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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