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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]