Supplementary Table 1. Primers used in the study. Primer Position (bp) Upstream primer (5 3 ) Downstream primer (5 3 ) Expected (bp) size 1 1 278 ACCAAACAGAGAATCTGTGAG CAGCAATCCGAAGGCAGAATAC 299 2 48 946 GAAATCGTACGGGTAGAAGGTG GGGCTGATGTCTTGGTATTG 918 3 788 1558 CATTCTCTGGCAGTCCGCATTT GTCGGTGTCGTTGTCCTGAGAT 792 4 1192 2006 ATCATTCTGGAGACTCGGGGTGG CTTTGTCTTGCCTTGTGGGATT 836 5-1 1829 2930 TCAGAGATCAGGACGAGCCAC GTCCTTCTCCACTCCCATATCA 1123 5-2 1773 3042 AACGATCCGTGCAGACCCCAG GCGCTTGACCTTCCTGATCTC 1290 6 2785 3895 TCGCTCGATCCCACCCAGTTTT CATTGAGCGCGAGGTTGTATAGG 1133 7 3768 4909 AAGCACCCGAGAAGATCCCTG AGAGCTACACTGCCGATAATG 1162 8 4753 5622 TATGCCCAAGGACAAAGAGG CGCTCAGGCAGGAATAAATAC 890 9 5435 6460 AACAATATGCGTGCCACCTACC CCATGTGTTCTTTGCTTCTCT 1046 10 6150 7379 AGACCTTGCTATGGCTTGG TTGAGCCCTCCGTAAACT 1230 11 6918 7974 TACAGGATCAGGTTGCACTCGG TATGCTGCCTTGGTACTGCTT 1077 12 7769 8761 GTAGTGTCCCTTGTCAGGCATC CACAGCTTGGCGAACAGGTCT 1013 13 8168 9384 ATGGCTGGGAGGATGATGCTG AGGCGATTGCGTGAGTTACTG 1237 14-1 9240 10394 TTGTAGCATTGATGGAGGG ATGGCATGGGCGAATAGCTT 1129 14-2 9238 10344 TGTCGTAGCATTGATGGAGGG CATGGGCGAATAGCTTAACTG 1127 15 10108 11421 CCAGATTGCACCTTTTTTCC TCTGCCTCATTGTCCTCTGTGT 1335 16 11191 12326 GACTACTGCTTTTGCGGAG GGCCCAGGAGCATAATTTGTTG 1157 17 12033 13376 AGGCAGCACTAAGGGCATC TGGCATCTCTGTCCTCTCGTTC 1365
18 12660 13747 GCCAATCCGTGGTTTCTTATG AAGACTCATGATGGCTCCG 1088 19 13568 14597 GAGCACACATTGCCGAACCCAG TCAGCCTCCATGTAAATCAC 1049 20 14566 15173 TGCCAGCCACATTGACACAG ACCAAACAAAGATTTGGTGA 627
Supplementary Table 2. NDV strains and their accession numbers used for phylogenetic analysis. Virus strains Year Country Host Genotype Accession number Chicken/N. Ireland/Ulster/67 1967 U.K. Chicken I AY562991 D3 2007 China Mallard I HM063422 B1 2000 U.S. Chicken II AF309418 LaSota 1999 Netherlands Chicken II AF077761 HX01 2009 China Swine II JF795531 JS/9/05/Go 2008 China Chicken III FJ430160 Mukteswar 2006 China Avian III EF201805 Herts/33 1933 U.K. Chicken IV AY741404 Italien 1944 IV EU293914 NDV-P05 2005 Mexico Chicken V HM117720 Iraq AG68 1998 Iraq Fowl VIa AF001108 Kuwait 256 1998 Kuwait Fowl VIa AF001109 Pi/CH/LGD/110208 2011 China Pigeon VIb JX486550 Pi/CH/LGD/110945 2011 China Pigeon VIb JX486555 Pi/CH/LGD/110947 2011 China Pigeon VIb JX486556 Pi/CH/LHLJ/110813 2011 China Pigeon VIb JX486553 Pi/CH/LHLJ/110822 2011 China Pigeon VIb JX486554 Pi/CH/LLN/110713 2011 China Pigeon VIb JX486552 AV324/96 1996 Ireland Pigeon VIb GQ429292 PPMV-1/Belgium/05-01824/2005 2005 Belgium Pigeon VIb JX901119 PPMV-1/Belgium/07-04943/2007 2007 Belgium Pigeon VIb JX901121 NDV05-027 2005 China Pigeon VIb DQ439884 ND/05-028 2005 China Pigeon VIb GQ338311 NDV05-029 2005 China Pigeon VIb FJ766528 P4 2003 China Wild pigeon VIb HM063425 PPMV-1/Belgium/11-07574/2011 2011 Belgium Pigeon VIb JX901122 PPMV-1/Belgium/11-08304/2011 2011 Belgium Pigeon VIb JX901123 PPMV-1/Belgium/11-09620/2011 2011 Belgium Pigeon VIb JX901124 IT-227/82 1982 Italy Pigeon VIb AJ880277 PPMV-1/Maryland/1984 1984 U.S. Pigeon VIb FJ410147 PPMV-1/New York/1984 1984 U.S. Pigeon VIb FJ410145 PPMV-1/pigeon/IE/806/04 2004 Ireland Pigeon VIb JN986839 W4 2005 China White-breasted VIb HM063423 waterhen STP96 2006 China Pigeon VIb DQ417113 PHKPI86358 1986 Hong Kong Pigeon VIbiia AY471856
PUKPI84259 1984 U.K. Pigeon VIbiia AY471847 PUKPI86239 1986 U.K. Pigeon VIbiia AY471854 PUKPI89124 1989 U.K. Pigeon VIbiia AY175768 PUKPI89226 1989 U.K. Pigeon VIbiia AY471836 PATPI96335 1996 Austria Pigeon VIbiib AY471844 PITDO00289 2000 Italy Pigeon VIbiib AY471846 PITPH95294 1995 Italy Pigeon VIbiib AY471839 PUKPH96441 1996 U.K. Pigeon VIbiic AY471818 PUKPI88224 1988 U.K. Pigeon VIbiic AY471830 PUKPI90126 1990 U.K. Pigeon VIbiic AY175769 PUKPI90221 1990 U.K. Pigeon VIbiic AY471801 PUKPI90222 1990 U.K. Pigeon VIbiic AY471802 PUKPI90275 1990 U.K. Pigeon VIbiic AY471825 PUKPI90397 1990 U.K. Pigeon VIbiic AY471810 PUKPI93399 1993 U.K. Pigeon VIbiic AY471813 Ch/98-1 1998 China Pigeon VIbiid AF358785 PUKPI88286 1988 U.K. Pigeon VIbiid AY471793 PUKPI89228 1989 U.K. Pigeon VIbiid AY471790 PUKPI94400 1994 U.K. Pigeon VIbiie AY471764 PUKPI98355 1998 U.K. Pigeon VIbiie AY471766 Dove/Italy/2736/00 2000 Italy Dove VIbiie GQ429293 PATPI97345 1997 Austria Pigeon VIbiif AY471778 PIEPI02436 2002 Ireland Pigeon VIbiif AY471737 PPTPI98388 1998 Portugal Pigeon VIbiif AY471776 PPTPI01315 2001 Portugal Pigeon VIbiif AY471774 PPTPI99393 1999 Portugal Pigeon VIbiif AY471777 PPTPI99395 1999 Portugal Pigeon VIbiif AY471775 PUKPI01421 2001 U.K. Pigeon VIbiif AY471736 PUKPI02423 2002 U.K. Pigeon VIbiif AY471730 PUKPI02428 2002 U.K. Pigeon VIbiif AY471725 PUKPI02431 2002 U.K. Pigeon VIbiif AY471755 PUKPI99131 1999 U.K. Pigeon VIbiif AY175773 H-310/82 1982 Hungary Fowl VIc AF001112 A-24/96 1996 Austria Fowl VId AF001133 BBGPI95039 1995 Bulgaria Pigeon VId AY135742 DK-1/95 1995 Denmark Fowl VId AF001129 Wawr VIe Z12111 XJ-1/91 1991 China Chicken VIf AF458020 XJ-3/97 1997 China Chicken VIf AF458019 ZhJ-2/86 1986 China Chicken VIg AF458016 Sh-2/98 1998 China Chicken VIg AF458017
BHKPI89172 1989 Hong Kong Pigeon VIi AY175673 Pigeon/China/Shaanxi/g10/2006 2006 China Pigeon VIi JX855040 Chicken/China/SDLY01/2010 2010 China Chicken VII JN400897 Chicken/China/SD04/2011 2011 China Chicken VII JQ015296 Chicken/TC/9/2011 2011 China Chicken VII KC461214 Duck/China/SD03/2009 2009 China Duck VII JN400895 Egret/China/Guangxi/2011 2011 China Egret VII JX193074 GD450/2011 2011 China Goose VII KC152048 GD1003/2010 2010 China Goose VII KC152049 GM 2006 China Chicken VII DQ486859 Pheasant/MM20/Pakistan/2011 2011 Pakistan Pheasant VII JX854452 AF2240-I 2010 Malaysia Avian VIII JX012096 QH4 1985 China Chicken VIII FJ751919 F48E8 1946 China Chicken IX FJ436302 MG-1992 1992 Madagascar Chicken XI HQ266603 MG-725/08 2008 Madagascar Chicken XI HQ266602 9a5b 2009 Japan Waterfowl Class I AB524406 Ch-ZJ-10-03 2010 China Chicken embryo Class I JN688863 D-AH-10-02 2010 China Chicken Class I JN688864