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H5N1 Vietnam 2008 Clade 7

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  • #1

    H5N1 Vietnam 2008 Clade 7

    LOCUS FJ842481 1713 bp cRNA linear VRL 27-MAR-2009
    DEFINITION Influenza A virus (A/chicken/Vietnam/NCVD-03/2008(H5N1)) segment 4
    hemagglutinin (HA) gene, complete cds.
    ACCESSION FJ842481
    VERSION FJ842481.1 GI:225697337
    KEYWORDS .
    SOURCE Influenza A virus (A/chicken/Vietnam/NCVD-03/2008(H5N1))
    ORGANISM Influenza A virus (A/chicken/Vietnam/NCVD-03/2008(H5N1))
    Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
    Influenzavirus A.
    REFERENCE 1 (bases 1 to 1713)
    AUTHORS Nguyen,T., Davis,T., Stembridge,W., Shu,B., Balish,A., Inui,K.,
    Do,H., Ngo,H., Wan,X.-F., McCarron,M., Lindstrom,S., Cox,N.,
    Nguyen,C., Klimov,A. and Donis,R.
    TITLE Characterization of a highly pathogenic avian influenza H5N1 virus
    sublineage in poultry seized at ports of entry into Vietnam
    JOURNAL Virology (2009) In press
    REFERENCE 2 (bases 1 to 1713)
    AUTHORS Nguyen,T., Davis,T., Stembridge,W., Shu,B., Balish,A., Inui,K.,
    Do,H., Ngo,H., Wan,X.-F., McCarron,M., Lindstrom,S., Cox,N.,
    Nguyen,C., Klimov,A. and Donis,R.
    TITLE Direct Submission
    JOURNAL Submitted (19-MAR-2009) Influenza Division, CDC, 1600 Clifton Rd.,
    Atlanta, GA 30333, USA
    FEATURES Location/Qualifiers
    source 1..1713
    /organism="Influenza A virus
    (A/chicken/Vietnam/NCVD-03/2008(H5N1))"
    /mol_type="viral cRNA"
    /strain="A/chicken/Vietnam/NCVD-03/2008"
    /serotype="H5N1"
    /isolation_source="cloacal swab"
    /host="chicken"
    /db_xref="taxon:629212"
    /segment="4"
    /country="Viet Nam"
    /collection_date="2008"
    gene 1..1713
    /gene="HA"
    CDS 1..1713
    /gene="HA"
    /codon_start=1
    /product="hemagglutinin"
    /protein_id="ACO07038.1"
    /db_xref="GI:225697338"
    /translation="MEKIVLLLAIISLVKSDQICIGYHANNSTEQVDTIME KNVTVTH
    AQDILEKTHNGKLCNLDGVKPLILKDCSVAGWLLGNPMCDEFLNVSEWSY IVEKASPA
    NGLCYPGDFNDYEELKHLLNRITHLKKIKIIPKSYWSNHEASSGVSAACS YMGEPSFF
    RNVVWLIKKNNTYPPIKVNYTNTNQEDLLVLWGIHHPNNEAEQIQIYQNL ITHISVGT
    STLNQRLIPKIATRSKVNGQSGRMEFFWTILKPNDSINFDSNGNFIAPEY AYIVKKGD
    SAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRL VLATGLRN
    APQREREGGRRRKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAA DKESTQKA
    IDGITNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTY NAELLVLM
    ENERTLDFHDSNVKNLYEKVRLQLRDNAKELGNGCFEFYHKCDNECMESV RNGTYDYS
    QYSEEARLSREEINGVKLESMVTYQILSIYSTVASSLALAIMVAGLSLWM CSNGSLQC
    RICI"
    ORIGIN
    1 atggagaaaa tagtgcttct tcttgcaata atcagccttg ttaaaagtga tcagatttgc
    61 attggttacc atgcaaacaa ctcgacagag caggttgaca caataatgga aaagaacgtt
    121 actgttacac atgctcaaga catactggag aagacacaca acgggaagct ctgcaaccta
    181 gatggagtga agcctctaat tctaaaagac tgtagtgtag ctggatggct cctcgggaac
    241 ccaatgtgtg acgaatttct caatgtgtca gaatggtctt acatagtgga gaaggccagt
    301 ccagccaatg gcctctgtta cccaggggat ttcaatgact atgaagaact gaaacaccta
    361 ttaaacagaa taacacatct taagaaaatt aagatcatcc ccaaaagtta ttggtccaat
    421 catgaagcct catcaggggt gagcgcagca tgttcctata tgggggagcc ctcctttttc
    481 agaaatgtgg tatggcttat caaaaagaat aatacatacc caccaataaa ggtgaactac
    541 accaatacca atcaagaaga tcttttggta ctgtggggga ttcaccatcc caataatgag
    601 gcagagcaga tacagatcta tcaaaaccta atcacccata tttcagttgg aacatcaaca
    661 ctaaaccaga gattgatacc aaaaatagct actagatcca aagtgaacgg gcaaagtgga
    721 agaatggagt tcttctggac aattttaaag ccgaatgatt ctatcaattt cgatagcaat
    781 ggaaatttca ttgctccaga atatgcctac attgtcaaga aaggggactc ggcaattatg
    841 aaaagtgaat tggagtatgg taactgcaac accaagtgtc aaactccaat gggggcgata
    901 aattctagta tgccattcca caacatacac cctctcacca tcggggaatg ccccaaatat
    961 gtgaagtcaa acagattagt cctcgcgact ggactcagaa atgcccctca aagagaaaga
    1021 gaggggggaa gaagaagaaa aagaggacta tttggagcca tagcagggtt tatagaggga
    1081 ggatggcagg gaatggtaga tggttggtat gggtaccacc atagcaatga gcaggggagt
    1141 gggtacgctg cagacaaaga atccactcaa aaggcaatag atggaatcac taataaggtc
    1201 aactcgatca ttgacaaaat gaacactcaa tttgaggccg ttggaaggga atttaataac
    1261 ttagagagga gaatagaaaa tttaaacaaa aagatggagg acggattcct agatgtctgg
    1321 acttataacg ctgaacttct ggttctcatg gaaaatgaga gaactctaga ctttcatgac
    1381 tcaaatgtca agaaccttta cgaaaaggtc cgactacagc ttagggataa tgcaaaggag
    1441 ctgggtaacg gttgtttcga gttctaccac aaatgtgata atgaatgtat ggaaagtgta
    1501 agaaacggaa cgtatgacta ctcgcagtat tcagaagaag caagactaag cagagaggaa
    1561 ataaatggag taaaattgga atcaatggta acttaccaaa tactgtcaat ttattcaaca
    1621 gtggcgagtt ccctagcatt ggcaatcatg gtggctggtc tatctttatg gatgtgctcc
    1681 aatggatcgt tacaatgcag aatttgcatt tga
    Tags: None
  • #2
    Re: H5N1 Vietnam 2008 Clade 7

    Sequence has a 3 BP deletion (downstream from Shanxi/2 deletion) as well as 9 BP insertion at HA cleavages site, reflection clade 7 instability in Northern Vietnam ex-China.

    Comment

    • #3
      Re: H5N1 Vietnam 2008 Clade 7

      Originally posted by niman View Post
      Sequence has a 3 BP deletion (downstream from Shanxi/2 deletion) as well as 9 BP insertion at HA cleavages site, reflection clade 7 instability in Northern Vietnam ex-China.
      Earlier clade 7 sequence from Vietnam has a 3 BP insertion to create novel cleavage site REGGRRRKR (the above sequence matches but has a 6 BP duplication to create REREGGRRRKR).

      It is VERY likely that both of these sequences originated in China.

      Comment

      • #4
        Re: H5N1 Vietnam 2008 Clade 7

        Note title:

        TITLE Characterization of a highly pathogenic avian influenza H5N1 virus
        sublineage in poultry seized at ports of entry into Vietnam

        Comment

        • #5
          Re: H5N1 Vietnam 2008 Clade 7

          Commentary at

          http://www.recombinomics.com/News/03300901/H5N1_China_7_Unstable.html

          Comment

          • #6
            Re: H5N1 Vietnam 2008 Clade 7

            Originally posted by niman View Post
            Commentary at

            http://www.recombinomics.com/News/03..._Unstable.html
            Commentary

            Unstable Clade 7 H5N1 In China Raises Concerns

            Recombinomics Commentary 10:34
            March 30, 2009

            A recent clade 7 HA sequence from a chicken in Vietnam, A/chicken/Vietnam/NCVD-03/2008 was released at Genbank under the title, "Characterization of a highly pathogenic avian influenza H5N1 sublineage in poultry seized at ports of entry into Vietnam". It was proposed as a vaccine target in the recent WHO update because it was antigenically distinct from another recent clade 7 target, A/chicken/Vietnam/NCVD-016/2008, which was isolate in northern Vietnam near the border with China. Both of these sequences have a cleavage site similar to clade 7 isolated in 2006 in China, except the cleavage site has a 3 BP insertion, encoding for an additional basic amino acid.

            However, the recent sequence also has a duplication of sequences encoding the two amino acids at the beginning of the cleavage site, creating the novel cleavage site, REREGGRRRKR. The sequence also has an addition 3 BP deletion, which is distinct from the 3 BP deletion found in earlier clade 7 isolates from China, as well as clade 2.2 isolates in Egypt.

            The selection of two 2008 clade 7 targets from Vietnam is unusual, but follows a spate of cases in China in January. These cases followed confirmed clade 7 outbreaks in poultry in Jiangsu in December, 2008 and strongly suggest that most of the human cases in China were clade 7.

            The sequences form these patients have not been released and have only been described in general terms in reports from China. The WHO report was silent on all cases from China except for two that were the Fujian strain (clade 2.3.2 and 2.3.4), further supporting concerns that vaccine resistant clade 7 is widely circulating in China.

            The recent sequences from northern Vietnam demonstrate considerable genetic instability that involves a large number of non-synonymous changes as well as insertions and deletions in the HA sequence.

            Release of sequences from the Jiangsu poultry outbreaks in China, as well as recent human cases in China and northern Vietnam would be useful.

            .
            "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

            Comment

            • #7
              Re: H5N1 Vietnam 2008 Clade 7

              REREGGRRRKR
              These are all cleavage site positions?

              If so, that's more than in the past, so is H5N1 adapting to be cleaved my more enzymes with one strain?

              .
              "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

              Comment

              • #8
                Re: H5N1 Vietnam 2008 Clade 7

                Originally posted by AlaskaDenise View Post
                These are all cleavage site positions?

                If so, that's more than in the past, so is H5N1 adapting to be cleaved my more enzymes with one strain?

                .
                Cleavage is after an R or K.

                Comment

                • #9
                  Re: H5N1 Vietnam 2008 Clade 7

                  Originally posted by niman View Post
                  Cleavage is after an R or K.
                  ???

                  Could you provide more detail?

                  .
                  "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                  Comment

                  • #10
                    Re: H5N1 Vietnam 2008 Clade 7

                    Commentary

                    http://www.recombinomics.com/News/03300902/H5N1_China_7_Cleavage.html

                    Comment

                    • #11
                      Re: H5N1 Vietnam 2008 Clade 7

                      <table cellpadding="0" width="100%"><tbody><tr><td style="white-space: nowrap;" valign="top" width="20%">1: FJ538950</td><td align="left" valign="top">
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                      <script language="JavaScript1.2"><!-- var Menu218137997 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=218137997&ordinalpos=1&itool=EntrezSystem2.P Entrez.Sequence.Sequence_ResultsPanel.Sequence_RVD ocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=218137997&ordinalpos=1&itool=EntrezSystem2.PEnt rez.Sequence.Sequence_ResultsPanel.Sequence_RVDocS um' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=218137997&ordinalpos=1&itool=EntrezSystem 2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_ RVDocSum' ", "", ""] ] --></script>Links</td></tr><tr><td colspan="3" style="padding-left: 2.8em;" align="left" valign="top">Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1)) segment 7 matrix protein 2 (M2) and matrix protein 1 (M1) genes, complete cds
                      gi|218137997|gb|FJ538950.1|[218137997]
                      </td></tr></tbody></table> <!--docsumok 218137995 218137995 1 0 1349--> <dl><dt><table cellpadding="0" width="100%"><tbody><tr><td style="white-space: nowrap;" valign="top" width="20%"><input name="EntrezSystem2.PEntrez.Sequence.Sequence_Resu ltsPanel.Sequence_RVDocSum.uid" sid="2" value="218137995" id="UidCheckBox" type="checkbox">2: FJ538949</td><td align="left" valign="top">
                      Reports<script language="JavaScript1.2"><!-- var PopUpMenu2_LocalConfig_Reports218137995 = [ ["TitleText","Reports"] ]; var Reports218137995 = [ ["UseLocalConfig","Reports218137995","",""], ["ASN.1","window.top.location='/nuccore/218137995?report=asn1'","",""], ["XML","window.top.location='/nuccore/218137995?report=xml'","",""], ["Summary","window.top.location='/nuccore/218137995?report=docsum'","",""], ["Brief","window.top.location='/nuccore/218137995?report=brief'","",""], ["FASTA","window.top.location='/nuccore/218137995?report=fasta'","",""], ["TinySeq XML","window.top.location='/nuccore/218137995?report=fasta_xml'","",""], ["GenBank","window.top.location='/nuccore/218137995?report=genbank'","",""], ["INSDSeq XML","window.top.location='/nuccore/218137995?report=gbc_xml'","",""], ["GenBank(Full)","window.top.location='/nuccore/218137995?report=gbwithparts'","",""], ["Feature table","window.top.location='/nuccore/218137995?report=ft'","",""], ["GI List","window.top.location='/nuccore/218137995?report=gilist'","",""], ["Graphic","window.top.location='/nuccore/218137995?report=graph'","",""], ["Revision History","window.top.location='/entrez/sutils/girevhist.cgi?val=FJ538949'","",""] ] --></script></td><td align="right" valign="top">
                      <script language="JavaScript1.2"><!-- var Menu218137995 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=218137995&ordinalpos=2&itool=EntrezSystem2.P Entrez.Sequence.Sequence_ResultsPanel.Sequence_RVD ocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=218137995&ordinalpos=2&itool=EntrezSystem2.PEnt rez.Sequence.Sequence_ResultsPanel.Sequence_RVDocS um' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=218137995&ordinalpos=2&itool=EntrezSystem 2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_ RVDocSum' ", "", ""] ] --></script>Links</td></tr><tr><td colspan="3" style="padding-left: 2.8em;" align="left" valign="top">Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1)) segment 6 neuraminidase (NA) gene, partial cds
                      gi|218137995|gb|FJ538949.1|[218137995]
                      </td></tr></tbody></table></dt></dl>
                      <!--docsumok 218137992 218137992 1 0 983--> <dl><dt><table cellpadding="0" width="100%"><tbody><tr><td style="white-space: nowrap;" valign="top" width="20%"><input name="EntrezSystem2.PEntrez.Sequence.Sequence_Resu ltsPanel.Sequence_RVDocSum.uid" sid="3" value="218137992" id="UidCheckBox" type="checkbox">3: FJ538948</td><td align="left" valign="top">
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                      <script language="JavaScript1.2"><!-- var Menu218137992 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=218137992&ordinalpos=3&itool=EntrezSystem2.P Entrez.Sequence.Sequence_ResultsPanel.Sequence_RVD ocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=218137992&ordinalpos=3&itool=EntrezSystem2.PEnt rez.Sequence.Sequence_ResultsPanel.Sequence_RVDocS um' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=218137992&ordinalpos=3&itool=EntrezSystem 2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_ RVDocSum' ", "", ""] ] --></script>Links</td></tr><tr><td colspan="3" style="padding-left: 2.8em;" align="left" valign="top">Influenza A virus (A/duck/Vietnam/NCVD-100/2007(H5N1)) segment 7 matrix protein 2 (M2) and matrix protein 1 (M1) genes, complete cds
                      gi|218137992|gb|FJ538948.1|[218137992]
                      </td></tr></tbody></table></dt></dl>
                      <!--docsumok 218137990 218137990 1 0 1349--> <table cellpadding="0" width="100%"><tbody><tr><td style="white-space: nowrap;" valign="top" width="20%"><input name="EntrezSystem2.PEntrez.Sequence.Sequence_Resu ltsPanel.Sequence_RVDocSum.uid" sid="4" value="218137990" id="UidCheckBox" type="checkbox">4: FJ538947</td><td align="left" valign="top">
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                      <script language="JavaScript1.2"><!-- var Menu218137990 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=218137990&ordinalpos=4&itool=EntrezSystem2.P Entrez.Sequence.Sequence_ResultsPanel.Sequence_RVD ocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=218137990&ordinalpos=4&itool=EntrezSystem2.PEnt rez.Sequence.Sequence_ResultsPanel.Sequence_RVDocS um' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=218137990&ordinalpos=4&itool=EntrezSystem 2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_ RVDocSum' ", "", ""] ] --></script>Links</td></tr><tr><td colspan="3" style="padding-left: 2.8em;" align="left" valign="top">Influenza A virus (A/duck/Vietnam/NCVD-100/2007(H5N1)) segment 6 neuraminidase (NA) gene, partial cds
                      gi|218137990|gb|FJ538947.1|[218137990] </td></tr></tbody></table>

                      Comment

                      • #12
                        Re: H5N1 Vietnam 2008 Clade 7

                        LOCUS FJ538949 1349 bp cRNA linear VRL 04-APR-2009
                        DEFINITION Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1)) segment 6
                        neuraminidase (NA) gene, partial cds.
                        ACCESSION FJ538949
                        VERSION FJ538949.1 GI:218137995
                        KEYWORDS .
                        SOURCE Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))
                        ORGANISM Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))
                        Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
                        Influenzavirus A.
                        REFERENCE 1 (bases 1 to 1349)
                        AUTHORS Deyde,V.M., Nguyen,T., Bright,R.A., Balish,A., Shu,B.,
                        Lindstrom,S., Klimov,A.I. and Gubareva,L.V.
                        TITLE Detection of molecular markers of antiviral resistance in influenza
                        A (H5N1) viruses using a pyrosequencing method
                        JOURNAL Antimicrob. Agents Chemother. 53 (3), 1039-1047 (2009)
                        PUBMED 19124660
                        REFERENCE 2 (bases 1 to 1349)
                        AUTHORS Davis,T. and Nguyen,T.
                        TITLE Direct Submission
                        JOURNAL Submitted (09-DEC-2008) MVVB, CDC, 1600 Clifton Rd., Atlanta, GA
                        30333, USA
                        FEATURES Location/Qualifiers
                        source 1..1349
                        /organism="Influenza A virus
                        (A/chicken/Vietnam/NCVD-093/2008(H5N1))"
                        /mol_type="viral cRNA"
                        /strain="A/chicken/Vietnam/NCVD-093/2008"
                        /serotype="H5N1"
                        /host="chicken"
                        /db_xref="taxon:581024"
                        /segment="6"
                        /country="Viet Nam"
                        /collection_date="2008"
                        gene 1..>1349
                        /gene="NA"
                        CDS 1..>1349
                        /gene="NA"
                        /codon_start=1
                        /product="neuraminidase"
                        /protein_id="ACK57573.1"
                        /db_xref="GI:218137996"
                        /translation="MNPNQKIITIGSICVVIGIVSLMLQIGNMISIWVSHS IQTENQC
                        QAESISNTKFLTEKAVASVTLMGNSSLCPISGWAVHSKDNSIRIGSKGDV FVIREPFI
                        SCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMSCPVGEAPSPYNS RFESVAWS
                        ASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESE CACVNGSC
                        FTVMTDGPSNGQASYKIFKLEKGKVVKSVELDAPNYHYEECSCYPDAGEI TCVCRDNW
                        HGSNGPWVSFNHYLEYQIGYICSGVFGDNPRPNDGTGSCGPVSPNGAYGV KGFSFKYG
                        NGVWIGRTKSTNSRSGFEMIWDPNGWTGTDSSFSVKQDIVAITDWSGYSG SFVQHPEL
                        TGLDCIRPCFWVELVRGRPKESTIWTSGSSISFCGVNSDTVGWSWPDGAE VPFTIDK"
                        ORIGIN
                        1 atgaatccaa atcagaagat aataaccatc ggatcaatct gtgtggtaat tggaatagtt
                        61 agcttaatgt tacaaattgg gaacatgatc tcaatatggg tcagtcattc aattcagaca
                        121 gagaatcaat gccaagctga atcgatcagc aatactaaat ttctcactga gaaggctgtg
                        181 gcttcagtaa cattaatggg caattcatct ctttgcccca ttagcggatg ggctgtacac
                        241 agtaaggaca acagcataag gatcggttcc aagggggatg tgtttgttat aagagagccg
                        301 ttcatctcat gctcccactt ggaatgcaga actttctttt tgactcaggg agccttgctg
                        361 aatgacaagc actccaatgg gactgtcaaa gacagaagcc ctcacagaac attaatgagt
                        421 tgtcctgtgg gtgaggctcc ctctccatat aactcaaggt ttgagtctgt tgcttggtca
                        481 gcaagtgctt gccatgatgg caccagttgg ttgacaattg gaatttctgg cccagacaat
                        541 ggggctgtgg ctgtattgaa atacaatggt ataataacag acactatcaa aagttggagg
                        601 aacaacatac tgagaactca agagtctgaa tgtgcatgtg taaatggctc ttgctttact
                        661 gtaatgactg atggaccaag taatgggcag gcatcatata agatcttcaa attggaaaaa
                        721 gggaaagtgg ttaaatcagt tgaattggat gctcctaatt atcactatga ggaatgctcc
                        781 tgttatcctg atgctggcga aatcacatgt gtgtgcaggg ataattggca tggctcaaat
                        841 gggccatggg tatctttcaa tcactatttg gagtatcaaa taggatatat atgcagtgga
                        901 gttttcggag acaatccacg ccccaatgat ggaacaggga gctgtggtcc ggtgtcccct
                        961 aatggggcat atggggtaaa agggttttca tttaaatacg gcaatggtgt ttggatcggg
                        1021 agaaccaaaa gcactaattc caggagcggc tttgaaatga tttgggatcc gaatgggtgg
                        1081 actggaacgg acagcagctt ttcggtgaag caagatatcg tagcaataac tgattggtca
                        1141 ggatatagcg ggagttttgt ccagcatcca gaactgacag gattagattg cataagacct
                        1201 tgtttctggg ttgagttagt cagagggcgg cccaaagaga gcacaatctg gactagtggg
                        1261 agcagcatat ccttttgtgg tgtaaatagt gacactgtgg gttggtcttg gccagacggt
                        1321 gctgaggtgc cattcaccat tgacaagta
                        </pre>

                        Comment

                        • #13
                          Re: H5N1 Vietnam 2008 Clade 7

                          The above isolate (clade 7) is in the HA tree of WHO vaccine targets and the above NA sequence has OBVIOUS recombination (with vaccine resistant clade 2.2 in Egypt).

                          Comment

                          • #14
                            Re: H5N1 Vietnam 2008 Clade 7

                            NA travel log

                            gb|FJ538949.1| Influenza A virus (A/chicken/Vietnam/NCVD-093/... 38.2 0.17
                            gb|FJ719836.1| Influenza A virus (A/chicken/Manipur/NIV9743/2... 38.2 0.17
                            gb|FJ667187.1| Influenza A virus (A/chicken/Domodedovo/MK/200... 38.2 0.17
                            gb|FJ688369.1| Influenza A virus (A/chicken/Egypt/24NLQP-CLEV... 38.2 0.17
                            gb|FJ688367.1| Influenza A virus (A/chicken/Egypt/17NLQP-CLEV... 38.2 0.17
                            gb|FJ688366.1| Influenza A virus (A/chicken/Egypt/15NLQP-CLEV... 38.2 0.17
                            gb|FJ688365.1| Influenza A virus (A/chicken/Egypt/10NLQP-CLEV... 38.2 0.17
                            gb|FJ688364.1| Influenza A virus (A/chicken/Egypt/4NLQP-CLEVB... 38.2 0.17
                            gb|FJ688363.1| Influenza A virus (A/chicken/Egypt/1NLQP-CLEVB... 38.2 0.17
                            emb|AM911101.1| Influenza A virus (A/Anas acuta/Slovenia/470/... 38.2 0.17
                            emb|AM911091.1| Influenza A virus (A/Ardea cinerea/Slovenia/1... 38.2 0.17
                            emb|AM911086.1| Influenza A virus (A/cygnus olor/Slovenia/156... 38.2 0.17
                            emb|AM911074.1| Influenza A virus (A/Mergus albellus/Slovakia... 38.2 0.17
                            emb|AM911073.1| Influenza A virus (A/Peregrine falcon/Slovaki... 38.2 0.17
                            gb|EU636810.1| Influenza A virus (A/great crested grebe/Basqu... 38.2 0.17
                            gb|FJ461659.1| Influenza A virus (A/Egypt/3401-NAMRU3/2008(H5... 38.2 0.17
                            gb|FJ461658.1| Influenza A virus (A/Egypt/3300-NAMRU3/2008(H5... 38.2 0.17
                            gb|FJ461652.1| Influenza A virus (A/Egypt/10217-NAMRU3/2007(H... 38.2 0.17
                            gb|FJ461651.1| Influenza A virus (A/Egypt/10216-NAMRU3/2007(H... 38.2 0.17
                            gb|FJ461650.1| Influenza A virus (A/Egypt/10215-NAMRU3/2007(H... 38.2 0.17
                            gb|FJ461648.1| Influenza A virus (A/Egypt/6251-NAMRU3/2007(H5... 38.2 0.17
                            gb|FJ461644.1| Influenza A virus (A/Egypt/2751-NAMRU3/2007(H5... 38.2 0.17
                            gb|FJ461641.1| Influenza A virus (A/Egypt/2630-NAMRU3/2007(H5... 38.2 0.17
                            gb|FJ461632.1| Influenza A virus (A/Egypt/1731-NAMRU3/2007(H5... 38.2 0.17
                            gb|FJ461631.1| Influenza A virus (A/Egypt/1604-NAMRU3/2007(H5... 38.2 0.17
                            gb|FJ461629.1| Influenza A virus (A/Egypt/2991-NAMRU3/2006(H5... 38.2 0.17
                            gb|FJ461628.1| Influenza A virus (A/Egypt/2947-NAMRU3/2006(H5... 38.2 0.17
                            gb|EU889100.1| Influenza A virus (A/herring gull/Sweden/V1116... 38.2 0.17
                            gb|EU889099.1| Influenza A virus (A/tufted duck/Sweden/V599/2... 38.2 0.17
                            gb|EU748905.1| Influenza A virus (A/falcon/Saudi Arabia/D1795... 38.2 0.17
                            gb|EU717858.1| Influenza A virus (A/chicken/Egypt/1709-6/2008... 38.2 0.17
                            gb|EU717856.1| Influenza A virus (A/chicken/Egypt/1709-5/2008... 38.2 0.17
                            gb|EU717854.1| Influenza A virus (A/chicken/Egypt/1709-4VIR08... 38.2 0.17
                            gb|EU717852.1| Influenza A virus (A/duck/Egypt/1709-3VIR08/20... 38.2 0.17
                            gb|EU717850.1| Influenza A virus (A/chicken/Egypt/1709-1VIR08... 38.2 0.17
                            gb|EU697218.1| Influenza A virus (A/chicken/Nigeria/228-5/200... 38.2 0.17
                            gb|EU697225.1| Influenza A virus (A/chicken/Nigeria/228-6/200... 38.2 0.17
                            gb|EU697233.1| Influenza A virus (A/chicken/Nigeria/228-10/20... 38.2 0.17
                            gb|EU574921.1| Influenza A virus (A/chicken/Israel/1055/2008(... 38.2 0.17
                            gb|EU443567.1| Influenza A virus (A/Cygnus olor/Czech Republi... 38.2 0.17
                            gb|EU443566.1| Influenza A virus (A/Mergus albellus/Slovakia/... 38.2 0.17
                            gb|EU443565.1| Influenza A virus (A/Peregrine falcon/Slovakia... 38.2 0.17
                            gb|EU443564.1| Influenza A virus (A/Cygnus olor/Czech Republi... 38.2 0.17
                            emb|AM498620.1| Influenza A virus (A/mute swan/France/06254a/... 38.2 0.17
                            emb|AM498619.1| Influenza A virus (A/mute swan/France/06303/2... 38.2 0.17
                            emb|AM498617.1| Influenza A virus (A/common pochard/France/06... 38.2 0.17
                            gb|EU146881.1| Influenza A virus (A/chicken/Egypt/3/2006(H5N1... 38.2 0.17
                            gb|EU146882.1| Influenza A virus (A/Egypt/902782/2006(H5N1)) ... 38.2 0.17
                            gb|EU146883.1| Influenza A virus (A/Egypt/902786/2006(H5N1)) ... 38.2 0.17
                            gb|EU146891.1| Influenza A virus (A/chicken/Egypt/1/2006(H5N1... 38.2 0.17
                            gb|EU146892.1| Influenza A virus (A/chicken/Egypt/2/2006(H5N1... 38.2 0.17
                            gb|EF619973.1| Influenza A virus (A/turkey/Turkey/1/2005(H5N1... 38.2 0.17
                            emb|AM262563.1| Influenza A virus (A/chicken/Nigeria/SO494/20... 38.2 0.17
                            emb|AM262562.1| Influenza A virus (A/chicken/Nigeria/SO493/20... 38.2 0.17
                            emb|AM262561.1| Influenza A virus (A/chicken/Nigeria/SO452/20... 38.2 0.17
                            emb|AM262560.1| Influenza A virus (A/chicken/Nigeria/SO300/20... 38.2 0.17
                            gb|EF532643.1| Influenza A virus (A/duck/Gaza/760/2006(H5N1))... 38.2 0.17
                            gb|EF532642.1| Influenza A virus (A/chicken/Gaza/714/2006(H5N... 38.2 0.17
                            gb|EF532641.1| Influenza A virus (A/chicken/Gaza/713/2006(H5N... 38.2 0.17
                            gb|EF532640.1| Influenza A virus (A/chicken/Israel/625/2006(H... 38.2 0.17
                            gb|EF532639.1| Influenza A virus (A/chicken/Gaza/450/2006(H5N... 38.2 0.17
                            gb|EF532638.1| Influenza A virus (A/turkey/Israel/446/2006(H5... 38.2 0.17
                            gb|EF532637.1| Influenza A virus (A/chicken/Israel/397/2006(H... 38.2 0.17
                            gb|EF532636.1| Influenza A virus (A/turkey/Israel/365/2006(H5... 38.2 0.17
                            gb|EF532635.1| Influenza A virus (A/turkey/Israel/364/2006(H5... 38.2 0.17
                            gb|EF532634.1| Influenza A virus (A/turkey/Israel/345/2006(H5... 38.2 0.17
                            gb|EF532633.1| Influenza A virus (A/duck/Gaza/834/2006(H5N1))... 38.2 0.17
                            gb|EF486250.1| Influenza A virus (A/goose/Egypt/13009N3-SM2/2... 38.2 0.17
                            gb|EF486249.1| Influenza A virus (A/duck/Egypt/1888N3-SM25/20... 38.2 0.17
                            gb|EF486248.1| Influenza A virus (A/duck/Egypt/13010N3-CLEVB/... 38.2 0.17
                            gb|EF486247.1| Influenza A virus (A/duck/Egypt/12380N3-CLEVB/... 38.2 0.17
                            gb|EF486246.1| Influenza A virus (A/chicken/Egypt/1892N3-HK49... 38.2 0.17
                            gb|EF486245.1| Influenza A virus (A/chicken/Egypt/1891N3-CLEV... 38.2 0.17
                            gb|EF486244.1| Influenza A virus (A/chicken/Egypt/1890N3-HK45... 38.2 0.17
                            gb|EF486243.1| Influenza A virus (A/chicken/Egypt/1889N3-SM26... 38.2 0.17
                            gb|EF486242.1| Influenza A virus (A/chicken/Egypt/12379N3-CLE... 38.2 0.17
                            gb|EF486241.1| Influenza A virus (A/chicken/Egypt/12378N3-CLE... 38.2 0.17
                            gb|EF486240.1| Influenza A virus (A/chicken/Egypt/1129N3-HK9/... 38.2 0.17
                            gb|EF447431.1| Influenza A virus (A/chicken/Russia_Moscow obl... 38.2 0.17
                            gb|CY020655.1| Influenza A virus (A/turkey/Egypt/2253-2/2006(... 38.2 0.17
                            gb|CY020647.1| Influenza A virus (A/chicken/Egypt/2253-1/2006... 38.2 0.17
                            gb|CY020351.1| Influenza A virus (A/cygnus olor/Italy/808/200... 38.2 0.17
                            gb|EF474448.1| Influenza A virus (A/chicken/Moscow/2/2007(H5N... 38.2 0.17
                            gb|EF222324.1| Influenza A virus (A/Egypt/12374-NAMRU3/2006(H... 38.2 0.17
                            gb|EF222323.1| Influenza A virus (A/Egypt/14724-NAMRU3/2006(H... 38.2 0.17
                            gb|EF165588.1| Influenza A virus (A/great crested grebe/Bavar... 38.2 0.17
                            gb|EF165578.1| Influenza A virus (A/mute swan/Bavaria/12/2006... 38.2 0.17
                            gb|CY017045.1| Influenza A virus (A/swan/Slovenia/760/2006(H5... 38.2 0.17
                            gb|CY016901.1| Influenza A virus (A/duck/Egypt/2253-3/2006(H5... 38.2 0.17
                            gb|DQ659680.1| Influenza A virus (A/common bussard/Bavaria/2/... 38.2 0.17
                            gb|DQ534021.1| Influenza A virus A/Cygnus olor/Czech Republic... 38.2 0.17

                            Comment

                            • #15
                              Re: H5N1 Vietnam 2008 Clade 7

                              gb|FJ538949.1| Influenza A virus (A/chicken/Vietnam/NCVD-093/... 40.1 0.044
                              gb|FJ688369.1| Influenza A virus (A/chicken/Egypt/24NLQP-CLEV... 40.1 0.044
                              gb|FJ688367.1| Influenza A virus (A/chicken/Egypt/17NLQP-CLEV... 40.1 0.044
                              gb|FJ688365.1| Influenza A virus (A/chicken/Egypt/10NLQP-CLEV... 40.1 0.044
                              gb|FJ688364.1| Influenza A virus (A/chicken/Egypt/4NLQP-CLEVB... 40.1 0.044
                              gb|FJ461658.1| Influenza A virus (A/Egypt/3300-NAMRU3/2008(H5... 40.1 0.044
                              gb|EU717858.1| Influenza A virus (A/chicken/Egypt/1709-6/2008... 40.1 0.044
                              gb|EU717856.1| Influenza A virus (A/chicken/Egypt/1709-5/2008... 40.1 0.044
                              gb|EU574921.1| Influenza A virus (A/chicken/Israel/1055/2008(... 40.1 0.044
                              gb|EU430497.1| Influenza A virus (A/domestic green-winged tea... 40.1 0.044
                              gb|EU430510.1| Influenza A virus (A/domestic green-winged tea... 40.1 0.044
                              gb|EF587279.1| Influenza A virus (A/Beijing/01/2003(H5N1)) se... 40.1 0.044
                              gb|EF124329.1| Influenza A virus (A/goose/Yunnan/3644/2005(H5... 40.1 0.044
                              gb|EF124310.1| Influenza A virus (A/goose/Yunnan/3315/2005(H5... 40.1 0.044
                              gb|DQ997539.1| Influenza A virus (A/chicken/Jilin/xv/2002(H5N... 40.1 0.044
                              gb|DQ997378.1| Influenza A virus (A/chicken/Jilin/hf/2002(H5N... 40.1 0.044
                              gb|DQ997284.1| Influenza A virus (A/chicken/Jilin/hd/2002(H5N... 40.1 0.044
                              gb|AY653195.1| Influenza A virus (A/chicken/Jilin/9/2004(H5N1... 40.1 0.044

                              Comment

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