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Table 4 Results of testing selecteda Newcastle disease viruses analyzed in this study by real-time RT-PCR using different sets of primers and probes

From: Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa

Isolate name

sub/genotype

Cycle threshold (Ct) valuesb

Matrix gene testc

Fusion-specific gene testd

New pigeon-specific fusion gene primers and probe (annealing

temperature 56 °C)

pigeon/Egypt/Giza/11/2015

VI g

16.12

0

13.55

pigeon/Egypt/Helwan/44/2015

VI g

12.07

0

20.27

pigeon/Egypt/Qena/56/2015

VI g

12.27

0

15.92

pigeon/Egypt/El Fayom/73/2015

VI g

12.11

0

19.97

pigeon/Egypt/El Fayom /79/2015

VI g

14.72

0

15.57

pigeon/Egypt/El Fayom/84/2015

VI g

12.42

0

14.34

pigeon/Ukraine/Kharkiv/2301/2013

VI g

15.53

0

18.4

pigeon/Ukraine/Doneck/3/2007

VI g

12.11

0

21.62

pigeon/Pakistan/ Lahore/21A/2015

VI m

12.03

23.35

19.66

pigeon/Pakistan/Lahore/22A/2015

VI m

12.99

26.92

22.45

pigeon/Pakistan/Lahore/25A/2015

VI m

16.38

26.49

17.81

chicken/Bulgaria/Mokresh/1982

VI

13.72

24.25

21.83

chicken/Bulgaria/Dolnolinevo/1992

VI c

12.94

18.3

15.54

chicken/South Korea/9358GG/1993

VI c

12.31

26.61

24.84

quail/South Korea /88 M/1988

VI c

12.08

16.51

24.52

hawk/Mexico 663-ZM03/2008 (KC808489.1)

II

18.52

0

38.85

chicken/Belize/4224–3/08 (JN872163.1)

V b

16.23

18.95

28.02

parrot/Israel/2012/841 (KF792020.1)

VI a

16.63

26.41

32.42

chicken/KY-Israel/2013/50 (KF792019.1)

VII i

13.35

26.29

33.29

poultry/Peru/1918–03/2008 (JN800306.1)

XII

13.16

20.31

35.68

NG-707/GM.GMM.17-18 T (KC568207.1)

XIV b

12.29

17.07

32.05

chicken/DominicanRepublic499–31/2008 (JX119193.1)

XVI

17.44

17.92

0

NG-694/YB.GSH1.9-10C (KC568215.1)

XVII a

13.67

17.18

29.33

  1. a some Pakistani viruses were characterized only in Pakistan and were not submitted to SEPRL for further studies (designated in Table 1)
  2. b the pigeon-specific F-gene assay [39] failed to detect all fifteen NDV (the viruses sequenced in Pakistan were not tested)
  3. c,d primers and probes previously described by Wise et al. [24]