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H5N1 Assam 2008 (November)

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  • H5N1 Assam 2008 (November)

    <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="12" value="225422944" id="UidCheckBox" type="checkbox">12: FJ839923</td><td align="left" valign="top">
    Reports<script language="JavaScript1.2"><!-- var PopUpMenu2_LocalConfig_Reports225422944 = [ ["TitleText","Reports"] ]; var Reports225422944 = [ ["UseLocalConfig","Reports225422944","",""], ["ASN.1","window.top.location='/nuccore/225422944?report=asn1'","",""], ["XML","window.top.location='/nuccore/225422944?report=xml'","",""], ["Summary","window.top.location='/nuccore/225422944?report=docsum'","",""], ["Brief","window.top.location='/nuccore/225422944?report=brief'","",""], ["FASTA","window.top.location='/nuccore/225422944?report=fasta'","",""], ["TinySeq XML","window.top.location='/nuccore/225422944?report=fasta_xml'","",""], ["GenBank","window.top.location='/nuccore/225422944?report=genbank'","",""], ["INSDSeq XML","window.top.location='/nuccore/225422944?report=gbc_xml'","",""], ["GenBank(Full)","window.top.location='/nuccore/225422944?report=gbwithparts'","",""], ["Feature table","window.top.location='/nuccore/225422944?report=ft'","",""], ["GI List","window.top.location='/nuccore/225422944?report=gilist'","",""], ["Graphic","window.top.location='/nuccore/225422944?report=graph'","",""], ["Revision History","window.top.location='/entrez/sutils/girevhist.cgi?val=FJ839923'","",""] ] --></script></td><td align="right" valign="top">
    <script language="JavaScript1.2"><!-- var Menu225422944 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=225422944&ordinalpos=12&itool=EntrezSystem2. PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RV DocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=225422944&ordinalpos=12&itool=EntrezSystem2.PEn trez.Sequence.Sequence_ResultsPanel.Sequence_RVDoc Sum' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=225422944&ordinalpos=12&itool=EntrezSyste m2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence _RVDocSum' ", "", ""], ["Related Sequences" , "window.top.location='/sites/entrez?Db=nuccore&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_nuccore&LinkReadableName=Related%20Sequen ces&IdsFromResult=225422944&ordinalpos=12&itool=En trezSystem2.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/Assam/140203/2008(H5N1)) segment 6 neuraminidase (NA) gene, partial cds
    gi|225422944|gb|FJ839923.1|[225422944]
    </td></tr></tbody></table> <!--docsumok 225422942 225422942 1 0 1707--> <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="13" value="225422942" id="UidCheckBox" type="checkbox">13: FJ839922</td><td align="left" valign="top">
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    <script language="JavaScript1.2"><!-- var Menu225422942 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=225422942&ordinalpos=13&itool=EntrezSystem2. PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RV DocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=225422942&ordinalpos=13&itool=EntrezSystem2.PEn trez.Sequence.Sequence_ResultsPanel.Sequence_RVDoc Sum' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=225422942&ordinalpos=13&itool=EntrezSyste m2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence _RVDocSum' ", "", ""], ["Related Sequences" , "window.top.location='/sites/entrez?Db=nuccore&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_nuccore&LinkReadableName=Related%20Sequen ces&IdsFromResult=225422942&ordinalpos=13&itool=En trezSystem2.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/Assam/140203/2008(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds
    gi|225422942|gb|FJ839922.1|[225422942]
    </td></tr></tbody></table></dt></dl>
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    <script language="JavaScript1.2"><!-- var Menu225422940 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=225422940&ordinalpos=14&itool=EntrezSystem2. PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RV DocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=225422940&ordinalpos=14&itool=EntrezSystem2.PEn trez.Sequence.Sequence_ResultsPanel.Sequence_RVDoc Sum' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=225422940&ordinalpos=14&itool=EntrezSyste m2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence _RVDocSum' ", "", ""], ["Related Sequences" , "window.top.location='/sites/entrez?Db=nuccore&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_nuccore&LinkReadableName=Related%20Sequen ces&IdsFromResult=225422940&ordinalpos=14&itool=En trezSystem2.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/Assam/140187/2008(H5N1)) segment 6 neuraminidase (NA) gene, partial cds
    gi|225422940|gb|FJ839921.1|[225422940]
    </td></tr></tbody></table></dt></dl>
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    <script language="JavaScript1.2"><!-- var Menu225422938 = [ ["UseLocalConfig", "jsmenu3Config", "", ""], ["Protein" , "window.top.location='/sites/entrez?Db=protein&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_protein&LinkReadableName=Protein&IdsFromR esult=225422938&ordinalpos=15&itool=EntrezSystem2. PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RV DocSum' ", "", ""], ["PubMed" , "window.top.location='/sites/entrez?Db=pubmed&DbFrom=nuccore&Cmd=Link&LinkName= nuccore_pubmed&LinkReadableName=PubMed&IdsFromResu lt=225422938&ordinalpos=15&itool=EntrezSystem2.PEn trez.Sequence.Sequence_ResultsPanel.Sequence_RVDoc Sum' ", "", ""], ["Taxonomy" , "window.top.location='/sites/entrez?Db=taxonomy&DbFrom=nuccore&Cmd=Link&LinkNam e=nuccore_taxonomy&LinkReadableName=Taxonomy&IdsFr omResult=225422938&ordinalpos=15&itool=EntrezSyste m2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence _RVDocSum' ", "", ""], ["Related Sequences" , "window.top.location='/sites/entrez?Db=nuccore&DbFrom=nuccore&Cmd=Link&LinkName =nuccore_nuccore&LinkReadableName=Related%20Sequen ces&IdsFromResult=225422938&ordinalpos=15&itool=En trezSystem2.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/Assam/140187/2008(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds
    gi|225422938|gb|FJ839920.1|[225422938] </td></tr></tbody></table>

  • #2
    Re: H5N1 Assam 2008 (November)

    Both isolates are clade 2.2.3 (Uvs Lake version)

    Comment


    • #3
      Re: H5N1 Assam 2008 (November)

      NA does NOT have G743A

      Comment


      • #4
        Re: H5N1 Assam 2008 (November)

        Top 100 HA matches

        gb|FJ839922.1| Influenza A virus (A/chicken/Assam/140203/2008... 3079 0.0
        gb|FJ839920.1| Influenza A virus (A/chicken/Assam/140187/2008... 3079 0.0
        gb|EU700511.1| Influenza A virus (A/saker falcon/Kuwait/0286/... 2966 0.0
        gb|CY029988.1| Influenza A virus (A/chicken/Kuwait/KISR8/2007... 2966 0.0
        gb|CY029980.1| Influenza A virus (A/chicken/Kuwait/KISR7/2007... 2966 0.0
        gb|CY029972.1| Influenza A virus (A/chicken/Kuwait/KISR6/2007... 2966 0.0
        gb|EU391537.1| Influenza A virus (A/falcon/Kuwait/1019-7/2007... 2962 0.0
        gb|CY029964.1| Influenza A virus (A/chicken/Kuwait/KISR5/2007... 2962 0.0
        gb|CY029996.1| Influenza A virus (A/chicken/Kuwait/KISR9/2007... 2957 0.0
        gb|CY029956.1| Influenza A virus (A/chicken/Kuwait/KISR3/2007... 2957 0.0
        gb|EU424135.1| Influenza A virus (A/houbara bustard/Saudi Ara... 2957 0.0
        dbj|AB284324.1| Influenza A virus (A/common goldeneye/Mongoli... 2957 0.0
        dbj|AB263752.1| Influenza A virus (A/whooper swan/Mongolia/2/... 2957 0.0
        gb|CY029948.1| Influenza A virus (A/chicken/Kuwait/KISR2/2007... 2953 0.0
        gb|EU233691.1| Influenza A virus (A/chicken/Korea/CA7/2006(H5... 2953 0.0
        gb|DQ914808.1| Influenza A virus (A/grebe/Tyva/Tyv06-1/2006(H... 2953 0.0
        emb|AM914026.1| Influenza A virus (A/domestic duck/Germany/R2... 2947 0.0
        emb|AM914004.1| Influenza A virus (A/domestic goose/Germany/R... 2947 0.0
        emb|FM177119.1| Influenza A virus (A/chicken/Germany/R3234/20... 2947 0.0
        emb|FM177127.1| Influenza A virus (A/chicken/Germany/R3272/20... 2947 0.0
        gb|EU871936.1| Influenza A virus (A/common gull/Chany/P/2006(... 2947 0.0
        gb|EU233707.1| Influenza A virus (A/duck/Korea/Asan5/2006(H5N... 2947 0.0
        gb|EU233715.1| Influenza A virus (A/duck/Korea/Asan6/2006(H5N... 2947 0.0
        gb|EU233731.1| Influenza A virus (A/environment/Korea/W149/20... 2947 0.0
        emb|AM914012.1| Influenza A virus (A/great crested grebe/Germ... 2944 0.0
        emb|FM177135.1| Influenza A virus (A/chicken/Germany/R3294/20... 2944 0.0
        emb|FM165530.1| Influenza A virus (A/Peking duck/Germany/R195... 2944 0.0
        gb|CY034733.1| Influenza A virus (A/chicken/Manshera/NARC1033... 2944 0.0
        gb|EU401795.1| Influenza A virus (A/goose/Lahore-Pakistan/NAR... 2944 0.0
        emb|AM773724.1| Influenza A virus (A/black-necked grebe/Germa... 2944 0.0
        gb|CY021373.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2944 0.0
        gb|CY020621.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2944 0.0
        gb|CY037770.1| Influenza A virus (A/chicken/Sihala/NARC3303.4... 2938 0.0
        gb|CY037762.1| Influenza A virus (A/chicken/Rawalakot/NARC244... 2938 0.0
        gb|EU443555.1| Influenza A virus (A/Cygnus olor/Czech Republi... 2938 0.0
        gb|EU443554.1| Influenza A virus (A/turkey/Czech Republic/103... 2938 0.0
        gb|EU443553.1| Influenza A virus (A/chicken/Czech Republic/11... 2938 0.0
        gb|CY020637.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2938 0.0
        gb|DQ861291.1| Influenza A virus (A/duck/Tuva/01/2006(H5N1)) ... 2938 0.0
        emb|AM914014.1| Influenza A virus (A/domestic duck/Germany/R1... 2935 0.0
        gb|CY020629.1| Influenza A virus (A/chicken/Afghanistan/1573-... 2935 0.0
        gb|FJ390028.1| Influenza A virus (A/chicken/Astana/6/2005(H5N... 2931 0.0
        emb|AM914021.1| Influenza A virus (A/domestic duck/Germany/R1... 2929 0.0
        gb|CY034725.1| Influenza A virus (A/goose/Islamabad/NARC7757/... 2929 0.0
        gb|EU233675.1| Influenza A virus (A/chicken/Korea/IS/2006(H5N... 2929 0.0
        gb|EU233683.1| Influenza A virus (A/chicken/Korea/IS2/2006(H5... 2929 0.0
        emb|AM749443.1| Influenza A virus (A/mute swan/Germany/R1359/... 2929 0.0
        gb|DQ863503.1| Influenza A virus (A/Grebe/Tyva/Tyv06-8/2006(H... 2929 0.0
        gb|DQ852600.1| Influenza A virus (A/grebe/Tyva/Tyv06-2/06(H5N... 2929 0.0
        emb|AM914016.1| Influenza A virus (A/domestic duck/Germany/R1... 2926 0.0
        gb|EU401794.1| Influenza A virus (A/turkey/Islamabad-Pakistan... 2926 0.0
        gb|EU233739.1| Influenza A virus (A/environment/Korea/W150/20... 2926 0.0
        gb|EU257631.1| Influenza A virus (A/Cygnus cygnus/Krasnodar/3... 2926 0.0
        gb|EU163431.1| Influenza A virus (A/chicken/Krasnodar/300/07(... 2926 0.0
        gb|CY016787.1| Influenza A virus (A/chicken/Afghanistan/1207/... 2926 0.0
        emb|FM165522.1| Influenza A virus (A/Cygnus olor/Germany/R137... 2920 0.0
        gb|FJ183472.1| Influenza A virus (A/mallard/Bavaria/10/2007(H... 2920 0.0
        gb|EF362426.1| Influenza A virus (A/chicken/India/NIV33491/06... 2920 0.0
        gb|EF362418.1| Influenza A virus (A/chicken/India/NIV33487/06... 2920 0.0
        emb|AM749442.1| Influenza A virus (A/mute swan/Germany/R1349/... 2920 0.0
        gb|EU401796.1| Influenza A virus (A/peacock/Mansehra-Pakistan... 2919 0.0
        emb|FM163448.1| Influenza A virus (A/turkey/Poland/R3249/2007... 2917 0.0
        emb|FM163440.1| Influenza A virus (A/chicken/Poland/R3248/200... 2917 0.0
        gb|FJ602811.1| Influenza A virus (A/common cormorant/Qinghai/... 2917 0.0
        gb|CY034729.1| Influenza A virus (A/crow/Peshawer/NARC7914/20... 2917 0.0
        gb|CY034727.1| Influenza A virus (A/turkey/Islamabad/NARC7873... 2917 0.0
        gb|DQ864715.1| Influenza A virus (A/chicken/Adygea/203/06(H5N... 2917 0.0
        gb|EU233723.1| Influenza A virus (A/quail/Korea/KJ4/2006(H5N1... 2913 0.0
        gb|FJ602813.1| Influenza A virus (A/bar-headedgoose/Qinghai/1... 2911 0.0
        gb|FJ602810.1| Influenza A virus (A/great black-headed gull/Q... 2911 0.0
        gb|FJ476174.1| Influenza A virus (A/swan/England/26-70/2008(H... 2911 0.0
        gb|CY016779.1| Influenza A virus (A/cygnus cygnus/Iran/754/20... 2911 0.0
        gb|FJ602867.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
        gb|FJ602866.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
        gb|FJ602815.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
        gb|FJ602812.1| Influenza A virus (A/common cormorant/Qinghai/... 2908 0.0
        gb|FJ602807.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
        gb|FJ602806.1| Influenza A virus (A/brown-headed gull/Qinghai... 2908 0.0
        gb|FJ602805.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2908 0.0
        gb|CY034731.1| Influenza A virus (A/peacock/Chakshahzad/NARC9... 2908 0.0
        gb|EF605603.1| Influenza A virus (A/chicken/Russia_Krasnodar/... 2904 0.0
        gb|DQ864720.1| Influenza A virus (A/cat/Dagestan/87/06(H5N1))... 2904 0.0
        gb|DQ864717.1| Influenza A virus (A/goose/Crimea/615/05(H5N1)... 2904 0.0
        gb|FJ602814.1| Influenza A virus (A/great black-headed gull/Q... 2902 0.0
        gb|FJ602809.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2902 0.0
        gb|FJ602808.1| Influenza A virus (A/bar-headed goose/Qinghai/... 2902 0.0
        gb|EU650486.1| Influenza A virus (A/falcon/Saudi Arabia/6732-... 2902 0.0
        gb|EF205159.1| Influenza A virus (A/chicken/Krasnodar/123/06(... 2902 0.0
        gb|EU233699.1| Influenza A virus (A/chicken/Korea/IS3/2006(H5... 2899 0.0
        gb|DQ887061.1| Influenza A virus (A/chicken/Navapur/7972/2006... 2899 0.0
        gb|EF205155.1| Influenza A virus (A/chicken/Omsk/14/05(H5N1))... 2899 0.0
        gb|DQ864711.1| Influenza A virus (A/duck/Novosibirsk/02/05(H5... 2899 0.0
        gb|DQ095617.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
        gb|DQ095613.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
        gb|DQ095612.2| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
        gb|DQ095620.1| Influenza A virus (A/Bar-headed Goose/Qinghai/... 2895 0.0
        gb|EU190482.1| Influenza A virus (A/domestic goose/Pavlodar/1... 2893 0.0
        gb|CY016819.1| Influenza A virus (A/cygnus olor/Croatia/1/200... 2893 0.0
        gb|DQ650663.1| Influenza A virus (A/chicken/Crimea/08/2005(H5... 2893 0.0
        gb|DQ676834.1| Influenza A virus (A/chicken/Krasnodar/01/2006... 2893 0.0

        Comment


        • #5
          Re: H5N1 Assam 2008 (November)

          S. Nagarajan, H. V. Murugkar, C. Tosh, P. Behera, R. Jain, S. Tripathi, R. Khandia, V. Gupta, D. D. Kulkarni, and S. C. Dubey Avian influenza virus (H5N1) in chickens in India
          Vet Rec. 2009 164: 128. <dl><dt>
          </dt><dd><nobr> [Full Text] [PDF]
          </nobr></dd></dl>

          Comment


          • #6
            Re: H5N1 Assam 2008 (November)

            Commentary

            http://www.recombinomics.com/News/03...ake_Assam.html

            Comment


            • #7
              Re: H5N1 Assam 2008 (November)

              Commentary

              Uvs Lake H5N1 Flies Into Assam India

              Recombinomics Commentary 21:39
              March 31, 2009

              HA and NA sequences from the H5N1 outbreak in Assam, India were released at Genbank. The two HA sequences, A/chicken/Assam/140187/2008 and A/chicken/Assam/140203/2008 were identical and clade 2.2.3, as seen previously in isolates from south Asia (India, Pakistan, Afghanistan). However, the current sequences are the Uvs Lake strain that was initially isolated from a massive wild bird outbreak at Uvs Lake in Mongolia and the adjacent region in Siberia (Tyva) in the summer of 2006. These sequences were subsequently found in outbreaks in South Korea and Japan at the end of 2006 / beginning of 2007. However, another set of sequences was found in early 2007, and these sequences had acquired G743A, which was also acquired by distinct clade 2.2 isolates in Egypt, Russia, Ghana, and Nigeria in early 2007.

              However, the Assam sequences do not have G743A, suggesting they originated from sequences that did not fly west to the Middle East and Europe (the sequences in Kuwait, including G743A, were subsequently reported throughout Europe, beginning in the summer of 2007). Phylogenetic analysis also shows that the Assam sequences are on a lower branch that is distinct from the isolates with G743A. Moreover, the newly acquired polymorphisms in the Assam sequences were not clade 2.2 sequences, but were largely polymorphisms found in other H5N1 clades circulating in Asia.

              These data support migration of the H5N1 sequences from Mongolia or Russia to India via the south Asia flyway, which connects those countries. This connection was expected, because all prior outbreaks in the region were clade 2.2, which was initially reported in countries to the north of India that were in this flyway.

              However, the linkage with Uvs Lake sequences, populated with Asian polymorphisms further supports the migration of H5N1 into India via migratory birds.

              .
              "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

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