Pavia/180/2015 | NS | 1.7x108 | 5155 | D (100) | D | 11 |
| BAL | 2.9x105 | 6463 | D (100) | D | 11 | ||
| 6 | A/Pavia/24/2015 | NS | 7.1x103 | ND, LVL | - | - | - |
| Brasp | 1.3x106 | 7969 | D (61.06), N (21.23), G (17.71) | D/N/G | 21 | ||
| 7 | A/Pavia/160/2015 | NS | negative | NA | - | D | - |
| BAL | 5.3x105 | 7092 | D (100) | D | 8 | ||
| 8 | A/Pavia/271/2015 | NS | 1.0x109 | 6818 | D (100) | D | 4 |
| Brasp | 2.7x109 | 6847 | D (100) | D | 16 | ||
| 9 | A/Pavia/247/2015 | NS | 4.5x102 | ND, LVL | - | - | - |
| Brasp | 9.0x104 | 4798 | D (100) | D | 3 | ||
| 10 | A/Pavia/55/2015 | NS | 1.1x104 | NA | - | - | - |
| Brasp | 1.7x106 | 5473 | D (34.04), N (65.96) | D/N | 18 | ||
| 11 | A/Pavia/25/2015 | BAL | 5.3x104 | 428 | D (100) | D | 2 |
| 12 | A/Pavia/196/2015 | BAL | 2.8x106 | 4895 | D (100) | D | 7 |
| 13 | A/Pavia/267/2015 | BAL | 1.8x102 | ND, LVL | - | - | - |
NS, nasal swab; BAL, bronchoalveolar lavage; Brasp, broncho aspirate; NA, not applicable, ND, not done; LVL, low viral load