TABLE 2.
Deep sequencing analysis of A/H5N6 BHG inoculum and ferret tissues a
| Percentage of reads having the indicated substitution | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene segment | PB2 | PB1 | NA | ||||||||
| AA substitution | K80R | E188G | K339E | S489P | G590S | I647M | D701N | P596S | P708S | E268K | |
| MDCK2 stock | <1 b | 3.2 | 1.3 | <1 | <1 | <1 | 2.4 | 2.3 | <1 | <1 | |
| Ferret 1 (3 dpi) | Nasal turb. | <5 c | 5.5 | 7.2 | <5 | <5 | <5 | 23.7 | <5 | <5 | <5 |
| Lung | 17.1 | <5 | 41.9 | 5.9 | <5 | <5 | 35.8 | <5 | 12.3 | <5 | |
| Cerebrum | 10.9 | <5 | <5 | <5 | <5 | <5 | 35.8 | <5 | <5 | <5 | |
| Spleen | <5 | <5 | <5 | <5 | <5 | <5 | 87.2 | <5 | <5 | <5 | |
| Ferret 2 (3 dpi) | Nasal turb. | <5 | <5 | 10.0 | <5 | <5 | <5 | 29.5 | <5 | <5 | <5 |
| Lung | <5 | <5 | <5 | <5 | <5 | <5 | 43.7 | 10.9 | <5 | <5 | |
| Cerebrum | ND d | ND | ND | ND | ND | ND | ND | ND | ND | ND | |
| Spleen | <5 | <5 | 82.2 | <5 | <5 | <5 | 52.9 | <5 | <5 | 20.8 | |
| Ferret 3 (3 dpi) | Nasal turb. | <5 | <5 | 10.7 | <5 | <5 | <5 | 29.1 | <5 | <5 | <5 |
| Lung | <5 | 43.0 | 13.8 | <5 | <5 | <5 | 58.5 | <5 | <5 | <5 | |
| Cerebrum | <5 | <5 | 50.5 | <5 | <5 | <5 | 43.9 | <5 | <5 | <5 | |
| Spleen | <5 | <5 | 19.4 | <5 | <5 | <5 | 89.6 | <5 | <5 | <5 | |
| Ferret 4 (5 dpi) | Nasal turb. | ND | ND | ND | ND | ND | ND | ND | ND | ND | ND |
| Lung | <5 | <5 | 41.9 | <5 | <5 | <5 | 94.7 | <5 | <5 | <5 | |
| Cerebrum | <5 | <5 | <5 | <5 | 92.2 | 92.9 | <5 | <5 | <5 | <5 | |
| Spleen | <5 | <5 | 11.9 | <5 | <5 | <5 | 97.5 | <5 | <5 | <5 | |
| Ferret 5 (6 dpi) | Nasal turb. | <5 | <5 | 11.9 | <5 | <5 | <5 | 37.6 | <5 | <5 | <5 |
| Lung | <5 | <5 | 56.8 | <5 | <5 | <5 | 99.1 | <5 | <5 | <5 | |
| Cerebrum | <5 | <5 | <5 | <5 | <5 | <5 | 99.4 | <5 | <5 | <5 | |
| Spleen | <5 | <5 | 63.3 | <5 | <5 | <5 | 98.5 | <5 | <5 | 6.2 | |
| Ferret 6 (6 dpi) | Nasal turb. | <5 | <5 | 17.7 | <5 | <5 | <5 | 49.8 | <5 | <5 | <5 |
| Lung | <5 | <5 | 44.5 | <5 | <5 | <5 | 26.1 | <5 | <5 | <5 | |
| Cerebrum | 24.8 | <5 | 19.9 | 22.7 | <5 | <5 | 38.7 | 26.5 | 9.8 | <5 | |
| Spleen | <5 | 6.0 | 47.4 | <5 | <5 | <5 | 85.4 | <5 | <5 | <5 | |
a
Substitutions that were <5% present in the virus genome of the MDCK2 virus stock, but >5% present in two or more ferret samples are shown. In addition, two substitutions are depicted that were present in the cerebrum of ferret 4, the only sample that did not contain the D701N substitution. Nasal turb., nasal turbinates.
b
The detection limit of the MDCK2 virus stock was set at 1%.
c
The detection limit of the ferret tissues samples was set at 5%.
d
Not done, no PCR products were amplified from this material.