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  • mixin
    replied
    Re: Two Reports: Influenza Virus Characterization, WHO Vax Reports

    We were watching changes in amino acid positions 170-174 in connection with low reactors. Gs searched the Genbank records and found 43 with changes in those positions. Those are in positions 511 to 519 (shown vertical for formatting).

    He says it transmits in Athen,Swine,Salekhard/Nanjing

    Code:
            
 
 
                                                0000000000000000001111111111111 
                                                1111224[COLOR="Red"]5[/COLOR][COLOR="Red"]5555[/COLOR]5677790112334456666 
                                                1245193[COLOR="#ff0000"]1[/COLOR][COLOR="#ff0000"]1111[/COLOR]5511451278190003788 
                                                6654683[COLOR="#ff0000"]12579[/COLOR]5867857811852840823 
-codon-position---------------------------------2 11 111221  12 11  1 1 111112  
---Index----------------------------------------AACGTTTAAGATTTATCAGAGAGGACGGCAG 
   1 >A/******/index/2009/02/01                 ............................... 
   2 >A/Oklahoma/3052/2009/04/30                ........C..........------------ 
   3 >A/Bayern/62/2009/04/29                    .........A..................... 
   4 >A/Lisboa/120/2009/12/21                   .........A...A.....------------ 
   5 >A/Yamaguchi/21/2009/06/03                 ..........R..A...........T..... 
   6 >A/Oregon/20/2009                          .............A.......G...T..... 
   7 >A/Wisconsin/629-D00223/2009/05/30         .........................T..... 
   8 >A/NY/4459/2009/06/19                      .......G.....A...........T..... 
   9 >A/Delhi/NIV3610/2009/08/                  .......G.....A...........T..... 
  10 >A/Pennsylvania/14/2009                    .........R...A...........T..... 
  11 >A/Bahrain/N11659/2009/10/                 .........A...A...........T..... 
  12 >A/Catalonia/S1207/2009/08/06              --.......A...A...........T..--- 
  13 >A/Netherlands/2243/2009/11/17             .........A...AG......G...T..... 
  14 >A/Salekhard/01/2009                       .........A...AG......G...T..... 
  15 >A/Nanjing/2/2010/06/30                    ......C..A...AG.........GTA.... 
  16 >A/Nanjing/1/2010/06/30                    ......C..A...AG.........GTA.... 
  17 >A/Daejeon/1871/2009/12/15                 G.....C..A...A...........T..... 
  18 >A/Nagano/RC1/2009/08/27                   .G...A...A...A....T......T..... 
  19 >A/Nagano/RC1/2009/08/27                   .G...A...R...AR...T......T..... 
  20 >A/Texas/47/2009                           ..A......RR.................... 
  21 >A/Silver Spring/WRAIRSP510P2/2009/06/18   ..A.C....A...................GC 
  22 >A/Silver Spring/WRAIRSP510P3/2009/06/18   ..A.C.....G...........A......GC 
  23 >A/Moscow/WRAIR1621N/2009/11/02            ..A.C.....G...........A......GC 
  24 >A/Mexico city/CIA2/2009/07/06             ...........A.............T..... 
  25 >A/Wisconsin/629-D01935/2009/09/16         ...........A.A...........T..... 
  26 >A/Athens/INS347/2009/12/20                G..........A.A.AT......A.T.T... 
  27 >A/Athens/INS348/2009/12/20                G..........A.A.AT......A.T.T... 
  28 >A/Athens/INS355/2009/12/22                G..........A.A.AT......A.T.T... 
  29 >A/Japan/AF2278/2009/11/10                 ...........A.A.......---------- 
  30 >A/Sw/Minnesota/02979/2010/02/17           ...T.........A...-------------- 
  31 >A/Sw/MN/8762-1/2010/02/16                 ...T.....A...A...G.T.GT..T..... 
  32 >A/Sw/MN/8762-2/2010/02/16                 ...T.....A...A...G.T.GT..T..... 
  33 >A/Sw/IL/12660/2010/02/23                  ...T.....A...A...G.T.GT..T..... 
  34 >A/Sw/NC/19646/2010/04/20                  .........A...A.......G...T..... 
  35 >A/turkey/Ontario/FAV110-4/2009/11/03      .........A...............T..... 
  36 >A/Niigata/700/2009/06/22                  .....Y....R..............T..... 
  37 >A/CA/27/2009/05/01                        .......R....................... 
  38 >A/Roma/ISS1941/2009/08/27                 .........A..CAGA......--------- 
  39 >A/Bangkok/INS425/2010/02/25               .........A..CA.......G...T..T.. 
  40 >A/Texas/AF2589/2009/10/04                 .............A......A---------- 
  41 >A/NY/3230/2010/01/25                      ...........A.A......A....T..... 
  42 >A/Shandong-Weishan/SWL36/2009/10/05       -------....G.A...........T.C--- 
  43 >A/Santo Domingo/WR1068N/2009/06/25        ..A.....C...................TGA 
  44 >A/Singapore/GP2316/2009/07/31             ..........N..N...........T..... 
                                                                                
---Index----------------------------------------AACGTTTAAGATTTATCAGAGAGGACGGCAG 
-codon-position---------------------------------2 11 111221  12 11  1 1 111112  
                                                0000000000000000001111111111111 
                                                1111224555555677790112334456666 
                                                1245193111115511451278190003788 
                                                6654683125795867857811852840823

    Leave a comment:

  • mixin
    replied
    Re: Two Reports: Influenza Virus Characterization, WHO Vax Reports

    Gs gave values to the numbers; he rated the reactions from 1-9
    0 = No test
    1 = <40
    2 = 40
    3 = 80
    4 = 160
    5 = 320
    6 = 640
    7 = 1280
    8 = 2560
    9 = >5120


    Table 6. Antigenic analyses of pandemic influenza A(H1N1) viruses
    [all isolates with > 4-fold reduction against at least one ferret antiserum]
    Haemagglutination inhibition titre
    Post infection ferret sera

    1 2 3 4 5 6 7 8
    -------------------------------------------------- ----------------
    1 A/New Jersey/8/76 R15/79 ,1976,Ex , 9,7,5,6,6,7,5,6
    2 A/New Jersey/8/76 F34/82 ,1976,Ex , 9,7,5,6,6,7,5,6
    3 A/CA/4/09 ,2009,C1/E2 , 9,5,8,8,8,8,7,8
    4 A/CA/7/09 ,2009,E5 , 8,6,8,8,8,8,7,9
    5 A/England/156/09 ,2009,MDCK5 , 8,5,8,8,8,8,7,8
    6 A/Auckland/3/09 ,2009,Ex+4 , 9,6,8,8,9,8,8,9
    7 A/Bayern/69/09 ,2009,Siat2/MDCK1/Siat1 , 6,1,3,5,4,4,6,6
    8 A/Lviv/N6/09 ,2009,MDCK3/Siat1 , 6,1,5,6,4,4,7,7

    A/Sachsen-Anhalt101/09 ,04/05/2009,Siat4 , 7,1,5,4,3,4,0,0
    A/Hungary/20/09 ,15/06/2009,E2/E1 , 8,4,6,5,5,6,0,0
    A/Bayern/69/09 ,07/09/2009,Siat2/MDCK1 , 6,1,3,3,2,3,0,0
    A/Sachsen/92/09 ,04/07/2009,Siat4 , 6,1,4,3,3,4,0,0
    A/Netherlands/1132/09 ,12/08/2009,xMDCK3 , 7,3,6,6,7,7,0,0
    A/Norway/3206-3/09 ,01/09/2009,MDCK3 , 6,1,5,6,3,3,0,0
    A/Belarus/24/09 ,07/10/2009,MDCK2/Siat1 , 6,0,6,6,6,6,6,6
    A/Norway/4011/09 ,25/10/2009,MDCK1/Siat1 , 7,3,7,7,6,5,6,6
    A/Lviv/N6/09 ,27/10/2009,MDCK2 , 6,1,5,6,3,3,0,0
    A/Lyon/2288/09 ,03/11/2009,MDCK3/Siat1 , 6,1,5,6,5,5,6,6
    A/Belgium/G4405/09 ,23/11/2009,Siat2 , 8,2,6,8,6,6,7,7
    A/Azores/13092/09 ,12/11/2009,Siat2 , 7,3,6,6,6,7,0,0
    A/Athens/16606/09 ,26/12/2009,Siat2 , 0,0,5,6,5,5,8,7
    A/Brandenburg/19/09 ,02/05/2009,Siatx , 8,4,4,5,4,4,0,0
    A/Stockholm/63/09 ,11/07/2009,p2/SIAT1 , 0,0,6,7,5,6,7,7
    A/Nordrhein-Westfalen/74/09,20/07/2009,Siat4 , 8,1,3,4,3,3,0,0
    A/Nordrhein-Westfalen/79/09,20/07/2009,Siat3 , 6,1,4,4,4,4,0,0
    A/Slovenia/3347/09 ,08/09/2009,MDCK1/Siat1 , 6,2,6,6,6,7,0,0
    A/Nordrhein-Westfalen/99/09,07/08/2009,Siat3+1 , 8,0,6,7,6,5,8,7
    A/Lisboa/51/09 ,19/08/2009,MDCK2/Siat1 , 8,0,4,6,4,4,6,6
    A/Switzerland/2243133/09 ,27/08/2009,MDCK3 , 6,3,6,6,7,7,0,0
    A/Iraq/8529/09 ,08/09/2009,E3/E1 , 0,0,5,6,5,5,6,6
    A/St.Etienne/2024/09 ,14/09/2009,MDCK4/Siat1 , 7,3,6,7,6,6,6,6
    A/South Carolina/18/09 ,16/09/2009,M1/E3/E1 , 0,0,5,7,5,5,7,7
    A/Ontario/RV3226/09 ,18/09/2009,C1/E2/E1 , 0,0,5,6,4,5,6,6
    A/Norway/3568/09 ,20/09/2009,MDCK6 , 6,2,6,6,6,7,0,0
    A/Slovenia/4025/09 ,25/10/2009,MDCK1/Siat1 , 7,3,6,6,7,7,0,0
    A/Norway/3670/09 ,05/10/2009,MDCK5 , 6,2,5,6,6,7,0,0
    A/Thuringen/176/09 ,17/10/2009,Siat3+1 , 9,0,6,7,6,6,7,7
    A/Madagascar/9018/09 ,26/10/2009,Siat2 , 0,0,6,7,6,5,8,8
    A/Belgium/1044/09 ,28/10/2009,Siat3 , 6,1,5,7,5,4,7,7
    A/Rivne/214/09 ,30/10/2009,Siat4 , 9,2,4,7,4,4,6,7
    A/Belarus/119/09 ,02/11/2009,MDCK2/Siat1 , 8,0,6,6,6,6,6,6
    A/Lisboa/99/09 ,02/11/2009,MDCK2/Siat1 , 0,0,7,6,6,7,6,6
    A/Dnipropetrovsk/267/09 ,04/11/2009,MDCK1/Siat1 , 6,2,6,6,6,6,0,0
    A/Volin/226/09 ,05/11/2009,Siat3 , 8,3,7,7,6,6,5,7
    A/Bremen/20/09 ,16/11/2009,Siat3/Siat1 , 7,2,6,7,6,6,7,7
    A/Berlin/133/09 ,16/11/2009,Siat3/Siat1 , 9,2,5,7,5,5,7,7
    A/Sweden/25/09 ,16/11/2009,p2/SIAT1 , 0,0,6,6,6,7,6,7
    A/Neidersachsen/366/09 ,16/11/2009,Siat3/Siat1 , 6,3,6,7,6,7,5,6
    A/Brandenburg/55/09 ,17/11/2009,Siat3/Siat1 , 6,1,5,6,5,5,7,7
    A/Kosovo/275/09 ,18/11/2009,Siat3 , 0,0,7,6,6,7,6,7
    A/England/869/09 ,18/11/2009,Siat1/Siat1 , 0,0,4,5,4,4,7,6
    A/England/876/09 ,20/11/2009,Siat1/Siat1 , 0,0,4,5,4,4,5,5
    A/Sachsen/177/09 ,14/12/2009,Siat4/Siat1 , 0,0,5,7,6,6,7,6
    A/Albania/2385/09 ,18/12/2009,P1/SIAT1 , 0,0,7,6,6,7,6,7

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  • mixin
    started a topic Two Reports: Influenza Virus Characterization, WHO Vax Reports

    Two Reports: Influenza Virus Characterization, WHO Vax Reports

    These are both big reports put out this spring but they are full of charts, graphs showing antigenic sites. Seasonal H1N1, pandemic H1N1, H3N2...

    http://www.ecdc.europa.eu/en/publications/Publications/1001_Influenza_virus_characterisation_2010_JAN.pdf


    http://www.nimr.mrc.ac.uk/documents/about/interim_report_feb_2010.pdf


    From one of the .pdf's; I had trouble sizing it but it gives an idea of the type of charts that are included. It's on page 20 of the nimr .pdf for a better look. This is a list of viruses that had a >4-fold reduction against at least one ferret antiserum

    Click image for larger version Name: Low Reactor List pdf.jpg Views: 1 Size: 207.2 KB ID: 665213
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