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PostPosted: Fri May 07, 2010 8:29 am 
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China's national labs in Harbin released 10 HA sequences from Egyptian poultry, including 2 from 2010. None of the sequences had 125del. However, one had a deletion in the HA cleavage site that matched the Fujian subclade (2.3.2) found in wild birds at Uvs lake as well as the 2008 outbreak in Japan. South Korea, and Russia. The cleavage site and flanking regions were identical matches with the above sub-clade.

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Last edited by niman on Sun May 09, 2010 9:33 am, edited 1 time in total.

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PostPosted: Fri May 07, 2010 8:30 am 
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Travel log of A/chicken/Egypt/36-4/2008

gb|GQ412056.1| Influenza A virus (A/chicken/Korea/YAQ173/2008... 119 1e-24
gb|GQ412055.1| Influenza A virus (A/chicken/Korea/USQ284/2008... 119 1e-24
gb|GQ412054.1| Influenza A virus (A/duck/Korea/NSQ263/2008(H5... 119 1e-24
gb|GQ412053.1| Influenza A virus (A/chicken/Korea/Gimje/2008(... 119 1e-24
gb|GQ412052.1| Influenza A virus (A/duck/Korea/JEQ149/2008(H5... 119 1e-24
gb|GQ412051.1| Influenza A virus (A/chicken/Korea/ISQ250/2008... 119 1e-24
gb|GU182198.1| Influenza A virus (A/environment/Hunan/5-25/20... 119 1e-24
dbj|AB523775.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB523767.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB523759.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523368.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523366.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB522001.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB521999.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB520708.1| Influenza A virus (A/whooper swan/Mongolia/6/... 119 1e-24
dbj|AB517667.1| Influenza A virus (A/whooper swan/Mongolia/8/... 119 1e-24
dbj|AB517665.1| Influenza A virus (A/whooper swan/Mongolia/2/... 119 1e-24
gb|GQ227383.1| Influenza A virus (A/pika/Qinghai/SHK/2007(H5N... 119 1e-24
gb|GQ227380.1| Influenza A virus (A/pika/Qinghai/GRL/2007(H5N... 119 1e-24
gb|GQ227367.1| Influenza A virus (A/pika/Qinghai/HMH/2007(H5N... 119 1e-24
gb|GQ386150.1| Influenza A virus (A/bean goose/Tyva/10/2009(H... 119 1e-24
gb|GQ386142.1| Influenza A virus (A/grebe/Tyva/3/2009(H5N1)) ... 119 1e-24
gb|GQ338087.1| Influenza A virus (A/great crested grebe/Tyva/... 119 1e-24
gb|GQ338084.1| Influenza A virus (A/black-headed gull/Tyva/11... 119 1e-24
gb|GQ290463.1| Influenza A virus (A/environment/Dongting Lake... 119 1e-24
gb|FJ654295.1| Influenza A virus (A/chicken/Primorsky/85/2008... 119 1e-24
gb|CY036229.1| Influenza A virus (A/black-crowned night heron... 119 1e-24
gb|CY036221.1| Influenza A virus (A/common buzzard/Hong Kong/... 119 1e-24
gb|CY036205.1| Influenza A virus (A/little egret/Hong Kong/88... 119 1e-24
gb|CY036189.1| Influenza A virus (A/house crow/Hong Kong/5288... 119 1e-24
gb|CY036181.1| Influenza A virus (A/Daurian starling/Hong Kon... 119 1e-24
gb|CY036173.1| Influenza A virus (A/common magpie/Hong Kong/5... 119 1e-24
gb|CY036165.1| Influenza A virus (A/red-billed starling/Hong ... 119 1e-24
gb|CY036093.1| Influenza A virus (A/peregrine falcon/Hong Kon... 119 1e-24
gb|CY036045.1| Influenza A virus (A/peregrine falcon/Hong Kon... 119 1e-24
gb|EU676174.1| Influenza A virus (A/chicken/Primorje/1/2008(H... 119 1e-24
dbj|AB436902.1| Influenza A virus (A/whooper swan/Hokkaido/2/... 119 1e-24

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PostPosted: Fri May 07, 2010 9:00 am 
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LOCUS CY062606 1776 bp cRNA linear VRL 05-MAY-2010
DEFINITION Influenza A virus (A/chicken/Egypt/36-4/2008(H5N1)) segment 4
sequence.
ACCESSION CY062606
VERSION CY062606.1 GI:295789203
KEYWORDS .
SOURCE Influenza A virus (A/chicken/Egypt/36-4/2008(H5N1))
ORGANISM Influenza A virus (A/chicken/Egypt/36-4/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1776)
AUTHORS Li,Y., Liu,L., El-Sanousi,A.A., Soliman,R.T., Hussein,H.A., Bu,Z.
and Chen,H.
TITLE Genetic charaterization of Egyptian highly pathogenic avian
influenza H5N1
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1776)
AUTHORS Li,Y., Liu,L., El-Sanousi,A.A., Soliman,R.T., Hussein,H.A., Bu,Z.
and Chen,H.
TITLE Direct Submission
JOURNAL Submitted (04-MAY-2010) National avian influenza reference
laboratory, Harbin Veterinary Research Institute, 427 Maduan,
Harbin, Heilongjiang 150001, China
FEATURES Location/Qualifiers
source 1..1776
/organism="Influenza A virus
(A/chicken/Egypt/36-4/2008(H5N1))"
/mol_type="viral cRNA"
/strain="A/chicken/Egypt/36-4/2008"
/serotype="H5N1"
/isolation_source="Swab"
/host="chicken"
/db_xref="taxon:761832"
/segment="4"
/lab_host="E1 passage(s)"
/country="Egypt"
/collection_date="02-Jul-2008"
gene 29..1732
/gene="HA"
CDS 29..1732
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADG28681.1"
/db_xref="GI:295789204"
/translation="MEKIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFLNVSEWSYIVEKINPA
NDLCYPGNFNNYEELKHLLSRINRFEKIQIIPKSSWPDHEASLGVSAACPYQGGPSFY
RNVVWLIKKNNTYPTIEKSYHNTNQEDLLVLWGIHHTNDAAEQTRIYKNPTTYISVGT
STLNQRLVPKIATRSKVNGQSGRVEFLWTILKSNDTINFESNGNFIAPEYAYKIVKKG
DSTIMKSELEYGNCNTRCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR
NSPQRERRRKRGLFGAIAGCIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDG
VTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENE
RTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHRCDNECMESVRNGTYDYPQYS
EEARLKREEISGVKLESIRTYQILSIYSTVASSLALAIMVAGLSLCMCSNGSLQCRIC
I"
sig_peptide 29..76
/gene="HA"
mat_peptide 77..1063
/gene="HA"
/product="HA1"
mat_peptide 1064..1729
/gene="HA"
/product="HA2"
ORIGIN
1 agcaaaagca ggggtataat ctgtcaaaat ggagaaaata gtgcttcttc ttgcaatagt
61 cagtcttgtt aaaagtgatc agatttgcat tggttaccat gcaaacaact caacagagca
121 ggttgacaca ataatggaaa agaacgtcac tgttacacac gctcaagaca tactggaaaa
181 gacacacaac gggaaactct gcgatctaga tggagtgaag cctctaattt taagagattg
241 tagtgtagct ggatggctcc tcgggaaccc aatgtgtgac gaattcctca atgtgtcgga
301 atggtcttac atagtggaga agatcaatcc agccaatgac ctctgttacc cagggaattt
361 caacaactat gaagaactga aacacctatt gagcagaata aaccgttttg agaaaattca
421 gatcatcccc aaaagttctt ggccagatca tgaagcctca ttaggagtga gcgcagcatg
481 tccataccag ggaggaccct ccttttatag aaatgtggta tggcttatca aaaagaacaa
541 tacataccca acaatagaga aaagttacca taataccaat caagaagatc ttttggtgct
601 gtgggggatt caccatacta atgatgcggc agagcagaca aggatctata aaaacccaac
661 tacctatatt tccgttggga catcaacact aaaccagaga ttggtaccaa agatagccac
721 tagatctaaa gtaaacgggc aaagtggaag ggtggagttc ctttggacaa ttttaaaatc
781 gaatgataca ataaacttcg agagtaatgg aaatttcatt gctccagaat atgcatacaa
841 aattgtcaag aaaggagact caacaattat gaaaagtgaa ttggaatatg gtaactgcaa
901 caccaggtgt cagactccgg tgggggcgat aaactctagt atgccattcc acaacataca
961 ccctctcacc atcggagaat gtcccaaata tgtgaaatca aacaaattag tccttgcgac
1021 tgggctcaga aatagtcctc aaagagagag aagaagaaaa agaggactgt ttggagctat
1081 agcaggttgt atagagggag gatggcaggg aatggtagat ggttggtatg ggtaccacca
1141 cagcaatgag cagggaagtg ggtacgctgc agacaaagaa tccactcaaa aggcaataga
1201 tggagtcacc aataaggtca actcgatcat tgacaaaatg aacactcagt ttgaggctgt
1261 tggaagggaa tttaataact tggaaaggag aatagaaaat ttaaacaaga agatggaaga
1321 cgggttccta gatgtctgga cttataatgc tgaacttctg gttctcatgg aaaatgagag
1381 aactctagac tttcatgact caaatgtcaa gaacctttac gacaaggtgc gactacagct
1441 tagggataat gcaaaggagc ttggtaacgg ttgtttcgag ttctatcaca gatgcgataa
1501 tgaatgtatg gaaagtgtaa gaaacggaac gtatgactac ccgcagtatt cagaagaagc
1561 aagattaaaa agagaggaaa taagtggagt aaaattggaa tcaataagaa cttaccaaat
1621 actatcaatt tattcaacag tggcaagttc cctagcactg gcaatcatgg tggctggtct
1681 atctttatgc atgtgctcca atggatcgtt acaatgcaga atttgcattt aaatttgtga
1741 gttcagatag tagttaaaaa cacccttgtt tctact

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PostPosted: Fri May 07, 2010 9:19 am 
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Upstream identity

dbj|AB557633.1| Influenza A virus (A/oriental magpie robin/Ho... 119 1e-24
dbj|AB557629.1| Influenza A virus (A/feral pigeon/Hong Kong/3... 119 1e-24
gb|GQ412056.1| Influenza A virus (A/chicken/Korea/YAQ173/2008... 119 1e-24
gb|GQ412055.1| Influenza A virus (A/chicken/Korea/USQ284/2008... 119 1e-24
gb|GQ412054.1| Influenza A virus (A/duck/Korea/NSQ263/2008(H5... 119 1e-24
gb|GQ412053.1| Influenza A virus (A/chicken/Korea/Gimje/2008(... 119 1e-24
gb|GQ412052.1| Influenza A virus (A/duck/Korea/JEQ149/2008(H5... 119 1e-24
gb|GQ412051.1| Influenza A virus (A/chicken/Korea/ISQ250/2008... 119 1e-24
gb|GU182142.1| Influenza A virus (A/chicken/Hunan/3/2007(H5N1... 119 1e-24
gb|GU182150.1| Influenza A virus (A/duck/Hunan/3/2007(H5N1)) ... 119 1e-24
gb|GU182158.1| Influenza A virus (A/chicken/Hunan/8/2008(H5N1... 119 1e-24
gb|GU182166.1| Influenza A virus (A/duck/Hunan/8/2008(H5N1)) ... 119 1e-24
gb|GU182174.1| Influenza A virus (A/environment/Hunan/7-73/20... 119 1e-24
gb|GU182190.1| Influenza A virus (A/environment/Hunan/6-45/20... 119 1e-24
gb|GU182198.1| Influenza A virus (A/environment/Hunan/5-25/20... 119 1e-24
gb|GU182206.1| Influenza A virus (A/environment/Hunan/5-32/20... 119 1e-24
dbj|AB523775.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB523767.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB523759.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523368.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523366.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB522001.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB521999.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB521163.1| Influenza A virus (A/crested myna/Hong Kong/1... 119 1e-24
dbj|AB521161.1| Influenza A virus (A/large billed crow/Hong K... 119 1e-24
dbj|AB520708.1| Influenza A virus (A/whooper swan/Mongolia/6/... 119 1e-24
dbj|AB517667.1| Influenza A virus (A/whooper swan/Mongolia/8/... 119 1e-24
dbj|AB517665.1| Influenza A virus (A/whooper swan/Mongolia/2/... 119 1e-24
dbj|AB517663.1| Influenza A virus (A/grey heron/Hong Kong/779... 119 1e-24
dbj|AB517661.1| Influenza A virus (A/house crow/Hong Kong/767... 119 1e-24
gb|GQ386150.1| Influenza A virus (A/bean goose/Tyva/10/2009(H... 119 1e-24
gb|GQ386142.1| Influenza A virus (A/grebe/Tyva/3/2009(H5N1)) ... 119 1e-24
gb|GQ338087.1| Influenza A virus (A/great crested grebe/Tyva/... 119 1e-24
gb|GQ338084.1| Influenza A virus (A/black-headed gull/Tyva/11... 119 1e-24
gb|GQ290463.1| Influenza A virus (A/environment/Dongting Lake... 119 1e-24
gb|CY041049.1| Influenza A virus (A/chicken/Laos/XDM006/2008(... 119 1e-24
gb|CY041048.1| Influenza A virus (A/chicken/Laos/OX005/2008(H... 119 1e-24
gb|CY041047.1| Influenza A virus (A/chicken/Laos/LPQ001/2008(... 119 1e-24
gb|FJ654295.1| Influenza A virus (A/chicken/Primorsky/85/2008... 119 1e-24
gb|CY036261.1| Influenza A virus (A/magpie robin/Hong Kong/18... 119 1e-24
gb|CY036253.1| Influenza A virus (A/magpie robin/Hong Kong/10... 119 1e-24
gb|CY036245.1| Influenza A virus (A/grey heron/Hong Kong/1046... 119 1e-24
gb|CY036237.1| Influenza A virus (A/great egret/Hong Kong/807... 119 1e-24
gb|CY036229.1| Influenza A virus (A/black-crowned night heron... 119 1e-24
gb|CY036221.1| Influenza A virus (A/common buzzard/Hong Kong/... 119 1e-24
gb|CY036213.1| Influenza A virus (A/grey heron/Hong Kong/3088... 119 1e-24
gb|CY036205.1| Influenza A virus (A/little egret/Hong Kong/88... 119 1e-24
gb|CY036197.1| Influenza A virus (A/little egret/Hong Kong/85... 119 1e-24
gb|CY036093.1| Influenza A virus (A/peregrine falcon/Hong Kon... 119 1e-24
dbj|AB458247.1| Influenza A virus (A/whooper swan/Aomori/2/20... 119 1e-24
dbj|AB458239.1| Influenza A virus (A/whooper swan/Aomori/1/20... 119 1e-24
dbj|AB436736.1| Influenza A virus (A/whooper swan/Akita/1/200... 119 1e-24
gb|EU676174.1| Influenza A virus (A/chicken/Primorje/1/2008(H... 119 1e-24
dbj|AB436902.1| Influenza A virus (A/whooper swan/Hokkaido/2/... 119 1e-24
dbj|AB436550.1| Influenza A virus (A/whooper swan/Hokkaido/1/... 119 1e-24

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PostPosted: Fri May 07, 2010 12:15 pm 
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More sequences have stretches of identitie with Fujian clade 2.3.2

Here is another travel log covering three consecutive polymorphisms

dbj|AB557629.1| Influenza A virus (A/feral pigeon/Hong Kong/3... 75.8 8e-12
gb|GQ412056.1| Influenza A virus (A/chicken/Korea/YAQ173/2008... 75.8 8e-12
gb|GQ412055.1| Influenza A virus (A/chicken/Korea/USQ284/2008... 75.8 8e-12
gb|GQ412054.1| Influenza A virus (A/duck/Korea/NSQ263/2008(H5... 75.8 8e-12
gb|GQ412053.1| Influenza A virus (A/chicken/Korea/Gimje/2008(... 75.8 8e-12
gb|GQ412052.1| Influenza A virus (A/duck/Korea/JEQ149/2008(H5... 75.8 8e-12
gb|GQ412051.1| Influenza A virus (A/chicken/Korea/ISQ250/2008... 75.8 8e-12
gb|GU182142.1| Influenza A virus (A/chicken/Hunan/3/2007(H5N1... 75.8 8e-12
gb|GU182150.1| Influenza A virus (A/duck/Hunan/3/2007(H5N1)) ... 75.8 8e-12
gb|GU182158.1| Influenza A virus (A/chicken/Hunan/8/2008(H5N1... 75.8 8e-12
gb|GU182198.1| Influenza A virus (A/environment/Hunan/5-25/20... 75.8 8e-12
gb|GU182206.1| Influenza A virus (A/environment/Hunan/5-32/20... 75.8 8e-12
gb|GQ290463.1| Influenza A virus (A/environment/Dongting Lake... 75.8 8e-12
gb|CY041049.1| Influenza A virus (A/chicken/Laos/XDM006/2008(... 75.8 8e-12
gb|CY041048.1| Influenza A virus (A/chicken/Laos/OX005/2008(H... 75.8 8e-12
gb|CY041047.1| Influenza A virus (A/chicken/Laos/LPQ001/2008(... 75.8 8e-12
gb|FJ654295.1| Influenza A virus (A/chicken/Primorsky/85/2008... 75.8 8e-12
gb|CY036229.1| Influenza A virus (A/black-crowned night heron... 75.8 8e-12
gb|CY036221.1| Influenza A virus (A/common buzzard/Hong Kong/... 75.8 8e-12
gb|CY036205.1| Influenza A virus (A/little egret/Hong Kong/88... 75.8 8e-12
dbj|AB458247.1| Influenza A virus (A/whooper swan/Aomori/2/20... 75.8 8e-12
dbj|AB458239.1| Influenza A virus (A/whooper swan/Aomori/1/20... 75.8 8e-12
dbj|AB436736.1| Influenza A virus (A/whooper swan/Akita/1/200... 75.8 8e-12
gb|EU676174.1| Influenza A virus (A/chicken/Primorje/1/2008(H... 75.8 8e-12
dbj|AB436902.1| Influenza A virus (A/whooper swan/Hokkaido/2/... 75.8 8e-12
dbj|AB436550.1| Influenza A virus (A/whooper swan/Hokkaido/1/... 75.8 8e-12

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PostPosted: Fri May 07, 2010 1:28 pm 
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Posts: 1835
Location: germany
why does Harbin sequence Egypt sequences

not listed yet at genbank-ftp ?
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/


Egypt 2010 sequences at genbank:

accession length host segment subtype country year Virus name 27 nucleotide sequences Age Gender
CY062464 1704 Human 4 (HA) H5N1 Egypt 2010/01/11 Influenza A virus (A/Egypt/N00269/2010(H5N1))
CY062465 1350 Human 6 (NA) H5N1 Egypt 2010/01/11 Influenza A virus (A/Egypt/N00269/2010(H5N1))
CY062466 1704 Human 4 (HA) H5N1 Egypt 2010/01/12 Influenza A virus (A/Egypt/N00270/2010(H5N1))
CY062467 1350 Human 6 (NA) H5N1 Egypt 2010/01/12 Influenza A virus (A/Egypt/N00270/2010(H5N1))
GU811748 1584 Avian 4 (HA) H5N1 Egypt 2010/02 Influenza A virus (A/chicken/Egypt/1052S-NLQP/2010(H5N1))
CY062468 1704 Human 4 (HA) H5N1 Egypt 2010/02/02 Influenza A virus (A/Egypt/N01360/2010(H5N1))
CY062469 1350 Human 6 (NA) H5N1 Egypt 2010/02/02 Influenza A virus (A/Egypt/N01360/2010(H5N1))
CY062470 1704 Human 4 (HA) H5N1 Egypt 2010/02/07 Influenza A virus (A/Egypt/N01644/2010(H5N1))
CY062471 1350 Human 6 (NA) H5N1 Egypt 2010/02/07 Influenza A virus (A/Egypt/N01644/2010(H5N1))
CY062472 1704 Human 4 (HA) H5N1 Egypt 2010/02/12 Influenza A virus (A/Egypt/N01982/2010(H5N1))
CY062473 1350 Human 6 (NA) H5N1 Egypt 2010/02/12 Influenza A virus (A/Egypt/N01982/2010(H5N1))
CY062476 1704 Human 4 (HA) H5N1 Egypt 2010/02/13 Influenza A virus (A/Egypt/N02127/2010(H5N1))
CY062477 1350 Human 6 (NA) H5N1 Egypt 2010/02/13 Influenza A virus (A/Egypt/N02127/2010(H5N1))
CY062474 1704 Human 4 (HA) H5N1 Egypt 2010/02/15 Influenza A virus (A/Egypt/N02038/2010(H5N1))
CY062475 1350 Human 6 (NA) H5N1 Egypt 2010/02/15 Influenza A virus (A/Egypt/N02038/2010(H5N1))
CY062478 1704 Human 4 (HA) H5N1 Egypt 2010/02/23 Influenza A virus (A/Egypt/N02554/2010(H5N1))
CY062479 1350 Human 6 (NA) H5N1 Egypt 2010/02/23 Influenza A virus (A/Egypt/N02554/2010(H5N1))
CY062480 1704 Human 4 (HA) H5N1 Egypt 2010/02/27 Influenza A virus (A/Egypt/N02770/2010(H5N1))
CY062481 1350 Human 6 (NA) H5N1 Egypt 2010/02/27 Influenza A virus (A/Egypt/N02770/2010(H5N1))
CY062482 1704 Human 4 (HA) H5N1 Egypt 2010/03/03 Influenza A virus (A/Egypt/N03071/2010(H5N1))
CY062483 1350 Human 6 (NA) H5N1 Egypt 2010/03/03 Influenza A virus (A/Egypt/N03071/2010(H5N1))
CY062484 1704 Human 4 (HA) H5N1 Egypt 2010/03/07 Influenza A virus (A/Egypt/N03072/2010(H5N1))
CY062485 1350 Human 6 (NA) H5N1 Egypt 2010/03/07 Influenza A virus (A/Egypt/N03072/2010(H5N1))
CY062609 1779 Avian 4 (HA) H5N1 Egypt 2010/03/20 Influenza A virus (A/chicken/Egypt/6-A/2010(H5N1))
CY062610 1779 Avian 4 (HA) H5N1 Egypt 2010/03/20 Influenza A virus (A/chicken/Egypt/8-C/2010(H5N1))
CY062486 1704 Human 4 (HA) H5N1 Egypt 2010/03/31 Influenza A virus (A/Egypt/N04434/2010(H5N1))
CY062487 1350 Human 6 (NA) H5N1 Egypt 2010/03/31 Influenza A virus (A/Egypt/N04434/2010(H5N1))



22.Mar 2010 http://www.ncbi.nlm.nih.gov/nuccore/295 ... rt=genbank
20.Mar.2010 http://www.ncbi.nlm.nih.gov/nuccore/295 ... rt=genbank

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no patents on genes, publish the GISAID sequences !


Last edited by gsgs on Fri May 07, 2010 1:44 pm, edited 2 times in total.

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PostPosted: Fri May 07, 2010 1:38 pm 
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Posts: 56044
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niman wrote:
Travel log of A/chicken/Egypt/36-4/2008

gb|GQ412056.1| Influenza A virus (A/chicken/Korea/YAQ173/2008... 119 1e-24
gb|GQ412055.1| Influenza A virus (A/chicken/Korea/USQ284/2008... 119 1e-24
gb|GQ412054.1| Influenza A virus (A/duck/Korea/NSQ263/2008(H5... 119 1e-24
gb|GQ412053.1| Influenza A virus (A/chicken/Korea/Gimje/2008(... 119 1e-24
gb|GQ412052.1| Influenza A virus (A/duck/Korea/JEQ149/2008(H5... 119 1e-24
gb|GQ412051.1| Influenza A virus (A/chicken/Korea/ISQ250/2008... 119 1e-24
gb|GU182198.1| Influenza A virus (A/environment/Hunan/5-25/20... 119 1e-24
dbj|AB523775.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB523767.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB523759.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523368.1| Influenza A virus (A/ruddy shelduck/Mongolia/... 119 1e-24
dbj|AB523366.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB522001.1| Influenza A virus (A/common goldeneye/Mongoli... 119 1e-24
dbj|AB521999.1| Influenza A virus (A/bar-headed goose/Mongoli... 119 1e-24
dbj|AB520708.1| Influenza A virus (A/whooper swan/Mongolia/6/... 119 1e-24
dbj|AB517667.1| Influenza A virus (A/whooper swan/Mongolia/8/... 119 1e-24
dbj|AB517665.1| Influenza A virus (A/whooper swan/Mongolia/2/... 119 1e-24
gb|GQ227383.1| Influenza A virus (A/pika/Qinghai/SHK/2007(H5N... 119 1e-24
gb|GQ227380.1| Influenza A virus (A/pika/Qinghai/GRL/2007(H5N... 119 1e-24
gb|GQ227367.1| Influenza A virus (A/pika/Qinghai/HMH/2007(H5N... 119 1e-24
gb|GQ386150.1| Influenza A virus (A/bean goose/Tyva/10/2009(H... 119 1e-24
gb|GQ386142.1| Influenza A virus (A/grebe/Tyva/3/2009(H5N1)) ... 119 1e-24
gb|GQ338087.1| Influenza A virus (A/great crested grebe/Tyva/... 119 1e-24
gb|GQ338084.1| Influenza A virus (A/black-headed gull/Tyva/11... 119 1e-24
gb|GQ290463.1| Influenza A virus (A/environment/Dongting Lake... 119 1e-24
gb|FJ654295.1| Influenza A virus (A/chicken/Primorsky/85/2008... 119 1e-24
gb|CY036229.1| Influenza A virus (A/black-crowned night heron... 119 1e-24
gb|CY036221.1| Influenza A virus (A/common buzzard/Hong Kong/... 119 1e-24
gb|CY036205.1| Influenza A virus (A/little egret/Hong Kong/88... 119 1e-24
gb|CY036189.1| Influenza A virus (A/house crow/Hong Kong/5288... 119 1e-24
gb|CY036181.1| Influenza A virus (A/Daurian starling/Hong Kon... 119 1e-24
gb|CY036173.1| Influenza A virus (A/common magpie/Hong Kong/5... 119 1e-24
gb|CY036165.1| Influenza A virus (A/red-billed starling/Hong ... 119 1e-24
gb|CY036093.1| Influenza A virus (A/peregrine falcon/Hong Kon... 119 1e-24
gb|CY036045.1| Influenza A virus (A/peregrine falcon/Hong Kon... 119 1e-24
gb|EU676174.1| Influenza A virus (A/chicken/Primorje/1/2008(H... 119 1e-24
dbj|AB436902.1| Influenza A virus (A/whooper swan/Hokkaido/2/... 119 1e-24

More upstream matches

gb|GU182166.1| Influenza A virus (A/duck/Hunan/8/2008(H5N1)) ... 119 1e-24
dbj|AB557629.1| Influenza A virus (A/feral pigeon/Hong Kong/3... 111 3e-22
gb|GQ412056.1| Influenza A virus (A/chicken/Korea/YAQ173/2008... 111 3e-22
gb|GQ412055.1| Influenza A virus (A/chicken/Korea/USQ284/2008... 111 3e-22
gb|GQ412054.1| Influenza A virus (A/duck/Korea/NSQ263/2008(H5... 111 3e-22
gb|GQ412053.1| Influenza A virus (A/chicken/Korea/Gimje/2008(... 111 3e-22
gb|GQ412052.1| Influenza A virus (A/duck/Korea/JEQ149/2008(H5... 111 3e-22
gb|GQ412051.1| Influenza A virus (A/chicken/Korea/ISQ250/2008... 111 3e-22
gb|GU182142.1| Influenza A virus (A/chicken/Hunan/3/2007(H5N1... 111 3e-22
gb|GU182150.1| Influenza A virus (A/duck/Hunan/3/2007(H5N1)) ... 111 3e-22
gb|GU182158.1| Influenza A virus (A/chicken/Hunan/8/2008(H5N1... 111 3e-22
gb|GU182174.1| Influenza A virus (A/environment/Hunan/7-73/20... 111 3e-22
gb|GU182190.1| Influenza A virus (A/environment/Hunan/6-45/20... 111 3e-22
gb|GU182198.1| Influenza A virus (A/environment/Hunan/5-25/20... 111 3e-22
gb|GU182206.1| Influenza A virus (A/environment/Hunan/5-32/20... 111 3e-22
dbj|AB521163.1| Influenza A virus (A/crested myna/Hong Kong/1... 111 3e-22
dbj|AB521161.1| Influenza A virus (A/large billed crow/Hong K... 111 3e-22
dbj|AB517663.1| Influenza A virus (A/grey heron/Hong Kong/779... 111 3e-22
dbj|AB517661.1| Influenza A virus (A/house crow/Hong Kong/767... 111 3e-22
gb|GQ227383.1| Influenza A virus (A/pika/Qinghai/SHK/2007(H5N... 111 3e-22
gb|GQ227380.1| Influenza A virus (A/pika/Qinghai/GRL/2007(H5N... 111 3e-22
gb|GQ227367.1| Influenza A virus (A/pika/Qinghai/HMH/2007(H5N... 111 3e-22
gb|GQ290463.1| Influenza A virus (A/environment/Dongting Lake... 111 3e-22
gb|CY041049.1| Influenza A virus (A/chicken/Laos/XDM006/2008(... 111 3e-22
gb|CY041048.1| Influenza A virus (A/chicken/Laos/OX005/2008(H... 111 3e-22
gb|CY041047.1| Influenza A virus (A/chicken/Laos/LPQ001/2008(... 111 3e-22
gb|FJ654295.1| Influenza A virus (A/chicken/Primorsky/85/2008... 111 3e-22
gb|CY036261.1| Influenza A virus (A/magpie robin/Hong Kong/18... 111 3e-22
gb|CY036253.1| Influenza A virus (A/magpie robin/Hong Kong/10... 111 3e-22
gb|CY036245.1| Influenza A virus (A/grey heron/Hong Kong/1046... 111 3e-22
gb|CY036237.1| Influenza A virus (A/great egret/Hong Kong/807... 111 3e-22
gb|CY036229.1| Influenza A virus (A/black-crowned night heron... 111 3e-22
gb|CY036221.1| Influenza A virus (A/common buzzard/Hong Kong/... 111 3e-22
gb|CY036213.1| Influenza A virus (A/grey heron/Hong Kong/3088... 111 3e-22
gb|CY036205.1| Influenza A virus (A/little egret/Hong Kong/88... 111 3e-22
gb|CY036197.1| Influenza A virus (A/little egret/Hong Kong/85... 111 3e-22
gb|CY036189.1| Influenza A virus (A/house crow/Hong Kong/5288... 111 3e-22
gb|CY036181.1| Influenza A virus (A/Daurian starling/Hong Kon... 111 3e-22
gb|CY036173.1| Influenza A virus (A/common magpie/Hong Kong/5... 111 3e-22
gb|CY036165.1| Influenza A virus (A/red-billed starling/Hong ... 111 3e-22
gb|CY036093.1| Influenza A virus (A/peregrine falcon/Hong Kon... 111 3e-22
dbj|AB458247.1| Influenza A virus (A/whooper swan/Aomori/2/20... 111 3e-22
dbj|AB458239.1| Influenza A virus (A/whooper swan/Aomori/1/20... 111 3e-22
dbj|AB436736.1| Influenza A virus (A/whooper swan/Akita/1/200... 111 3e-22

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PostPosted: Fri May 07, 2010 2:09 pm 
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gsgs wrote:
why does Harbin sequence Egypt sequences

not listed yet at genbank-ftp ?
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/



My guess is Harbin is the only lab willing to thumb their nose at the ranters in denial of recombination. Most of the recombinant sequences come from northern China, but this time the jig is up for real (and there WILL be consequences).

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PostPosted: Fri May 07, 2010 2:46 pm 
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if you'd showed me just the title of this thread and asked,
what lab I guessed had done the sequencing, I think
I'd said: Harbin

why can't we have it from two different labs in such cases ?
why didn't Egypt find that cleavage site in hundreds of sequences -
and then comes Harbin and finds it in the very first ?

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no patents on genes, publish the GISAID sequences !


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PostPosted: Fri May 07, 2010 2:47 pm 
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Posts: 56044
Location: Pittsburgh, PA USA
gsgs wrote:
if you'd showed me just the title of this thread and asked,
what lab I guessed had done the sequencing, I think
I'd said: Harbin

why can't we have it from two different labs in such cases ?
why didn't Egypt find that cleavage site in hundreds of sequences -
and then comes Harbin and finds it in the very first ?

No. Harbin PUBLISHES first. Have you looked at the hard drives in Egypt?

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