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 siteâ–¡ |
|---|---|---|---|---|---|---|---|
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 |