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Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)

Giuseppe

Emeritus
Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan
Yuko Uchida, Masaji Mase, Kumiko Yoneda, Atsumu Kimura, Tsuyoshi Obara, Seikou Kumagai, Takehiko Saito, Yu Yamamoto, Kikuyasu Nakamura, Kenji Tsukamoto, and Shigeo Yamaguchi

Author affiliations: National Institute of Animal Health, Kannondai, Japan (Y. Uchida, M. Mase, T. Saito, Y. Yamamoto, K. Nakamura, K. Tsukamoto, S. Yamaguchi); Japan Wildlife Research Center, Taito-ku, Tokyo, Japan (K. Yoneda); Akita Animal Hygiene Service Center of Akita Prefecture, Akita, Japan ( A. Kimura, T. Obara, S. Kumagai)

On April 21, 2008, four whooper swans were found dead at Lake Towada, Akita prefecture, Japan. Highly pathogenic avian influenza virus of the H5N1 subtype was isolated from specimens of the affected birds. The hemagglutinin (HA) gene of the isolate belongs to clade 2.3.2 in the HA
phylogenetic tree. (...)

Conclusions
Whooper swans breed in northern Eurasia and winter in Europe and eastern Asia i.e., China, the Korean peninsula, and Japan.

In Japan, ≈35,000–38,000 whooper swans spend every winter primarily in Hokkaido, Tohoku, and the Hokuriku area (10).

In the Lake Towada area, ≈300 whooper swans arrive beginning in late October; they leave the area between late March and late April (11).

In late March, summer birds begin to arrive.

According to results of satellite tracking of 8 swans (12), as well as the results of banding studies since 1961 (13), whooper swans that winter in Japan migrate from the northern end of Honshu Island to eastern Hokkaido, by means of Sakhalin, and reach eastern Siberia, where they breed.

To our knowledge, there have been no reports of whooper swans that winter on the Eurasian continent migrating north through Japan.

In light of the migratory route mentioned above, the whooper swans found dead at Lake Towada were most likely recently infected with HPAIV (H5N1) in Japan.

It is unlikely that the swans were infected before they flew to Japan in autumn, maintained the virus within the flock, and then suddenly developed the disease after no apparent infections for several months.

Although the susceptibility of a certain species of birds to a subtype H5N1 virus may be different depending on the virus strain (14), whooper swans as well as mute swans have been considered to be susceptible species to HPAIV (H5N1), as they showed a fulminant course of disease at the outbreak in Germany in 2006 (7).

The possibility that the swans were infected by domestic fowl is low because there has been no report of HPAI among domestic fowl in Japan since the beginning of 2008.

One possible explanation is that other wild birds brought the virus from outside the country.

Although it is not known whether any birds wintering on the continent migrate north through Japan, passage visitor birds such as wader birds migrate from south to north through Japan in spring; summer birds, e.g., egrets, swallows, songbirds, and some raptors, come to Japan from the south in spring for breeding.

Also, the possibility of anthropogenic introduction of virus, such as by inappropriate importation of birds, meats, or materials, cannot be excluded.

In conclusion, genetic analysis demonstrates that the virus that killed the 4 swans in Japan in 2008 is genetically distinguishable from the strains that caused previous poultry outbreaks in Japan, ruling out a possibility of resurgence of previously introduced HPAIV in Japan.

After the incident we describe, 2 other whooper swan cases of HPAIV (H5N1) infection were confirmed in eastern Hokkaido in early May.

Possible involvement of wild birds in the introduction of the virus to Japan requires further scrutiny.
-
http://www.cdc.gov/eid/content/14/9/pdfs/08-0655.pdf
-------
 

Attachments

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Sequencing analysis of the entire genome of WsAk08 (GenBank accession nos.​
AB436731?AB436738)
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

All 8 inoculated chickens died by 26 hours after inoculation. This result coincides with the sequence analysis of the hemagglutinin
(HA) gene, showing that the HA protein possesses a series of basic amino acids (PQRERRRKR) at the cleavage site.
Phylogenetic analysis of the HA1 region of the HA gene (Figure 2) showed that WsAk08 belongs to clade 2.3.2


RERRRKR = Fujian H5N1
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

<TABLE id=logo cellSpacing=0 cellPadding=0 width="100%" border=0><TBODY><TR><TD><LABEL class=searchbar_text for=db>Search </LABEL><SELECT id=db name=EntrezSystem2.PEntrez.Nuccore.SearchBar.Db cmd="" tab="" dbname="" sid="1"><OPTION value=pubmed>PubMed</OPTION><OPTION value=protein>Protein</OPTION><OPTION value=nuccore selected>Nucleotide</OPTION><OPTION value=nucgss>GSS</OPTION><OPTION value=nucest>EST</OPTION><OPTION value=structure>Structure</OPTION><OPTION value=genome>Genome</OPTION><OPTION value=books>Books</OPTION><OPTION value=cancerchromosomes>CancerChromosomes</OPTION><OPTION value=cdd>Conserved Domains</OPTION><OPTION value=gap>dbGaP</OPTION><OPTION value=domains>3D Domains</OPTION><OPTION value=gene>Gene</OPTION><OPTION value=genomeprj>Genome Project</OPTION><OPTION value=gensat>GENSAT</OPTION><OPTION value=geo>GEO Profiles</OPTION><OPTION value=gds>GEO DataSets</OPTION><OPTION value=homologene>HomoloGene</OPTION><OPTION value=journals>Journals</OPTION><OPTION value=mesh>MeSH</OPTION><OPTION value=ncbisearch>NCBI Web Site</OPTION><OPTION value=nlmcatalog>NLM Catalog</OPTION><OPTION value=omia>OMIA</OPTION><OPTION value=omim>OMIM</OPTION><OPTION value=pmc>PMC</OPTION><OPTION value=popset>PopSet</OPTION><OPTION value=probe>Probe</OPTION><OPTION value=proteinclusters>Protein Clusters</OPTION><OPTION value=pcassay>PubChem BioAssay</OPTION><OPTION value=pccompound>PubChem Compound</OPTION><OPTION value=pcsubstance>PubChem Substance</OPTION><OPTION value=snp>SNP</OPTION><OPTION value=taxonomy>Taxonomy</OPTION><OPTION value=toolkit>ToolKit</OPTION><OPTION value=unigene>UniGene</OPTION><OPTION value=unists>UniSTS</OPTION></SELECT><LABEL class=searchbar_text for=term> for </LABEL><INPUT id=term size=45 value=AB436731 name=EntrezSystem2.PEntrez.Nuccore.SearchBar.Term cmd="Go" sid="1"><BUTTON id=Go name=EntrezSystem2.PEntrez.Nuccore.SearchBar.Go submit="yes" cmd="Go" sid="1">Go</BUTTON><BUTTON id=Clear name=EntrezSystem2.PEntrez.Nuccore.SearchBar.Clear sid="1" prop1="">Clear</BUTTON>
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Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Sequencing analysis of the entire genome of WsAk08 (GenBank accession nos.​

AB436731?AB436738)
These sequences will be available in Japan shortly.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

</PRE>
LOCUS AB436731 2280 bp RNA linear VRL 02-AUG-2008DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) PB2 gene for polymerase basic protein 2, complete cds.ACCESSION AB436731VERSION AB436731.1KEYWORDS .SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1)) ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1)) Viruses; ssRNA negative-strand viruses; Orthomyxoviridae; Influenzavirus A.REFERENCE 1 (bases 1 to 2280) AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S. TITLE Direct Submission JOURNAL Submitted (08-MAY-2008) to the DDBJ/EMBL/GenBank databases. Contact:Yuko Uchida National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Research Teams for Zoonotic Diseases and Viral Diseases; 3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL :http://niah.naro.affrc.go.jp/index-j.htmlREFERENCE 2 AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S., Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S. TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan JOURNAL Emerging Infect. Dis. (2008) In pressCOMMENT FEATURES Location/Qualifiers source 1..2280 /country="Japan" /db_xref="taxon:527687" /mol_type="genomic RNA" /organism="Influenza A virus (A/whooper swan/Akita/2008(H5N1))" /serotype="H5N1" /strain="A/whooper swan/Akita/2008" CDS 1..2280 /codon_start=1 /gene="PB2" /product="polymerase basic protein 2" /protein_id="BAG68173.1" /transl_table=1 /translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA LRMKWMMAMKYPITADKRIIEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQ DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADP LASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS GSSVTKEEEVLTGNLQTLKIRVHEGYEEFTMVGQRATAILRKATRRLIQLIVSGRNEQ SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG IEPIDNVMGMIGLLPDMTPSTELSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQR GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQ DPTMLYNKMEFEPFQSLVPKATRSQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA PPEQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTILGKDAGALTEDPDEG TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD SSILTDSQTATKRIRMAIN"BASE COUNT 772 a 436 c 578 g 494 tORIGIN 1 atggaaagaa taaaagaatt aagagatcta atgtcacagt cccgcactcg cgagatacta 61 acaaaaacca ctgtggacca tatggccata atcaagaaat acacatcagg aagacaagag 121 aagaatcctg ctctcagaat gaaatggatg atggcaatga agtatccgat cacagcggac 181 aagagaataa tagagatgat tcctgaaagg aatgaacaag ggcagacgct ctggagcaag 241 acaaatgatg ctgggtcgga cagggtgatg gtgtcccccc tagctgtaac ttggtggaat 301 aggaatgggc cgacgacaag tacagttcat tatccaaaag tttacaaaac atacttcgag 361 aaggttgaaa ggttaaaaca tggaaccttt ggtcccgttc atttccgaaa ccaagttaaa 421 atacgccgcc gagttgatac aaaccctggc catgcagatc tcagtgctaa agaagcacaa 481 gatgttatca tggaagttgt cttcccaaat gaagtgggag ctagaatatt gacttcagag 541 tcgcaattga caataacgaa agagaaaaaa gaagagctcc aagactgtaa gattgctccc 601 ttaatggttg catacatgtt ggagagggaa ctggtccgca aaaccagatt cctaccggta 661 gcaggcggaa caagcagtgt gtacattgaa gtactgcatt tgactcaagg aacctgctgg 721 gaacagatgt acactccggg cggagaagta agaaatgacg atgttgacca gagtttgatc 781 attgctgcca gaaacattgt taggagagca acggtatcag cggacccatt ggcatcactg 841 ctggagatgt gtcacagcac acaaattggt gggataagga tggtggacat ccttaggcaa 901 aatccaactg aagaacaagc tgtggatata tgcaaagcag caatgggtct gaggatcagt 961 tcatccttta gttttggagg tttcaccttc aaaagaacaa gtgggtcatc cgtcacgaag 1021 gaagaggaag tgctcacggg caacctccaa acattgaaaa taagagtaca tgaggggtat 1081 gaagaattca caatggttgg gcagagggca acagctatcc tgaggaaagc aactagaagg 1141 ctgattcagt tgatagtaag cggaagaaac gaacaatcaa tcgctgaggc aatcattgta 1201 gcgatggtgt tctcacagga ggattgcatg ataaaggcag tccgaggcga tctaaatttc 1261 gtaaacagag caaaccaaag attaaacccc atgcatcaac tcctgagaca ttttcaaaag 1321 gacgcaaaag tgctatttca gaattgggga attgaaccca ttgataatgt catggggatg 1381 atcggattat tacctgacat gactcccagc acagaactgt cactgagagg agtaagagtt 1441 agtaaaatgg gagtggatga atattcaagc actgaaagag tagttgtaag cattgaccgc 1501 ttcttaaggg ttagagatca gcgggggaat gtactcttat ctcccgaaga ggtcagcgaa 1561 acccagggaa cagagaagtt gacaataaca tattcgtcat caatgatgtg ggaaatcaac 1621 ggtcctgagt cagtgcttgt caacacctat caatggatca tcagaaactg ggagaccgta 1681 aaaattcaat ggtctcagga ccccacgatg ctgtacaata agatggagtt cgaaccgttc 1741 caatccttgg tacctaaagc taccagaagt caatacagtg gatttgtgag aacattattc 1801 caacaaatgc gtgacgtact ggggacattt gatactgtcc agataataaa gctgctacca 1861 tttgcagcag caccacctga gcagagcaga atgcagtttt cttctctaac tgtgaatgta 1921 agaggctcag gaatgagaat acttgtaagg ggcaattctc ctgtgttcaa ctacaataag 1981 gcaaccaaaa ggcttaccat tcttggaaag gacgcaggtg cattaacaga ggatccagac 2041 gaggggacag ccggagtgga atctgcagta ctgaggggat tcctaattct aggcaaggag 2101 gacaaaagat atggaccagc attgagcatc aatgaactga gcaatcttgc aaaaggggag 2161 aaagctaatg tgctgatagg acaaggagac gtagtgttgg taatgaaacg gaaacgggac 2221 tctagcatac ttactgacag ccagacagcg accaaaagaa ttcggatggc catcaattag</PRE>
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

The Akita PB2 differs from A/whooper swan/Hokkaido/1/2008 at 1 position.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436732 2274 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) PB1 gene for
polymerase basic protein 1, complete cds.
ACCESSION AB436732
VERSION AB436732.1 GI:195536902
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 2274)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..2274
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene 1..2274
/gene="PB1"
CDS 1..2274
/gene="PB1"
/codon_start=1
/product="polymerase basic protein 1"
/protein_id="BAG68174.1"
/db_xref="GI:195536903"
/translation="MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVN
RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI
FENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEIFRSNGLTANES
GRLIDFLKDVMESMDKEEMEITTHFQRKRRVRDNMTKKMITQRTIGKKKQRLNKRSYL
IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN
EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR
DVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLANIDLKYFNDLTKKKIEKI
RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSME
LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT
QIQTRRSFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRL
CNPLNPFVSHKEIESVNNAIVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI
LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF
AEIMKICSTIEELRRQK"
ORIGIN
1 atggatgtca acccgacttt acttttcttg aaagtgccag tgcaaaatgc tataagtacc
61 acattccctt atactggaga ccctccatac agccatggaa cagggacagg atacactatg
121 gacacagtca acagaacaca ccaatattcg gaaaaaggga agtggacaac aaacacagag
181 actggagcac cccaactcaa cccgattgat ggaccactac ctgaggataa tgagcccagt
241 gggtatgcac aaacagattg tgtattggaa gcaatggctt tccttgaaga atcccaccca
301 gggatctttg aaaattcgtg tcttgaaacg atggaaattg ttcaacaaac aagagtggat
361 aaactgaccc aaggtcgcca gacttatgac tggacattga atagaaacca accggctgcg
421 actgctttgg ccaacactat agaaatcttc agatcaaacg gtctgacagc aaatgaatct
481 ggacggctga tagatttcct caaggatgtg atggaatcaa tggataagga agaaatggag
541 ataacaacac atttccagag aaagagaaga gtaagggaca acatgaccaa gaaaatgata
601 acacaaagaa caatagggaa gaaaaaacaa aggctgaaca aaaggagcta cctgataaga
661 gcactgacat tgaacacaat gaccaaggat gcagaaagag gcaaattgaa gaggcgagca
721 attgcaacac ccgggatgca aatcagagga ttcgtgtatt ttgttgaaac actagcgagg
781 agtatctgtg agaaacttga gcaatctgga ctcccagtcg gagggaatga gaagaaagct
841 aaattggcaa acgtcgtgag gaagatgatg actaactcac aggatactga actctccttt
901 acaattactg gggacaatac aaaatggaat gagaatcaaa atcctaggat gtttctggca
961 atgataacgt acatcacaag gaaccagcca gaatggtttc gagatgtctt aagcattgcc
1021 cccataatgt tctcaaacaa aatggcgaga ttagggaaag gatacatgtt cgaaagtaag
1081 agcatgaagt tacgaacaca aataccagca gaaatgcttg caaacattga ccttaaatac
1141 ttcaatgact taacgaaaaa gaaaattgag aagataagac ctctattaat agatggtaca
1201 gcctcattga gccctggaat gatgatgggc atgttcaaca tgctgagtac agtcctagga
1261 gtttcaatcc tgaatcttgg acagaaaagg tacaccaaaa ccacatattg gtgggacggg
1321 ctccaatcct ctgatgattt cgctctcatc gtaaatgcac cgaatcatga gggaatacaa
1381 gcaggggtgg atagatttta taggacttgt aaactagttg ggatcaatat gagcaagaag
1441 aagtcttaca taaatcggac agggacattt gaattcacga gctttttcta ccgctatgga
1501 tttgtagcca atttcagtat ggagctgccc agttttggag tgtctggaat taatgaatcg
1561 gccgacatga gcattggtgt tacagtgata aagaacaata tgataaacaa cgaccttggg
1621 ccagcaacag ctcagatggc tcttcagcta ttcatcaagg actacagata cacataccga
1681 tgccacaggg gagatacgca aatccaaacg aggagatcat tcgagctgaa gaagctatgg
1741 gagcaaaccc gttcaaaggc agggctgttg gtttcagatg gaggaccaaa tctatacaat
1801 atccgaaatc tccatattcc tgaggtctgc ttgaaatggg aattgatgga tgaagactac
1861 cagggcagac tgtgcaatcc tctgaatcca ttcgtcagcc ataaggaaat tgaatctgtc
1921 aataatgcta tagtaatgcc agctcatggt ccagccaaga gtatggaata tgatgccgtt
1981 gcaaccacac attcatggat tcctaaaagg aatcgttcca ttctcaacac gagtcaaagg
2041 ggaattcttg aggatgagca gatgtaccaa aagtgctgca acctattcga gaaattcttc
2101 cccagcagtt cgtatcggag gccagttgga atttccagca tggtggaggc catggtgtct
2161 cgggcccgaa ttgacgcacg aattgatttc gagtctggga ggatcaagaa agaagagttt
2221 gctgagatca tgaagatctg ttccaccatt gaagagctca gacggcaaaa atag
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436733 2151 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) PA gene for
polymerase acidic protein, complete cds.
ACCESSION AB436733
VERSION AB436733.1 GI:195536904
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 2151)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..2151
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene 1..2151
/gene="PA"
CDS 1..2151
/gene="PA"
/codon_start=1
/product="polymerase acidic protein"
/protein_id="BAG68175.1"
/db_xref="GI:195536905"
/translation="MEDFVRQCFNPMIVELAEKAMKEYGENPKIETNKFAAICTHLEV
CFMYSDFHFIDERGESIIAESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVDK
PKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKAD
YTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEEKFEITGTMRRLADQS
LPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFMKKTPRPLRLPDGPPC
SQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNY
LLAWKQVLAELQDIENEEKIPKTKNMKKTSQLKWTLGENMAPEKVDFEDCKDVSDLKQ
YDSDEPEPRSLSSWIQSEFNKACELTDSSWIELDEIGEDIAPIEHIASMRRNYFTAEV
SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGR
SHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVR
TNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFETKSETWPIGES
PKGVEESSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFD
LGGLYEAIEECLINDPWVLLNASWFNSFLTHALK"
ORIGIN
1 atggaagact ttgtgcgaca atgcttcaat ccaatgatcg tcgagcttgc ggaaaaggca
61 atgaaagaat atggggaaaa tccgaaaatc gaaacgaaca aattcgccgc aatatgcaca
121 cacttagaag tctgcttcat gtattcggat ttccacttta ttgatgaacg aggcgaatca
181 ataattgcag aatctggcga tccgaatgca ttattgaaac accgatttga gataattgaa
241 gggagagacc gaacaatggc ttggacagtg gtaaatagta tctgcaacac cacaggagtc
301 gataagccta aattcctccc agatttgtat gactacaaag agaaccgatt cattgaaatt
361 ggagtgacac ggagggaagt tcacatatac tacctagaaa aagcaaataa gataaaatca
421 gagaagacac acattcacat attctcattc actggagagg aaatggccac caaagcagac
481 tatactcttg atgaggagag cagagcaaga atcaaaacca ggctattcac tataagacaa
541 gaaatggcca gtaggggcct atgggattcc tttcgtcaat ccgagagagg cgaagagaca
601 attgaagaaa aatttgaaat cacaggaacc atgcgcaggc ttgccgacca aagtctccca
661 ccgaacttct ccagccttga aaattttaga gcctatgtgg atggattcga accgaacggc
721 tgcattgagg gcaagctttc tcaaatgtca aaagaagtga acgccagaat tgagccattt
781 atgaagaaaa caccacgccc tctcagacta cccgatgggc ctccctgctc ccagcggtcg
841 aagttcttac tgatggatgc acttaaatta agtatcgaag atccaagcca tgagggggaa
901 ggtataccac tatatgatgc aatcaaatgc atgaagacat ttttcggctg gaaagagccc
961 aacatcgtaa aaccacatga aaaaggcata aatcccaatt acctcctagc ttggaagcag
1021 gtgctggcag aactccaaga cattgaaaat gaagagaaaa tcccaaaaac aaagaacatg
1081 aagaaaacaa gccaattaaa gtggacactt ggtgagaaca tggcaccaga aaaagtagac
1141 tttgaggact gcaaagatgt tagcgatcta aaacagtatg acagtgatga accagagcct
1201 agatcattat caagctggat tcagagcgaa ttcaacaaag catgcgaatt gacagattcg
1261 agttggattg aacttgatga aataggagaa gatattgctc caattgagca cattgcaagt
1321 atgagaagaa actatttcac agcggaagtg tctcattgca gggctactga atacataatg
1381 aagggagtgt atataaatac agccctgttg aatgcatcct gtgcagccat ggatgacttc
1441 caactgattc caatgataag caagtgcaga accaaagaag gaagacggaa gacaaatctg
1501 tatggattca ttataaaagg aaggtcccat ttgaggaacg acaccgatgt ggtaaatttt
1561 gtgagcatgg aattctctct tactgacccg aggctggaac cacacaagtg ggaaaagtac
1621 tgtgttctcg agataggaga catgctccta cgaactgcaa taggccaagt gtcaagaccc
1681 atgttcctgt atgtgagaac caatgggact tccaagatta agatgaaatg gggcatggag
1741 atgaggcgat gccttcttca atcccttcaa caaattgaga gcatgattga ggccgagtct
1801 tctgtcaaag agaaagacat gaccaaagaa ttctttgaaa ccaaatcaga aacgtggcca
1861 attggggaat cacctaaagg ggtggaggaa agctccattg gaaaggtgtg tagaacgtta
1921 ctagcaaaat ctgtattcaa cagcctgtat gcatctccac aacttgaggg attttcagct
1981 gaatcaagaa aattgcttct cattgttcag gcacttaggg acaacctgga acctggaacc
2041 ttcgatcttg gggggctata tgaagcaatt gaggagtgcc tgattaatga tccctgggtt
2101 ttgcttaatg catcttggtt caactccttc ctcacacatg cactgaaata g
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436734 1497 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) NP gene for
nucleoprotein, complete cds.
ACCESSION AB436734
VERSION AB436734.1 GI:195536906
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 1497)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..1497
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene 1..1497
/gene="NP"
CDS 1..1497
/gene="NP"
/codon_start=1
/product="nucleoprotein"
/protein_id="BAG68176.1"
/db_xref="GI:195536907"
/translation="MASQGTKRSYEQMETGGERQNATEIRASVGRMVSGIGRFYIQMC
TELKLSDYEGRLIQNSITIERMVLSAFDERRNRYLEEHPSAGKDPKKTGGPIYRRRDG
KWVRELILYDKEEIRRIWRQANNGEDATAGLTHLMIWHSNLNDATYQRTRALVRTGMD
PRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIA
YERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCL
PACVYGLAVASGYDFEREGYSLVGIDPFRLLQNSQVFSLIRPNENPAHKSQLVWMACH
SAAFEDLRVSSFIRGTRVVPRGQLSTRGVQIASNENMEAMDSNTLELRSRYWAIRTRS
GGNTNQQRASAGQISVQPTFSVQRNLPFERATIMAAFTGNTEGRTSDMRTEIIRMMES
ARPEDVSFQGRGVFELSDEKATNPIVPSFDMNNEGSYFFGDNAEEYDN"
ORIGIN
1 atggcgtccc aaggcaccaa acgatcttat gaacagatgg aaactggtgg agagcgccag
61 aatgctactg agatcagggc atccgttgga agaatggtta gtggcattgg gagattctac
121 atacagatgt gcacagaact caaactcagt gactatgaag gaagactgat ccagaacagc
181 ataacaatag agagaatggt actttctgca tttgatgaaa gaaggaacag gtacctggaa
241 gaacacccca gtgcggggaa ggacccgaag aaaactggag gtccaattta tcggaggaga
301 gacggaaaat gggtgaggga gctgattctg tacgacaaag aggagatcag gaggatttgg
361 cgtcaagcga acaatggaga ggacgcaact gctggtctta cccacctgat gatatggcat
421 tccaatctaa atgatgccac atatcagaga acgagagctc tcgtgcgtac tggaatggat
481 cccaggatgt gctctctgat gcaaggatca accctcccga ggagatctgg agctgccggt
541 gcagcagtga agggggtagg aacaatggtg atggagctga ttcggatgat aaaacgggga
601 atcaacgacc ggaatttttg gagaggtgaa aatggaagaa gaacaaggat tgcatatgag
661 agaatgtgca acatcctcaa agggaaattc caaacagcag cacaaagagc aatgatggat
721 caagtgcgag agagcagaaa tcctgggaat gctgaaattg aagatctcat ttttctggca
781 cggtctgcac tcatcctgag aggatcagtg gcccataagt cctgcttgcc tgcctgtgtg
841 tacggacttg cagtggccag tggatatgac tttgagagag aagggtactc tctggttgga
901 atagatcctt tccgtctgct tcaaaacagc caggtcttta gtctcattag accaaatgag
961 aatccagcac ataagagtca attagtgtgg atggcatgcc actctgcagc atttgaggac
1021 cttagagtct caagtttcat cagagggaca agagtggtcc caaggggaca gctatccacc
1081 agaggggttc aaattgcttc aaatgagaat atggaagcaa tggactccaa cactcttgaa
1141 ctgagaagta gatattgggc tataagaacc agaagcggag gaaacaccaa ccagcagagg
1201 gcatctgcag ggcagatcag cgttcagccc actttctcgg tacagagaaa ccttcccttc
1261 gaaagagcga ccattatggc agcatttaca ggaaatactg agggcagaac gtctgacatg
1321 aggactgaaa tcataagaat gatggaaagt gccagaccag aagatgtgtc attccagggg
1381 cggggagtct tcgagctctc ggacgaaaag gcaacgaacc cgatcgtgcc ttcctttgac
1441 atgaataatg aaggatctta tttcttcgga gacaatgcag aggagtatga caattaa
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436735 1350 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) NA gene for
neuraminidase, complete cds.
ACCESSION AB436735
VERSION AB436735.1 GI:195536908
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 1350)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..1350
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene 1..1350
/gene="NA"
CDS 1..1350
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="BAG68177.1"
/db_xref="GI:195536909"
/translation="MNPNQKIITIGSVCMIIGIVSLMLQIGNMISIWVSHSIQTGNQH
QAEPIRNTNFLTENAVASVTLAGNSSLCPIRGWAVHSKDNSIRIGSKGDVFVIREPFI
SCSHMECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNSRFESVAWS
ASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC
FTVMTDGPSNGQASYKIFKIEKGKVVKSVELNAPNYHYEECSCYPDAGEIICVCRDNW
HGSNRPWISFNQNLEYQIGYICSGVFGDNPRPNDGTGSCGPMSLNGAYGIKGFSFKYG
NGVWIGRTKSTNSRSGFEMIWDPNGWTGTDSEFSVKQDIVAITDWSGYSGSFVQHPEL
TGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNSDTVSWSWPDGAELPFTIDK"
ORIGIN
1 atgaatccaa atcagaagat aataaccatt ggatcagtct gtatgataat tggaatagtt
61 agcttaatgt tacagattgg gaacatgatc tcaatatggg tcagtcattc aattcaaaca
121 gggaatcaac accaagctga accaatcaga aataccaatt ttcttactga gaacgctgtg
181 gcttcagtaa cattagcggg caattcatct ctttgcccca ttagaggatg ggctgtacac
241 agtaaagaca acagtataag gattgggtcc aagggggatg tgtttgtaat tagagagccg
301 ttcatctcat gctcccatat ggaatgcaga actttctttt tgactcaggg agccttactg
361 aatgacaagc actccaacgg gactgtcaaa gacaggagcc ctcacagaac actaatgagt
421 tgtcctgtgg gtgaggctcc ctccccatat aactcgaggt ttgagtctgt tgcttggtca
481 gcaagtgctt gccatgatgg caccagttgg ttgacaattg gaatttctgg tccagacaat
541 ggggctgtgg ctgtattgaa atacaatggc ataataacag acactatcaa gagttggagg
601 aacaacatac tgaggactca agagtctgaa tgtgcatgtg taaatggctc ttgctttact
661 gtaatgacag atggaccaag taatggacag gcatcatata agatcttcaa aatagaaaaa
721 gggaaagtag ttaaatcggt cgaattgaat gctcctaatt atcactatga ggaatgctcc
781 tgttatcctg atgctggcga aataatatgt gtgtgcaggg acaattggca tggctcaaat
841 aggccatgga tatctttcaa tcagaatttg gagtatcaaa taggatatat ttgcagtggg
901 gttttcggag acaatccacg gccaaatgat gggacaggta gttgtggtcc aatgtccctt
961 aacggggcat atgggataaa agggttttca tttaaatacg gtaatggtgt ttggatcggg
1021 agaaccaaaa gcactaattc caggagcggt tttgaaatga tttgggatcc aaatgggtgg
1081 actggaacgg acagtgaatt ttcggtgaaa caagatatag tagcaataac tgattggtca
1141 ggatatagcg ggagttttgt ccagcatccg gaactgacag gattagactg cataagacct
1201 tgcttctggg ttgagttaat cagggggcgg ccaaaagaga gcacaatttg gactagtggg
1261 agcagcatat ctttttgtgg tgtaaatagt gacactgtga gttggtcttg gccagacggt
1321 gctgagttgc cattcaccat tgacaagtag
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436736 1704 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) HA gene for
hemagglutinin, complete cds.
ACCESSION AB436736
VERSION AB436736.1 GI:195536910
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 1704)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..1704
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene 1..1704
/gene="HA"
CDS 1..1704
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="BAG68178.1"
/db_xref="GI:195536911"
/translation="MEKIVLLFAIVSLVKSDHICIGYHANNSTEQVDTIMEKNVTVTH
AQDILERTHNGRLCDLNGVKPLILKDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPA
NDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKDSWSDHEASLGVSSACPYQGNSSFF
RNVVWLIKKDNAYPTIKKSYNNTNQEDLLVLWGIHHPNDEAEQTRLYQNPTTYISIGT
STLNQRLVPKIATRSKVNGQSGRIDFFWTILKPNDAINFESNGNFIAPEYAYKIVKKG
DSTIMKSEVEYGNCNTRCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR
NNPQRERRRKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDG
VTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENE
RTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYS
EEARLKREEISGVKLESIGTYQILSIYSTVASSLVLAIMMAGLSLWMCSNGSLQCRIC
I"
ORIGIN
1 atggagaaaa tagtgcttct ttttgcaata gtcagccttg ttaaaagcga tcatatttgc
61 attggttacc atgcaaacaa ctcgacagag caggttgaca caataatgga aaagaacgtt
121 actgttacac atgcccaaga catactggaa aggacacaca acgggaggct ctgcgatcta
181 aatggagtga agcctctgat tttaaaagat tgtagtgtag caggatggct cctcggaaac
241 ccaatgtgtg acgaattcat caatgtgcca gaatggtctt acatagtaga gaaggccaat
301 ccagccaatg acctctgtta cccagggaat ttcaacgatt atgaagaact gaaacaccta
361 ttgagcagaa taaaccattt tgagaaaata cagatcatcc ccaaagattc ttggtcagat
421 catgaagcct cattgggggt gagctcagca tgtccatacc agggaaattc ctcctttttc
481 agaaatgtgg tatggcttat caaaaaggac aatgcatacc caacaataaa gaaaagctac
541 aataatacca accaagaaga tctcttggta ctgtggggga ttcaccatcc taatgatgag
601 gcagagcaga caaggctcta tcaaaaccca accacctata tttccatcgg gacatcaaca
661 ctaaaccaga gattggtacc aaaaatagcc actagatcca aagtaaacgg gcaaagtgga
721 aggatagatt tcttctggac aattttaaaa ccgaatgatg caatcaactt cgagagtaat
781 ggaaatttca ttgctccaga atatgcatac aaaattgtca agaaaggaga ctcaacaatt
841 atgaaaagtg aagtggaata tggtaactgc aacaccaggt gtcagactcc gatgggggcg
901 ataaactcta gtatgccatt ccacaacata caccctctca ccatcggaga atgtcccaaa
961 tatgtgaaat caaacaaatt agtccttgcg actgggctca gaaataatcc tcaaagagag
1021 agaagaagaa aaagaggact gtttggagct atagcaggtt ttatagaggg aggatggcag
1081 ggaatggtag atggttggta tgggtaccac cacagcaatg agcagggaag tgggtacgct
1141 gcagacaaag aatccactca aaaggcaata gacggagtca ccaataaggt caactcgatc
1201 attgacaaaa tgaacactca gtttgaggcc gtaggaaggg aatttaataa cttagagagg
1261 agaatagaga atttaaacaa gaagatggaa gacggattcc tagatgtctg gacttataat
1321 gctgaacttc tggttctcat ggaaaatgag agaactctag acttccatga ctcaaatgtc
1381 aagaaccttt acgacaaggt cagactacag cttagggata atgcaaaaga gctgggtaac
1441 ggttgtttcg agttctatca caaatgtgat aatgaatgta tggaaagtgt aagaaacgga
1501 acgtatgact acccgcaata ttcagaagaa gcaagattaa aaagagagga aataagtgga
1561 gtaaaattgg aatcaatagg aacttaccaa atactgtcaa tttattcaac agtggcgagt
1621 tccctagtac tggcaatcat gatggctggt ctatctttat ggatgtgttc taacgggtcg
1681 ttacaatgca gaatttgcat ctaa
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

HA has 3-4 differences with the sequences from Hokkaido or Primorie, but each change matches at least one of the three earlier sequences (signaling recombination).

All sequences have M230I.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436737 982 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) M2, M1 genes
for matrix protein 2, matrix protein 1, complete cds.
ACCESSION AB436737
VERSION AB436737.1 GI:195536912
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 982)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..982
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene join(1..26,715..982)
/gene="M2"
CDS join(1..26,715..982)
/gene="M2"
/codon_start=1
/product="matrix protein 2"
/protein_id="BAG68179.1"
/db_xref="GI:195536913"
/translation="MSLLTEVETPTRHEWECRCSDSSDPLVIAASIIGILHLILWILD
RLFFKCIYRRLKYGLKRGPSTGGVPESMREEYRQEQQSAVDVDDGHFVNIELE"
gene 1..759
/gene="M1"
CDS 1..759
/gene="M1"
/codon_start=1
/product="matrix protein 1"
/protein_id="BAG68180.1"
/db_xref="GI:195536914"
/translation="MSLLTEVETYVLSIIPSGPLKAEIAQKLEDVFAGKNTDLEALME
WLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYKK
LKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQHR
SHRQMATITNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVANQARQMVQAMRT
IGTHPNSSAGLRDNLLENLQAYQTRMGVQMQRFK"
ORIGIN
1 atgagtcttc taaccgaggt cgaaacgtac gttctctcta tcatcccgtc aggccccctc
61 aaagccgaga tcgcgcagaa acttgaggat gtctttgcag gaaagaacac cgatctcgag
121 gctctcatgg agtggctaaa gacaagacca atcctgtcac ctctgactaa agggatcttg
181 ggatttgtat tcacgctcac cgtgcccagt gagcgaggac tgcagcgtag acgttttgtc
241 cagaatgccc taaatggaaa tggagatcca aataatatgg atagagcagt taagctatat
301 aagaagctga aaagagaaat aacattccat ggggctaagg aggttgcact cagctactca
361 accggtgcac ttgccagttg catgggtctc atatacaaca ggatgggaac ggtgactacg
421 gaagtggctt ttggcctagt gtgtgccact tgtgagcaga ttgcagattc acagcatcgg
481 tctcacagac agatggcaac catcaccaac ccactaatca ggcatgagaa cagaatggtg
541 ctggccagca ctacagctaa ggctatggag cagatggcgg gatcaagcga gcaggcagcg
601 gaagccatgg aggtcgctaa tcaggctagg cagatggtgc aggcaatgag gacaattgga
661 actcatccta actctagtgc tggtctgaga gataatcttc ttgaaaattt gcaggcctac
721 cagacacgaa tgggagtgca gatgcagcga ttcaagtgat cctcttgtta ttgccgcaag
781 tatcattggg atcttgcact tgatattgtg gattcttgat cgtcttttct tcaaatgcat
841 ttatcgtcgc cttaaatacg gtttgaaaag agggccttct acgggagggg tacctgagtc
901 tatgagggaa gagtaccggc aggaacagca gagtgctgtg gatgttgacg atggtcattt
961 tgtcaacata gaattggagt aa
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

LOCUS AB436738 823 bp RNA linear VRL 02-AUG-2008
DEFINITION Influenza A virus (A/whooper swan/Akita/2008(H5N1)) NS2, NS1 genes
for nonstructural protein 2, nonstructural protein 1, complete cds.
ACCESSION AB436738
VERSION AB436738.1 GI:195536915
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Akita/2008(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Akita/2008(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Uchida,Y., Mase,M., Yoneda,K., Kimura,A., Obara,T., Kumagai,S.,
Saito,T., Yamamoto,Y., Nakamura,K., Tsukamoto,K. and Yamaguchi,S.
TITLE Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from
Whooper Swans, Japan
JOURNAL Emerging Infect. Dis. (2008) In press
REFERENCE 2 (bases 1 to 823)
AUTHORS Uchida,Y., Mase,M., Saito,T. and Yamaguchi,S.
TITLE Direct Submission
JOURNAL Submitted (08-MAY-2008) Contact:Yuko Uchida National Institute of
Animal Health, National Agriculture and Food Research Organization
(NARO), Research Teams for Zoonotic Diseases and Viral Diseases;
3-1-5, Kannonndai, Tsukuba, Ibaraki 305-0856, Japan URL
:http://niah.naro.affrc.go.jp/index-j.html
FEATURES Location/Qualifiers
source 1..823
/organism="Influenza A virus (A/whooper
swan/Akita/2008(H5N1))"
/mol_type="genomic RNA"
/strain="A/whooper swan/Akita/2008"
/serotype="H5N1"
/db_xref="taxon:527687"
/country="Japan"
gene join(1..30,488..823)
/gene="NS2"
CDS join(1..30,488..823)
/gene="NS2"
/codon_start=1
/product="nonstructural protein 2"
/protein_id="BAG68181.1"
/db_xref="GI:195536916"
/translation="MDSNTVSSFQDILVRMSKMQLASSSEDLNGMITQFGSLKLYRDS
LGEAVMRVGDFHSLQIRNGKWREQLSQKFEEIRWLIEEVRHRLKITENSFEQITFMQA
LQLLLEVEQEIRAFSFQLI"
gene 1..678
/gene="NS1"
CDS 1..678
/gene="NS1"
/codon_start=1
/product="nonstructural protein 1"
/protein_id="BAG68182.1"
/db_xref="GI:195536917"
/translation="MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDKKSLR
GRGNTLGLDIETATRAGKQIVERILEEETDEALKMPTSRYLTDMTLEEMSRDWFMLMP
KQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPS
LPGHTGEDVKNAIGVLIGGLEWNDNTVRVSETIQRFAWRSSDEGGRLPLPPNQKRKMA
RTIESEV"
ORIGIN
1 atggattcca acactgtgtc aagctttcag gtagactgct ttctttggca tgtccgcaaa
61 cgatttgcag accaagaact gggtgatgcc ccattccttg accggctccg ccgagataag
121 aagtccctaa gaggaagagg caacactctt ggtctggaca tcgaaacagc tactcgtgcg
181 ggaaaacaga tagtggagcg gattctggag gaggaaaccg atgaggcact taaaatgccg
241 acttcacgct acctaactga catgactctc gaagaaatgt caagggactg gttcatgctc
301 atgcccaagc agaaagtggc gggttccctt tgcatcaaaa tggaccaggc aataatggat
361 aaaaccatca tattgaaagc aaacttcagt gtgatttttg accggttaga aaccctaata
421 ctgcttagag ctttcacaga agaaggagca atcgtgggag aaatctcacc attaccttct
481 cttccaggac atactggtga ggatgtcaaa aatgcaattg gcgtcctcat cggaggactt
541 gaatggaatg ataacacagt tcgggtctct gaaactatac agagattcgc ttggagaagc
601 agtgatgagg gtgggagact tccactccct ccaaatcaga aacggaaaat ggcgagaaca
661 attgagtcag aagtttgaag aaataaggtg gctaattgaa gaagtacgac atagattgaa
721 aattacagaa aacagcttcg aacagataac gtttatgcaa gccttacaac tactgcttga
781 agtggagcaa gagataagag ccttctcgtt tcagcttatt taa
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

NS differs from the other 3 at 1 position.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

MP matches A/whooper swan/Hokkaido/1/2008.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

NA differs at 2 positions.
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

NP matches A/whooper swan/Hokkaido/1/2008
 
Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

Re: _|EID: Highly Pathogenic Avian Influenza Virus (H5N1) Isolated from Whooper Swans, Japan (2008)|_

PA has 4 differences.
 
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