Volume 12, Number 9—September 2006
Research
Genomic Signatures of Human versus Avian Influenza A Viruses
Guang-Wu Chen*1, Shih-Cheng Chang*1, Chee-Keng Mok*, Yu-Luan Lo*, Yu-Nong Kung*, Ji-Hung Huang*, Yun-Han Shih*, Ji-Yi Wang*, Chiayn Chiang*, Chi-Jene Chen*, and Shin-Ru Shih*
Table A2
Listing of 60 human-isolated avian influenza viruses used in this study, with the first 29 strains contain at least one accession per genomic segment. All accessions here are according to GenBank, except those ones begin with 'ISD', which are from Influenza Sequence Database (ISD). Cells with 'n/a' in PB1-F2 column indicate that the PB1 RNA sequence did not contain the PB1-F2 ORF, while 'truncated' represent early-terminated PB1-F2 with a length less than 87-aa. Exclusion of those PB1-F2 leaves us 21 genomes for inspecting the species-associated mutations as described in the text.
| Strain Name | PB2 | PB1 | PB1-F2 | PA | HA | NP | NA | M1 | M2 | NS1 | NS2 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A/HongKong/156/97(H5N1) | AF036363 | AF036362 | AF036362 | AF084267 | AF028709 | AF028710 | AF036357 | AF036358 | AF036358 | AF036360 | AF036360 |
| A/HongKong/481/97(H5N1) | AF115290 | AF258818 | AF258818 | AF115294 | AF046096 | AJ289873 | AF084271 | AF115286 | AF115286 | AF115288 | AF115288 |
| A/HongKong/482/97(H5N1) | AF258838 | AF258819 | AF084264 | AF084268 | AF046098 | AF255745 | AF084272 | AF084282 | AF084282 | AF084285 | AF084285 |
| A/HongKong/483/97(H5N1) | AF258839 | AF258820 | AF084265 | AF084269 | AF046097 | AF084277 | AF084273 | AF255367 | AF255367 | AF084286 | AF084286 |
| A/HongKong/485/97(H5N1) | AF084263 | AF084266 | truncated | AF084270 | AF102681 | AF084278 | AF084274 | AF084284 | AF084284 | AF084287 | AF084287 |
| A/HongKong/486/97(H5N1) | AF115291 | AF115293 | AF115293 | AF115295 | AF102671 | AF115285 | AF084275 | AF255368 | AF255368 | AF256181 | AF256181 |
| A/HongKong/488/97(H5N1) | AF258848 | AF258829 | n/a | AF257204 | AF102672 | AF255756 | AF102657 | AF255377 | AF255378 | AF256190 | AF256190 |
| A/HongKong/491/97(H5N1) | AF258849 | AF258830 | n/a | AF257205 | AF102677 | AF255758 | AF102665 | AF255379 | AF255380 | AF256191 | AF256191 |
| A/HongKong/503/97(H5N1) | AF258850 | AF258831 | n/a | AF257206 | AF102679 | AF255760 | AF102666 | AF255381 | AF255381 | AF256192 | AF256192 |
| A/HongKong/507/97(H5N1) |
AF258851 |
AF258832 |
n/a |
AF257207 |
AF102675 |
AF255762 |
AF102659 |
AF255382 |
AF255382 |
AF256193 |
AF256193 |
| A/HongKong/514/97(H5N1) | AF258852 | AF258833 | n/a | AF257208 | AF102682 | AF255764 | AF102669 | AF255383 | AF255383 | AF256184 | AF256184 |
| A/HongKong/516/97(H5N1) | AF258853 | AF258834 | n/a | AF257209 | AF102673 | AF255766 | AF102660 | AF255384 | AF255384 | AF256194 | AF256194 |
| A/HongKong/532/97(H5N1) | AF258843 | AF258824 | AF258824 | AF257199 | AF102680 | AF255750 | AF102667 | AF255371 | AF255371 | AF256185 | AF256185 |
| A/HongKong/538/97(H5N1) | AF258844 | AF258825 | AF258825 | AF257200 | AF102674 | AF255751 | AF102662 | AF255372 | AF255372 | AF256186 | AF256186 |
| A/HongKong/542/97(H5N1) | AF258845 | AF258826 | AF258826 | AF257201 | AF102678 | AF255752 | AF102670 | AF255373 | AF255373 | AF256187 | AF256187 |
| A/HongKong/97/98(H5N1) | AF258846 | AF258827 | AF258827 | AF257202 | AF102676 | AF255753 | AF102661 | AF255374 | AF255374 | AF256188 | AF256188 |
| A/HongKong/212/03(H5N1) | AY576380 | AY576392 | AY576392 | AY576404 | AY575869 | AY575905 | AY575881 | AY575893 | AY575893 | AY576368 | AY576368 |
| A/HongKong/213/2003(H5N1) | AY576381 | AB212052 | AY576393 | AB212053 | AB212054 | AB212055 | AB212056 | AB212057 | AB212057 | AY576369 | AY576369 |
| A/Thailand/16/2004(H5N1) | ISDN40383 | ISDN40859 | ISDN40859 | ISDN40940 | ISDN40341 | ISDN40086 | ISDN48790 | ISDN45755 | ISDN45755 | ISDN40040 | ISDN40040 |
| A/Thailand/SP83/2004(H5N1) |
ISDN49457 |
ISDN40931 |
ISDN40931 |
ISDN121933 |
ISDN40917 |
ISDN41067 |
ISDN48792 |
ISDN111182 |
ISDN111182 |
ISDN41028 |
ISDN41028 |
| A/Vietnam/1194/2004(H5N1) | AY651718 | AY651664 | AY651664 | AY651610 | AY651333 | AY651498 | ISDN38703 | ISDN39957 | ISDN39957 | AY651552 | AY651552 |
| A/Vietnam/1196/04(H5N1) | AY526752 | AY526751 | AY526751 | AY526750 | AY526745 | AY526749 | AY526746 | AY526748 | AY526748 | AY526747 | AY526747 |
| A/Vietnam/1203/2004(H5N1) | AY651719 | AY818129 | AY651665 | AY818132 | ISDN38687 | AY818138 | AY651447 | AY651388 | AY651388 | AY651553 | AY651553 |
| A/Vietnam/3046/2004(H5N1) | AY651720 | AY651666 | AY651666 | AY651613 | AY651335 | AY651500 | AY651446 | AY651389 | AY651389 | AY651554 | AY651554 |
| A/Vietnam/3062/2004(H5N1) | AY651721 | AY651667 | AY651667 | AY651612 | AY651336 | AY651501 | AY651448 | AY651390 | AY651390 | AY651555 | AY651555 |
| A/Netherlands/219/03(H7N7) | AAR04358 | AAR05983 | AY340083 | AAR04363 | AAR02640 | AAR04370 | AAR11367 | AAR11371 | AY340089 | AAR04367 | AY342422 |
| A/Guangzhou/333/99(H9N2) | AY043030 | AY043029 | truncated | AY043028 | AY043019 | AY043026 | AY043024 | AY043025 | AY043025 | AY043027 | AY043027 |
| A/HongKong/1073/99(H9N2) | AF258835 | AF258816 | AF258816 | AF257191 | AJ404626 | AJ289871 | AJ404629 | AF255363 | AF255363 | AJ278649 | AJ278649 |
| A/HongKong/1074/99(H9N2) | AF258836 | AF258817 | AF258817 | AF257192 | AJ404627 | AJ289872 | AJ404628 | AF255364 | AF255364 | AF256177 | AF256177 |
| A/England/268/96(H7N7) |
|
|
|
|
AF028020 |
|
|
|
|
|
|
| A/Shantou/239/98(H9N2) | AY043015 | AY043021 | |||||||||
| A/Shaoguan/408/98(H9N2) | AY043017 | AY043022 | |||||||||
| A/Shaoguan/447/98(H9N2) | AY043018 | AY043023 | |||||||||
| A/unknown/149717-12/2002(H7N2) | DQ107480 | DQ107480 | |||||||||
| A/Netherlands/124/03(H7N7) | AAR04355 | AAR05980 | AY340080 | AAR04360 | AAR11364 | AAR11368 | AY340086 | ||||
| A/Netherlands/126/03(H7N7) | AAR04356 | AAR05981 | AY340081 | AAR04361 | AAR11363 | AAR11369 | AY340087 | ||||
| A/Netherlands/127/03(H7N7) | AAR04357 | AAR05982 | AY340082 | AAR04362 | AAR02636 | AAR11370 | AY340088 | AAR04366 | AY342421 | ||
| A/Netherlands/33/03(H7N7) | AAR05984 | AY340084 | AAR04364 | AAR02638 | AAR04371 | AAR11366 | AAR11372 | AY340090 | AAR04368 | AY342423 | |
| A/Hanoi/03/2004(H5N1) | AJ715872 | AJ715873 | |||||||||
| A/Hatay/2004(H5N1) |
|
|
|
|
AJ867074 |
AJ867076 |
AJ867075 |
AM040045 |
AM040045 |
AM040046 |
AM040046 |
| A/Prachinburi/6231/2004(H5N1) | ISDN110940 | ISDN110939 | |||||||||
| A/Thailand/1-KAN-1/2004(H5N1) | AY555150 | AY555151 | |||||||||
| A/Thailand/2-SP-33/2004(H5N1) | AY555153 | AY555152 | |||||||||
| A/Thailand/Chaiyaphum/622/2004(H5N1) | ISDN49460 | ISDN48793 | ISDN111184 | ISDN111184 | |||||||
| A/Thailand/EKA2NF/2004(H5N1) | AY535029 | ||||||||||
| A/Thailand/Kamphaengphet-Nontaburi/04(H5N1) | AY786078 | AY786079 | |||||||||
| A/Thailand/Kan353/2004(H5N1) | ISDN40918 | ISDN48791 | ISDN111183 | ISDN111183 | |||||||
| A/Thailand/Prachinburi/6231/2004(H5N1) | ISDN111185 | ISDN111185 | |||||||||
| A/Thailand/LFPN-2004/2004(H5N1) | AY679514 | AY679513 | |||||||||
| A/Vietnam/1194/2004(H5N1) |
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ISDN38686 |
|
AY651445 |
AY651387 |
AY651387 |
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| A/Vietnam/1204/2004(H5N1) | ISDN40380 | ISDN40843 | ISDN40843 | ISDN121932 | ISDN38688 | ISDN40017 | ISDN40017 | ||||
| A/Vietnam/3212/2004(H5N1) | ISDN40278 | ||||||||||
| A/Vietnam/DN-33/2004(H5N1) | AY720950 | AY720948 | AY720949 | AY720949 | |||||||
| A/Vietnam/JP178/2004(H5N1) | ISDN69608 | ISDN69610 | |||||||||
| A/Vietnam/HN/2004(H5N1) | AY720954 | AY720955 | n/a | AY720952 | AY720953 | AY720951 | AY720951 | ||||
| A/Cambodia/JP52a/2005(H5N1) | ISDN121986 | ISDN122818 | |||||||||
| A/Hanoi/30408/2005(H5N1) | ISDN129400 | ||||||||||
| A/Vietnam/HN30408/2005(H5N1) | ISDN119678 | ISDN119679 | |||||||||
| A/Vietnam/JP14/2005(H5N1) | ISDN117778 | ISDN117783 | |||||||||
| A/Vietnam/JP4207/2005(H5N1) | ISDN117777 | ISDN117782 | |||||||||
| A/Vietnam/JPHN30321/2005(H5N1) | ISDN118371 |
1These authors contributed equally to this article.
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