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Table 4 Identification and virulence prediction of NDV genotypes in clinical samples collected during outbreaks in 2015 (run 5, 6, and 7)
| Sample ID | Miseq genotypes | MinION genotypes | ID of the MinION hit | Reads/ cluster | Consensus length | Percent identity | Fusion protein cleavage site□ |
|---|---|---|---|---|---|---|---|
| 44 | VIIi | VIIi | chicken/Pakistan/Wadana_Kasur/PNI_PF_(14F)/2015 | 200 | 734 | 100 | virulent |
| 45 |
VIIi II |
VIIi II |
chicken/Pakistan/Wadana_Kasur/PNI_PF_(14F)/2015 chicken/USA/LaSota/1946 |
28 5 |
734 733 |
99.31 96.44 |
virulent low virulent |
| 46 |
VIIi II |
VIIi II |
chicken/Pakistan/Wadana_Kasur/PNI_PF_(14F)/2015 chicken/USA/LaSota/1946 |
10 17 |
733 733 |
99.13 98.51 |
virulent low virulent |
| 47 |
VIIi II |
NDd II |
NAe chicken/USA/LaSota/1946 |
NA 139 |
NA 732 |
NA 99.32 |
NA low virulent |
| 48 |
ND
VIIi |
II
VIIi |
chicken/USA/LaSota/1946
chicken/Pakistan/Wadana_Kasur/PNI_PF_(14F)v/2015 |
200
21 |
732
733 |
99.59
99.13 |
low virulent
virulent |
| 49 |
VIIi II |
ND II |
NA chicken/USA/LaSota/1946 |
NA 200 |
NA 732 |
NA 99.32 |
NA low virulent |
| 50 | VIIi | VIIi | chicken/Pakistan/Wadana_Kasur/PNI_PF_(14F)/2015 | 113 | 734 | 100 | virulent |
| 51 | VIIi | VIIi | chicken/Pakistan/Mirpur_Khas/3EOS/2015 | 200 | 734 | 100 | virulent |
| 52a | VIIi | ND | NA | NA | NA | NA | NA |
| 53 | VIIi | VIIi | exotic Parakeets/Pakistan/Charah/Pk29/29A/2015 | 5 | 726 | 98.5 | virulent |
| 54 | NO NDV | ND | NA | NA | NA | NA | NA |
| 55 | NO NDV | ND | NA | NA | NA | NA | NA |
| 56 | NO NDV | ND | NA | NA | NA | NA | NA |
| 57 | NO NDV | ND | NA | NA | NA | NA | NA |
| 58 | VIIi | VIIi | chicken/Pakistan/Gharoo/Three_star_PF_(7G)/2015 | 8 | 729 | 99.32 | virulent |
| TNb | NA | ND | NA | NA | NA | NA | NA |
| ENc | NA | ND | NA | NA | NA | NA | NA |
