Supplementary Table: Influenza sequences used in the analysis
PB2 sequences:
Abbreviation / Strain name and Serotype / GenBank No.Brevig Mission/1918 / A/Brevig Mission/1/1918 H1N1 / DQ208309
Akita/94 / A/Akita/1/94 H3N2 / U71132
Akita/95 / A/Akita/1/95 H3N2 / U71133
Ann Arbor/60 / A/Ann Arbor/6/60 H2N2 / M23970
budgerigar/Hokkaido/77 / A/budgerigar/Hokkaido/1/77 H4N6 / M73523
Charlottesville/95 / A/Charlottesville/31/95 H1N1 / AF398866
chicken/California/00 / A/chicken/California/1002a/00 H6N2 / AF457714
chicken/California/01 / A/chicken/California/139/01 H6N2 / AF457705
chicken/Rostock/34 / A/chicken/FPV/Rostock/34 H7N1 / M21851
chicken/Hong Kong/97 / A/chicken/Hong Kong/G9/97 H9N2 / AF156430
chicken/Shanghai/98 / A/chicken/Shanghai/F/98 H9N2 / AY253750
chicken/Taiwan/99 / A/chicken/Taiwan/7-5/99 H6N1 / AF255624
Chile/83 / A/Chile/1/83 H1N1 / X15283
chukka/Hong Kong/00 / A/chukka/Hong Kong/FY295/00 H6N1 / AJ410501
duck/North Carolina/01 / A/duck/NC/91347/01 H1N2 / AY233387
equine/Kentucky/86 / A/equine/Kentucky/2/86 H3N8 / M73526
equine/London/73 / A/equine/London/1416/73 H7N7 / M73520
equine/Prague/56 / A/equine/Prague/1/56 H7N7 / M73519
Fiji/83 / A/Fiji/15899/83 H1N1 / AJ564805
Fort Monmouth/47 / A/Fort Monmouth/1/47 H1N1 / X99035
FPV/Weybridge / A/FPV/Weybridge H7N7 / M38291
Fukushima/96 / A/Fukushima/114/96 H3N2 / AF037414
goose/Guangdong/96 / A/goose/Guangdong/1/96 H5N1 / AF144300
goose/Guangdong/97 / A/goose/Guangdong/3/97 H5N1 / AY038798
Great Lakes/65 / A/Great Lakes/389/65 H2N2 / M91713
gull/Astrakhan/84 / A/gull/Astrakhan/227/84 H13N6 / M73516
gull/Maryland/77 / A/gull/Maryland/704/77 H13N6 / M73525
Hong Kong/68 / A/Hong Kong/1/68 H3N2 / AF348170
Hong Kong/97a / A/Hong Kong/156/97 H5N1 / AF036363
Hong Kong/97b / A/Hong Kong/470/97 H1N1 / AF258524
Hong Kong/98a / A/Hong Kong/427/98 H1N1 / AF258525
Hong Kong/98b / A/Hong Kong/97/98 H5N1 / AF258846
Hong Kong/99c / A/Hong Kong/1774/99 H3N2 / AJ293920
Hong Kong/99d / A/Hong Kong/1073/99 H9N2 / AF258835
Kiev/79 / A/Kiev/59/79 H1N1 / M38277
Kitakyushu/93 / A/Kitakyushu/159/93 H3N2 / AF037412
Korea/68 / A/Korea/426/68 H2N2 / M73524
Leningrad/57 / A/Leningrad/134/17/57 H2N2 / M81581
Los Angeles/87 / A/Los Angeles/2/87 H3N2 / U62543
Memphis/88 / A/Memphis/8/88 H3N2 / M73517
Miyagi/95 / A/Miyagi/29/95 H3N2 / U71135
Niigata/96 / A/Niigata/137/96 H3N2 / AF037415
NT/68 / A/NT/60/68 H3N2 / J02140
parakeet/Chiba/97 / A/parakeet/Chiba/1/97 H9N2 / AB049153
parakeet/Narita/98 / A/parakeet/Narita/92A/98 H9N2 / AB049154
Paris/97 / A/Paris/908/97 H3N2 / AF483602
pheasant/Hong Kong/99 / A/pheasant/Hong Kong/SH39/99 H6N1 / AJ410495
Pheasant/Hong Kong/00 / A/pheasant/Hong Kong/FY294/00 H6N1 / AJ427305
Puerto Rico/34 / A/Puerto Rico/8/34 H1N1 / NC 002023
quail/Hong Kong/99 / A/quail/Hong Kong/1721-20/99 H6N1 / AJ410496
quail/Hong Kong/00 / A/quail/Hong Kong/SF550/00 H6N1 / AJ410498
ruddy turnstone/New Jersey/85 / A/ruddy turnstone/New Jersey/47/85 H4N6 / M73518
seal/Massachusetts/82 / A/seal/Massachusetts/133/82 H4N5 / M73522
Shiga/95 / A/Shiga/20/95 H3N2 / U71134
Shiga/97 / A/Shiga/25/97 H3N2 / AF037417
Singapore/57 / A/Singapore/1/57 H2N2 / M73521
swine/31 / A/swine/1976/31 H1N1 / M55469
swineColorado/77 / A/swine/Colorado/1/77 H3N2 / AF251394
swine/Cotes d'Armor/84 / A/swine/Cotes d'Armor/3633/84 H3N2 / AJ311458
swine/Germany/81 / A/swine/Germany/2/81 H1N1 / M55471
swine/Hong Kong/98 / A/swine/Hong Kong/10/98 H9N2 / AF222817
swine/Illinois/01 / A/swine/Illinois/100084/01 H1N2 / AF455738
swine/Indiana/99 / A/swine/Indiana/9K035/99 H1N2 / AF250131
swine/Indiana/00 / A/swine/Indiana/P12439/00 H1N2 / AF455736
swine/Iowa/30 / A/swine/Iowa/15/30 H1N1 / M73515
swine/Iowa/99 / A/swine/Iowa/533/99 H3N2 / AF251418
swine/Iowa/01 / A/swine/Iowa/930/01 H1N2 / AF455735
swine/Italy/98 / A/swine/Italy/1523/98 H3N2 / AJ311459
swine/Korea/02 / A/swine/Korea/CY02/02 H1N2 / AY129163
swine/Minnesota/99 / A/swine/Minnesota/593/99 H3N2 / AF251434
swine/Minnesota/00 / A/swine/Minnesota/55551/00 H1N2 / AF455734
swine/Nebraska/98 / A/swine/Nebraska/209/98 H3N2 / AF251410
swine/North Carolina/01 / A/swine/North Carolina/93523/01 H1N2 / AF455733
swine/Ohio/01 / A/swine/Ohio/891/01 H1N2 / AF455731
swine/Ontario/97 / A/swine/Ontario/41848/97 H3N2 / AF251402
swine/Ontario/99 / A/swine/Ontario/1911-1/99 H4N6 / AF285892
Swine/Shizuoka/97 / A/swine/Shizuoka/110/97 H3N2 / AF225514
swine/Tennessee/77 / A/swine/Tennessee/24/77 H1N1 / M73513
teal/Hong Kong/97 / A/teal/Hong Kong/W312/97 H6N1 / AF250476
Tochigi/95 / A/Tochigi/44/95 H3N2 / AF037413
turkey/Minnesota/80 / A/turkey/Minnesota/833/80 H4N2 / M73514
Udorn/72 / A/Udorn/307/72 H3N2 / M91712
WSN/33 / A/wsn/33 H1N1 / J02179
X-31 / A/X-31 H3N2 / AB036782
PB1 sequences:
Abbreviation / Strain name and Serotype / GenBank No.Brevig Mission/1918 / A/Brevig Mission/1/18 H1N1 / DQ208310
Akita/94 / A/Akita/1/94 H3N2 / U71128
Akita/95 / A/Akita/1/95 H3N2 / U71129
Albany/58 / A/Albany/6/58 / AY210010
Albany/65 / A/Albany/1/65 / AY210016
Ann Arbor/60 / A/Ann Arbor/6/60 H2N2 / M23972
AnnArbor/67 / A/Ann Arbor/7/67 / AY210024
avian/Netherlands/03 / A/Avian/Netherlands/219/03 H7N7 / AY340083
Beijing/56 / A/Beijing/11/56 H1N1 / M25932
Berkley/68 / A/Berkeley/1/68 / AY210025
Califonia/66 / A/California/1/66 / AY210019
chicken/California/00 / A/chicken/California/1002a/00 H6N2 / AF457671
chicken/California/01 / A/chicken/California/139/01 H6N2 / AF457706
chicken/Hong Kong/97 / A/chicken/Hong Kong/220/97 H5N1 / AF046085
chicken/Pakistan/99 / A/Chicken/Pakistan/2/99 H9N2 / AJ291396
chicken/Shanghai/98 / A/chicken/Shanghai/F/98 H9N2 / AY253751
chicken/Taiwan/99 / A/chicken/Taiwan/7-5/99 H6N1 / AF262210
Chile/57 / A/Chile/13/57 / AY210008
chukka/Hong Kong/00 / A/chukka/Hong Kong/FY295/00 H6N1 / AJ410508
duck/Anyang/01 / A/duck/Anyang/AVL-1/2001 H5N1 / AF468839
duck/Hong Kong/99 / A/duck/Hong Kong/3096/99 H6N2 / AJ410509
duck/North Carolina/01 / A/Duck/NC/91347/01 H1N2 / AY233388
Dunedin/73 / A/Dunedin/4/73 N2 / M74899
England/67 / A/England/10/67 / AY210021
equine/London/73 / A/equine/London/1416/73 H7N7 / M25928
equine/Tennessee86 / A/equine/Tennessee/5/86 H3N8 / M25929
Fort Monmouth/47 / A/Fort Monmouth/1/47 H1N1 / X99037
Fukushima/96 / A/Fukushima/114/96 H3N2 / AF037421
Georgia/67 / A/Georgia/1/67 / AY210022
goose/Guangdong/96 / A/goose/Guangdong/1/96 H5N1 / AF144301
goose/Guangdong/97 / A/goose/Guangdong/3/97 H5N1 / AY035888
Gull/Maryland/77 / A/gull/Maryland/704/77 H13N6 / M25933
Hong Kong/68 / A/Hong Kong/1/68 H3N2 / AF348172
Hong Kong/97 / A/Hong Kong/156/97 H5N1 / AF036362
Hong Kong/98 / A/Hong Kong/427/98 H1N1 / AF258526
Hong Kong/99 / A/Hong Kong/1073/99 H9N2 / AJ404634
Japan/62 / A/Japan/170/62 / AY210014
Kiev/79 / A/Kiev/59/79 H1N1 / M38376
Kitakyushu/93 / A/Kitakyushu/159/93 H3N2 / AF037418
Korea/68 / A/Korea/426/68 H2N2 / M25935
Kumamoto/65 / A/Kumamoto/1/65 / AY210017
Leningrad/57a / A/Leningrad/134/17/57 H2N2 / M81580
Leningrad/57b / A/Leningrad/134/47/57 / M81586
Leningrad/57c / A/Leningrad/134/57 / M81574
mallard/Alberta/88 / A/mallard/Alberta/321/88 H9N2 / AY633282
mallard/Alberta/98 / A/mallard/Alberta/242/98 H3N8 / AY633250
mallard/New York/78 / A/mallard/New York/6750/78 H2N2 / M25926
Memphis/88 / A/Memphis/8/88 H3N2 / M25936
Miyagi/95 / A/Miyagi/29/95 H3N2 / U71131
Murakami/64 / A/Murakami/4/64 / AY210015
Niigata/96 / A/Niigata/137/96 H3N2 / AF037420
NT/68 / A/NT/60/68 H3N2 / J02138
Panama/61 / A/Panama/1/61 / AY210013
Panama/66 / A/Panama/1/66 / AY210020
parakeetChiba/97 / A/parakeet/Chiba/1/97 H9N2 / AB049155
parakeetNarita/98 / A/parakeet/Narita/92A/98 H9N2 / AB049156
Paris/97 / A/Paris/908/97 H3N2 / AF483601
pheasant/Hong Kong/00 / A/pheasant/Hong Kong/FY294/00 H6N1 / AJ421061
pheasant/Hong Kong/99 / A/pheasant/Hong Kong/SH39/99 H6N1 / AJ410502
Pittsburgh/65 / A/Pittsburgh/2/65 / AY210018
Puerto Rico/34 / A/Puerto Rico/8/34 H1N1 / NC_002021
Puerto Rico/34 / A/Puerto Rico/8/34 H1N1 / ISDN13420
quail/Hong Kong/00 / A/quail/Hong Kong/SF550/00 H6N1 / AJ410505
quail/Hong Kong/99 / A/quail/Hong Kong/1721-20/99 H6N1 / AJ410503
Shiga/97 / A/Shiga/25/97 H3N2 / AF037423
Singapore/57 / A/Singapore/1/57 H2N2 / M25924
Singapore/57b / A/Singapore/1/57 / M25924
swine/31 / A/swine/1976/31 H1N1 / M55472
swine/Cote d'Armour/84 / A/swine/Cote d'Armour/3633/84 H3N1 / AJ311461
swine/Finistere82 / A/swine/Finistere/2899/82 H1N1 / AJ311462
swine/Hong Kong/82 / A/swine/Hong Kong/126/82 H3N2 / M25927
swine/Illinois/01 / A/swine/Illinois/100084/01 H1N2 / AF455730
swine/Indiana/00 / A/swine/Indiana/P12439/00 H1N2 / AF455728
swine/Indiana/99 / A/swine/Indiana/9K035/99 H1N2 / AF250130
swine/Iowa/99 / A/swine/Iowa/533/99 H3N2 / AF251413
swine/Iowa/01 / A/swine/Iowa/930/01 H1N2 / AF455727
swine/Korea/02 / A/swine/Korea/CY02/02 H1N2 / AY129162
swine/Minnesota/00 / A/swine/Minnesota/55551/00 H1N2 / AF455726
swine/North Carolina/01 / A/swine/North Carolina/93523/01 H1N2 / AF455725
swine/Ontario/81 / A/swine/Ontario/2/81 H1N1 / M25930
swine/Ontario/97 / A/swine/Ontario/41848/97 H3N2 / AF251397
swine/Ontario/99 / A/Swine/Ontario/1911-1/99 H4N6 / AF285891
swine/Shizuoka/97 / A/swine/Shizuoka/110/97 H3N2 / AF225518
swine/Tennessee/77 / A/swine/Tennessee/26/77 H1N1 / M25931
teal/Hong Kong/97 / A/teal/Hong Kong/W312/97 H6N1 / AF250477
Tokyo/67 / A/Tokyo/3/67 / AY210023
turkey/Minnesota/80 / A/turkey/Minnesota/833/80 H4N2 / M25925
Victoria/59 / A/Victoria/15681/59 / AY210011
Vietnam/04 / A/Vietnam/1194/2004 H5N1 / AY651664
Wisconsin/88 / A/Wisconsin/3523/88 H1N1 / M25934
WSN/33 / A/WSN/33 H1N1 / J02178
PA sequences:
Abbreviation / Strain / Genbank No.Brevig Mission/1918 / A/Brevig Mission/1/18 H1N1 / DQ208311
WSN/33 / A/WSN/33 H1N1 / X17336
Akita/94 / A/Akita/1/94 H3N2 / U71136
Akita/95 / A/Akita/1/95 H3N2 / U71137
Ann Arbor/60 / A/Ann Arbor/6/60 H2N2 / M23974
avian/Netherlands/03 / A/avian/Netherlands/033/03 H7N7 / AY342419
Charlottesville/95 / A/Charlottesville/28/95 H1N1 / AF398864
chicken/Beijing/94 / A/chicken/Beijing/1/94 H9N2 / AF156452
chicken/California/00 / A/chicken/California/1002a/00 H6N2 / AF457716
chickenCalifornia/01 / A/chicken/California/139/01 H6N2 / AF457707
chicken/Rostock/34 / A/chicken/FPV/Rostock/34 H7N1 / M21850
chicken/Germany/03 / A/chicken/Germany/R28/03 H7N7 / AJ619677
chicken/Guangdong/00 / A/chicken/Guangdong/10/00 H9N2 / AF508672
chicken/Hidalgo/94 / A/chicken/Hidalgo/26654-1368/94 H5N2 / AF098612
chicken/Hong Kong/01 / A/chicken/Hong Kong/FY150/01 H5N1 / AY221569
chicken/Hong Kong/94 / A/chicken/Hong Kong/739/94 H9N2 / AF156450
chicken/Hong Kong/97 / A/chicken/Hong Kong/220/97 H5N1 / AF046087
chicken/Hong Kong/97 / A/chicken/Hong Kong/G23/97 H9N2 / AF156445
chicken/Korea/96 / A/chicken/Korea/25232-96006/96 H9N2 / AF156454
chicken/Mexico/94 / A/chicken/Mexico/26654-1374/94 H5N2 / AF098613
chicken/Pakistan/99 / A/chicken/Pakistan/2/99 H9N2 / AJ291397
chicken/Puebla/94 / A/chicken/Puebla/14585-622/94 H5N2 / AF098615
chicken/Queretaro/95 / A/chicken/Queretaro/14588-19/95 H5N2 / AF098616
chicken/Rostock/34 / A/FPV/Rostock/34 H7N1 / X17223
chicken/Shanghai/98 / A/chicken/Shanghai/F/98 H9N2 / AY253752
chicken/Taiwan/99 / A/chicken/Taiwan/7-5/99 H6N1 / AF262211
chukka/Hong Kong/00 / A/chukka/Hong Kong/FY295/00 H6N1 / AJ410517
duck/Anyang/2001 / A/duck/Anyang/AVL-1/2001 H5N1 / AF468841
duck/China/03 / A/duck/China/E319-2/03 H5N1 / AY518365
duck/Hokkaido/80 / A/duck/Hokkaido/8/80 H3N8 / M26083
duck/Hong Kong/00 / A/duck/Hong Kong/2986.1/2000 H5N1 / AY059532
duck/Hong Kong/97 / A/duck/Hong Kong/Y280/97 H9N2 / AF156447
duck/North Carolina/01 / A/duck/NC/91347/01 H1N2 / AY233389
England/69 / A/England/939/69 H3N2 / AJ605763
equine/London/73 / A/equine/London/1416/73 H7N7 / M26087
equine/Tennessee/86 / A/equine/Tennessee/5/86 H3N8 / M26082
Fiji/83 / A/Fiji/15899/83 H1N1 / AJ605762
Fort Monmouth/47 / A/Fort Monmouth/1/47 H1N1 / X99039
Fukushima/96 / A/Fukushima/114/96 H3N2 / AF037427
goose/Guangdong/96 / A/goose/Guangdong/1/96 H5N1 / AF144302
goose/Guangdong/97 / A/goose/Guangdong/3/97 H5N1 / AF380163
goose/Hong Kong/00 / A/goose/Hong Kong/3014.8/2000 H5N1 / AY059533
Guangzhou/99 / A/Guangzhou/333/99 H9N2 / AY043028
gull/Maryland/77 / A/gull/Maryland/704/77 H13N6 / M26088
Hong Kong/68 / A/Hong Kong/1/68 H3N2 / AF348174
Hong Kong/97 / A/Hong Kong/156/97 H5N1 / AF046095
Hong Kong/98 / A/Hong Kong/427/98 H1N1 / AF258519
Hong Kong/99 / A/Hong Kong/1073/99 H9N2 / AF257191
Kitakyushu/93 / A/Kitakyushu/159/93 H3N2 / AF037424
Korea/68 / A/Korea/426/68 H2N2 / M26079
Leningrad/57 / A/Leningrad/134/17/57 H2N2 / M81579
Mallard/New York/78 / A/mallard/New York/6750/78 H2N2 / AJ243994
Miyagi/95 / A/Miyagi/29/95 H3N2 / U71139
Niigata/96 / A/Niigata/137/96 H3N2 / AF037426
NT/68 / A/NT/60/68/11 H3N2 / J02139
parakeet/Chiba/97 / A/parakeet/Chiba/1/97 H9N2 / AB049157
parakeet/Narita/98 / A/parakeet/Narita/92A/98 H9N2 / AB049158
Paris/97 / A/Paris/908/97 H3N2 / AF483603
pheasant/Hong Kong/00 / A/pheasant/Hong Kong/FY294/00 H6N1 / AJ427307
pheasant/Hong Kong/99 / A/pheasant/Hong Kong/SH39/99 H6N1 / AJ410511
pheasant/HongKong01 / A/Pheasant/Hong Kong/FY155/01 H5N1 / AY221571
pigeon/Hong Kong/97 / A/Pigeon/Hong Kong/Y233/97 H9N2 / AF156446
pintail/Alberta/79 / A/pintail/Alberta/119/79 H4N6 / M26085
Puerto Rico/34 / A/Puerto Rico/8/34 H1N1 / NC_002022
Puerto Rico/34 / A/Puerto Rico/8/34 H1N1 / ISDN13421
Puerto Rico/34 M.S. / A/Puerto Rico/8/34/Mount Sinai H1N1 / AF389117
quail/Arkansas/93 / A/quail/Arkansas/29209-1/93 H9N2 / AF156456
quail/Hong Kong/00 / A/quail/Hong Kong/SF550/00 H6N1 / AJ410514
quail/Hong Kong/92 / A/quail/Hong Kong/AF157/92 H9N2 / AF156451
quail/Hong Kong/97 / A/quail/Hong Kong/G1/97 H9N2 / AF156449
quail/Hong Kong/99 / A/quail/Hong Kong/1721-20/99 H6N1 / AJ410512
ruddy turnstone/New Jersey/85 / A/ruddy turnstone/New Jersey/47/85 H4N6 / M26086
Shiga/95 / A/Shiga/20/95 H3N2 / U71138
Shiga/97 / A/Shiga/25/97 H3N2 / AF037429
shorebird/Delaware/96 / A/shorebird/Delaware/9/96 H9N2 / AF156455
Singapore/57 / A/Singapore/1/57 H2N2 / M26078
swine/Colorado/77 / A/swine/Colorado/1/77 H3N2 / AF251393
swine/Cotes d'Armor/84 / A/swine/Cotes d'Armor/3633/84 H3N2 / AJ311464
swine/Cotes d'Armor/97 / A/swine/Cotes d'Armor/790/97 H1N2 / AJ311207
swine/Cotes d'Armor/98 / A/swine/Cotes d'Armor/2433/98 H1N2 / AJ311205
swine/Cotes d'Armor/99 / A/swine/Cotes d'Armor/604/99 H1N2 / AJ312838
swine/Finistere/82 / A/swine/Finistere/2899/82 H1N1 / AJ311463
swine/Hong Kong/78 / A/swine/Hong Kong/81/78 H3N2 / M26080
swine/Hong Kong/82 / A/swine/Hong Kong/126/82 H3N2 / M26081
swine/Ille et Vilaine/99 / A/swine/Ille et Vilaine/1455/99 H1N1 / AJ312836
swine/Illinois/01 / A/swine/Illinois/100084/01 H1N2 / AF455722
swine/Indiana/00 / A/swine/Indiana/P12439/00 H1N2 / AF455720
swine/Iowa/01 / A/swine/Iowa/930/01 H1N2 / AF455719
swine/Iowa/30 / A/swine/Iowa/15/30 H1N1 / M26076
swine/Iowa/31 / A/swine/Iowa/1976/31 H1N1 / M55473
swine/Italy/00 / A/swine/Italy/1081/00 H1N2 / AJ311209
swine/Italy/98 / A/swine/Italy/1513-1/98 H1N1 / AJ311465
swine/Italy/98b / A/swine/Italy/1521/98 H1N2 / AJ311206
swine/Italy/99 / A/swine/Italy/2064/99 H1N2 / AJ311210
swine/Korea/02 / A/swine/Korea/CY02/02 H1N2 / AY129161
swine/Minnesota/00 / A/swine/Minnesota/55551/00 H1N2 / AF455718
swine/Nebraska/98 / A/swine/Nebraska/209/98 H3N2 / AF251409
swine/North Carolina/01 / A/swine/North Carolina/93523/01 H1N2 / AF455717
swine/Ontario/99 / A/swine/Ontario/1911-1/99 H4N6 / AF285890
swine/Shizuoka/97 / A/swine/Shizuoka/110/97 H3N2 / AF225522
swine/Tennessee/77 / A/swine/Tennessee/26/77 H1N1 / M26077
teal/Hong Kong/97 / A/teal/Hong Kong/W312/97 H6N1 / AF250478
Tochigi/95 / A/Tochigi/44/95 H3N2 / AF037425
turkey/Minnesota/80 / A/turkey/Minnesota/833/80 H4N2 / M26084
X-31 / A/X-31 H3N2 / AB036780
Yokohama/02 / A/Yokohama/22/2002 H1N2 / AB126627