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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)

From: Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

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
  1. aAfter bead purification, the barcoded amplicon concentration of this sample was lowest in this pool
  2. bTemplate control negative
  3. cNegative extraction control
  4. dNot detected
  5. eNot applicable
  6. The fusion protein cleavage sites did not vary between AmpSeq and previous MiSeq
  7. Note: Isolates known to have low virulence are highlighted in bold