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Table 3 Identification and virulence prediction of NDV genotypes from 33 egg-grown samples (runs 3 and 4)

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

Sample ID Input genotypea Output genotypeb BLAST search Alignment length Percent identity Fusion protein cleavage sitec, □
1 II* II MH392212/chicken/USA/LaSota/1946 732 100 low virulent
2 II II KJ607167/LHLJ/2/goose/2006/China 734 100 low virulent
3 II II KJ607167/LHLJ/2/goose/2006/China 732 100 low virulent
4 II II EU289029/turkey/USA/VG/GA-clone_5/1987 734 99.86 low virulent
5 Ia* Ia MH392213/chicken/Australia/Queensland/V-4/10/1966 734 100 low virulent
15 Ia Ia MH392213/chicken/Australia/Queensland/V-4/10/1966 734 99.86 low virulent
16 VIId VIId KU295454/chicken/Ukraine/Lyubotyn/961/2003 735 99.46 virulent
17 II* II MH392228/poultry/Canada/Ontario/Berwick/853/1948 735 100 virulent
18 II II MH392228/poultry/Canada/Ontario/Berwick/853/1948 732 98.36 virulent
19 III* III *MH392214/chicken/India/Mukteswar/519/1940 734 100 virulent
20 IV* IV MH392215/chicken/Nigeria/Kano/1973/N52/899/1973 734 99.86 virulent
21 IV IV EU293914/Italy/Italien/1944 734 99.05 virulent
22 XIVb* XIVb KT948996/domestic_duck/Nigeria/NG-695/KG.LOM.11–16/2009 734 100 virulent
23 Va* Va MH392216/cormorant/USA/MN/92–40,140/250/1992 734 100 virulent
24 Vb* Vb MH392217/turkey/Belize/4338-4/607/2008 734 100 virulent
25 Vc* Vc MH392218/chicken/Mexico/NC/23/686/2011 733 99.73 virulent
26 VIc* VIc KY042125/chicken/Bulgaria/Dolno_Linevo/1992 734 100 virulent
27 VIm* VIm KX236101/pigeon/Pakistan/Lahore/25A/2015 734 100 virulent
28 VIIj* VIIj MH392219/chicken/Egypt/Sohag/18/1020/2014 734 100 virulent
29 VIIe VIIe KJ782375/goose/China/GD-QY/1997 734 97.82 virulent
30 VIIi* VIIi KX496962/ wild_pigeon/Pakistan/Lahore/20A/996//2015 734 100 virulent
31 IX* IX MH392220/poultry/China/04-23/C12/647/2004 734 100 virulent
32 IX IX MH392220/poultry/China/04–23/C12/647/2004 734 99.86 virulent
33 Xb* Xb MH392221/mallard/USA/MN/99–376/163/1999 734 100 low virulent
34 Xa* Xa GQ288378/ northern_pintail/USA/OH/87–486/1987 734 100 low virulent
35 XIIa* XIIa JN800306/poultry/Peru/1918-03/2008 734 100 virulent
36 XIIIb* XIIIb MH392222/chicken/Pakistan/SPVC/Karachi/27/558/2007 734 99.18 virulent
37d VIc/XIIIb* XIIIb MH392223/chicken/Pakistan/SPVC/Karachi/33/556-XIII/2007 734 99.46 virulent
38 XIVb* XIVb MH392225/chicken/Nigeria/KD/TW/03 T/N45/720/2009 734 100 virulent
39 XVI* XVI MH392226/chicken/Dominican_Republic/FO/499–31/505/2008 734 100 virulent
40 XVIIa* XVIIa KY171995/VRD124/06/N11/867/chicken/2006/Nigeria 734 100 virulent
41 XVII* XVII KU058680/903/domestic_duck/Nigeria/KUDU-113/1992 734 100 virulent
42 XVIIIb* XVIIIb MH392227/chicken/Nigeria/OOT/4/1/N69/914/2009 734 100 virulent
  1. aInput genotype was determined with MiSeq sequencing (*) or previous Sanger sequencing
  2. bDetermined by MinION sequencing
  3. cF protein cleavage sites of virulent NDV genotypes contains more than 3 basic amino acids [(112(R/K)-R-(Q/K/R)-(R/K)-R-F117)] and low virulent NDV genotypes has monobasic amino acids [(112(G/E)-(R/K)-Q-(G/E)-R-L117)]
  4. dIllumina Miseq detected two NDV genotypes
  5. *Matching MiSeq result from same isolate
  6. The fusion protein cleavage sites did not vary between AmpSeq and either previous Sanger or previous MiSeq
  7. Note: Isolates known to have low virulence are highlighted in bold