Table 3.
Comparison of RT-qPCR assays
| Sample description | RT-qPCR assays | ||||
|---|---|---|---|---|---|
| AI type A (generic) | H5 duplex (generic H5) | H5 2.3.4.4-BHQ1 | H5 2.3.4.4-MGB | AI N6 | |
| A/shearwater/Australia/75(H5N3) | 22.9 | 25.3 | U | U | U |
| A/Chicken/Myanmar/295/2010(H5N1); clade 2.3.2.1 | 20.8 | 22.8 | U | U | U |
| A/Duck/VN/2064/13(H5N1); clade 2.3.2.1 | 19.8 | 20.8 | U | U | U |
| A/Swallow/Vietnam/4696/2013(H5N1); clade 2.3.2.1 | 17.7 | 19.3 | U | U | U |
| A/Ch/LaoPDR/LK001/2010(H5N1); clade 2.3.4.1 | 17.6 | 21.3 | U | U | U |
| A/Ch/LaoPDR/LK002/2010(H5N1); clade 2.3.4.1 | 17.7 | 21.6 | U | U | U |
| A/Duck/VN/4804/13(H5N1); clade 1.1 | 22.7 | 24.2 | 28.8 | U | 44.8/U |
| A/Chicken/Indonesia/Subang/2007(H5N1); clade 2.1.3 | 23.2 | 24.6 | 30.2 | U | U |
| A/Chicken/Laos/Xaythani/26/2006(H5N1); clade 2.3.4 | 24.0 | 27.4 | 31.7 | U | U |
| A/Avian/Myanmar/182/2010(H5N1); clade 2.3.4.2 | 20.7 | 23.5 | 26.8 | U | 42.3/U |
| A/duck/Lao/XBY004/2014(H5N6); clade 2.3.4.4 | 20.8 | 24.9 | 22.7 | 18.2 | 22.1 |
| A/MALLARD/GURJEV/244/82(H14N6) | 21.5 | U | U | U | 23.0 |
| A/silver gull/Tasmania/349/2006(H13N6) | 27.1 | U | U | U | U |
| A/gull/Maryland/704/1977(H13N6) | 15.7 | U | U | U | 40.2/U |
| No template (negative control) | U | U | U | U | U |
AI reference assays and candidate clade-specific and N6 assays were compared using selected AI strains.
U = Undetected. Results are displayed as averaged CT values of two replicates. Assay results considered positive are indicated by CT values in bold. Strain A/duck/Lao/XBY004/2014(H5N6) representative of proposed clade 2.3.4.4 is indicated in bold.