Rhiza Labs FluTracker Forum

The National Laboratory for Veterinary Quality Control on Poultry Production has released a series of H5 sequences (at Genbank) from samples collected in late 2011 / early 2012. All except A/chicken/Egypt/113Q/2011 had the 3 BP deletion, S133del.

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None of the above recent sequences have N224K.

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JQ858477 Avian 4 H5N1 Egypt 2011/10/05 1676 Influenza A virus (A/chicken/Egypt/1119AF/2011(H5N1)) yes
JQ858472 Avian 4 H5N1 Egypt 2011/07/26 1764 Influenza A virus (A/chicken/Egypt/113Q/2011(H5N1)) yes
JQ858469 Avian 4 H5N1 Egypt 2011/07/08 1726 Influenza A virus (A/chicken/Egypt/11506SF/2011(H5N1)) yes
JQ858475 Avian 4 H5N1 Egypt 2011/07/27 1726 Influenza A virus (A/chicken/Egypt/11667s/2011(H5N1)) yes
JQ858473 Avian 4 H5N1 Egypt 2011/07/26 1738 Influenza A virus (A/chicken/Egypt/11672s/2011(H5N1)) yes
JQ858471 Avian 4 H5N1 Egypt 2011/07/18 1749 Influenza A virus (A/chicken/Egypt/1176/2011(H5N1)) yes
JQ858481 Avian 4 H5N1 Egypt 2011/12/04 1715 Influenza A virus (A/chicken/Egypt/11764s/2011(H5N1)) yes
JQ858482 Avian 4 H5N1 Egypt 2011/12/13 1770 Influenza A virus (A/chicken/Egypt/11765s/2011(H5N1)) yes
JQ858479 Avian 4 H5N1 Egypt 2011/10/25 1789 Influenza A virus (A/chicken/Egypt/1188/2011(H5N1)) yes
JQ858483 Avian 4 H5N1 Egypt 2012/01/06 1704 Influenza A virus (A/chicken/Egypt/121/2012(H5N1)) yes
JQ858488 Avian 4 H5N1 Egypt 2012/02 1760 Influenza A virus (A/chicken/Egypt/12186F-12/2012(H5N1)) yes
JQ858487 Avian 4 H5N1 Egypt 2012/02 1761 Influenza A virus (A/chicken/Egypt/12186F-9/2012(H5N1)) yes
JQ858486 Avian 4 H5N1 Egypt 2012/01/12 1701 Influenza A virus (A/chicken/Egypt/1219s/2012(H5N1)) yes
JQ858484 Avian 4 H5N1 Egypt 2012/01/04 1710 Influenza A virus (A/chicken/Egypt/125s/2012(H5N1)) yes
JQ858485 Avian 4 H5N1 Egypt 2012/01/09 1680 Influenza A virus (A/chicken/Egypt/128s/2012(H5N1)) yes
JQ858470 Avian 4 H5N1 Egypt 2011/07/14 1771 Influenza A virus (A/duck/Egypt/1120SMF/2011(H5N1)) yes
JQ858476 Avian 4 H5N1 Egypt 2011/08/22 1767 Influenza A virus (A/duck/Egypt/11685s/2011(H5N1)) yes
JQ858480 Avian 4 H5N1 Egypt 2011/11/29 1771 Influenza A virus (A/duck/Egypt/11762s/2011(H5N1)) yes
JQ858478 Avian 4 H5N1 Egypt 2011/10/22 1701 Influenza A virus (A/duck/Egypt/1187/2011(H5N1)) yes
JQ858474 Avian 4 H5N1 Egypt 2011/07/27 1652 Influenza A virus (A/duck/Egypt/1198AS/2011(H5N1))

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LOCUS JQ858472 1764 bp cRNA linear VRL 29-APR-2012
DEFINITION Influenza A virus (A/chicken/Egypt/113Q/2011(H5N1)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION JQ858472
VERSION JQ858472.1 GI:385198465
KEYWORDS .
SOURCE Influenza A virus (A/chicken/Egypt/113Q/2011(H5N1))
ORGANISM Influenza A virus (A/chicken/Egypt/113Q/2011(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1764)
AUTHORS Arafa,A., Hagag,N., Yehia,N., Mady,W., Adel,A., Naguib,M.,
Elhuseiny,M. and Abdel-Wanees,S.
TITLE Effect of co-circulation of highly pathogenic avian influenza H5N1
subtype with low pathogenic H9N2 subtype on the epizootiological
nature of outbreaks
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1764)
AUTHORS Arafa,A., Hagag,N., Yehia,N., Mady,W., Adel,A., Naguib,M.,
Elhuseiny,M. and Abdel-Wanees,S.
TITLE Direct Submission
JOURNAL Submitted (30-MAR-2012) National Laboratory for Veterinary Quality
Control on Poultry Production, Animal Health Research Institute,
Nadi Elsaid Street, Dokki, Giza 12618, Egypt
COMMENT ##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..1764
/organism="Influenza A virus
(A/chicken/Egypt/113Q/2011(H5N1))"
/mol_type="viral cRNA"
/strain="A/chicken/Egypt/113Q/2011"
/serotype="H5N1"
/isolation_source="oro-pharyngeal swabs"
/host="chicken"
/db_xref="taxon:1168482"
/segment="4"
/country="Egypt: Qalyobia"
/collection_date="26-Jul-2011"
gene 13..1719
/gene="HA"
CDS 13..1719
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AFI44342.1"
/db_xref="GI:385198466"
/translation="MERIVLLLAIVSLVKSDQICIGYHANNSTQQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFPNVSEWSYIVEKVNPA
NDLCYPGNFNNYEELKHLLSRINRFEKIQIIPKNSWPDHEASLGVSSACPYQGELSFY
KNVVWLIKKNNTYPTIKESYHNTNQEDLLVLWGIHHPNDEKEQKSIYKNPITYISVGT
STLNQRLVPKIATRPKVNGQSGRVEFFWTILKSNDTINFESNGNFIAPEYAYKIVKKG
SSTIMKSELEYGNCSTKCQTPIGAINSSMPFHNIHPLTIGECPKYVKSTRLVLATGLR
NSPQGEGRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGTGYAADKESTQKAID
GVTNKVNSIIDKMNTQFEAVGREFNNLEKRIENLNKKMEDGFLDVWTYNAELLVLMEN
ERTLDFHDSNVRNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQY
SEEARLKREEISGVKLESIGNYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCRI
CI"
ORIGIN
1 caatctgtca aaatggagag aatagtgctt cttcttgcaa tagtcagtct tgttaaaagt
61 gatcagattt gcattggtta ccatgcaaac aactcaacac agcaggttga cacaataatg
121 gaaaagaacg tcactgttac acacgctcaa gacatactgg aaaagacaca caatgggaaa
181 ctctgcgatc tagatggagt gaagcctcta attttaagag attgtagtgt agctggatgg
241 ctcctcggga acccaatgtg tgacgaattc cccaatgtgt ctgaatggtc ctacatagtg
301 gagaaggtca atccagccaa tgacctctgt tacccaggga atttcaacaa ctatgaagaa
361 ctgaaacacc tattgagcag aataaaccgg tttgagaaaa ttcagatcat ccccaaaaat
421 tcttggccag accatgaagc ctcattagga gtgagctcag catgtccata ccagggagaa
481 ctctcctttt ataaaaatgt ggtatggctt atcaaaaaga acaatacata cccaacaata
541 aaggaaagtt accataatac caatcaagaa gatcttttgg tgctgtgggg gatccaccat
601 ccaaatgatg aaaaagagca aaaaagtatc tataaaaacc caattaccta tatttccgtt
661 gggacatcaa cactaaacca gagattggta ccaaagatag ccactagacc taaggtaaac
721 ggacaaagtg gaagagtgga gttcttttgg acaattttaa aatcaaatga tacaataaac
781 tttgaaagta atggaaattt cattgctcca gagtatgcat ataaaattgt caagaaaggg
841 agctcaacaa ttatgaaaag tgagttggaa tatggtaact gcagcaccaa gtgtcaaact
901 ccaatagggg cgataaactc cagtatgcca ttccacaaca tccaccctct caccatcggg
961 gaatgcccca aatatgtgaa atcaaccaga ttagtccttg ctactgggct cagaaatagc
1021 cctcaaggag aaggaagaag aaaaaagaga ggactatttg gagctatagc aggttttata
1081 gagggaggat ggcagggaat ggtagatggt tggtatgggt accaccatag caacgagcag
1141 gggactgggt acgctgcaga caaagaatcc actcaaaagg caatagatgg agtcaccaat
1201 aaggtcaact cgatcattga caaaatgaat actcagtttg aggctgttgg gagggaattt
1261 aataacttgg aaaagagaat agaaaattta aacaagaaga tggaagacgg gttcctagat
1321 gtctggactt ataatgctga acttctggtt ctcatggaaa atgagagaac tctagacttt
1381 catgactcaa atgtcaggaa cctttacgac aaggtgcgac tacagcttag ggacaatgca
1441 aaggagcttg gtaacggttg tttcgagttc tatcacaaat gcgataatga atgtatggaa
1501 agtgtaagaa acggaacgta tgactaccct cagtattcag aagaagcaag attaaaaaga
1561 gaggaaataa gtggagtaaa attggaatca ataggaaatt accaaatatt atcaatttat
1621 tcaacagtgg caagttccct agcactggca atcatggtgg ctggtctatc tttatggatg
1681 tgctccaatg gatcgctaca atgcagaatt tgcatttaaa tttgtgagtt cagattgtag
1741 ttaaaaacac ccttgtttcc tact

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Commentary

http://www.recombinomics.com/News/05011 ... Adapt.html

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