Table 1. Number of clones sequenced from inoculum and from swabs collected at each time point from turkeys infected with Italy/1279 H7N1 virus.
| Swabs | Number of clones sequenced at each time point (number of birds sampled) | Total number of clones analysed | Clones with cleavage site identical to LPAI virus | ||||||||
| Days pi* | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ||
| Inoculum | 180 | all | |||||||||
| Buccal | 190 (9) | 189 (2) | 1191 (18) | 134 (8) | 86 (1) | 159 (6) | 182 (1) | 88 (1) | 769 (15) | 2988 | all |
| Cloacal | – | – | 319 (4) | 43 (3) | – | 16 (1) | – | – | 226 (7) | 604 | all |
Clones containing HA gene cDNA amplicons made from selected swab samples (described in tables S1, S2 and [28]) were analysed using Sanger sequencing ABI 3730 XL DNA analyser.
*
Days post infection.