Table 2. Real-time RT-PCR results (based on 15 µl swab fluids), GEC values and TCID50 (both based on 100 µl swab fluids) of tracheal and cloacal samples obtained from ducks after challenge with HPAIV H5N1 strain.
| Group | Cloacal swabs (dpc) | Tracheal swabs (dpc) | |||||||||||||||
| 1* | 2 | 3 | 4 | 7 | 10 | 14 | 21 | 1 | 2 | 3 | 4 | 7 | 10 | 14 | 21 | ||
| H5 | Pos. No. 1 | 0/12 | 0/12 | 0/12 | 0/12 | 0/12 | 0/12 | 0/12 | 0/12 | 3/12 | 3/12 | 2/12 | 1/12 | 0/12 | 0/12 | 0/12 | 0/12 |
| Average Ct 2 | neg | neg | neg | neg | neg | neg | neg | Neg | 34.8 | 34.07 | 34.25 | 34.24 | neg | neg | neg | neg | |
| Ct Range3 | - | - | - | - | - | - | - | - | 34.2–35.1 | 33.5–34.8 | 33.3–35.3 | - | - | - | - | - | |
| Average GEC 4 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | 1.1×103 | 1.7×103 | 1.8×103 | 1.5×103 | <1 | <1 | <1 | <1 | |
| GEC range 5 | - | - | - | - | - | - | - | - | 9.0×102–1.6×103 | 1.1×103–2.4×103 | 8.0×102–1.8×103 | - | - | - | - | - | |
| Average TCID50 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | 1.0×101 | 1.3×101 | 1.7×101 | 1.5×103 | <1 | <1 | <1 | <1 | |
| TCID50 Range | - | - | - | - | - | - | - | - | 7.0–1.3×101 | 7.0–2.0×101 | 7.0–2.6×101 | - | - | - | - | - | |
| H4 | Pos. No. | 0/12 | 0/12 | 0/12 | 0/12 | 0/11 7 | 0/11 | 0/11 | 0/11 | 12/12 | 12/12 | 12/12 | 10/12 | 4/11 | 1/11 | 0/11 | 0/11 |
| Average Ct | neg | neg | neg | neg | Neg | neg | neg | Neg | 29.84 | 29.8 | 30.67 | 32.39 | 33.99 | 34.16 | neg | neg | |
| Ct Range | - | - | - | - | - | - | - | - | 24.2–34.5 | 24.1–33 | 27–33.2 | 29.8–35.1 | 33.2–35.1 | - | - | - | |
| Average GEC | <1 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | 7.5×104 | 7.1×104 | 2.3×104 | 8.6×103 | 1.9×103 | 1.6×103 | <1 | <1 | |
| GEC Range | - | - | - | - | - | - | - | - | 1.3×103–5.8×105 | 3.1×103–6.1×105 | 2.9×103–1.1×105 | 8.9×102–2.1×104 | 8.9×102–2.8×103 | - | - | - | |
| Average TCID50 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | <1 | 1.4×103 | 1.3×103 | 3.1×102 | 7.5×101 | 1.7×101 | 1.3×101 | <1 | <1 | |
| TCID50 Range | - | - | - | - | - | - | - | - | 1.3×101–1.2×104 | 2.6×101–1.3×104 | 2.6×101–1.8×103 | 7.0×100–2.4×102 | 7.0×100–2.6×101 | - | - | - | |
| Control | Pos. No. | 4/8 | 4/8 | 6/8 | 4/8 | 1/6 6 | 0/6 | 0/6 | 0/6 | 8/8 | 8/8 | 8/8 | 8/8 | 6/6 | 4/6 | 2/6 | 1/6 |
| Average Ct | 33.91 | 32.71 | 32.15 | 32.17 | 35.2 | neg | neg | Neg | 28.12 | 27.54 | 27.83 | 29.44 | 33.26 | 33.9 | 34.45 | 34.3 | |
| Ct Range | 32.7–34.8 | 30.33–34.37 | 26.9–34.6 | 28.4–35.2 | - | - | - | - | 22.7–33.6 | 24.6–31.6 | 26.3–30.1 | 27.0–31.4 | 29.3–35.6 | 31.8–34.4 | 34.0–34.9 | - | |
| Average GEC | 2.1×103 | 5.9×103 | 2.2×104 | 1.6×104 | 8.6×102 | <1 | <1 | <1 | 2.5×105 | 1.4×105 | 8.7×104 | 3.6×104 | 5.8×103 | 2.9×103 | 1.4×103 | 1.5×103 | |
| GEC range | 1.1×103–3.9×103 | 1.8×103–1.5×104 | 1.2×103–1.1×105 | 8.2×102–4.9×104 | - | - | - | - | 2.1×103–1.4×106 | 7.3×103–4.6×105 | 1.8×104–1.7×105 | 8.2×103–1.1×105 | 6.6×102–2.8×104 | 7.3×102–6.6×103 | 1.0×103–1.7×103 | - | |
| Average TCID50 | 1.8×101 | 6.1×101 | 3.3×102 | 2.1×102 | 7.0×100 | <1 | <1 | <1 | 5.7×103 | 2.5×103 | 1.4×103 | 5.0×102 | 6.8×101 | 2.9×101 | 1.0×101 | 1.1×101 | |
| TCID50 range | 7.0×100–3.3×101 | 1.3×101–1.7×102 | 2.0×101–1.8×103 | 1.0×101–6.7×102 | - | - | - | - | 2.1×101–3.4×104 | 7.3×101–9.4×103 | 2.1×102–2.9×103 | 7.9×101–1.7×103 | 1.3×101–3.5×102 | 1.3×101–6.6×101 | 7.0×100–1.3×101 | - | |
*
The numbers indicate days post-challenge (dpc).
1
Number of positive birds as indicated by real-time RT-PCT. Ct-values<36 considered as positive.
2
Average ct-value of positive ducks per 15 µl of swab fluid.
3
The max and min range of positive ct-values.
4
Average genome equivalent copy (GEC) number of positive samples/100 µl of swab fluid.
5
Average tissue culture infectious dose (TCID50) titre/100 µl of swab fluid.
6
At this stage one of the control birds died.
7
Two ducks lost the wing tags at 5 dpc, and one of them died at 5 dpc, since their assignment to either H4 or control groups was not possible, both were excluded from calculations after day 5.