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Receptor Binding Sites Altered by Egg Passage

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  • Receptor Binding Sites Altered by Egg Passage

    After reading the recent study possibly linking mutations at position225 with egg passaging, I decided to look at all the records at GISAID and see if the sequence data agreed with the study.
    Here's a direct link to the study (hat-tip to IOH); http://vir.sgmjournals.org/cgi/conte...r.0.016691-0v1

    All of this information came from the GISAID database, currently containing 4418 pH1N1 isolates.
    Thanks to all the originating labs for their work on these sequences.

    Here is a list of all the sequences using egg passage which do not have any mutations in positions D225 and Q226:

    *note: Some of these were submitted in large groups; where you see "also" means those are part of that group and are of the same time frame with the same passage and no mutations.

    RDQ gat
    A/Cherkasy/353/2009 RDQ gat 11-02-09 E1
    A/Cherkasy/346/2009 RDQ gat 11-02-09 E1
    A/Cherkasy/332/2009 RDQ gat 10-30-09 E1
    A/Cherkasy/333/2009 RDQ gat 11-02-09 E1
    A/Cherkasy/335/2009 RDQ gat 11-02-09 E1
    A/Cherkasy/321/2009 RDQ gat 11-01-09 E1
    A/Russia/61/2009 11-01-09 RDQ gat E1
    A/Russia/4/2009 11-01-09 RDQ gat E1
    A/Russia/180/2009 11-05-09 RDQ gat E1
    A/Russia/171/2009 11-12-09 RDQ gat E1
    A/Russia/12/2009 11-01-09 RDQ gat E1
    A/Russia/191/2009 11-01-09 RDQ gat E1
    A/Russia/14/2009 11-01-09 RDQ gat E1
    A/Russia/74,178,190,200 RDQ gat E1
    A/Argentina/HNRG5/2009 06-22-09 RDQ gat E1
    Also:>48,45,44,42,41,40,39,37,36,33,32,31,30,3,23, 21,
    18,17,15,14,13>all gat E1
    A/Russia/165/2009 11-10-09 RDQ gat E1
    A/Russia/19/2009 11-01-09 RDQ gat E1 1151-
    A/Fujian/SWL3/2009 05-29-09 RDQ gat E1
    A/Panama/303373/2009 05-18-09 RDQ gat E1
    Also: 303370, 303360, 303328, 303270, 303246
    Also: 303238, 303066, 303053, 303052
    A/Mexico/4108/2009 04-03-09 RDQ gat E1
    A/Delaware/03/2009 04-28-09 RDQ gat E1
    A/Delaware/02/2009 04-28-09 RDQ gat E1
    A/Guangdong/1/2009 05-18-09 RDQ gat E1
    A/Auckland/3/2009 04-25-09 RDQ gat E1
    ***** Total of 57 with E1

    A/Bangladesh/3009/2009 12-19-09 RDQ gat E2
    A/Korea/9741/2009 09-22-09 RDQ gat E2
    A/Texas/70/2009 09-09-09 RDQ gat E2
    A/Tomsk/01/2009 00-00-09 RDQ gat Chicken embryo 2
    A/Iraq/8529/2009 09-08-09 RDQ gat E2
    A/TASMANIA/2005/2009 07-03-09 RDQ gat E2
    A/FIJI/2035/2009 07-02-09 RDQ gat E2
    A/FIJI/2029/2009 07-06-09 RDQ gat E2
    A/Texas/70/2009 09-09-09 RDQ gat E2
    A/Texas/04/2009 04-14-09 RDQ gat E2
    A/Korea/9741/2009 09-22-09 RDQ gat E2
    A/Fujian/SWL6/2009 05-31-09 RDQ gat E2
    A/GUAM/2049/2009 07-23-09 RDQ gat E2
    A/DARWIN/2131/2009 08-14-09 RDQ gat E2
    A/WELLINGTON/188/2009 07-10-09 RDQ gat E2
    A/WELLINGTON/9/2009 06-09-09 RDQ gat E2
    A/DARWIN/2124/2009 07-09-09 RDQ gat E2
    Also 2125,2126 and Victoria/2083
    A/New York/45/2009 04-25-09 RDQ gat E2
    A/California/17/2009 04-25-09 RDQ gat E2
    A/New York/35/2009 04-25-09 RDQ gat E2
    A/New York/39/2009 04-25-09 RDQ gat E2
    A/South Carolina/10/2009 04-26-09 RDQ gat E2
    A/New York/19/2009 04-25-09 RDQ gat E2
    A/New York/17/2009 04-00-09 RDQ gat E2
    A/New York/16/2009 04-24-09 RDQ gat E2
    A/Colorado/04/2009 04-26-09 RDQ gat E2
    A/Colorado/03/2009 04-27-09 RDQ gat E2
    A/California/11/2009 04-24-09 RDQ gat E2
    A/Arizona/03/2009 04-26-09 RDQ gat E2
    A/Arizona/02/2009 04-26-09 RDQ gat E2
    A/Shandong/1/2009 05-10-09 RDQ gat E2 4151-
    A/New York/21/2009 04-24-09 RDQ gat E2
    A/Texas/09/2009 04-25-09 RDQ gat E2
    A/New York/28/2009 04-00-09 RDQ gat E2
    A/New York/27/2009 04-00-09 RDQ gat E2
    Also: A/New York/26/2009 RDQ E2
    A/New York/24/2009 RDQ E2
    A/New York/23/2009 RDQ E2
    Also: NY/14,12,09,18,
    A/Mexico/4486/2009 04-14-09 RDQ gat E2
    A/Mexico/4482/2009 04-14-09 RDQ gat E2
    A/New York/20/2009 04-25-09 RDQ gat E2
    A/California/08/2009 04-09-09 RDQ gat E2
    A/Kansas/03/2009 04-24-09 RDQ gat E2
    A/Auckland/1/2009 04-25-09 RDQ gat E2
    A/Mexico/4108/2009 04-03-09 RDQ gat C1/E2
    **** Total 52 with E2

    A/North Carolina/38/2009 10-21-09 RDQ gat E3
    A/Argentina/HNRG20/2009 06-00-09 RDQ gat E3
    A/California/08/2009 04-09-09 RDQ gat E3
    A/Iraq/8531/2009 09-08-09 RDQ gat E3
    A/PORT MORESBY/2009 00-00-09 RDQ gat E3
    ***** Total 5 with E3

    A/Belgorod/05/2009 11-30-09 RDQ gat E3/E1
    A/Belarus/94/2009 09-02-09 RDQ gat E1,E1
    A/Brazil/441/2009 08-06-09 RDQ gat E1C2/C1
    A/Iran/2521/2009 08-00-09 RDQ gat E2+E1
    ***** Total 4 multiple passages
    The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

  • #2
    Re: Receptor Binding Sites Altered by Egg Passage

    Here are the ones with mutations at 225, 226:

    RNQ aat D225
    A/Russia/100/2009 11-01-09 RNQ aat E1
    A/Argentina/HNRG8/2009 06-11-09 RNQ aat E1

    REQ gaa D225
    A/St-Petersburg/99/2009 11-30-09 REQ gaa E2,E1
    A/Egypt-Vacsera162/2009 12-00-09 REQ gaa E1,E1
    A/Egypt-Vacsera/138/2009 12-00-09 RGQ gga E1,E1
    A/St Petersburg/59/2009 11-30-09 REQ gaa E2/E1
    A/Uganda/0543/2009 10-24-09 REQ gaa E2

    RGQ ggt D225
    A/IIV-Anadyr/177/2009 1-04-09 RGQ ggt embryonated chicken eggs
    A/Voronezh/01/2009 11-30-09 RGQ ggt E1/E1
    A/Argentina/HNRG16/2009 06-29-09 E1 RGQ ggt
    A/Tianjin/SWL4/2009 06-11-09 RGQ ggt E3
    A/Hiroshima/201/2009 06-17-09 RGQ ggt E1+1
    A/Indiana/09/2009 04-22-09 RGQ ggt E2
    A/Texas/05/2009 04-15-09 RGQ ggt X/E2
    A/Mexico/InDRE4114/2009 00-00-09 RGQ ggt E2/E1
    A/New York/04/2009 04-00-09 RGQ ggt E2
    A/Mexico/3955/2009 04-03-09 RGQ ggt E2

    RXQ grt D225
    A/California/13/2009 04-21-09 RXQ grt E2
    A/Texas/10/2009 04-23-09 RXQ grt E2
    A/South Carolina/09/2009 04-26-09 RXQ rat E2
    A/Nebraska/02/2009 04-00-09 RXQ grt E2
    A/Arizona/04/2009 04-27-09 RXQ rat E2
    A/New York/31/2009 04-24-09 RXQ grt E2
    A/New York/11/2009 04-25-09 RXQ grt E2

    RDR cga Q226
    A/Hungary/33/2009 07-22-09 6yo M RDR cga E3/E2
    A/Hungary/20/2009 06-15-09 19 M RDR cga E2/E2
    A/England/195/2009 05-00-09 RDR cga X/E2
    A/Hungary/20/2009 06-15-09 RDR cga E2+1
    A/Hungary/36/2009 07-22-09 RDR cga E2+2
    A/St Petersburg/03/2009 09-21-09 RDR cga E2/E1
    A/El Salvador/1553/2009 07-14-09 RDR cga E3
    A/GUAM/2050/2009 08-10-09 RDR cga E2
    A/EAST TIMOR/2002/2009 00-00-09 RDR cga E2
    A/PORT MORESBY/2008/2009 00-00-09 RDR cga E3
    A/TASMANIA/2004/2009 07-05-09 RDR cga E2
    A/Verona-Italy/2810/2009 05-28-09 RDR cga E1
    A/Mexico/InDRE4487/2009 04-14-09 RDR cga E2/E1
    A/Texas/17/2009 04-24-09 RDR cga E2
    A/Mexico/4603/2009 04-19-09 RDR cga C1/E2

    RDX cra Q226
    A/California/12/2009 04-22-09 RDX cra E2
    A/Delaware/05/2009 04-28-09 RDX cra E2
    A/New York/07/2009 00-00-09 RDX cra E2
    A/New York/18/2009 00-00-09 RDX cra E4
    A/New York/13/2009 04-25-09 RDX cra E2
    A/New York/34/2009 04-25-09 RDX cra E2
    A/New York/37/2009 04-25-09 RDX cra E2
    A/New York/33/2009 04-25-09 RDX cra E2
    A/New York/25/2009 04-24-09 RDX cra E2
    A/New York/18/2009 00-00-09 RDX cra E3
    A/New York/08/2009 04-25-09 RDX cra E2
    A/Texas/08/2009 4-24-09 RDX cra E2
    A/Texas/20/2009 04-25-09 RDX cra E2
    A/Mexico/4108/2009 04-03-09 RDX cra E2
    A/Belgorod/01/2009 11-30-09 RDX cra E3/E1

    D225 + Q226 positions
    A/Kaliningrad/01/2009 11-02-09 RER gaa cga E2/E1
    A/St Petersburg/5/2009 09-21-09 REX gaa cra E3+1
    A/California/07/2009 04-09-09 RXX grt cra E2
    A/Texas/04/2009 04-14-09 RXX grt cra X/E2
    The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

    Comment


    • #3
      Re: Receptor Binding Sites Altered by Egg Passage

      Gs's research from GenBank:

      50 sequences from genbank with mutation at 716(4)
      716 mxha7a 50 -:127 A:1924 G:33 M:1 R:15 T:1

      8 have "E2", 2 have "X/E2", 1 has "E2/E1" , 2 have "C1", 1 has "MDCK", 6 have no passage data
      1 has E1, 1 has E1+1, 3 have P0 , 1 CE , 1 M1 , 1 MDCK1, 1 MDCK2,

      total: 14 egg , 6 MDCK , 30 ?

      ----------------------------------------------------------------------

      4114: Passage_history E2/E1
      4114(2): ? /mol_type="viral cRNA"
      vostok/01: ?
      Abakan/02: /isolation_source="lung"
      Tomsk/07: /isolation_source="lung"
      Salekhard/01:/isolation_source="lung"
      Tomsk/08: /isolation_source="lung"
      NY/04: Passage_history E2
      Nebraska/02: Passage_history C1
      Swine/4/Mex:/isolation_source="age:Adult; trachea" /lab_host="MDCK passage(s)"
      G >A/Mexico/3955,2009/04/02 Passage_history E2
      R >A/CA/07,2009/04/09 Passage_history E2
      R >A/Texas/04,2009/04/14 Passage_history X/E2
      G >A/Texas/05,2009/04/15 Passage_history X/E2
      R >A/CA/13,2009/04/21 Passage_history E2
      R >A/Texas/10,2009/04/23 Passage_history E2
      G >A/Texas/11,2009/04/23 Passage_history E2
      R >A/NY/31,2009/04/24 Passage_history E2
      R >A/NY/11,2009/04/25 Passage_history E2
      G >A/Georgia/01,2009/04/27 Passage_history C1
      T >A/Sw/Alberta/OTH-33-3,2009/05/03 /lab_host="embryonated chicken eggs passage 1CE-4dpi"
      G >A/Hiroshima/201,2009/06/17 passage history: E1+1"
      G >A/CA/VRDL7,2009/06/17 /lab_host="P0 passage(s)"
      M >A/CA/VRDL31,2009/06/17 /lab_host="P0 passage(s)"
      G >A/CA/VRDL27,2009/06/27 /lab_host="P0 passage(s)"
      R >A/Texas/42291877,2009/06/29 ?
      G >A/Argentina/HNRG16,2009/06/29 /lab_host="E1 passage(s)"
      G >A/Sao Paulo/53206,2009/07/19 /isolation_source="necropsy tissue (lung)"
      R >A/Utah/42,2009/07/24 Passage_history Original
      G >A/Utah/42,2009/07/24 Passage_history M1
      R >A/Finland/614,2009/07/24 ?
      G >A/Rio de Janeiro/5826,2009/07/28 deceased patient" Nasopharyngeal secretion"
      G >A/Catalonia/NS1706,2009/07/29 nasopharyngeal
      G >A/Sao Paulo/53225,2009/08/01 ?
      G >A/Catalonia/NS2001,2009/08/03 nasopharyngeal"
      G >A/Catalonia/NS2008,2009/08/03 nasopharyngeal"
      R >A/Norway/2924,2009/08/10 /lab_host="MDCK1 passage(s)" nasopharyngeal
      G >A/Norway/3206-3,2009/09/01 /lab_host="MDCK2 passage(s)" post mortem lung
      G >A/Zhejiang-Yiwu/11,2009/09/06 severe symptoms
      G >A/Zhejiang/DTID-ZJU02,2009/09/07 ?
      G >A/Zhejiang/DTID-ZJU03,2009/09/07 ?
      R >A/Mexico/InDRE43149,2009/09/28 9m,pharyngeal,deceased,Mex.City
      R >A/Mexico/InDRE50625,2009/10/31 25m,pharyngeal,deceased,SLP
      R >A/Mexico/InDRE50617,2009/11/01 40m,pharyngeal,deceased,SLP
      G >A/Bryansk/IIV2971,2009/11/11 29m,lung
      G >A/Tver/IIV2969,2009/11/14 26f,autopsy material; lung whole cell-tissue lysate"
      G >A/Perm/01,2009/11/25 lung
      G >A/Taraz/01,2009/12/ ?
      G >A/Catalonia/NS092145684,2009/12/10 62m, M; age:62; bronchoalveolar lavage"
      G >A/Karasuk/01/2010(H1N1),2010/01/04 lung
      The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

      Comment


      • #4
        Re: Receptor Binding Sites Altered by Egg Passage

        Gs, here's some info on the number of sequences at GISAID; do we have stats for Genbank?

        H1N1 2251 isolates
        2127 HA
        1718 HA complete
        1455 NA complete
        1198 HA + NA complete
        414 PB2 complete
        290 all 8 segments complete
        The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

        Comment

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