Rhiza Labs FluTracker Forum

The first reported H5N1 fatally in 2012 was a case (2M) in Cambodia (discussed at link below)

viewtopic.php?f=5&t=7858

In 2011 Cambodia reported 8 human cases and all 8 were fatal. Sequences from these 2011 cases were recently reelased at GISAID and Genbank. The most recent sequence was from a June 6, 2011 case, A/Cambodia/V0606311/2011, and the HA sequence had S227N which increases affinity for human 2/6 gal receptors, as well as PB2 E627K, which allows the H5N1 to replicate more efficiently at a lower temperature, leading to enhanced transmission.

_________________
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LOCUS JN588809 1743 bp cRNA linear VRL 01-NOV-2011
DEFINITION Influenza A virus (A/Cambodia/V0606311/2011(H5N1)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION JN588809
VERSION JN588809.1 GI:345098974
KEYWORDS .
SOURCE Influenza A virus (A/Cambodia/V0606311/2011(H5N1))
ORGANISM Influenza A virus (A/Cambodia/V0606311/2011(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1743)
AUTHORS Buchy,P. and Mardy,S.
TITLE Direct Submission
JOURNAL Submitted (16-AUG-2011) Virology Unit, Institut Pasteur in
Cambodia, 5 Monivong Blvd, BP 983, Phnom Penh BP 983, Cambodia
FEATURES Location/Qualifiers
source 1..1743
/organism="Influenza A virus
(A/Cambodia/V0606311/2011(H5N1))"
/mol_type="viral cRNA"
/strain="A/Cambodia/V0606311/2011"
/serotype="H5N1"
/host="Homo sapiens"
/db_xref="taxon:1076957"
/segment="4"
/country="Cambodia: Prey Veng"
/collection_date="06-Jun-2011"
gene 10..1716
/gene="HA"
CDS 10..1716
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEN68938.1"
/db_xref="GI:345098975"
/translation="MEKIVLLFVIVNLVKSDQICIGYHANNSTEQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLDGIRPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPV
NDICYPGVFNDYEELKHLLSRINHFEKVQIIPKSSWPSHEASLGVSAACPYQGKSSFF
RNVVWLIKKNSTYPTIKRSYNNTGQEDLLIMWGIHHPNDAAEQTKLYQNPTTYISVGT
STLNQRLTPRIATRSKVNGQNGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKG
DSTIMKSELEYGNCNTRCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLR
NSPQREGRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAID
GVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMEN
ERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQY
SEEARLKREEISGVKLESIGVYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCRI
CI"
ORIGIN
1 tctgtcaaaa tggagaaaat agtgcttctt tttgtgatag tcaatcttgt taaaagtgat
61 cagatttgca ttggctacca tgcaaacaac tcgacagagc aggttgacac gataatggaa
121 aagaacgtta ctgttacaca tgcccaagac atactggaaa agacacataa cgggaagctc
181 tgtgacctag atggaattag gcctctaatt ttgagggatt gcagtgtagc tggatggctc
241 ctcggaaacc caatgtgtga cgaattcatc aatgtgccag aatggtctta catagtggag
301 aaggccaatc cagtcaacga catctgttac ccaggagttt tcaatgacta tgaagaattg
361 aaacacctac tgagccgaat aaaccatttt gagaaagttc agatcatccc caagagttct
421 tggcccagtc atgaagcctc attgggggtg agcgcagcat gtccatacca gggaaagtcc
481 tcttttttca gaaatgtggt atggcttatc aaaaagaaca gtacataccc aacaataaag
541 aggagttaca ataatacagg ccaagaagat cttttgataa tgtgggggat ccaccatcct
601 aatgatgcgg cagagcaaac aaaactctac caaaatccaa ccacctatat ctccgttggg
661 acatcaacgc taaaccagag attgacacca agaatagcta ctagatccaa agtaaacggg
721 caaaatggga ggatggagtt cttctggaca attttaaaac cgaatgatgc aatcaacttc
781 gagagtaatg gaaatttcat tgctccagaa tatgcataca aaattgtcaa gaaaggggac
841 tcaacaatta tgaaaagtga attggaatat ggcaactgca acaccaggtg tcaaactcca
901 atgggggcga taaactctag tatgccattc cacaatatac atcctctcac tattggggaa
961 tgccccaaat atgtgaaatc aaacagacta gtacttgcga ccgggctcag aaatagccct
1021 caaagagagg gaagaagaaa aaagagagga ttatttggag ctatagcagg ttttatagag
1081 ggaggatggc aggggatggt agatggttgg tatgggtacc accatagcaa tgagcaggga
1141 agcgggtacg ctgcagacaa agaatccact caaaaggcta tagatggagt caccaataag
1201 gtcaactcga tcattgacaa aatgaacact cagtttgagg ccgttggaag ggaatttaac
1261 aacttagaaa gaagaataga gaatttaaac aagaagatgg aagacgggtt cttagatgtc
1321 tggacctata atgctgaact tctggttctc atggaaaatg agagaactct agacttccat
1381 gactcaaatg taaagaacct ttacgacaag gtccgattac agcttaggga taatgcaaag
1441 gagctgggta acggttgttt cgagttctat cacaaatgtg acaatgaatg tatggaaagt
1501 gtgagaaacg ggacgtatga ctacccgcag tattcagaag aagcgagatt aaaaagagag
1561 gaaataagtg gagtgaaatt ggaatcgata ggagtttacc aaatactgtc aatttattct
1621 acagtggcga gttccctagc attggcaatc atggtagctg gtctatcctt atggatgtgc
1681 tccaatgggt cgttacaatg cagaatctgc atttaaatct gtgagttcag attgtagtta
1741 aaa

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S227N at GISAID

EPI341364 A/Cambodia/V0606311/2011 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI255349 A/Egypt/10217-NAMRU3/2007 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI165070 A/Egypt/2546-NAMRU3/2008 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI118835 A/Turkey/65596/2006 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI118798 A/Turkey/12/2006 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI116501 A/Hong Kong/213/2003 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI110237 A/Egypt/2947-NAMRU3/2006 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI20508 A/Hong Kong/213/03 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI20506 A/HK/212/03 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)
EPI1161 A/Hong Kong/213/03 (A/H5N1) segment 4 (HA) 27.0 7.439545e+00 14/14 (100%)

_________________
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S227N at Genbank

JN588809.1 Influenza A virus (A/Cambodia/V0606311/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 38.2 38.2 100% 0.26 100%
EF541401.1 Influenza A virus (A/Hong Kong/213/2003(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 38.2 38.2 100% 0.26 100%
AY575870.1 Influenza A virus (A/HK/213/03 (H5N1)) hemagglutinin (HA) gene, partial cds 38.2 38.2 100% 0.26 100%
AY575869.1 Influenza A virus (A/HK/212/03 (H5N1)) hemagglutinin (HA) gene, partial cds 38.2 38.2 100% 0.26 100%
AB212054.1 Influenza A virus (A/Hong Kong/213/2003(H5N1)) HA gene for hemagglutinin, complete cds, MDCK isolate, embryonated chicken egg isolate 38.2 38.2 100% 0.26 100%

_________________
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LOCUS JN588929 2315 bp cRNA linear VRL 01-NOV-2011
DEFINITION Influenza A virus (A/Cambodia/V0606311/2011(H5N1)) segment 1
polymerase PB2 (PB2) gene, complete cds.
ACCESSION JN588929
VERSION JN588929.1 GI:345098838
KEYWORDS .
SOURCE Influenza A virus (A/Cambodia/V0606311/2011(H5N1))
ORGANISM Influenza A virus (A/Cambodia/V0606311/2011(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2315)
AUTHORS Buchy,P. and Mardy,S.
TITLE Direct Submission
JOURNAL Submitted (16-AUG-2011) Virology Unit, Institut Pasteur in
Cambodia, 5 Monivong Blvd, BP 983, Phnom Penh BP 983, Cambodia
FEATURES Location/Qualifiers
source 1..2315
/organism="Influenza A virus
(A/Cambodia/V0606311/2011(H5N1))"
/mol_type="viral cRNA"
/strain="A/Cambodia/V0606311/2011"
/serotype="H5N1"
/host="Homo sapiens"
/db_xref="taxon:1076957"
/segment="1"
/country="Cambodia: Prey Veng"
/collection_date="06-Jun-2011"
gene 5..2284
/gene="PB2"
CDS 5..2284
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="AEN68870.1"
/db_xref="GI:345098839"
/translation="MERIKEIRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA
LRMKWMMAMKYPITADKRIIEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN
GPATSAVHYPKVYKTYFEKVERLKHGTFGPVRFRNQVKIRRRVDINPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL
PVTGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADP
LASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGMRISSSFSFGGFTFKRTS
GASIKKEEEVLTGNLQTLKIRVYEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNTMHQLLRHFQKDAKVLFQNWG
IEPIDDVMGMIGVLPDMTPSTEMSLRGVRVSKMGVDEYSSTERIVVSIDRFLRVRDQR
GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQ
DPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA
PPKQSRMQFSSLTVNVRGSGMRILIRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEG
TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRN
SSILTDSQTATKRIRMAIN"
ORIGIN
1 caatatggag agaataaaag aaatacgaga tttaatgtca caatcccgca ctcgcgagat
61 actaacaaaa accactgtgg accatatggc cataatcaag aaatacacat caggaagaca
121 agagaagaac cctgctctca gaatgaaatg gatgatggca atgaaatatc caatcacagc
181 agacaagaga ataatagaga tgatccctga aaggaatgaa caaggacaga cgctctggag
241 taagacaaat gatgctggat cggacagggt gatggtgtcc cccctagctg taacctggtg
301 gaataggaat gggccggcaa caagtgcagt tcattatcca aaggtttaca aaacatactt
361 tgagaaggtt gaaaggttaa aacacgggac cttcggtccc gtccgtttcc gaaatcaagt
421 caaaatacgc cgccgagttg atataaatcc tggccatgca gatctcagtg ctaaagaagc
481 gcaagatgtc atcatggagg tcgttttccc aaatgaagtg ggagctagaa tattgacatc
541 agagtcgcaa ttgacaataa cgaaagagaa gaaagaagag ctccaagatt gtaaaattgc
601 tcccttaatg gttgcatata tgttggaaag ggaactagtc cgcaaaacca ggttcctacc
661 ggtaacaggc ggaacaagca gtgtgtacat tgaggtattg catttgactc aagggacctg
721 ctgggaacag atgtacactc caggcggaga agtgagaaat gacgatgttg accagagttt
781 gatcatcgct gccagaaaca ttgttaggag agcaacggta tcagcagatc cactagcatc
841 actactggag atgtgtcaca gcacacaaat tggtgggata aggatggtgg acatccttag
901 gcaaaatcca actgaggaac aagctgtgga tatatgcaaa gcagcaatgg gtatgaggat
961 cagttcttcc tttagctttg gaggcttcac ttttaagaga acaagtggag catccatcaa
1021 gaaggaagag gaagtgctca caggcaacct ccaaacattg aaaataagag tctacgaagg
1081 gtatgaggaa ttcacaatgg ttgggcggag agcaacagct atcttgagga aagcaactag
1141 aaggctgatt cagttgatag taagtggaag agacgaacaa tcaatcgctg aggcaatcat
1201 tgtagcaatg gtattctcac aggaggattg catgataaag gcagtccgag gcgatctgaa
1261 tttcgtaaac agagcaaacc aaagattaaa caccatgcat caactcctga gacattttca
1321 aaaggatgca aaagtgttat ttcagaattg gggaattgaa cccattgatg atgtcatggg
1381 gatgatcgga gtattacctg acatgactcc cagcacagaa atgtcactaa gaggagtaag
1441 agttagtaaa atgggagtgg atgaatattc cagcactgag agaatagtag taagtattga
1501 ccgtttctta agggttcgag atcagagggg gaatgtactc ttatcccccg aggaggtcag
1561 cgaaacccag ggaacagaga aattgacaat aacatattca tcatcaatga tgtgggaaat
1621 caacggtcct gagtcagtgc ttgttaacac ctatcagtgg atcatcagaa actgggagac
1681 tgtgaagatt caatggtctc aagaccccac gatgctgtac aataagatgg agtttgaacc
1741 gttccaatcc ttggtaccca aagctgccag aggtcaatac agtggatttg tgagaacatt
1801 attccaacaa atgcgtgacg tgctggggac ttttgatact gtccagataa taaagctgct
1861 accatttgca gcagccccac cgaagcagag cagaatgcag ttttcttctc taactgtgaa
1921 tgtgagaggc tcaggaatga gaatactcat aagaggcaat tcccctgtgt tcaactacaa
1981 taaggcaacc aaaaggctta ccgtccttgg aaaggacgca ggtgcattaa cagaggatcc
2041 agatgagggg acagccggag tggaatctgc agtactgagg ggatttttaa tcctaggtaa
2101 ggaggacaaa aggtacggac cagcattgag catcaatgaa ttgagcaatc ttgcgaaggg
2161 ggagaaagct aatgtgctga tagggcaagg agacgtggtg ctggtaatga aacgaaaacg
2221 aaactctagc atacttactg acagccagac agcgaccaaa agaattcgga tggccatcaa
2281 ttagtgtcga attgtttaaa aacgaccttg tttct

_________________
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Top matches to most recent Cambodia human H5N1 HA sequence

EPI341364 A/Cambodia/V0606311/2011 (A/H5N1) segment 4 (HA) 3153.4 0.000000e+00 1707/1707 (100%)
EPI321744 A/muscovy duck/Vietnam/OIE-559/2011 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1690/1707 (99%)
EPI341366 A/Cambodia/V0401301/2011 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1687/1707 (98%)
EPI284580 A/duck/Vietnam/NCVD-010/2008 (A/H5N1) segment 4 (HA) 2987.2 0.000000e+00 1677/1707 (98%)
EPI284551 A/duck/Vietnam/NCVD-101/2008 (A/H5N1) segment 4 (HA) 2987.2 0.000000e+00 1677/1707 (98%)
EPI341362 A/chicken/Cambodia/TLC1/2009 (A/H5N1) segment 4 (HA) 2985.3 0.000000e+00 1670/1697 (98%)
EPI284536 A/duck/Vietnam/NCVD-118/2008 (A/H5N1) segment 4 (HA) 2970.5 0.000000e+00 1674/1707 (98%)
EPI284528 A/duck/Vietnam/NCVD-363/2009 (A/H5N1) segment 4 (HA) 2965.0 0.000000e+00 1674/1708 (98%)
EPI284581 A/duck/Vietnam/NCVD-011/2008 (A/H5N1) segment 4 (HA) 2959.5 0.000000e+00 1672/1707 (97%)
EPI284449 A/chicken/Vietnam/NCVD-117/2008 (A/H5N1) segment 4 (HA) 2959.5 0.000000e+00 1672/1707 (97%)
EPI284527 A/duck/Vietnam/NCVD-362/2009 (A/H5N1) segment 4 (HA) 2953.9 0.000000e+00 1671/1707 (97%)
EPI341348 A/chicken/Cambodia/67F1/2008 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI284552 A/duck/Vietnam/NCVD-103/2008 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI284518 A/duck/Vietnam/NCVD-371/2009 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI284517 A/duck/Vietnam/NCVD-370/2009 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI284433 A/chicken/Vietnam/NCVD-369/2009 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI284521 A/duck/Vietnam/NCVD-366/2009 (A/H5N1) segment 4 (HA) 2942.8 0.000000e+00 1669/1707 (97%)
EPI284441 A/chicken/Vietnam/NCVD-359/2009 (A/H5N1) segment 4 (HA) 2942.8 0.000000e+00 1669/1707 (97%)
EPI284431 A/chicken/Vietnam/NCVD-380/2009 (A/H5N1) segment 4 (HA) 2942.8 0.000000e+00 1669/1707 (97%)
EPI284529 A/duck/Vietnam/NCVD-364/2009 (A/H5N1) segment 4 (HA) 2939.1 0.000000e+00 1668/1707 (97%)
EPI284520 A/duck/Vietnam/NCVD-361/2009 (A/H5N1) segment 4 (HA) 2937.3 0.000000e+00 1668/1707 (97%)
EPI341361 A/chicken/Cambodia/TLC2/2009 (A/H5N1) segment 4 (HA) 2931.8 0.000000e+00 1637/1662 (98%)
EPI284523 A/duck/Vietnam/NCVD-368/2009 (A/H5N1) segment 4 (HA) 2931.8 0.000000e+00 1667/1707 (97%)
EPI284001 A/Cambodia/S1211394/2008 (A/H5N1) segment 4 (HA) 2931.8 0.000000e+00 1667/1707 (97%)
EPI284530 A/duck/Vietnam/NCVD-365/2009 (A/H5N1) segment 4 (HA) 2926.2 0.000000e+00 1666/1707 (97%)
EPI221601 A/Muscovy duck/Ca Mau/07-04/2007 (A/H5N1) segment 4 (HA) 2915.1 0.000000e+00 1665/1708 (97%)
EPI286378 A/duck/Soc Trang/07-25/2007 (A/H5N1) segment 4 (HA) 2909.6 0.000000e+00 1664/1708 (97%)
EPI140671 A/Muscovy duck/Vietnam/33/2007 (A/H5N1) segment 4 (HA) 2909.6 0.000000e+00 1663/1707 (97%)
EPI123752 A/Duck/Vietnam/Ca Mau498A/2006 (A/H5N1) segment 4 (HA) 2909.6 0.000000e+00 1664/1708 (97%)
EPI284522 A/duck/Vietnam/NCVD-367/2009 (A/H5N1) segment 4 (HA) 2904.1 0.000000e+00 1663/1708 (97%)
EPI123754 A/Duck/Vietnam/Ca Mau498/2006 (A/H5N1) segment 4 (HA) 2904.1 0.000000e+00 1664/1709 (97%)
EPI284519 A/duck/Vietnam/NCVD-360/2009 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1662/1708 (97%)
EPI284435 A/chicken/Vietnam/NCVD-387/2009 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1661/1707 (97%)
EPI221871 A/duck/Bac Lieu/07-06/2007 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1662/1708 (97%)
EPI221722 A/chicken/Bac Lieu/07-10/2007 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1662/1708 (97%)
EPI140631 A/duck/Vietnam/7/2007 (A/H5N1) segment 4 (HA) 2896.7 0.000000e+00 1655/1698 (97%)
EPI140599 A/duck/Vietnam/2/2007 (A/H5N1) segment 4 (HA) 2896.7 0.000000e+00 1655/1698 (97%)
EPI341360 A/duck/Cambodia/TK05D8T/2010 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI341359 A/duck/Cambodia/TK05D12T/2010 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI341358 A/chicken/Cambodia/TKCMB5T/2010 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI341357 A/chicken/Cambodia/TKCMB8F/2010 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI284584 A/ostrich/Vietnam/NCVD-373/2009 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI284535 A/duck/Vietnam/NCVD-372/2009 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI221879 A/duck/Bac Lieu/07-09/2007 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI140655 A/duck/Vietnam/18/2007 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1661/1708 (97%)
EPI140639 A/duck/Vietnam/8/2007 (A/H5N1) segment 4 (HA) 2891.1 0.000000e+00 1654/1698 (97%)
EPI140615 A/duck/Vietnam/5/2007 (A/H5N1) segment 4 (HA) 2891.1 0.000000e+00 1654/1698 (97%)
EPI140623 A/duck/Vietnam/6/2007 (A/H5N1) segment 4 (HA) 2889.3 0.000000e+00 1653/1697 (97%)
EPI341355 A/duck/Cambodia/TK007D1C/2010 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1660/1708 (97%)
EPI341354 A/duck/Cambodia/TK007D5T/2010 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1660/1708 (97%)
EPI140679 A/duck/Vietnam/34/2007 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1647/1689 (97%)
EPI341369 A/Cambodia/U0417030/2010 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1659/1708 (97%)
EPI341353 A/chicken/Cambodia/PV025LC1/2010 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1659/1708 (97%)
EPI341352 A/duck/Cambodia/PV027D1/2010 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1659/1708 (97%)
EPI123758 A/Muscovy Duck/Vietnam/Ben Tre 342/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1659/1708 (97%)
EPI123756 A/Duck/Vietnam/Tien Giang 409/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1659/1708 (97%)
EPI341351 A/chicken/Cambodia/PV025LC2/2010 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1657/1708 (97%)
EPI341350 A/chicken/Cambodia/PV025LC4/2010 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1657/1708 (97%)
EPI283916 A/duck/Cambodia/D5KC167/2006 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1657/1708 (97%)
EPI283903 A/duck/Cambodia/D3KC167/2006 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1657/1708 (97%)
EPI140591 A/duck/Vietnam/1/2007 (A/H5N1) segment 4 (HA) 2867.1 0.000000e+00 1649/1697 (97%)
EPI283895 A/duck/Cambodia/D2KC167/2006 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1656/1708 (96%)
EPI283888 A/duck/Cambodia/D1KC167/2006 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1656/1708 (96%)
EPI221886 A/duck/Hau Giang/07-12/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1656/1708 (96%)
EPI341349 A/chicken/Cambodia/008LC1/2011 (A/H5N1) segment 4 (HA) 2854.2 0.000000e+00 1654/1708 (96%)
EPI123957 A/duck/Vietnam/An Giang 680B/2005 (A/H5N1) segment 4 (HA) 2854.2 0.000000e+00 1654/1708 (96%)
EPI167625 A/chicken/Vietnam/NCVD-21/2007 (A/H5N1) segment 4 (HA) 2850.5 0.000000e+00 1619/1657 (97%)
EPI140607 A/Muscovy duck/Vietnam/4/2007 (A/H5N1) segment 4 (HA) 2850.5 0.000000e+00 1634/1679 (97%)
EPI341368 A/Cambodia/V0203306/2011 (A/H5N1) segment 4 (HA) 2848.7 0.000000e+00 1653/1708 (96%)
EPI341365 A/Cambodia/V0417301/2011 (A/H5N1) segment 4 (HA) 2848.7 0.000000e+00 1653/1708 (96%)
EPI140663 A/chicken/Vietnam/29/2007 (A/H5N1) segment 4 (HA) 2848.7 0.000000e+00 1653/1708 (96%)
EPI140647 A/chicken/Vietnam/15/2007 (A/H5N1) segment 4 (HA) 2845.0 0.000000e+00 1633/1679 (97%)
EPI167649 A/chicken/Vietnam/NCVD-24/2007 (A/H5N1) segment 4 (HA) 2843.1 0.000000e+00 1618/1657 (97%)
EPI167641 A/Muscovy duck/Vietnam/NCVD-23/2007 (A/H5N1) segment 4 (HA) 2839.4 0.000000e+00 1617/1657 (97%)
EPI167577 A/chicken/Vietnam/NCVD-15/2007 (A/H5N1) segment 4 (HA) 2832.0 0.000000e+00 1615/1657 (97%)
EPI167569 A/duck/Vietnam/NCVD-13/2007 (A/H5N1) segment 4 (HA) 2832.0 0.000000e+00 1616/1657 (97%)
EPI167657 A/duck/Vietnam/NCVD-25/2007 (A/H5N1) segment 4 (HA) 2826.5 0.000000e+00 1615/1657 (97%)
EPI341367 A/Cambodia/V0219301/2011 (A/H5N1) segment 4 (HA) 2821.0 0.000000e+00 1648/1708 (96%)
EPI167585 A/duck/Vietnam/NCVD-16/2007 (A/H5N1) segment 4 (HA) 2821.0 0.000000e+00 1614/1657 (97%)
EPI167505 A/Muscovy duck/Vietnam/NCVD-5/2007 (A/H5N1) segment 4 (HA) 2821.0 0.000000e+00 1614/1657 (97%)
EPI123760 A/Chicken/Vietnam/Long An 636/2005 (A/H5N1) segment 4 (HA) 2821.0 0.000000e+00 1648/1708 (96%)
EPI167545 A/chicken/Vietnam/NCVD-10/2007 (A/H5N1) segment 4 (HA) 2815.4 0.000000e+00 1613/1657 (97%)
EPI167537 A/duck/Vietnam/NCVD-9/2007 (A/H5N1) segment 4 (HA) 2815.4 0.000000e+00 1613/1657 (97%)
EPI164826 A/duck/Vietnam/177/2005 (A/H5N1) segment 4 (HA) 2815.4 0.000000e+00 1647/1708 (96%)
EPI167489 A/chicken/Vietnam/NCVD-3/2007 (A/H5N1) segment 4 (HA) 2811.7 0.000000e+00 1612/1657 (97%)
EPI327584 A/quail/Vietnam/7B/2004 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1646/1708 (96%)
EPI167513 A/duck/Vietnam/NCVD-6/2007 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1612/1657 (97%)
EPI160689 A/Duck/Viet Nam/367/2005 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1646/1708 (96%)
EPI152849 A/muscovy duck/Vietnam/NCVD02/2005 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1646/1708 (96%)
EPI117155 A/Duck/Viet Nam/367/2005 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1644/1705 (96%)
EPI115173 A/Viet Nam/JP14/2005 (A/H5N1) segment 4 (HA) 2809.9 0.000000e+00 1646/1708 (96%)
EPI341363 A/chicken/Cambodia/67F4/2008 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1645/1708 (96%)
EPI341347 A/chicken/Cambodia/67F8/2008 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1646/1709 (96%)
EPI283995 A/chicken/Cambodia/047LC3/2005 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1645/1708 (96%)
EPI283959 A/chicken/Cambodia/047LC3b/2005 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1645/1708 (96%)
EPI123772 A/Duck/Vietnam/Dong Thap 680D/2005 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1646/1709 (96%)
EPI123762 A/Chicken/Vietnam/Binh Duong477/2005 (A/H5N1) segment 4 (HA) 2804.3 0.000000e+00 1645/1708 (96%)
EPI167497 A/Muscovy duck/Vietnam/NCVD-4/2007 (A/H5N1) segment 4 (HA) 2800.6 0.000000e+00 1612/1659 (97%)
EPI317081 A/Cambodia/408008/2005 (A/H5N1) segment 4 (HA) 2798.8 0.000000e+00 1644/1708 (96%)
EPI283988 A/chicken/Cambodia/LC3AL/2007 (A/H5N1) segment 4 (HA) 2798.8 0.000000e+00 1644/1708 (96%)

_________________
www.twitter.com/hniman

Top 100 PB2 matches at GISAID
EPI341428 A/Cambodia/V0606311/2011 (A/H5N1) segment 1 (PB2) 4211.5 0.000000e+00 2280/2280 (100%)
EPI321741 A/muscovy duck/Vietnam/OIE-559/2011 (A/H5N1) segment 1 (PB2) 4122.8 0.000000e+00 2264/2280 (99%)
EPI341430 A/Cambodia/V0401301/2011 (A/H5N1) segment 1 (PB2) 4111.8 0.000000e+00 2262/2280 (99%)
EPI341427 A/chicken/Cambodia/TLC1/2009 (A/H5N1) segment 1 (PB2) 4073.0 0.000000e+00 2255/2280 (98%)
EPI167646 A/chicken/Vietnam/NCVD-24/2007 (A/H5N1) segment 1 (PB2) 4034.2 0.000000e+00 2248/2280 (98%)
EPI167574 A/chicken/Vietnam/NCVD-15/2007 (A/H5N1) segment 1 (PB2) 4034.2 0.000000e+00 2248/2280 (98%)
EPI167566 A/duck/Vietnam/NCVD-13/2007 (A/H5N1) segment 1 (PB2) 4034.2 0.000000e+00 2248/2280 (98%)
EPI167550 A/Muscovy duck/Vietnam/NCVD-11/2007 (A/H5N1) segment 1 (PB2) 4034.2 0.000000e+00 2248/2280 (98%)
EPI221608 A/Muscovy duck/Ca Mau/07-04/2007 (A/H5N1) segment 1 (PB2) 4028.7 0.000000e+00 2247/2280 (98%)
EPI167638 A/Muscovy duck/Vietnam/NCVD-23/2007 (A/H5N1) segment 1 (PB2) 4028.7 0.000000e+00 2247/2280 (98%)
EPI167502 A/Muscovy duck/Vietnam/NCVD-5/2007 (A/H5N1) segment 1 (PB2) 4028.7 0.000000e+00 2247/2280 (98%)
EPI167494 A/Muscovy duck/Vietnam/NCVD-4/2007 (A/H5N1) segment 1 (PB2) 4028.7 0.000000e+00 2247/2280 (98%)
EPI167486 A/chicken/Vietnam/NCVD-3/2007 (A/H5N1) segment 1 (PB2) 4028.7 0.000000e+00 2247/2280 (98%)
EPI167622 A/chicken/Vietnam/NCVD-21/2007 (A/H5N1) segment 1 (PB2) 4025.0 0.000000e+00 2246/2280 (98%)
EPI285715 A/duck/Soc Trang/07-25/2007 (A/H5N1) segment 1 (PB2) 4017.6 0.000000e+00 2245/2280 (98%)
EPI167654 A/duck/Vietnam/NCVD-25/2007 (A/H5N1) segment 1 (PB2) 4017.6 0.000000e+00 2245/2280 (98%)
EPI167582 A/duck/Vietnam/NCVD-16/2007 (A/H5N1) segment 1 (PB2) 4017.6 0.000000e+00 2245/2280 (98%)
EPI341424 A/chicken/Cambodia/TKCMB8F/2010 (A/H5N1) segment 1 (PB2) 4012.0 0.000000e+00 2244/2280 (98%)
EPI167510 A/duck/Vietnam/NCVD-6/2007 (A/H5N1) segment 1 (PB2) 4012.0 0.000000e+00 2244/2280 (98%)
EPI341425 A/chicken/Cambodia/TKCMB5T/2010 (A/H5N1) segment 1 (PB2) 4006.5 0.000000e+00 2243/2280 (98%)
EPI221878 A/duck/Bac Lieu/07-06/2007 (A/H5N1) segment 1 (PB2) 4006.5 0.000000e+00 2243/2280 (98%)
EPI167526 A/duck/Vietnam/NCVD-8/2007 (A/H5N1) segment 1 (PB2) 4006.5 0.000000e+00 2243/2280 (98%)
EPI341433 A/Cambodia/U0417030/2010 (A/H5N1) segment 1 (PB2) 4001.0 0.000000e+00 2242/2280 (98%)
EPI341421 A/chicken/Cambodia/PV025LC2/2010 (A/H5N1) segment 1 (PB2) 4001.0 0.000000e+00 2242/2280 (98%)
EPI140676 A/duck/Vietnam/34/2007 (A/H5N1) segment 1 (PB2) 3997.3 0.000000e+00 2228/2260 (98%)
EPI140668 A/Muscovy duck/Vietnam/33/2007 (A/H5N1) segment 1 (PB2) 3997.3 0.000000e+00 2228/2260 (98%)
EPI221885 A/duck/Bac Lieu/07-09/2007 (A/H5N1) segment 1 (PB2) 3995.4 0.000000e+00 2241/2280 (98%)
EPI221729 A/chicken/Bac Lieu/07-10/2007 (A/H5N1) segment 1 (PB2) 3995.4 0.000000e+00 2241/2280 (98%)
EPI167542 A/chicken/Vietnam/NCVD-10/2007 (A/H5N1) segment 1 (PB2) 3995.4 0.000000e+00 2241/2280 (98%)
EPI167534 A/duck/Vietnam/NCVD-9/2007 (A/H5N1) segment 1 (PB2) 3995.4 0.000000e+00 2241/2280 (98%)
EPI341434 A/Cambodia/S1211394/2008 (A/H5N1) segment 1 (PB2) 3989.9 0.000000e+00 2241/2281 (98%)
EPI341423 A/chicken/Cambodia/TKCMB1F/2010 (A/H5N1) segment 1 (PB2) 3989.9 0.000000e+00 2232/2268 (98%)
EPI341432 A/Cambodia/V0203306/2011 (A/H5N1) segment 1 (PB2) 3984.3 0.000000e+00 2239/2280 (98%)
EPI140652 A/duck/Vietnam/18/2007 (A/H5N1) segment 1 (PB2) 3975.1 0.000000e+00 2224/2260 (98%)
EPI140628 A/duck/Vietnam/7/2007 (A/H5N1) segment 1 (PB2) 3975.1 0.000000e+00 2224/2260 (98%)
EPI140596 A/duck/Vietnam/2/2007 (A/H5N1) segment 1 (PB2) 3975.1 0.000000e+00 2224/2260 (98%)
EPI341429 A/Cambodia/V0417301/2011 (A/H5N1) segment 1 (PB2) 3973.3 0.000000e+00 2237/2280 (98%)
EPI341420 A/chicken/Cambodia/008LC1/2011 (A/H5N1) segment 1 (PB2) 3973.3 0.000000e+00 2237/2280 (98%)
EPI140636 A/duck/Vietnam/8/2007 (A/H5N1) segment 1 (PB2) 3969.6 0.000000e+00 2223/2260 (98%)
EPI140620 A/duck/Vietnam/6/2007 (A/H5N1) segment 1 (PB2) 3964.0 0.000000e+00 2222/2260 (98%)
EPI140612 A/duck/Vietnam/5/2007 (A/H5N1) segment 1 (PB2) 3964.0 0.000000e+00 2222/2260 (98%)
EPI140588 A/duck/Vietnam/1/2007 (A/H5N1) segment 1 (PB2) 3958.5 0.000000e+00 2221/2260 (98%)
EPI140604 A/Muscovy duck/Vietnam/4/2007 (A/H5N1) segment 1 (PB2) 3953.0 0.000000e+00 2220/2260 (98%)
EPI341431 A/Cambodia/V0219301/2011 (A/H5N1) segment 1 (PB2) 3945.6 0.000000e+00 2233/2281 (97%)
EPI341422 A/duck/Cambodia/PV027D1/2010 (A/H5N1) segment 1 (PB2) 3940.0 0.000000e+00 2205/2241 (98%)
EPI341426 A/duck/Cambodia/TK05D8T/2010 (A/H5N1) segment 1 (PB2) 3938.2 0.000000e+00 2204/2240 (98%)
EPI167670 A/Muscovy duck/Vietnam/NCVD-29/2007 (A/H5N1) segment 1 (PB2) 3927.1 0.000000e+00 2229/2281 (97%)
EPI167677 A/duck/Vietnam/NCVD-30/2007 (A/H5N1) segment 1 (PB2) 3923.4 0.000000e+00 2229/2281 (97%)
EPI167606 A/duck/Vietnam/NCVD-19/2007 (A/H5N1) segment 1 (PB2) 3923.4 0.000000e+00 2229/2281 (97%)
EPI140644 A/chicken/Vietnam/15/2007 (A/H5N1) segment 1 (PB2) 3921.6 0.000000e+00 2199/2237 (98%)
EPI221893 A/duck/Hau Giang/07-12/2007 (A/H5N1) segment 1 (PB2) 3917.9 0.000000e+00 2228/2281 (97%)
EPI167558 A/duck/Vietnam/NCVD-12/2007 (A/H5N1) segment 1 (PB2) 3914.2 0.000000e+00 2227/2281 (97%)
EPI317088 A/Cambodia/408008/2005 (A/H5N1) segment 1 (PB2) 3912.3 0.000000e+00 2226/2280 (97%)
EPI297549 A/Cambodia/408008/2005 (A/H5N1) segment 1 (PB2) 3912.3 0.000000e+00 2226/2280 (97%)
EPI164833 A/duck/Vietnam/177/2005 (A/H5N1) segment 1 (PB2) 3912.3 0.000000e+00 2226/2280 (97%)
EPI160696 A/Duck/Viet Nam/367/2005 (A/H5N1) segment 1 (PB2) 3912.3 0.000000e+00 2226/2280 (97%)
EPI152856 A/muscovy duck/Vietnam/NCVD02/2005 (A/H5N1) segment 1 (PB2) 3912.3 0.000000e+00 2226/2280 (97%)
EPI167598 A/duck/Vietnam/NCVD-18/2007 (A/H5N1) segment 1 (PB2) 3906.8 0.000000e+00 2226/2281 (97%)
EPI167590 A/duck/Vietnam/NCVD-17/2007 (A/H5N1) segment 1 (PB2) 3906.8 0.000000e+00 2226/2281 (97%)
EPI167478 A/duck/Vietnam/NCVD-2/2007 (A/H5N1) segment 1 (PB2) 3901.2 0.000000e+00 2225/2281 (97%)
EPI171052 A/chicken/Vietnam/933/2004 (A/H5N1) segment 1 (PB2) 3890.2 0.000000e+00 2222/2280 (97%)
EPI160688 A/chicken/Vietnam/NCVD09/2005 (A/H5N1) segment 1 (PB2) 3890.2 0.000000e+00 2222/2280 (97%)
EPI171044 A/chicken/Vietnam/925/2004 (A/H5N1) segment 1 (PB2) 3884.6 0.000000e+00 2222/2281 (97%)
EPI171036 A/chicken/Vietnam/921/2004 (A/H5N1) segment 1 (PB2) 3884.6 0.000000e+00 2222/2281 (97%)
EPI105536 A/Vietnam/PEV16T/2005 (A/H5N1) segment 1 (PB2) 3884.6 0.000000e+00 2222/2281 (97%)
EPI300782 A/chicken/Cambodia/047LC3/2005 (A/H5N1) segment 1 (PB2) 3880.9 0.000000e+00 2213/2269 (97%)
EPI283964 A/chicken/Cambodia/047LC3b/2005 (A/H5N1) segment 1 (PB2) 3880.9 0.000000e+00 2213/2269 (97%)
EPI103513 A/Vietnam/CL01/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI98649 A/duck/Viet Nam/CM-V7/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI98647 A/duck/Viet Nam/TV-V2/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2222/2282 (97%)
EPI98641 A/chicken/Viet Nam/DN-045/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI98629 A/chicken/Viet Nam/AG-010/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI77519 A/chicken/Vietnam/23/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI23664 A/Ck/Viet Nam/39/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI23654 A/chicken/Viet Nam/33/2004 (A/H5N1) segment 1 (PB2) 3879.1 0.000000e+00 2221/2281 (97%)
EPI160672 A/chicken/Vietnam/18/2004 (A/H5N1) segment 1 (PB2) 3875.4 0.000000e+00 2220/2281 (97%)
EPI140660 A/chicken/Vietnam/29/2007 (A/H5N1) segment 1 (PB2) 3875.4 0.000000e+00 2207/2261 (97%)
EPI160680 A/chicken/Vietnam/890/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI156480 A/chicken/Vietnam/830/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI132013 A/chicken/Vietnam/15/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI98645 A/chicken/Viet Nam/LD-080/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2221/2282 (97%)
EPI98639 A/chicken/Viet Nam/HCM-022/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI98637 A/chicken/Viet Nam/LA-024/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI98635 A/chicken/Viet Nam/TG-023/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI98631 A/chicken/Viet Nam/DT-015/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI98625 A/quail/Viet Nam/TG-007B/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI23662 A/Ck/Viet Nam/38/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI23660 A/Ck/Viet Nam/37/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI23658 A/Ck/Viet Nam/36/2004 (A/H5N1) segment 1 (PB2) 3873.5 0.000000e+00 2220/2281 (97%)
EPI167518 A/duck/Vietnam/NCVD-7/2007 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2218/2280 (97%)
EPI167470 A/duck/Vietnam/NCVD-1/2007 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2218/2280 (97%)
EPI103517 A/Vietnam/CL26/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI98633 A/chicken/Viet Nam/CT-018/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI98627 A/chicken/Viet Nam/VL-008/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI98621 A/chicken/Viet Nam/TN-025/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI77500 A/chicken/Vietnam/10/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI25581 A/quail/Vietnam/36/04 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI23656 A/Ck/Viet Nam/35/2004 (A/H5N1) segment 1 (PB2) 3868.0 0.000000e+00 2219/2281 (97%)
EPI283990 A/chicken/Cambodia/LC3AL/2007 (A/H5N1) segment 1 (PB2) 3864.3 0.000000e+00 2217/2279 (97%)
EPI167325 A/chicken/Vietnam/NCVD12/2005 (A/H5N1) segment 1 (PB2) 3862.5 0.000000e+00 2218/2281 (97%)

_________________
www.twitter.com/hniman

Earlier reports of S227N in fatal clade 1 cases in Thailand

http://vir.sgmjournals.org/content/89/8/1805.full.pdf

Table 2. Numbers of all synonymous and non-synonymous substitutions and a list of non-synonymous substitutions in each dataset
RNA sample No. synonymous
substitutions
No. non-synonymous
substitutions
List of non-synonymous substitutions (frequency)

Patient A nasopharyngeal aspirate
17 138 S128R (1), L133V (54), S136G (1), A138V (53), A138E (1), Q142R (1), K157R
(3), Y161H (7), N172D (1), N186D (3), E190D (1), L194H (1), N224S (3),
N224D (2), S227N (2), S227G (1), N240S (1), N250S (2)

Patient B lung 98 94 S128G (1), A131V (1), A131T (3), Y141C (1), K144R (1), V152A (1), W153R
(1), I155V (1), N158D (1), Y161H (1), T163A (11), I164V (1), N169S (1),
V178A (2), D187G (1), D187N (2), E190G (1), K193R (18), K193S (3), K193E
(1), L194P (13), N197D (1), P198L (1), T200A (1), I202V (1), N210S (1),
I217V (1), K222E (2), G228E (2), M230T (10), F233S (1), F223L (1), N244D
(1), F245S (1), I252V (3), E255G (1)

Patient B intestine 35 62 E134V (2), S136G (2), R149K (2), S167G (1), S167C (1), Y168* (1), N172S (1),
H183R (1), H184R (1), N186D (2), R193K (11), L194P (2), Y195* (1), Q196R
(2), P198S (1), T199A (1), V204A (1), T206A (2), K222E (7), N224H (1),
G225R (1), S227N (2), M230T (1), F233S (1), P239S (1), N244S (1), I252V
(8), I268V (2), K270E (2)

Patient C lung 20 145 S128N (1), H129Q (1), L133V (6), S136G (4), A138V (55), S146P (1), W153*
(1), I155T (1), N158D (1), Y161H (3), Y161R (1), Y168C (2), N169H (1),
I182V (1), N186D (1), T199I (2), T206A (1), T208A (1), T219I (1), E222K
(56), R229G (1), S247N (2), F251S (2)

Patient C intestine 31 189 S127A (1), H129Q (3), A131D (1), L133V (19), L133F (1), S136G (1), A138V
(20), S146P (1), W153* (1), N158S (3), Y161C (1), Y161R (1), L177S (1),
W180R (2), I182T (1), N186D (37), K193R (1), Y201* (1), N210D (1), E222K
(51), S227N (36), I252V (4), K262R (1)

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S227N also identified in recent RBD study:

In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificityLi-Mei Chena, 1, Ola Blixtb, d, 1, 2, James Stevensa, c, Aleksandr S. Lipatova, Charles T. Davisa, Brian E. Collinsb, d, Nancy J. Coxa, James C. Paulsonb, d, 1, Ruben O. Donisa, , 1,

Purchase a Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, United States
b Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
c Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
d Glycan Array Synthesis Core-D, Consortium for Functional Glycomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
Received 27 August 2011; revised 26 September 2011; Accepted 10 October 2011. Available online 5 November 2011.


Abstract
Acquisition of α2-6 sialoside receptor specificity by α2-3 specific highly-pathogenic avian influenza viruses (H5N1) is thought to be a prerequisite for efficient transmission in humans. By in vitro selection for binding α2-6 sialosides, we identified four variant viruses with amino acid substitutions in the hemagglutinin (S227N, D187G, E190G, and Q196R) that revealed modestly increased α2-6 and minimally decreased α2-3 binding by glycan array analysis. However, a mutant virus combining Q196R with mutations from previous pandemic viruses (Q226L and G228S) revealed predominantly α2-6 binding. Unlike the wild type H5N1, this mutant virus was transmitted by direct contact in the ferret model although not by airborne respiratory droplets. However, a reassortant virus with the mutant hemagglutinin, a human N2 neuraminidase and internal genes from an H5N1 virus was partially transmitted via respiratory droplets. The complex changes required for airborne transmissibility in ferrets suggest that extensive evolution is needed for H5N1 transmissibility in humans.

Keywords: Highly pathogenic avian influenza virus; Hemagglutinin; Host cell receptor; Virus attachment; H5N1; Sialoglycan; Host range; Pandemic virus emergence


http://www.sciencedirect.com/science/ar ... 2211004752

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Commentary

http://www.recombinomics.com/News/01231 ... bodia.html

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