Table 8 Comparison of two RNA extraction methods for HA and NA classification using the portable system on sample set 3 with known AIV subtype (H7N6). Subtypes were characterised by manually mapping to a non-redundant reference gene set downloaded from GISAID. [+++] indicates the average depth of coverage is above quality threshold of > 30x. [—] indicates the average depth of coverage is below 30x and hence did not pass the quality threshold for generating a consensus sequence.
From: Development of a portable avian influenza virus characterisation system: bringing the inside-out
Sample No. | Sample Name | RNA extraction kit | Type of sample | GISAID mapping | HA average depth of coverage | NA average depth of coverage | |
|---|---|---|---|---|---|---|---|
13a | W24_02663-1 | QIAamp Viral RNA Mini kit | Oropharyngeal | H7 | N6 | +++ (109.3x) | +++ (494.5x) |
14a | W24_02665-7 | Oropharyngeal | H7 | N6 | +++ (150.4x) | +++ (625.4x) | |
15a | W24_02665-10 | Cloacal | H7 | N6 | +++ (149.6x) | +++ (524.3x) | |
16a | W24_02665-5 | Oropharyngeal | H7 | N6 | +++ (245.2x) | +++ (452.1x) | |
17a | W24_02665-4 | Cloacal | H7 | N6 | +++ (39.4x) | +++ (216.4x) | |
Number of samples successfully characterised as H7 or N6 | 5/5 (100%) | 5/5 (100%) | |||||
95% Confidence Interval | 56.55–99.49 | 47.82–100 | |||||
13b | W24_02663-1b | Zymo Quick-RNA viral kit | Oropharyngeal | H7 | N6 | +++ (419.3x) | +++ (990.9x) |
14b | W24_02665-7b | Oropharyngeal | H7 | N6 | +++ (100.8x) | +++ (537.2x) | |
15b | W24_02665-10b | Cloacal | Low read | N6 | — (28.5x) | +++ (275.9x) | |
16b | W24_02665-5b | Oropharyngeal | Low read | Low read | — (N/A) | — (N/A) | |
17b | W24_02665-4b | Cloacal | Low read | Low read | — (N/A) | — (N/A) | |
Number of samples successfully characterised as H7 or N6 | 2/5 (40%) | 3/5 (60%) | |||||
95% Confidence Interval | 5.27–85.34 | 14.66–94.73 | |||||
