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PostPosted: Mon Dec 22, 2014 5:22 pm 
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USDA has released an update OIE report from Oregon.

http://www.oie.int/wahis_2/public/wahid ... rtid=16810

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PostPosted: Mon Dec 22, 2014 5:27 pm 
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The USDA Animal and Plant Health Inspection Services (APHIS) and the Oregon Department of Agriculture (ODA) are conducting a comprehensive investigation of this outbreak. The USDA APHIS National Veterinary Services Laboratory (NVSL) confirmed avian influenza virus (AIV) H5N8 via sequencing directly from swab samples. Preliminary results indicate the HA sequence is 99.3% similar to A/bean goose/Korea/H40/2014 (H5N8 HPAI) based on a partial fragment of the HA gene. The neuraminidase sequence is 99.7% similar to A/Baikal teal/Korea/H80/2014 (H5N8) based on a partial fragment of the NA gene. The amino acid sequence at the hemagglutinin cleavage site is consistent with highly pathogenic avian influenza (HPAI). Whole genome sequencing is in progress. Enhanced surveillance by the USDA APHIS and ODA is being initiated. The H5N8 highly pathogenic avian influenza (HPAI) in Oregon is limited to a small backyard poultry premises only and does not involve commercial poultry.

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PostPosted: Mon Dec 22, 2014 5:32 pm 
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LOCUS KJ508924 1742 bp cRNA linear VRL 07-OCT-2014
DEFINITION Influenza A virus (A/bean goose/Korea/H40/2014(H5N8)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION KJ508924
VERSION KJ508924.1 GI:594705743
KEYWORDS .
SOURCE Influenza A virus (A/bean goose/Korea/H40/2014(H5N8))
ORGANISM Influenza A virus (A/bean goose/Korea/H40/2014(H5N8))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1742)
AUTHORS Jeong,J., Kang,H.M., Lee,E.K., Song,B.M., Kwon,Y.K., Kim,H.R.,
Choi,K.S., Kim,J.Y., Lee,H.J., Moon,O.K., Jeong,W., Choi,J.,
Baek,J.H., Joo,Y.S., Park,Y.H., Lee,H.S. and Lee,Y.J.
TITLE Highly pathogenic avian influenza virus (H5N8) in domestic poultry
and its relationship with migratory birds in South Korea during
2014
JOURNAL Vet. Microbiol. 173 (3-4), 249-257 (2014)
PUBMED 25192767
REFERENCE 2 (bases 1 to 1742)
AUTHORS Lee,Y.-J., Kang,H.-M., Lee,E.-K., Song,B.-M., Jeong,J., Lee,K.-J.
and Hong,M.-S.
TITLE Direct Submission
JOURNAL Submitted (28-FEB-2014) Avian Disease Division, Animal and Plant
Quarantine Agency (QIA), 175, Anyang-ro, Anyang-city, Gyeonggi-do
430-757, Republic of Korea
COMMENT GenBank Accession Numbers KJ508921-KJ508928 represent sequences
from the 8 segments of Influenza A virus (A/bean
goose/Korea/H40/2014(H5N8)).

##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..1742
/organism="Influenza A virus (A/bean
goose/Korea/H40/2014(H5N8))"
/mol_type="viral cRNA"
/strain="A/bean goose/Korea/H40/2014"
/serotype="H5N8"
/host="bean goose"
/db_xref="taxon:1470228"
/segment="4"
/country="South Korea"
/collection_date="19-Jan-2014"
/note="passage details: chicken embryo 1"
gene 15..1718
/gene="HA"
CDS 15..1718
/gene="HA"
/function="receptor binding and fusion protein"
/codon_start=1
/product="hemagglutinin"
/protein_id="AHM24673.1"
/db_xref="GI:594705744"
/translation="MEKIVLLLAVVSLVKSDQICIGYHANNSTKQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPA
NDLCYPGTLNDYEELKHLLSRINHFEKTLIIPKSSWPNHETSLGVSAACPYQGASSFF
RNVVWLIKKNDAYPTIKINYNNTNREDLLILWGIHHSNNAAEQTNLYKNPDTYVSVGT
STLNQRLVPKIATRSQVNGQRGRMDFFWTILKPNDAIHFESNGNFIAPEYAYKIVKKG
DSTIMKSEVEYGHCNTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR
NSPLRERRRKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDG
VTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENE
RTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPKYS
EEARLKREEISGVKLESIGTYQILSIYSTVASSLALAIIVAGLSLWMCSNGSLQCRIC
I"
sig_peptide 15..62
/gene="HA"
mat_peptide 63..1049
/gene="HA"
/product="HA1"
mat_peptide 1050..1715
/gene="HA"
/product="HA2"
ORIGIN
1 ttcaatctgt caaaatggag aaaatagtgc ttcttcttgc agtggttagc cttgttaaaa
61 gtgatcagat ttgcattggt taccatgcaa acaactcaac aaagcaggtt gacacgataa
121 tggaaaaaaa cgtcactgtt acacatgccc aagacatact ggaaaagaca cacaacggga
181 agctctgcga tcttaatgga gtgaagcccc tgattctaaa ggattgtagc gtagctgggt
241 ggctccttgg aaatccaatg tgcgacgagt tcatcagggt gccggaatgg tcttacatcg
301 tggagagggc taacccagcc aacgacctct gttacccagg gaccctcaat gactatgagg
361 aactgaaaca cctattgagc agaataaatc attttgagaa aactctgatc atccccaaga
421 gttcttggcc caatcatgaa acatcattag gggtgagcgc agcatgtcca taccagggag
481 catcctcatt tttcagaaat gtggtatggc tcatcaaaaa gaacgatgca tacccgacaa
541 taaagataaa ctacaataat accaatcggg aagatctttt gatactgtgg gggattcatc
601 attccaacaa tgcagcagag cagacaaatc tctataaaaa cccagacact tatgtttccg
661 ttgggacatc aacattaaac cagagattgg tgccaaaaat agctaccaga tcccaagtaa
721 acgggcaacg tggaagaatg gatttcttct ggacaatttt aaaaccgaat gatgcaatcc
781 actttgagag taatggaaat ttcattgctc cagaatatgc atacaaaatt gtcaagaaag
841 gggactcaac aattatgaaa agtgaagtgg agtatggcca ctgcaacacc aaatgtcaaa
901 ctccaatagg ggcgataaac tctagcatgc cattccacaa tatacaccct ctcaccatcg
961 gggaatgccc caaatacgtg aagtcaaaca aattagtcct tgcgactggg ctcagaaata
1021 gtcctctaag agaaagaaga agaaaaagag gactatttgg agctatagca gggtttatag
1081 agggaggatg gcagggaatg gtagacggtt ggtatgggta ccaccatagc aatgagcagg
1141 ggagtgggta cgctgcagac aaagaatcca cccaaaaggc aatagatgga gttaccaata
1201 aggtcaactc aatcattgac aaaatgaaca ctcaatttga ggccgttgga agggaattta
1261 ataacttaga aaggagaata gagaatttaa acaagaaaat ggaagacgga ttcctagatg
1321 tctggactta taatgctgaa cttttagttc tcatggaaaa tgagagaact ctagatttcc
1381 atgactcaaa tgtcaagaac ctttacgaca aagtccgact acagcttagg gataatgcaa
1441 aggagctggg taatggttgt ttcgagttct atcacaaatg tgataacgaa tgtatggaaa
1501 gcgtaagaaa tgggacgtat gactacccta agtattcaga agaagcaaga ttaaaaagag
1561 aagaaataag cggagtgaaa ttagaatcaa taggaactta ccaaatactg tcaatttatt
1621 caacagtggc gagttcccta gcactggcaa tcatagtggc tggtctatct ttatggatgt
1681 gctctaatgg gtcgttacaa tgcagaattt gcatctaaat ttgtgagctc agattgtaat
1741 ta

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PostPosted: Mon Dec 22, 2014 5:35 pm 
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Posts: 56044
Location: Pittsburgh, PA USA
EPI509704 A/broiler duck/Korea/Buan2/2014 (A/H5N8) segment 4 (HA) 3125.7 0.000000e+00 1700/1704 (99%)
EPI517161 A/Chicken/Kumamoto/1-7/2014 (A/H5N8) segment 4 (HA) 3120.1 0.000000e+00 1699/1704 (99%)
EPI509709 A/baikal teal/Korea/Donglim3/2014 (A/H5N8) segment 4 (HA) 3114.6 0.000000e+00 1698/1704 (99%)
EPI542628 A/mallard/Korea/W452/2014 (A/H5N8) segment 4 (HA) 3098.0 0.000000e+00 1695/1704 (99%)
EPI547673 A/duck/England/36254/14 (A/H5N8) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI552746 A/turkey/Germany/R2474-L00899/2014 (A/H5N8) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI548493 A/duck/Chiba/26-372-61/2014 (A/H5N8) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI548485 A/duck/Chiba/26-372-48/2014 (A/H5N8) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI547678 A/Chicken/Netherlands/14015526/2014 (A/H5N8) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI548623 A/chicken/Netherlands/14015531/2014 (A/H5N8) segment 4 (HA) 3059.2 0.000000e+00 1688/1704 (99%)
EPI544756 A/turkey/Germany-MV/R2472/2014 (A/H5N8) segment 4 (HA) 3042.6 0.000000e+00 1677/1692 (99%)
EPI552776 A/chicken/Netherlands/emc-3/2014 (A/H5N8) segment 4 (HA) 3018.5 0.000000e+00 1666/1682 (99%)
EPI552768 A/eurasian wigeon/Netherlands/emc-2/2014 (A/H5N8) segment 4 (HA) 3018.5 0.000000e+00 1673/1692 (98%)
EPI552760 A/eurasian wigeon/Netherlands/emc-1/2014 (A/H5N8) segment 4 (HA) 2976.1 0.000000e+00 1637/1650 (99%)
EPI551149 A/eurasian wigeon/Netherlands/emc-2/2014 (A/H5N8) segment 4 (HA) 2972.4 0.000000e+00 1648/1667 (98%)
EPI551143 A/eurasian wigeon/Netherlands/emc-1/2014 (A/H5N8) segment 4 (HA) 2909.6 0.000000e+00 1599/1611 (99%)
EPI543010 A/duck/Beijing/CT01/2014 (A/H5N8) segment 4 (HA) 2909.6 0.000000e+00 1597/1608 (99%)
EPI542617 A/duck/Beijing/FS01/2013 (A/H5N8) segment 4 (HA) 2893.0 0.000000e+00 1593/1608 (99%)
EPI475579 A/wild duck/Shandong/628/2011 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1660/1706 (97%)
EPI543002 A/duck/Beijing/FS01/2014 (A/H5N8) segment 4 (HA) 2887.4 0.000000e+00 1594/1609 (99%)
EPI442017 A/duck/Jiangsu/k1203/2010 (A/H5N8) segment 4 (HA) 2887.4 0.000000e+00 1659/1706 (97%)
EPI399960 A/duck/Jiangsu/m234/2012 (A/H5N2) segment 4 (HA) 2854.2 0.000000e+00 1654/1707 (96%)
EPI398966 A/goose/Eastern China/1112/2011 (A/H5N2) segment 4 (HA) 2854.2 0.000000e+00 1653/1706 (96%)
EPI431456 A/duck/Hebei/3/2011 (A/H5N2) segment 4 (HA) 2843.1 0.000000e+00 1651/1706 (96%)
EPI398965 A/duck/Eastern China/1111/2011 (A/H5N2) segment 4 (HA) 2837.6 0.000000e+00 1650/1706 (96%)
EPI509698 A/breeder duck/Korea/Gochang1/2014 (A/H5N8) segment 4 (HA) 2821.0 0.000000e+00 1647/1706 (96%)
EPI530054 A/duck/Jiangxi/95/2014 (A/H5N6) segment 4 (HA) 2815.4 0.000000e+00 1647/1707 (96%)
EPI544892 A/duck/Shandong/Q1/2013 (A/H5N8) segment 4 (HA) 2809.9 0.000000e+00 1647/1708 (96%)
EPI531456 A/duck/Guangdong/GD01/2014 (A/H5N6) segment 4 (HA) 2809.9 0.000000e+00 1646/1707 (96%)
EPI530986 A/duck/Zhejiang/6D18/2013 (A/H5N8) segment 4 (HA) 2793.3 0.000000e+00 1642/1706 (96%)
EPI507673 A/mallard duck/Shanghai/SH-9/2013 (A/H5N8) segment 4 (HA) 2793.3 0.000000e+00 1642/1706 (96%)
EPI553144 A/turkey/Italy/14VIR7898-10/2014 (A/H5N8) segment 4 (HA) 2789.6 0.000000e+00 1533/1545 (99%)
EPI530985 A/duck/Zhejiang/W24/2013 (A/H5N8) segment 4 (HA) 2787.7 0.000000e+00 1641/1706 (96%)
EPI530063 A/environment/Shenzhen/25-24/2013 (A/H5N6) segment 4 (HA) 2787.7 0.000000e+00 1642/1707 (96%)
EPI493825 A/duck/Guangdong/wy19/2008 (A/H5N5) segment 4 (HA) 2787.7 0.000000e+00 1642/1707 (96%)
EPI550768 A/duck/Laos/XBY004/2014 (A/H5N6) segment 4 (HA) 2776.6 0.000000e+00 1641/1708 (96%)
EPI550763 A/duck/Laos/XBY004/2014 (A/H5N6) segment 4 (HA) 2776.6 0.000000e+00 1641/1708 (96%)
EPI550759 A/chicken/Laos/XBY003/2014 (A/H5N6) segment 4 (HA) 2776.6 0.000000e+00 1641/1708 (96%)
EPI550757 A/duck/Laos/LPQ002/2014 (A/H5N6) segment 4 (HA) 2776.6 0.000000e+00 1641/1708 (96%)
EPI431448 A/duck/Hebei/2/2011 (A/H5N2) segment 4 (HA) 2772.9 0.000000e+00 1639/1707 (96%)
EPI550752 A/chicken/Laos/LPQ001/2014 (A/H5N6) segment 4 (HA) 2771.1 0.000000e+00 1640/1708 (96%)
EPI499478 A/chicken/China/AH/2012 (A/H5N1) segment 4 (HA) 2765.6 0.000000e+00 1637/1706 (95%)
EPI493817 A/duck/Guangdong/wy11/2008 (A/H5N5) segment 4 (HA) 2765.6 0.000000e+00 1639/1708 (95%)
EPI328878 A/duck/Eastern China/031/2009 (A/H5N5) segment 4 (HA) 2721.2 0.000000e+00 1629/1706 (95%)
EPI328870 A/duck/Eastern China/008/2008 (A/H5N5) segment 4 (HA) 2693.5 0.000000e+00 1625/1707 (95%)
EPI493833 A/duck/Guangdong/wy24/2008 (A/H5N5) segment 4 (HA) 2689.8 0.000000e+00 1627/1710 (95%)
EPI547402 A/environment/Zhenjiang/C13/2013 (A/H5N6) segment 4 (HA) 2688.0 0.000000e+00 1626/1709 (95%)
EPI328886 A/duck/Eastern China/108/2008 (A/H5N1) segment 4 (HA) 2688.0 0.000000e+00 1624/1707 (95%)
EPI533583 A/Sichuan/26221/2014 (A/H5N6) segment 4 (HA) 2682.5 0.000000e+00 1624/1708 (95%)
EPI442025 A/quail/Jiangsu/k0104/2010 (A/H5N5) segment 4 (HA) 2678.8 0.000000e+00 1625/1710 (95%)
EPI442001 A/goose/Shandong/k1204/2009 (A/H5N5) segment 4 (HA) 2632.6 0.000000e+00 1614/1707 (94%)
EPI442009 A/goose/Guangdong/k0103/2010 (A/H5N5) segment 4 (HA) 2612.3 0.000000e+00 1614/1711 (94%)
EPI127406 A/wild duck/Hunan/211/2005 (A/H5N1) segment 4 (HA) 2566.1 0.000000e+00 1602/1707 (93%)
EPI127384 A/wild duck/Hunan/021/2005 (A/H5N1) segment 4 (HA) 2566.1 0.000000e+00 1602/1707 (93%)
EPI439897 A/goose/Guangdong/08/2005 (A/H5N1) segment 4 (HA) 2564.3 0.000000e+00 1602/1707 (93%)
EPI399886 A/duck/HuBei/03/2010 (A/H5N5) segment 4 (HA) 2560.6 0.000000e+00 1602/1708 (93%)
EPI279949 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 2560.6 0.000000e+00 1601/1707 (93%)
EPI181297 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 2560.6 0.000000e+00 1601/1707 (93%)
EPI275982 A/duck/Hubei/49/2005 (A/H5N1) segment 4 (HA) 2555.0 0.000000e+00 1601/1708 (93%)
EPI227309 A/Mallard/Huadong/lk/2005 (A/H5N1) segment 4 (HA) 2555.0 0.000000e+00 1600/1707 (93%)
EPI107769 A/duck/Guangxi/288/2006 (A/H5N1) segment 4 (HA) 2555.0 0.000000e+00 1594/1698 (93%)
EPI337076 A/Sichuan/2/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI280104 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI276046 A/goose/Hubei/65/2005 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI275774 A/chicken/Hunan/21/2005 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1600/1708 (93%)
EPI224777 A/Shanghai/1/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI181301 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI181298 A/Sichuan/1/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI164232 A/Sichuan/2/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI164224 A/Sichuan/1/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1599/1707 (93%)
EPI107913 A/goose/Yunnan/1144/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1593/1698 (93%)
EPI107829 A/goose/Guiyang/1304/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1593/1698 (93%)
EPI107771 A/chicken/Guangxi/463/2006 (A/H5N1) segment 4 (HA) 2549.5 0.000000e+00 1593/1698 (93%)
EPI406406 A/Muscovy duck/Ca Mau/22/2007 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1600/1709 (93%)
EPI337107 A/Shanghai/1/2006 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI280112 A/Shanghai/1/2006 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI275966 A/duck/Anhui/56/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI275386 A/Anhui/2/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1599/1708 (93%)
EPI170615 A/chicken/Vietnam/216/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI170607 A/Muscovy duck/Vietnam/217/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI170599 A/duck/Vietnam/218/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI170591 A/duck/Vietnam/219/2005 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1598/1707 (93%)
EPI108329 A/goose/Guangxi/1898/2006 (A/H5N1) segment 4 (HA) 2544.0 0.000000e+00 1592/1698 (93%)
EPI270188 A/Vietnam/UT30850/2005 (A/H5N1) segment 4 (HA) 2542.1 0.000000e+00 1595/1703 (93%)
EPI106243 A/duck/Laos/3295/2006 (A/H5N1) segment 4 (HA) 2542.1 0.000000e+00 1599/1708 (93%)
EPI286383 A/chicken/Cao Bang/07-42/2007 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1599/1709 (93%)
EPI286381 A/chicken/Nam Dinh/07-32/2007 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1599/1709 (93%)
EPI275958 A/duck/Anhui/1/06 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1600/1710 (93%)
EPI275870 A/chicken/Sichuan/81/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI227371 A/muscovy duck/VietNam/209/2005 (A/H5) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI227010 A/chicken/Ninh Binh/209/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI181299 A/Fujian/1/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1598/1708 (93%)
EPI180956 A/duck/Laos/22/2006 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1598/1708 (93%)
EPI180951 A/duck/Laos/25/2006 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1598/1708 (93%)
EPI170742 A/duck/Vietnam/215/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI170741 A/Muscovy duck/Vietnam/213/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI170740 A/chicken/Vietnam/212/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI170739 A/Muscovy duck/Vietnam/211/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI170738 A/duck/Vietnam/210/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)
EPI170714 A/chicken/Vietnam/202/2005 (A/H5N1) segment 4 (HA) 2538.4 0.000000e+00 1597/1707 (93%)

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PostPosted: Mon Dec 22, 2014 5:37 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
LOCUS KJ509014 1425 bp cRNA linear VRL 07-OCT-2014
DEFINITION Influenza A virus (A/Baikal teal/Korea/H80/2014(H5N8)) segment 6
neuraminidase (NA) gene, complete cds.
ACCESSION KJ509014
VERSION KJ509014.1 GI:594705474
KEYWORDS .
SOURCE Influenza A virus (A/Baikal teal/Korea/H80/2014(H5N8))
ORGANISM Influenza A virus (A/Baikal teal/Korea/H80/2014(H5N8))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1425)
AUTHORS Jeong,J., Kang,H.M., Lee,E.K., Song,B.M., Kwon,Y.K., Kim,H.R.,
Choi,K.S., Kim,J.Y., Lee,H.J., Moon,O.K., Jeong,W., Choi,J.,
Baek,J.H., Joo,Y.S., Park,Y.H., Lee,H.S. and Lee,Y.J.
TITLE Highly pathogenic avian influenza virus (H5N8) in domestic poultry
and its relationship with migratory birds in South Korea during
2014
JOURNAL Vet. Microbiol. 173 (3-4), 249-257 (2014)
PUBMED 25192767
REFERENCE 2 (bases 1 to 1425)
AUTHORS Lee,Y.-J., Kang,H.-M., Lee,E.-K., Song,B.-M., Jeong,J., Lee,K.-J.
and Hong,M.-S.
TITLE Direct Submission
JOURNAL Submitted (28-FEB-2014) Avian Disease Division, Animal and Plant
Quarantine Agency (QIA), 175, Anyang-ro, Anyang-city, Gyeonggi-do
430-757, Republic of Korea
COMMENT GenBank Accession Numbers KJ509009-KJ509016 represent sequences
from the 8 segments of Influenza A virus (A/Baikal
teal/Korea/H80/2014(H5N8)).

##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..1425
/organism="Influenza A virus (A/Baikal
teal/Korea/H80/2014(H5N8))"
/mol_type="viral cRNA"
/strain="A/Baikal teal/Korea/H80/2014"
/serotype="H5N8"
/host="Baikal teal"
/db_xref="taxon:1470222"
/segment="6"
/country="South Korea"
/collection_date="22-Jan-2014"
/note="passage details: chicken embryo 1"
gene 6..1418
/gene="NA"
CDS 6..1418
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="AHM24543.1"
/db_xref="GI:594705475"
/translation="MNPNQKIVTIGSISLGLVVFNVLLHAVSIILTVLALGKSENNGI
CNGTVVREYNETVRIEKVTQWYNTSVVEYVPHWNEGTYINNTEPICDVKGFAPFSKDN
GIRVGSRGHIFVIREPFVSCSPVECRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVE
VGQSPNVYQARFEAVAWSATACHDGKKWMAIGVTGPDSKAVAVVHYGGVPTDVVNSWA
GDILRTQESSCTCIQGNCYWVMTDGPANRQAQYRIYKANQGKIIGRTDVSFSGGHIEE
CSCYPNDGKVECVCRDNWTGTNRPVLIISPDLSYRVGYLCAGLPSDTPRGEDTQFVGS
CTSPMGNQGYGVKGFGFRQGTDVWVGRTISRTSRSGFEIIRIKNGWTQTSKEQIRRQV
VVDNSNWSGYSGSFTLPVELSGRECLVPCFWVEMIRGRPEERTIWTSSSSIVMCGVDY
EIADWSWHDGAILPFDIDKM"
ORIGIN
1 ttaaaatgaa tccaaatcag aaaatagtaa ccattggctc catttcatta gggttggttg
61 tattcaatgt tctactgcat gccgtgagca tcatattaac agtgttagcc ctggggaaga
121 gtgaaaacaa tggaatctgc aatggaactg tagtgaggga atacaatgaa acagttagaa
181 tagagaaagt gactcaatgg tacaatacta gcgtagtcga atatgtaccg cattggaatg
241 agggcactta tataaataac accgaaccaa tatgtgatgt caagggcttt gcaccttttt
301 ccaaggacaa cgggataaga gttggctcca ggggacatat ttttgtcata agagagcctt
361 tcgtctcttg ttcacctgta gagtgcagga ctttcttcct cactcagggg tctctactca
421 atgacaaaca ctcaaatgga acagtgaagg atagaagccc attcagaact ctcatgagtg
481 tcgaagtggg ccaatcaccc aatgtatatc aagccaggtt tgaagctgtg gcatggtcag
541 caacagcctg tcatgatggt aagaagtgga tggcgattgg tgtaacaggg ccagattcta
601 aagcagtagc agtagttcat tacggagggg tgcctactga cgttgttaac tcctgggcag
661 gagatatatt aagaactcag gagtcatctt gtacttgcat tcaaggtaat tgttattggg
721 taatgactga cggtcctgcc aatagacagg cgcagtatag aatatacaaa gcaaatcaag
781 gcaaaataat tggccgaaca gatgttagct ttagtggagg acatattgag gaatgttctt
841 gttatccaaa tgatggtaaa gtggaatgcg tgtgtagaga caactggacg ggaactaaca
901 ggcctgtgct aattatttcg cctgatctct cttacagggt tgggtattta tgtgcagggt
961 tgcccagtga cactccaaga ggggaagata ctcaatttgt cggttcatgc actagtccca
1021 tgggaaatca gggatatggc gtaaaagggt tcgggtttcg acagggaact gatgtgtggg
1081 tggggcggac aattagtcga acctccagat caggatttga aataataagg ataaagaatg
1141 gttggacgca aacaagcaaa gaacagatta gaagacaggt ggttgttgat aactcgaatt
1201 ggtcgggata cagtgggtct ttcactttac cagtagaatt gtctgggagg gaatgtttgg
1261 ttccctgttt ttgggtcgaa atgatcagag gtaggccaga agagagaaca atctggacct
1321 ctagtagctc cattgtaatg tgtggagttg attatgaaat tgccgattgg tcatggcacg
1381 atggagctat tcttcccttt gacatcgata agatgtaatt tacga

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PostPosted: Mon Dec 22, 2014 5:39 pm 
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EPI509714 A/baikal teal/Korea/Donglim3/2014 (A/H5N8) segment 6 (NA) 2592.0 0.000000e+00 1405/1406 (99%)
EPI509706 A/broiler duck/Korea/Buan2/2014 (A/H5N8) segment 6 (NA) 2592.0 0.000000e+00 1405/1406 (99%)
EPI542632 A/mallard/Korea/W452/2014 (A/H5N8) segment 6 (NA) 2580.9 0.000000e+00 1403/1406 (99%)
EPI552748 A/turkey/Germany/R2474-L00899/2014 (A/H5N8) segment 6 (NA) 2575.3 0.000000e+00 1402/1406 (99%)
EPI544759 A/turkey/Germany-MV/R2472/2014 (A/H5N8) segment 6 (NA) 2575.3 0.000000e+00 1402/1406 (99%)
EPI543012 A/duck/Beijing/CT01/2014 (A/H5N8) segment 6 (NA) 2575.3 0.000000e+00 1402/1406 (99%)
EPI517163 A/Chicken/Kumamoto/1-7/2014 (A/H5N8) segment 6 (NA) 2575.3 0.000000e+00 1402/1406 (99%)
EPI543004 A/duck/Beijing/FS01/2014 (A/H5N8) segment 6 (NA) 2569.8 0.000000e+00 1401/1406 (99%)
EPI548495 A/duck/Chiba/26-372-61/2014 (A/H5N8) segment 6 (NA) 2564.3 0.000000e+00 1400/1406 (99%)
EPI548487 A/duck/Chiba/26-372-48/2014 (A/H5N8) segment 6 (NA) 2564.3 0.000000e+00 1400/1406 (99%)
EPI547683 A/Chicken/Netherlands/14015526/2014 (A/H5N8) segment 6 (NA) 2564.3 0.000000e+00 1400/1406 (99%)
EPI548626 A/chicken/Netherlands/14015531/2014 (A/H5N8) segment 6 (NA) 2558.7 0.000000e+00 1399/1406 (99%)
EPI553152 A/turkey/Germany-NI/R3372/2014 (A/H5N8) segment 6 (NA) 2553.2 0.000000e+00 1398/1406 (99%)
EPI547675 A/duck/England/36254/14 (A/H5N8) segment 6 (NA) 2553.2 0.000000e+00 1398/1406 (99%)
EPI551150 A/eurasian wigeon/Netherlands/emc-2/2014 (A/H5N8) segment 6 (NA) 2525.5 0.000000e+00 1379/1385 (99%)
EPI552778 A/chicken/Netherlands/emc-3/2014 (A/H5N8) segment 6 (NA) 2518.1 0.000000e+00 1375/1381 (99%)
EPI552770 A/eurasian wigeon/Netherlands/emc-2/2014 (A/H5N8) segment 6 (NA) 2516.3 0.000000e+00 1374/1380 (99%)
EPI552762 A/eurasian wigeon/Netherlands/emc-1/2014 (A/H5N8) segment 6 (NA) 2510.7 0.000000e+00 1371/1377 (99%)
EPI551144 A/eurasian wigeon/Netherlands/emc-1/2014 (A/H5N8) segment 6 (NA) 2510.7 0.000000e+00 1371/1377 (99%)
EPI542627 A/duck/Beijing/FS01/2013 (A/H5N8) segment 6 (NA) 2499.6 0.000000e+00 1373/1385 (99%)
EPI530990 A/duck/Zhejiang/6D18/2013 (A/H5N8) segment 6 (NA) 2442.4 0.000000e+00 1379/1407 (98%)
EPI530989 A/duck/Zhejiang/W24/2013 (A/H5N8) segment 6 (NA) 2436.9 0.000000e+00 1378/1407 (97%)
EPI544894 A/duck/Shandong/Q1/2013 (A/H5N8) segment 6 (NA) 2431.3 0.000000e+00 1376/1406 (97%)
EPI509700 A/breeder duck/Korea/Gochang1/2014 (A/H5N8) segment 6 (NA) 2431.3 0.000000e+00 1377/1407 (97%)
EPI507675 A/mallard duck/Shanghai/SH-9/2013 (A/H5N8) segment 6 (NA) 2431.3 0.000000e+00 1377/1407 (97%)
EPI442019 A/duck/Jiangsu/k1203/2010 (A/H5N8) segment 6 (NA) 2425.8 0.000000e+00 1367/1394 (98%)
EPI485330 A/common shelduck/Mongolia/2185/2011 (A/H3N8) segment 6 (NA) 2165.4 0.000000e+00 1330/1408 (94%)
EPI132266 A/duck/Eastern China/90/2004 (A/H3N8) segment 6 (NA) 2154.3 0.000000e+00 1328/1408 (94%)
EPI132262 A/duck/Eastern China/19/2004 (A/H3N8) segment 6 (NA) 2143.2 0.000000e+00 1326/1408 (94%)
EPI326921 A/environment/Korea/SH12-6/2008 (A/H3N8) segment 6 (NA) 2132.2 0.000000e+00 1323/1407 (94%)
EPI416940 A/duck/Vietnam/OIE-2577/2011 (A/H3N8) segment 6 (NA) 2098.9 0.000000e+00 1318/1408 (93%)
EPI438257 A/duck/Vietnam/G18-1/2011 (A/H3N8) segment 6 (NA) 2082.3 0.000000e+00 1315/1408 (93%)
EPI387415 A/ruddy shelduck/Mongolia/1-26/2007 (A/H3N8) segment 6 (NA) 2082.3 0.000000e+00 1288/1367 (94%)
EPI387510 A/ruddy shelduck/Mongolia/2-79/2007 (A/H3N8) segment 6 (NA) 2060.1 0.000000e+00 1284/1367 (93%)
EPI387494 A/pintail/Mongolia/2-65/2007 (A/H3N8) segment 6 (NA) 2054.6 0.000000e+00 1283/1367 (93%)
EPI326920 A/environment/Korea/SH12-8/2008 (A/H3N8) segment 6 (NA) 2052.7 0.000000e+00 1280/1364 (93%)
EPI363489 A/duck/Guangxi/2736/2006 (A/H6N8) segment 6 (NA) 2049.1 0.000000e+00 1309/1408 (92%)
EPI485320 A/ruddy shelduck/Mongolia/1787/2011 (A/H3N8) segment 6 (NA) 1980.7 0.000000e+00 1287/1391 (92%)
EPI485328 A/common shelduck/Mongolia/2076/2011 (A/H3N8) segment 6 (NA) 1871.8 0.000000e+00 1258/1378 (91%)
EPI128912 A/duck/Ukraine/1/1963 (A/H3N8) segment 6 (NA) 1755.4 0.000000e+00 1261/1413 (89%)
EPI407886 A/duck/Ukraine/1963 (A/H3N8) segment 6 (NA) 1749.9 0.000000e+00 1261/1414 (89%)
EPI42182 A/duck/Ukraine/1/1963 (A/H3N8) segment 6 (NA) 1749.9 0.000000e+00 1261/1414 (89%)
EPI3107 A/duck/Ukraine/1/1963 (A/H3N8) segment 6 (NA) 1744.4 0.000000e+00 1260/1414 (89%)
EPI132460 A/duck/Ukraine/1/1963 (A/H3N8) segment 6 (NA) 1738.8 0.000000e+00 1259/1414 (89%)
EPI251642 A/mallard/Netherlands/10/1999 (A/H1N8) segment 6 (NA) 1724.0 0.000000e+00 1214/1352 (89%)
EPI128904 A/duck/Burjatia/652/1988 (A/H3N8) segment 6 (NA) 1672.3 0.000000e+00 1249/1416 (88%)
EPI2999 A/duck/Hong Kong/438/1977 (A/H4N8) segment 6 (NA) 1672.3 0.000000e+00 1247/1414 (88%)
EPI314410 A/mallard/Czech Republic/14516/2007 (A/H3N8) segment 6 (NA) 1666.8 0.000000e+00 1242/1410 (88%)
EPI182043 A/common eider/Netherlands/1/2006 (A/H3N8) segment 6 (NA) 1666.8 0.000000e+00 1245/1413 (88%)
EPI336006 A/teal/Chany/444/2009 (A/H8N8) segment 6 (NA) 1661.3 0.000000e+00 1245/1414 (88%)
EPI316502 A/duck/Hubei/126/1985 (A/H7N8) segment 6 (NA) 1661.3 0.000000e+00 1247/1416 (88%)
EPI251715 A/mallard/Sweden/45/2002 (A/H11N8) segment 6 (NA) 1661.3 0.000000e+00 1243/1412 (88%)
EPI398948 A/mallard/Norway/10_779/2009 (A/H3N8) segment 6 (NA) 1655.7 0.000000e+00 1242/1412 (87%)
EPI372503 A/mallard/Ukraine/05842-NAMRU3/2006 (A/H3N8) segment 6 (NA) 1655.7 0.000000e+00 1241/1411 (87%)
EPI339175 A/mallard/Germany-BY/R1353/2010 (A/H6N8) segment 6 (NA) 1655.7 0.000000e+00 1240/1410 (87%)
EPI339174 A/goose/Germany/R1767/2007 (A/H6N8) segment 6 (NA) 1655.7 0.000000e+00 1241/1411 (87%)
EPI316762 A/mallard/Czech Republic/13577-24K/2010 (A/H3N8) segment 6 (NA) 1655.7 0.000000e+00 1240/1410 (87%)
EPI268303 A/duck/Hunan/3748/2004 (A/H6N8) segment 6 (NA) 1655.7 0.000000e+00 1241/1411 (87%)
EPI397605 A/duck/Germany-NW/R2185/2006 (A/H6N8) segment 6 (NA) 1650.2 0.000000e+00 1244/1415 (87%)
EPI339172 A/mallard/Germany-BE/R663/08 (A/H3N8) segment 6 (NA) 1650.2 0.000000e+00 1241/1412 (87%)
EPI310343 A/duck/Zambia/04/2008 (A/H3N8) segment 6 (NA) 1650.2 0.000000e+00 1241/1412 (87%)
EPI235185 A/Mallard/65112/03 (A/H3N8) segment 6 (NA) 1650.2 0.000000e+00 1241/1412 (87%)
EPI182115 A/mallard/Netherlands/33/2006 (A/H7N8) segment 6 (NA) 1650.2 0.000000e+00 1242/1413 (87%)
EPI182051 A/turnstone/Netherlands/1/2007 (A/H3N8) segment 6 (NA) 1650.2 0.000000e+00 1242/1413 (87%)
EPI14499 A/duck/Spain/543/2006 (A/H6N8) segment 6 (NA) 1650.2 0.000000e+00 1241/1412 (87%)
EPI268302 A/mallard/Jiangxi/6285/2004 (A/H6N8) segment 6 (NA) 1646.5 0.000000e+00 1239/1410 (87%)
EPI268301 A/mallard/Jiangxi/4408/2005 (A/H6N8) segment 6 (NA) 1646.5 0.000000e+00 1239/1410 (87%)
EPI296491 A/common eider/Netherlands2/2006 (A/H4N8) segment 6 (NA) 1644.6 0.000000e+00 1240/1412 (87%)
EPI182083 A/black-headed gull/Netherlands/1/2005 (A/H6N8) segment 6 (NA) 1644.6 0.000000e+00 1240/1412 (87%)
EPI182075 A/common teal/Netherlands/2/2005 (A/H6N8) segment 6 (NA) 1644.6 0.000000e+00 1240/1412 (87%)
EPI398924 A/common gull/Norway/10_1602/2009 (A/H6N8) segment 6 (NA) 1639.1 0.000000e+00 1239/1412 (87%)
EPI367575 A/mallard/Czech Republic/14333-1K/2011 (A/H3N8) segment 6 (NA) 1639.1 0.000000e+00 1240/1413 (87%)
EPI169324 A/Anas platyrhynchos/Belgium/12827/2007 (A/H3N8) segment 6 (NA) 1639.1 0.000000e+00 1239/1412 (87%)
EPI408014 A/duck/Chabarovsk/1610/1972 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1238/1412 (87%)
EPI296538 A/mallard/Netherlands/20/2005 (A/H12N8) segment 6 (NA) 1633.6 0.000000e+00 1239/1413 (87%)
EPI222081 A/gadwall/Altai/1328/2007 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1237/1411 (87%)
EPI222073 A/gadwall/Altai/1326/2007 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1237/1411 (87%)
EPI222065 A/gadwall/Altai/1325/2007 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1237/1411 (87%)
EPI42316 A/duck/Chabarovsk/1610/1972 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1238/1412 (87%)
EPI14495 A/duck/Spain/539/2006 (A/H6N8) segment 6 (NA) 1633.6 0.000000e+00 1238/1412 (87%)
EPI2277 A/Duck/Hokkaido/8/80 (A/H3N8) segment 6 (NA) 1633.6 0.000000e+00 1239/1413 (87%)
EPI13715 A/duck/Norway/1/03 (A/H3N8) segment 6 (NA) 1631.7 0.000000e+00 1236/1411 (87%)
EPI234646 A/duck/Beijing/40/04 (A/H3N8) segment 6 (NA) 1628.0 0.000000e+00 1238/1413 (87%)
EPI222057 A/gadwall/Altai/1324/2007 (A/H3N8) segment 6 (NA) 1628.0 0.000000e+00 1237/1412 (87%)
EPI184026 A/mallard/Hungary/19616/2007 (A/H3N8) segment 6 (NA) 1628.0 0.000000e+00 1238/1413 (87%)
EPI128908 A/Duck/Hokkaido/8/80 (A/H3N8) segment 6 (NA) 1628.0 0.000000e+00 1239/1414 (87%)
EPI251795 A/mallard/Sweden/7/2003 (A/H10N8) segment 6 (NA) 1622.5 0.000000e+00 1168/1311 (89%)
EPI251736 A/mallard/Sweden/50/2002 (A/H3N8) segment 6 (NA) 1622.5 0.000000e+00 1214/1379 (88%)
EPI221959 A/environment/Dongting Lake/Hunan/3-9/2007 (A/H10N8) segment 6 (NA) 1622.5 0.000000e+00 1238/1414 (87%)
EPI181955 A/mallard/Netherlands/3/2005 (A/H3N8) segment 6 (NA) 1622.5 0.000000e+00 1235/1411 (87%)
EPI105959 A/Bewick's swan/Netherlands/2/2005 (A/H6N8) segment 6 (NA) 1622.5 0.000000e+00 1237/1413 (87%)
EPI356301 A/Greater white-fronted goose/Germany-NW/R02/2009 (A/H6N8) segment 6 (NA) 1616.9 0.000000e+00 1235/1412 (87%)
EPI345774 A/duck/Eastern China/50/2002 (A/H6N8) segment 6 (NA) 1616.9 0.000000e+00 1236/1413 (87%)
EPI302179 A/Greater White-Fronted Goose/Germany-NW/R02/2009 (A/H6N8) segment 6 (NA) 1616.9 0.000000e+00 1235/1412 (87%)
EPI232400 A/duck/Beijing/61/05 (A/H3N8) segment 6 (NA) 1616.9 0.000000e+00 1236/1413 (87%)
EPI174847 A/duck/Denmark/75-65472-P34/2003 (A/H3N8) segment 6 (NA) 1616.9 0.000000e+00 1235/1412 (87%)
EPI132438 A/duck/Eastern China/163/2002 (A/H6N8) segment 6 (NA) 1616.9 0.000000e+00 1235/1412 (87%)
EPI439277 A/common teal/Georgia/1/2011 (A/H3N8) segment 6 (NA) 1611.4 0.000000e+00 1205/1368 (88%)
EPI272796 A/mallard/PT/29497-11/2006 (A/H3N8) segment 6 (NA) 1611.4 0.000000e+00 1234/1412 (87%)
EPI221967 A/environment/Dongting Lake/Hunan/3-9/2007 (A/H10N8) segment 6 (NA) 1611.4 0.000000e+00 1236/1414 (87%)

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PostPosted: Mon Dec 22, 2014 5:46 pm 
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niman wrote:
USDA has released an update OIE report from Oregon.

http://www.oie.int/wahis_2/public/wahid ... rtid=16810

Information received on 19/12/2014 from Dr John Clifford, Deputy Administrator, Animal and Plant Health Inspection Service, United States Department of Agriculture, Washington, United States of America
Summary
Report type Follow-up report No. 1
Date of start of the event 10/12/2014
Date of pre-confirmation of the event 14/12/2014
Report date 19/12/2014
Date submitted to OIE 19/12/2014
Reason for notification Reoccurrence of a listed disease
Date of previous occurrence 2004
Manifestation of disease Clinical disease
Causal agent Highly pathogenic avian influenza virus
Serotype H5N8
Nature of diagnosis Laboratory (advanced)
This event pertains to a defined zone within the country
Related reports Immediate notification (16/12/2014)
Follow-up report No. 1 (19/12/2014)
New outbreaks (1)
Outbreak 1 Douglas County, Douglas, OREGON
Date of start of the outbreak 16/12/2014
Outbreak status Continuing (or date resolved not provided)
Epidemiological unit Backyard
Affected animals
Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 130 28 28 0 0
Affected population The affected premises are a small backyard mixed flock of guinea fowl, chickens, ducks, and geese that are allowed access to the outdoors and regularly exposed to wild migratory waterfowl. The affected backyard flock was placed under quarantine.
Summary of outbreaks Total outbreaks: 1
Total animals affected
Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 130 28 28 0 0
Outbreak statistics
Species Apparent morbidity rate Apparent mortality rate Apparent case fatality rate Proportion susceptible animals lost*
Birds 21.54% 21.54% 100.00% 21.54%
*Removed from the susceptible population through death, destruction and/or slaughter
Epidemiology
Source of the outbreak(s) or origin of infection
Contact with wild species
Epidemiological comments The USDA Animal and Plant Health Inspection Services (APHIS) and the Oregon Department of Agriculture (ODA) are conducting a comprehensive investigation of this outbreak. The USDA APHIS National Veterinary Services Laboratory (NVSL) confirmed avian influenza virus (AIV) H5N8 via sequencing directly from swab samples. Preliminary results indicate the HA sequence is 99.3% similar to A/bean goose/Korea/H40/2014 (H5N8 HPAI) based on a partial fragment of the HA gene. The neuraminidase sequence is 99.7% similar to A/Baikal teal/Korea/H80/2014 (H5N8) based on a partial fragment of the NA gene. The amino acid sequence at the hemagglutinin cleavage site is consistent with highly pathogenic avian influenza (HPAI). Whole genome sequencing is in progress. Enhanced surveillance by the USDA APHIS and ODA is being initiated. The H5N8 highly pathogenic avian influenza (HPAI) in Oregon is limited to a small backyard poultry premises only and does not involve commercial poultry.
Control measures
Measures applied
Quarantine
Vaccination prohibited
No treatment of affected animals
Measures to be applied
Stamping out
Disinfection of infected premises/establishment(s)
Diagnostic test results
Laboratory name and type Species Test Test date Result
National Veterinary Services Laboratories (National laboratory) Birds real-time reverse transcriptase/polymerase chain reaction (RRT-PCR) 18/12/2014 Positive
National Veterinary Services Laboratories (National laboratory) Birds virus sequencing 18/12/2014 Positive
Future Reporting
The event is continuing. Weekly follow-up reports will be submitted.

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PostPosted: Mon Dec 22, 2014 6:01 pm 
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Map updated

https://mapsengine.google.com/map/edit? ... IjI0Pz2tn8

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PostPosted: Mon Dec 22, 2014 6:49 pm 
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Published Date: 2014-12-22 16:19:58
Subject: PRO/AH/EDR> Avian influenza (115): USA (OR) backyard poultry, HPAI H5N8, OIE
Archive Number: 20141222.3049031
AVIAN INFLUENZA (115): USA (OREGON), BACKYARD POULTRY, HPAI H5N8, OIE
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Date: Fri 19 Dec 2014
Source: OIE, WAHID weekly disease information 2014; 27(52) [edited]
http://www.oie.int/wahis_2/public/wahid ... rtid=16810


Highly pathogenic avian influenza, USA
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Information received on [and dated] 19 Dec 2014 from Dr John Clifford, deputy administrator, Animal and Plant Health Inspection Service, United States Department of Agriculture, Washington, USA

Summary
Report type: follow-up report No. 1
Date of start of the event: 10 Dec 2014
Date of pre-confirmation of the event: 14 Dec 2014
Reason for notification: reoccurrence of a listed disease
Date of previous occurrence: 2004
Manifestation of disease: clinical disease
Causal agent: highly pathogenic avian influenza virus
Serotype: H5N8
Nature of diagnosis: laboratory (advanced)
This event pertains to a defined zone within the country

New outbreaks (1)
Summary of outbreaks: Total outbreaks: 1
Outbreak 1: Douglas County, Douglas, Oregon
Date of start of the outbreak: 16 Dec 2014
Outbreak status: continuing (or date resolved not provided)
Epidemiological unit: backyard
Total animals affected:
Species / Susceptible / Cases / Deaths / Destroyed / Slaughtered
Birds / 130 / 28 / 28 / 0 / 0
Affected population: The affected premises are a small backyard mixed flock of guinea fowl, chickens, ducks, and geese that are allowed access to the outdoors and regularly exposed to wild migratory waterfowl. The affected backyard flock was placed under quarantine.

Outbreak statistics [rates apparent, expressed as percentages]:
Species / Morbidity rate / Mortality rate / Case fatality rate / Proportion susceptible animals lost*
Birds / 21.5 / 21.5 / 100 / 21.5
*Removed from the susceptible population through death, destruction and/or slaughter

Epidemiology
Source of the outbreak(s) or origin of infection: contact with wild species

Epidemiological comment: The USDA Animal and Plant Health Inspection Services (APHIS) and the Oregon Department of Agriculture (ODA) are conducting a comprehensive investigation of this outbreak. The USDA APHIS National Veterinary Services Laboratory (NVSL) confirmed avian influenza virus (AIV) H5N8 via sequencing directly from swab samples. Preliminary results indicate the HA sequence is 99.3 per cent similar to A/bean goose/Korea/H40/2014 (H5N8 HPAI) based on a partial fragment of the HA gene. The neuraminidase sequence is 99.7 per cent similar to A/Baikal teal/Korea/H80/2014 (H5N8) based on a partial fragment of the NA gene. The amino acid sequence at the hemagglutinin cleavage site is consistent with highly pathogenic avian influenza (HPAI). Whole genome sequencing is in progress. Enhanced surveillance by the USDA APHIS and ODA is being initiated. The H5N8 highly pathogenic avian influenza (HPAI) in Oregon is limited to a small backyard poultry premises only and does not involve commercial poultry.

Control measures
Measures applied: quarantine; vaccination prohibited; no treatment of affected animals
Measures to be applied: stamping out; disinfection of infected premises/establishment(s)

Diagnostic test results
Laboratory name and type: National Veterinary Services Laboratories (NVSL) (national laboratory)
Species / Test / Test date / Result
Birds / real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) / 18 Dec 2014 / Positive
Birds / virus sequencing / 18 Dec 2014 / Positive

Future reporting
The event is continuing. Weekly follow-up reports will be submitted.

[The location of the outbreak can be seen on the interactive map included in the OIE report at the source URL above.]

--
communicated by:
ProMED-mail
<promed@promedmail.org>

[The finding in Douglas County, Oregon, was quickly reported and identified due to increased surveillance for avian influenza in light of the HPAI H5N2 affecting commercial poultry in British Columbia, Canada, and the detection of HPAI in wild birds in Washington State. The H5N8 virus found in this backyard flock is the same virus that was found in the Washington State gyrfalcons.

While the United States is likely to be working with its trading partners to minimize trade impacts on poultry commodities, countries should respond to this reported detection according to OIE's science-based standards. Given that only backyard poultry were affected, that commercial production operations have heightened their state of alert, tightened their biosecurity, and increased their surveillance activities, there would be little justification in prohibiting poultry and poultry commodities from US integrated operations. - Mod.CRD

A HealthMap/ProMED-mail map can be accessed at: http://healthmap.org/promed/p/3613.]
See Also
Avian influenza (112): USA (WA) wild birds, HPAI H5N8, H5N2 20141218.3040607
Avian influenza (110): USA (WA) wild birds, HPAI H5N8, H5N2, OIE 20141217.3037995
Avian influenza (108): USA (WA) H5N2, H5N8, wild birds 20141217.3038018
Avian influenza (109): Canada (BC) HPAI H5N2, poultry 20141217.3038022
Avian influenza (107): Germany (NI) poultry, HPAI H5N8 20141216.3037531
Avian influenza (106): Italy (VN) poultry, HPAI H5N8, OIE 20141216.3036371
Avian influenza (104): Canada (BC) HPAI H5N2, poultry, update, OIE 20141210.3024271
Avian influenza (102): Canada (BC) HPAI H5N2, poultry 20141205.3012874
Avian influenza (101): Canada (BC) H5, poultry, RFI, OIE: 20141204.3011429
Avian influenza (99): Netherlands (ZH) HPAI H5N8 conf, poultry 20141201.3003249
Avian influenza (98): Netherlands (ZH) H5, poultry 20141130.3000468
Avian influenza (97): HPAI H5N8, Germany, prevention, Japan, wild bird 20141128.2997318
Avian influenza (94): Netherlands (OV) HPAI H5N8, update, alert, OIE, FAO 20141124.2986950
Avian influenza (93): Germany, HPAI H5N8, migratory birds 20141122.2982721
Avian influenza (92): Netherlands (OV) HPAI H5N8, spread, RFI 20141121.2980599
Avian influenza (91): Netherlands (SH), UK (ENG) update, HPAI H5N8, RFI 20141120.2977844
Avian influenza (90): UK (England) domestic duck, HPAI H5N8, control 20141118.2966461
Avian influenza (89): UK (England) domestic duck, HPAI H5, OIE 20141117.2963406
Avian influenza (88): UK (England) domestic duck, H5, HPAI 20141117.2963428
Avian influenza (87): Netherlands (UT) poultry, HPAI H5N8, OIE 20141117.2961931
Avian influenza (86): UK (England) domestic duck, H5, RFI 20141117.2961879
Avian influenza (85): Netherlands (UT) poultry, HPAI H5N8 20141116.2960394
Avian influenza (83): Germany (MV) poultry, HPAI H5N8, migratory birds 20141115.2957974
Avian influenza (82): Japan (SM) HPAI H5N8, wild bird, OIE 20141115.2955318
Avian influenza (81): Germany (MV) poultry, HPAI H5N8, genotype 20141114.2955469
Avian influenza (80): Germany (MV) poultry, HPAI H5N8 20141113.2953243
Avian influenza (79): Germany (MV), poultry, HPAI H5N8, OIE 20141106.2934925
Avian influenza (78): China, poultry, HPAI H5N3, H5N8, H5N1, OIE 20141026.2898069
Avian influenza (74): South Korea (CN) HPAI H5N8, duck, reoccurrence, OIE 20140926.2804737
Avian influenza (70): S Korea, HPAI H5N8, over, RFI 20140905.2751562
Avian influenza (65): South Korea (CN) HPAI H5N8, RFI 20140730.2646054
Avian influenza (63): South Korea, HPAI H5N8, RFI 20140619.2552686
Avian influenza (58): Japan (KM) HPAI H5N8, controlled 20140504.2448688
Avian influenza (56): South Korea, HPAI H5N8, geese, OIE, RFI 20140502.2444300
Avian influenza (53): Japan (KM) HPAI H5N8, update 20140421.2419552
Avian influenza (52): Japan (KM) HPAI serotyped H5N8 20140417.2412249
Avian influenza (17): S. Korea, HPAI H5N8, poultry, spread, OIE, N. Korea, RFI 20140210.2268635
Avian influenza (15): South Korea, HPAI H5N8, poultry, wildfowl 20140203.2252563
Avian influenza (12): South Korea, HPAI H5N8, chicken, migratory birds, spread 20140129.2240988
Avian influenza (07): South Korea (CB) HPAI H5N8, duck, OIE 20140120.2185629
Avian influenza (06): South Korea (CB) HPAI H5N8, duck, migratory birds 20140120.2191161
Avian influenza (05): South Korea (CB) HPAI H5N8, duck 20140119.2183768
.................................................crd/je/sh

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PostPosted: Mon Dec 22, 2014 7:16 pm 
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