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H9 China

76. ▲ Duck/Vietnam/OIE-3060/2011 (H6N2). 81. ▲ Duck/Vietnam/OIE-3247/2011 (H6N2). PB2. ▲ Duck/Vietnam/OIE-3141/2011 (H6N2). ▲ Duck/Vietnam/OIE-3021/2011 (H6N2). ▲ Duck/Vietnam/OIE-3406/2012 (H3N8). ▲ Duck/Vietnam/OIE-3426/2012 (H3N8). ● Duck/Vietnam/OIE-2530/2011 (H4N2).

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H9 China

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  1. 76 • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) 81 • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) PB2 • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) • ● Duck/Vietnam/OIE-2530/2011 (H4N2) • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 98 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) • ▲ Duck/Vietnam/OIE-0178/2012(H7N1) • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) 74 84 • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) • ● Duck/Vietnam/OIE-1287/2012(H5N1) JX8264-like 99 • ● Duck/Vietnam/OIE-2202/2012 (H5N1) Mallard/Jiangxi/8264/2004 (H6N2) • ● Duck/Vietnam/OIE-2747/2012 (H3N8) • ● Duck/Vietnam/OIE-1218/2012(H3N6) 94 • ● Duck/Vietnam/OIE-1212/2012(H3N2) Duck/Hunan/491/2005 (H6N2) • ▲ Duck/Vietnam/OIE-3321/2011 (H6N2) • ● Duck/Vietnam/OIE-2577/2011 (H3N8) 59 Vietnam/1203/2004 (H5N1) • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) • ▲ Duck/Vietnam/OIE-3354/2011(H5N1) 71 • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) 69 • ▲ Muscovy duck/Vietnam/OIE-0043/2012(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3312/2011(H5N1) 75 • ▲ Duck/Vietnam/OIE-3002/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3012/2011(H5N1) 98 • ▲ Muscovy duck/Vietnam/OIE-3314/2011(H5N1) Chicken/Beijing/1/1994(H9N2) Duck/Hong Kong/Y280/1997(H9N2) 99 Duck/Hong Kong/Y439/1997(H9N2) H9 China • ▲ Chicken/Vietnam/OIE-0056/2012(H9N2) • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) 79 98 • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) Vietnam I • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) 99 98 • ▲ Duck/Vietnam/OIE-0033/2012(H6N2) • ▲ Duck/Vietnam/OIE-0483/2012(H10N7) • ▲ Duck/Vietnam/OIE-0068/2012(H11N3) 64 68 • ▲ Duck/Vietnam/OIE-0155/2012(H4N6) Goose/Guangdong/1/1996(H5N1) Wild bird • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) 90 • ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) • ● Chicken/Vietnam/OIE-1611/2012(H9N2) 99 • ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 90 • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) H6 Group III • ● Duck/Vietnam/OIE-2749/2012 (H9N8) Duck/Eastern China/51/2002 (H6N2) Duck/Hunan/573/2002 (H6N2) 81 • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) • ● Duck/Vietnam/OIE-2533/2011 (H5N1) 69 • ● Duck/Vietnam/OIE-1213/2012(H6N6) 91 • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) H6 Group Ⅰ • ● Duck/Vietnam/OIE-2562/2011(H6N6) 96 Duck/Hunan/908/2005 (H6N2) Duck/Shantou/339/2000 (H6N2) 61 Wild Duck/Shantou/2853/2003 (H6N2) Quail/Hong Kong/G1/1997(H9N2) 99 Teal/Hong Kong/W312/1997 (H6N1) • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) 92 • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) Vietnam II • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) 89 • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) 83 81 • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) 0.02 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 1 Okamatsuet al.

  2. 88 • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 73 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) • ▲ Duck/Vietnam/OIE-0033/2012(H6N2) PB1 • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) • ▲ Duck/Vietnam/OIE-0068/2012(H11N3) • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) • ▲ Duck/Vietnam/OIE-0483/2012(H10N7) • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) • ▲ Duck/Vietnam/OIE-0178/2012(H7N1) Vietnam • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) 76 • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) 64 • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) • ▲ Duck/Vietnam/OIE-0155/2012(H4N6) 76 • ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) • ● Chicken/Vietnam/OIE-1611/2012(H9N2) • ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 82 • ▲ Chicken/Vietnam/OIE-0056/2012(H9N2) • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) • ● Duck/Vietnam/OIE-1287/2012(H5N1) • ● Duck/Vietnam/OIE-2202/2012 (H5N1) • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) Vietnam/1203/2004 (H5N1) 89 H5N1 Vietnam • ▲ Muscovy duck/Vietnam/OIE-3312/2011(H5N1) 60 • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3002/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3012/2011(H5N1) 64 • ▲ Muscovy duck/Vietnam/OIE-0043/2012(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3314/2011(H5N1) • ▲ Duck/Vietnam/OIE-3354/2011(H5N1) • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) 74 • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) 70 • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) Hunan491 -like • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) • ● Duck/Vietnam/OIE-2533/2011 (H5N1) • ● Duck/Vietnam/OIE-1218/2012(H3N6) 69 83 99 • ● Duck/Vietnam/OIE-1212/2012(H3N2) • ● Duck/Vietnam/OIE-2747/2012 (H3N8) 89 • ● Duck/Vietnam/OIE-2749/2012 (H9N8) • ● Duck/Vietnam/OIE-2530/2011 (H4N2) • Duck/Hunan/491/2005 (H6N2) 70 Mallard/Jiangxi/8264/2004 (H6N2) JX8264-like 65 • ● Duck/Vietnam/OIE-2577/2011 (H3N8) Duck/Eastern China/51/2002 (H6N2) • ▲Duck/Vietnam/OIE-3321/2011 (H6N2) Goose/Guangdong/1/1996(H5N1) 52 Duck/Hunan/908/2005 (H6N2) Duck/Hunan/573/2002(H6N2) Quail/Hong Kong/G1/1997(H9N2) Teal/Hong Kong/W312/1997 (H6N1) 99 Chicken/Beijing/1/1994 (H9N2) 57 Duck/Hong Kong/Y439/1997(H9N2) Duck/Hong Kong/Y280/1997(H9N2) Duck/Shantou/339/2000 (H6N2) 54 90 H6 Group Ⅰ Wild Duck/Shantou/2853/2003 (H6N2) 90 • ● Duck/Vietnam/OIE-1213/2012(H6N6) 52 • ● Duck/Vietnam/OIE-2562/2011 (H6N6) 99 0.01 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 2 Okamatsuet al.

  3. ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) PA • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) 63 • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) • ▲ Duck/Vietnam/OIE-0483/2012(H10N7) 98 • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 50 95 60 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) • ▲ Duck/Vietnam/OIE-0033/2012(H6N2) Vietnam 87 • ▲ Duck/Vietnam/OIE-0068/2012(H11N3) • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) • ▲ Duck/Vietnam/OIE-0155/2012(H4N6) • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) 89 • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) 58 60 64 • ▲ Duck/Vietnam/OIE-0178/2012(H7N1) 57 • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) 58 • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) Duck/Hong Kong/Y439/1997(H9N2) Vietnam/1203/2004 (H5N1) • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) 85 • ▲ Duck/Vietnam/OIE-3354/2011(H5N1) 94 • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) 75 • ▲ Muscovy duck/Vietnam/OIE-0043/2012(H5N1) 63 H5N1 Vietnam • ▲ Muscovy duck/Vietnam/OIE-3012/2011(H5N1) 74 • ▲ Muscovy duck/Vietnam/OIE-3314/2011(H5N1) • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) 68 • ▲ Duck/Vietnam/OIE-3002/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3312/2011(H5N1) • ● Duck/Vietnam/OIE-2533/2011 (H5N1) • ● Duck/Vietnam/OIE-1287/2012(H5N1) 99 • ● Duck/Vietnam/OIE-2202/2012 (H5N1) 99 • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) Duck/Hunan/491/2005 (H6N2) Duck/Hunan/573/2002 (H6N2) • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) 67 88 • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) • ● Duck/Vietnam/OIE-2530/2011 (H4N2) • ● Duck/Vietnam/OIE-2747/2012 (H3N8) • ● Duck/Vietnam/OIE-1218/2012(H3N6) 93 • ● Duck/Vietnam/OIE-1212/2012(H3N2) 60 • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) Wild bird • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) 97 • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) 70 • ▲ Duck/Vietnam/OIE-3321/2011 (H6N2) 78 • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) Goose/Gunagdong/1/1996(H5N1) Mallard/Jiangxi/8264/2004 (H6N2) Duck/Eastern China/51/2002 (H6N2) 99 • ● Duck/Vietnam/OIE-1213/2012(H6N6) 74 H6 Group Ⅰ • ● Duck/Vietnam/OIE-2562/2011(H6N6) 95 Duck/Shantou/339/2000 (H6N2) Wild Duck/Shantou/2853/2003 (H6N2) • ● Chicken/Vietnam/OIE-1611/2012(H9N2) H9 China 99 • ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 67 97 • ● Duck/Vietnam/OIE-2749/2012 (H9N8) 95 • ▲ Chicken/Vietnam/OIE-0056/2012(H9N2) Chicken/Beijing/1/1994 (H9N2) 99 Duck/Hong Kong/Y280/1997(H9N2) Duck/Hunan/908/2005 (H6N2) • ● Duck/Vietnam/OIE-2577/2011 (H3N8) H6 W312 Quail/Hong Kong/G1/1997(H9N2) 54 99 Teal/Hong Kong/W312/1997 (H6N1) 0.02 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 3 Okamatsuet al.

  4. ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 51 • ● Duck/Vietnam/OIE-2749/2012 (H9N8) • ● Chicken/Vietnam/OIE-1611/2012_(H9N2) NP • ▲ Chicken/Vietnam/OIE-0056/2012_(H9N2) • ● Duck/Vietnam/OIE-2202/2012 (H5N1) 95 • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) Vietnam/1203/2004 (H5N1) H5N1 Vietnam • ● Duck/Vietnam/OIE-2533/2011 (H5N1) 99 • ● Duck/Vietnam/OIE-1287/2012_(H5N1) • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) • ▲ Muscovy duck/Vietnam/OIE-3012/2011_(H5N1) 56 • ▲ Muscovy duck/Vietnam/OIE-0043/2012_(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3314/2011_(H5N1) • ▲ Duck/Vietnam/OIE-3354/2011_(H5N1) • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) • ▲ Duck/Vietnam/OIE-3002/2011_(H5N1) 66 • ▲ Muscovy duck/Vietnam/OIE-3312/2011_(H5N1) Duck/Hong Kong/Y439/1997_(H9N2) Duck/Hunan/573/2002 (H6N2) • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) Wild bird I • ● Duck/Vietnam/OIE-2747/2012 (H3N8) • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) 57 • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) 68 • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) 91 Duck/Shantou/339/2000 (H6N2) Wild Duck/Shantou/2853/2003 (H6N2) 84 • ● Duck/Vietnam/OIE-2562/2011_(H6N6) Gs/Gd-like • ● Duck/Vietnam/OIE-1213/2012_(H6N6) Goose/Guangdong/1/1996_(H5N1) Duck/Hunan/908/2005 (H6N2) Quail/Hong Kong/G1/1997_(H9N2) 99 Teal/Hong Kong/W312/1997 (H6N1) Hunan491-like • ● Duck/Vietnam/OIE-2530/2011 (H4N2) Duck/Eastern China/51/2002 (H6N2) 91 Duck/Hunan/491/2005 (H6N2) • ● Duck/Vietnam/OIE-2577/2011 (H3N8) • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) Wild bird II 74 • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3321/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) • ● Duck/Vietnam/OIE-1212/2012_(H3N2) 99 • ● Duck/Vietnam/OIE-1218/2012_(H3N6) • ▲ Duck/Vietnam/OIE-0178/2012_(H7N1) • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) VietnamI • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) 96 • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) JX8264-like Mallard/Jiangxi/8264/2004 (H6N2) • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) Chicken/Beijing/1/1994 (H9N2) 99 Duck/Hong Kong/Y280/1997_(H9N2) • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) 99 • ▲ Duck/Vietnam/OIE-0068/2012_(H11N3) • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) 75 • ▲ Duck/Vietnam/OIE-0155/2012_(H4N6) 51 96 • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) • ▲ Duck/Vietnam/OIE-0033/2012_(H6N2) 55 Vietnam II • ▲ Duck/Vietnam/OIE-0483/2012_(H10N7) • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) 90 • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) 58 • ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 55 80 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) 0.01 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 4 Okamatsuet al.

  5. 99 • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) 57 M 54 • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) 82 • ▲ Duck/Vietnam/OIE-0155/2012(H4N6) • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) 63 • ▲ Duck/Vietnam/OIE-0068/2012(H11N3) 58 • ▲ Duck/Vietnam/OIE-0033/2012(H6N2) • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) Vietnam 92 • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) 94 • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 98 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) 73 • ▲ Duck/Vietnam/OIE-0483/2012(H10N7) 97 • ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) 83 • ▲ Duck/Vietnam/OIE-0178/2012(H7N1) 65 • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) 95 • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) 98 • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) Goose/Guangdong/1/1996(H5N1) Vietnam/1203/2004 (H5N1) • ● Duck/Vietnam/OIE-2533/2011 (H5N1) 87 99 • ● Duck/Vietnam/OIE-1287/2012(H5N1) 95 99 • ● Duck/Vietnam/OIE-2202/2012 (H5N1) • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) 99 H5N1 Vietnam • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) 95 • ▲ Muscovy duck/Vietnam/OIE-3012/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3314/2011(H5N1) 85 • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3002/2011(H5N1) 78 • ▲ Muscovy duck/Vietnam/OIE-3312/2011(H5N1) • ▲ Duck/Vietnam/OIE-3354/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-0043/2012(H5N1) 54 65 • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) Mallard/Jiangxi/8264/2004 (H6N2) Duck/Hunan/573/2002 (H6N2) JX8264-like 88 Duck/Hunan/491/2005 (H6N2) 98 • ● Duck/Vietnam/OIE-2530/2011 (H4N2) • ● Duck/Vietnam/OIE-1218/2012(H3N6) 99 Duck/Hong Kong/Y439/1997(H9N2) • ● Duck/Vietnam/OIE-2577/2011 (H3N8) Wild bird Duck/Eastern China/51/2002 (H6N2) • ● Duck/Vietnam/OIE-1212/2012(H3N2) 98 • ● Duck/Vietnam/OIE-2747/2012 (H3N8) 99 • ● Duck/Vietnam/OIE-2749/2012 (H9N8) 99 Wild Duck/Shantou/2853/2003 (H6N2) Duck/Shantou/339/2000 (H6N2) 99 Duck/Hunan/908/2005 (H6N2) 83 • ● Duck/Vietnam/OIE-2562/2011(H6N6) 99 • ● Duck/Vietnam/OIE-1213/2012(H6N6) 61 • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) 92 89 • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) H6 Group Ⅰ 99 • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3321/2011 (H6N2) 70 • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) 54 • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) 99 Chicken/Beijing/1/1994 (H9N2) Duck/Hong Kong/Y280/1997(H9N2) Qail/Hong Kong/G1/1997(H9N2) 99 Teal/Hong Kong/W312/1997 (H6N1) H6 W312 98 • ▲ Chicken/Vietnam/OIE-0056/2012(H9N2) • ● Chicken/Vietnam/OIE-1611/2012(H9N2) 99 99 • ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 0.01 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 5 Okamatsuet al.

  6. 74 • ▲ Duck/Vietnam/OIE-3231/2011 (H6N2) 69 • ▲ Duck/Vietnam/OIE-3287/2011 (H3N6) • ▲ Duck/Vietnam/OIE-3071/2011 (H4N6) NS 82 • ▲ Duck/Vietnam/OIE-745/2011 (H11N9) 66 • ▲ Duck/Vietnam/OIE-3223/2011 (H4N6) • ▲ Duck/Vietnam/OIE-3022/2011 (H3N8) • ▲ Duck/Vietnam/OIE-3241/2012 (H3N8) 93 • ▲ Duck/Vietnam/OIE-3406/2012 (H3N8) JX8264-like 68 • ▲ Duck/Vietnam/OIE-3426/2012 (H3N8) • ● Duck/Vietnam/OIE-1218/2012(H3N6) 96 • ● Duck/Vietnam/OIE-1212/2012(H3N2) Duck/Eastern China/51/2002 (H6N2) Duck/Hunan/573/2002(H6N2) Duck/Hunan/491/2005 (H6N2) Mallard/Jiangxi/8264/2004 (H6N2) • ▲ Duck/Vietnam/OIE-0155/2012(H4N6) • ▲ Duck/Vietnam/OIE-3469/2012 (H4N6) Wild bird • ● Duck/Vietnam/OIE-2530/2011 (H4N2) • ● Duck/Vietnam/OIE-2747/2012 (H3N8) 86 • ● Duck/Vietnam/OIE-2533/2011 (H5N1) 86 • ● Duck/Vietnam/OIE-1287/2012(H5N1) • ● Duck/Vietnam/OIE-2202/2012 (H5N1) Vietnam/1203/2004 (H5N1) H5N1 Vietnam • ▲ Muscovy duck/Vietnam/OIE-559/2011 (H5N1) 85 • ▲ Muscovy duck/Vietnam/OIE-3012/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3314/2011(H5N1) 67 • ▲ Duck/Vietnam/OIE-3002/2011(H5N1) • ▲ Muscovy duck/Vietnam/OIE-3312/2011(H5N1) 77 • ▲ Duck/Vietnam/OIE-3354/2011(H5N1) 62 • ▲ Muscovy duck/Vietnam/OIE-0043/2012(H5N1) 70 • ▲ Duck/Vietnam/OIE-3038/2012 (H5N1) • ● Duck/Vietnam/OIE-2562/2011(H6N6) 57 H6 Group I 99 • ● Duck/Vietnam/OIE-1213/2012(H6N6) Duck/Shantou/339/2000 (H6N2) Wild Duck/Shantou/2853/2003 (H6N2) Duck/Hunan/908/2005 (H6N2) • ▲ Duck/Vietnam/OIE-3225/2011 (H6N2) 61 • ▲ Duck/Vietnam/OIE-0033/2012(H6N2) • ▲ Duck/Vietnam/OIE-404/2011 (H6N2) 88 • ▲ Duck/Vietnam/OIE-406/2011 (H6N2) 55 • ▲ Duck/Vietnam/OIE-4217/2010 (H6N2) • ▲ Duck/Vietnam/OIE-4429/2010 (H6N2) 62 • ▲ Duck/Vietnam/OIE-4439/2010 (H6N6) 89 • ▲ Duck/Vietnam/OIE-535/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3342/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3301/2011 (H6N9) Vietnam • ▲ Duck/Vietnam/OIE-3141/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3349/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3321/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3304/2011 (H6N2) 79 • ▲ Duck/Vietnam/OIE-527/2011 (H6N2) 83 • ▲ Duck/Vietnam/OIE-547/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3061/2012 (H6N2) • ▲ Duck/Vietnam/OIE-3479/2012 (H6N2) Allele A • ▲ Duck/Vietnam/OIE-3021/2011 (H6N2) 50 • ▲ Duck/Vietnam/OIE-3060/2011 (H6N2) • ▲ Duck/Vietnam/OIE-3247/2011 (H6N2) Duck/Hong Kong/Y439/1997(H9N2) Quail/Hong Kong/G1/1997(H9N2) 99 Teal/Hong Kong/W312/1997 (H6N1) Chicken/Beijing/1/1994 (H9N2) Duck/Hong Kong/Y280/1997(H9N2) 76 76 • ▲ Chicken/Vietnam/OIE-0056/2012(H9N2) • ● Chicken/Vietnam/OIE-1611/2012(H9N2) H9 China • ● Chicken/Vietnam/OIE-2468/2012 (H9N2) 76 • ● Chicken/Vietnam/OIE-2215/2012 (H5N2) 83 • ● Duck/Vietnam/OIE-2749/2012 (H9N8) Allele B Goose/Guangdong/1/1996(H5N1) • ● Duck/Vietnam/OIE-2577/2011 (H3N8) 54 • ▲ Duck/Vietnam/OIE-707/2011 (H11N5) 99 • ▲ Duck/Vietnam/OIE-0483/2012(H10N7) 74 • ▲ Duck/Vietnam/OIE-0068/2012(H11N3) 82 • ▲ Duck/Vietnam/OIE-0178/2012(H7N1) 0.05 ●NorthVietnam ▲South Vietnam (Nam Dihn) (Bac Lieu, Ca Mau, and Dong Thap) Supplement Fig. 6 Okamatsuet al.

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