Announcement

**gsgs** · January 25, 2014, 07:58 AM

Re: Sequences at Genbank!

44 human H1N1 , segment 4 from USA, Nov. and Dec. 2013

all have
C273T,G340A,T465C,A538C,A579G,G605C,T658A,
G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,
A1230G,A1386G,G1403A,C1408T,G1546A,T1653C

658,1408 are in Cancun (2009/04)
340,579,605,1056,1171,1386,1403 are in India/UK/Denmark/Ohio (Jan.2011)
273,898,966,1041,1546 are in India/Sep.2011 ... Washington Jul 2012
465,1158,1230 are in Washington,Jul.2012
538,817,1653 are in Pennsylvania,Nov.2012 , but together with 588,675,1683
without 588,675,1683 in India,Feb.2013 then Brazil, Apr.2013 , Florida Jun 2013

(A716G=D239G)

the other mutations have frequency:

Code:

 273  - 155   -:  1 C:269 T:155 
 465  -  67   C: 67 T:358 
 538  -  70   A:355 C: 64 G:6 
 817  -  62   A: 62 G:363 
 898  - 148   A:277 G:148 
 966  - 156   A:269 G:156 
1041  - 152   C:152 T:273 
1158  - 152   A:152 G:273 
1230  - 150   -:  1 A:274 G:150 
1546  - 156   -:  1 A:156 G:268 
1653  -  64   -:  9 C: 64 T:352

Code:

                                                  0000000000000000000000000000001111111111111111111111 
                                                  0000000122333445555556667788990000011111223333444556 
                                                  3334457667049061333790052319691145615779342889002465 
                                                  0473778873200856578945780878662716868131097066382633 
-codon-position----------------------------------- 1112     21    1 1  211  11  1      1   11  121 1   
---Index------------------------------------------TTGGAAGGACGGGGTAACAATGGTATGAACGGTTGTGGGTACTGAGGCCGGT 
   1 >A/******/index/2009/02/01                   ....................................................        0      0 ,      0      0       1:>A/******/index/2009/02/01                   
   2 >CY163495,A/Florida/3507/2013(H1N1)          .....T.T.T.A..C..TCG.C.A..AGGAA.CC..AA.CG...G.AT.A.C       30     26 ,     30     26       2:>CY163495,A/Florida/3507/2013(H1N1)          
   3 >CY163494,A/Alaska/3506/2013(H1N1)           .....T.T.T.A..C..TCG.C.A..AGGAA.CC..AA.CG...G.AT.A.C       27     26 ,     27     26       3:>CY163494,A/Alaska/3506/2013(H1N1)           
   4 >CY163475,A/Florida/3487/2013(H1N1)          ......A..T.A.AC...CG.C.A..AGG...CC..AA.CG...G.AT.A.C       25     23 ,     25     23       4:>CY163475,A/Florida/3487/2013(H1N1)          
   5 >CY163496,A/Texas/3508/2013(H1N1)            ....C.A..TAA.AC...CG.C.A..AGG...CC..AA.CG...G.AT.A.C       28     25 ,     28     25       5:>CY163496,A/Texas/3508/2013(H1N1)            
   6 >CY163483,A/Arkansas/3495/2013(H1N1)         ....C.A..T.A.AC...CG.C.A..AGG...CC..AA.CG...GAAT.A.C       29     25 ,     29     25       6:>CY163483,A/Arkansas/3495/2013(H1N1)         
   7 >CY163482,A/California/3494/2013(H1N1)       ..A......T.A..CG..CG.C.A..AGG...CC..AA..G...GAAT.A.C       28     23 ,     28     23       7:>CY163482,A/California/3494/2013(H1N1)       
   8 >CY163465,A/Mississippi/3477/2013(H1N1)      .........T.A..CG..CGCC.A..AGG...CC..AA..G...G.AT.AAC       25     23 ,     25     23       8:>CY163465,A/Mississippi/3477/2013(H1N1)      
   9 >CY163508,A/Texas/3520/2013(H1N1)            .C......GT.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       27     25 ,     27     25       9:>CY163508,A/Texas/3520/2013(H1N1)            
  10 >CY163484,A/Arkansas/3496/2013(H1N1)         .C......GT.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       26     25 ,     26     25      10:>CY163484,A/Arkansas/3496/2013(H1N1)         
  11 >CY163487,A/Louisiana/3499/2013(H1N1)        .C......GT.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       25     25 ,     25     25      11:>CY163487,A/Louisiana/3499/2013(H1N1)        
  12 >CY163498,A/Texas/3510/2013(H1N1)            .C......GT.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       26     25 ,     26     25      12:>CY163498,A/Texas/3510/2013(H1N1)            
  13 >CY163503,A/Texas/3515/2013(H1N1)            .........T.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       24     23 ,     24     23      13:>CY163503,A/Texas/3515/2013(H1N1)            
  14 >CY163507,A/Florida/3519/2013(H1N1)          .........T.A..C...CGCC.A.CAGG...CC..AA..G...G.AT.AAC       24     23 ,     24     23      14:>CY163507,A/Florida/3519/2013(H1N1)          
  15 >CY163499,A/Mississippi/3511/2013(H1N1)      .........T.A..C...CGCC.A..AGG...CC..AA..G...G.AT.AAC       22     22 ,     22     22      15:>CY163499,A/Mississippi/3511/2013(H1N1)      
  16 >CY163467,A/Florida/3479/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CC..AA..G...G.AT.A.C       23     21 ,     23     21      16:>CY163467,A/Florida/3479/2013(H1N1)          
  17 >CY163473,A/Florida/3485/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       22     22 ,     22     22      17:>CY163473,A/Florida/3485/2013(H1N1)          
  18 >CY163492,A/Georgia/3504/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CCACAA..G...G.AT.A.C       25     23 ,     25     23      18:>CY163492,A/Georgia/3504/2013(H1N1)          
  19 >CY163502,A/Colorado/3514/2013(H1N1)         .........T.A..C...CGCC.A..AGG...CCACAA..G...G.AT.A.C       24     23 ,     24     23      19:>CY163502,A/Colorado/3514/2013(H1N1)         
  20 >CY163497,A/Texas/3509/2013(H1N1)            .........T.A..C...CGCC.A..AGG...CCACAA..G...G.AT.A.C       25     23 ,     25     23      20:>CY163497,A/Texas/3509/2013(H1N1)            
  21 >CY163478,A/Utah/3490/2013(H1N1)             .........T.A..C...CGCC.A..AGG...CCACAA..G...G.AT.A.C       25     23 ,     25     23      21:>CY163478,A/Utah/3490/2013(H1N1)             
  22 >CY163476,A/Arkansas/3488/2013(H1N1)         .........T.A..C.C.CGCCAA..AGG...CCA.AA..G...G.AT.A.C       24     24 ,     24     24      22:>CY163476,A/Arkansas/3488/2013(H1N1)         
  23 >CY163481,A/South Dakota/3493/2013(H1N1)     .........T.A..C.C.CGCCAA..AGG...CCA.AA..G...G.AT.A.C       25     24 ,     25     24      23:>CY163481,A/South Dakota/3493/2013(H1N1)     
  24 >CY163491,A/Georgia/3503/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       24     22 ,     24     22      24:>CY163491,A/Georgia/3503/2013(H1N1)          
  25 >CY163489,A/Florida/3501/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       23     22 ,     23     22      25:>CY163489,A/Florida/3501/2013(H1N1)          
  26 >CY163486,A/North Carolina/3498/2013(H1N1)   .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       23     22 ,     23     22      26:>CY163486,A/North Carolina/3498/2013(H1N1)   
  27 >CY163469,A/Colorado/3481/2013(H1N1)         .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       23     22 ,     23     22      27:>CY163469,A/Colorado/3481/2013(H1N1)         
  28 >CY163480,A/Florida/3492/2013(H1N1)          .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       22     22 ,     22     22      28:>CY163480,A/Florida/3492/2013(H1N1)          
  29 >CY163479,A/California/3491/2013(H1N1)       .........TAA..C...CGCC.AG.AGG...CCA.AA..G...G.AT.A.C       24     24 ,     24     24      29:>CY163479,A/California/3491/2013(H1N1)       
  30 >CY163471,A/Florida/3483/2013(H1N1)          .........TAA..C...CGCC.AG.AGG...CCA.AA..G...G.AT.A.C       24     24 ,     24     24      30:>CY163471,A/Florida/3483/2013(H1N1)          
  31 >CY163488,A/Colorado/3500/2013(H1N1)         .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       24     22 ,     24     22      31:>CY163488,A/Colorado/3500/2013(H1N1)         
  32 >CY163477,A/Mississippi/3489/2013(H1N1)      .........T.A..C...CGCC.A..AGG...CCA.AA..G...G.AT.A.C       22     22 ,     22     22      32:>CY163477,A/Mississippi/3489/2013(H1N1)      
  33 >CY163485,A/North Carolina/3497/2013(H1N1)   .........T.A..C...CGCC.A..AGG...CCA.AA..G..AG.AT.A.C       23     23 ,     23     23      33:>CY163485,A/North Carolina/3497/2013(H1N1)   
  34 >CY163505,A/South Dakota/3517/2013(H1N1)     .........T.A..C...CG.C.A..AGG...CC..AA..G..AG.AT.A.C       21     21 ,     21     21      34:>CY163505,A/South Dakota/3517/2013(H1N1)     
  35 >CY163504,A/Louisiana/3516/2013(H1N1)        .........T.A..C...CG.C.A..AGG...CC..AA..G...G.AT.A.C       20     20 ,     20     20      35:>CY163504,A/Louisiana/3516/2013(H1N1)        
  36 >CY163490,A/Florida/3502/2013(H1N1)          ..A......T.A..C...CG.C.A..AGG...CC..AA..G...G.AT.A.C       22     21 ,     22     21      36:>CY163490,A/Florida/3502/2013(H1N1)          
  37 >CY163466,A/Georgia/3478/2013(H1N1)          .........T.A..C...CG.C.A..AGG...CC..AA..G...G.AT.A.C       22     20 ,     22     20      37:>CY163466,A/Georgia/3478/2013(H1N1)          
  38 >CY163470,A/Ohio/3482/2013(H1N1)             .........T.A..C...CG.C.A..AGG...CC..AA..G...G.AT.A.C       22     20 ,     22     20      38:>CY163470,A/Ohio/3482/2013(H1N1)             
  39 >CY163506,A/Mississippi/3518/2013(H1N1)      ...A.....T.A..C...CG.C.A..AGG...CC..AA..G...G.ATAA.C       22     22 ,     22     22      39:>CY163506,A/Mississippi/3518/2013(H1N1)      
  40 >CY163472,A/Alabama/3484/2013(H1N1)          ...A.....T.A..C...CG.C.A..AGG...CC..AA..G...G.ATAA.C       22     22 ,     22     22      40:>CY163472,A/Alabama/3484/2013(H1N1)          
  41 >CY163493,A/California/3505/2013(H1N1)       C........T.AA.C...CG.C.A..AGG..ACC..AAA.GTC.G.AT.A.C       27     26 ,     27     26      41:>CY163493,A/California/3505/2013(H1N1)       
  42 >CY163468,A/Oklahoma/3480/2013(H1N1)         C........T.AA.C...CG.C.A..AGG..ACC..AAA.GTC.G.AT.A.C       26     26 ,     26     26      42:>CY163468,A/Oklahoma/3480/2013(H1N1)         
  43 >CY163500,A/Texas/3512/2013(H1N1)            C........T.AA.C...CG.C.A..AGG..ACC..AAA.GTC.G.AT.AAC       27     27 ,     27     27      43:>CY163500,A/Texas/3512/2013(H1N1)            
  44 >CY163501,A/Texas/3513/2013(H1N1)            C........T.AA.C...CG.C.A..AGG..ACC..AAA.GTC.G.AT.A.C       26     26 ,     26     26      44:>CY163501,A/Texas/3513/2013(H1N1)            
  45 >CY163474,A/Virginia/3486/2013(H1N1)         C........T.AA.C...CG.C.A..AGGA.ACC..AAA.G.C.G.AT.A.C       27     26 ,     27     26      45:>CY163474,A/Virginia/3486/2013(H1N1)         
                                                                                                       
---Index------------------------------------------TTGGAAGGACGGGGTAACAATGGTATGAACGGTTGTGGGTACTGAGGCCGGT 
-codon-position----------------------------------- 1112     21    1 1  211  11  1      1   11  121 1   
                                                  0000000000000000000000000000001111111111111111111111 
                                                  0000000122333445555556667788990000011111223333444556 
                                                  3334457667049061333790052319691145615779342889002465 
                                                  0473778873200856578945780878662716868131097066382633

Code:

                                                                              00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111 
                                                                              00000001111112222233333333333333344444455555555555555666666666666677777777788888888899999000000011111112222333334444555555666666 
                                                                              01233444569991466700001111346788912566711123334478999000012224567911224557713667788903468112445822567793445056890019122346567888 
                                                                              86204134950236018323472358703589943025205657890398489357910120855056698194776571908803561126176025851310494522663866224963388036 
-codon-position---------------------------------------------------------------211 121   1 1   1 2 11 1  11  12      1 2   12     12 21 22 1112  12  11   121 1 1 1      1        11   21  2  121 2 1  1   1    
---Index----------------------------------------------------------------------CGCTTCGCGCGAGTACGCGTTGTGAGAGAGAGATCGTTGAGACCAAACATTTCTGGTAGTCGTGGAGAGACGGACGGGCGTATAGTCAATGATCTGGGGAGGTAACATCCAGGCCGAGGCGGTTCAGT 
   1 >A/******/index/2009/02/01                                               ................................................................................................................................        0      0 ,      0      0       1:>A/******/index/2009/02/01                                               
   2 >KF280663,A/India/P1114854/2011,2011/09/23,India,H1N1,Human,4            .................T.........A....................G.....C.......A....................G...G...GC.C.....A.........G.AT......A.......       16     15 ,     16     15       2:>KF280663,A/India/P1114854/2011,2011/09/23,India,H1N1,Human,4            

   7 >KC891213,A/Washington/34/2012,2012/07/30,USA,H1N1,Human,4               .............C...T.........A.........C..........G.....C.......A..............A.....G...G....C.C...A.A..G......G.AT......A.......       22     19 ,     22     19       7:>KC891213,A/Washington/34/2012,2012/07/30,USA,H1N1,Human,4               

  13 >KF647938,A/Pennsylvania/25/2012,2012/11/23,USA,H1N1,Human,4             .................T.........A.........C......C...GC....C.......A.A..........A.......G...G....C.C...A.A..G......G.AT......A.C...A.       23     23 ,     23     23      13:>KF647938,A/Pennsylvania/25/2012,2012/11/23,USA,H1N1,Human,4             

  80 >KF280743,A/India/P131845/2013,2013/02/15,India,H1N1,Human,4             .................T.........A.........C......C...G.....C.......A...A........A.......G...G....C.C...A.A..G......G.AT......A.C.....       28     21 ,     28     21      80:>KF280743,A/India/P131845/2013,2013/02/15,India,H1N1,Human,4             
  81 >KF280751,A/India/P132194/2013,2013/02/18,India,H1N1,Human,4             .................T.......A.A.........C......C...G.....C.......A....................G...G....C.C...A.A..G......G.AT......A.C.....       22     20 ,     22     20      81:>KF280751,A/India/P132194/2013,2013/02/18,India,H1N1,Human,4             
  92 >KF142475,A/Sao Paulo/15835/2013,2013/03/10,Brazil,H1N1,Human,4          .................T.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       22     22 ,     22     22      92:>KF142475,A/Sao Paulo/15835/2013,2013/03/10,Brazil,H1N1,Human,4          
  93 >KF648036,A/New Jersey/04/2013,2013/03/19,USA,H1N1,Human,4               .A.C.............T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT......A.C.....       22     22 ,     22     22      93:>KF648036,A/New Jersey/04/2013,2013/03/19,USA,H1N1,Human,4               
 102 >KF041891,A/Para/122682/2013,2013/04/09,Brazil,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       23     23 ,     23     23     102:>KF041891,A/Para/122682/2013,2013/04/09,Brazil,H1N1,Human,4              
 103 >KF041893,A/Para/122687/2013,2013/04/09,Brazil,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       23     23 ,     23     23     103:>KF041893,A/Para/122687/2013,2013/04/09,Brazil,H1N1,Human,4              
 104 >KF041892,A/Para/122686/2013,2013/04/09,Brazil,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A.AG......G.AT......A.C.....       32     24 ,     32     24     104:>KF041892,A/Para/122686/2013,2013/04/09,Brazil,H1N1,Human,4              
 106 >KF648196,A/North Carolina/07/2013,2013/04/09,USA,H1N1,Human,4           .................T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT...A..A.C.....       21     21 ,     21     21     106:>KF648196,A/North Carolina/07/2013,2013/04/09,USA,H1N1,Human,4           
 108 >KF151216,A/Sao Paulo/28426/2013,2013/04/11,Brazil,H1N1,Human,4          ....A............T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A.CG......G.AT......A.C.....       22     22 ,     22     22     108:>KF151216,A/Sao Paulo/28426/2013,2013/04/11,Brazil,H1N1,Human,4          
 109 >KF648164,A/Louisiana/05/2013,2013/04/11,USA,H1N1,Human,4                .................T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT...A..A.C.....       22     21 ,     22     21     109:>KF648164,A/Louisiana/05/2013,2013/04/11,USA,H1N1,Human,4                
 111 >KF151218,A/Sao Paulo/3-13108/2013,2013/04/13,Brazil,H1N1,Human,4        .................T.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       24     22 ,     24     22     111:>KF151218,A/Sao Paulo/3-13108/2013,2013/04/13,Brazil,H1N1,Human,4        
 113 >KF041894,A/Para/122805/2013,2013/04/15,Brazil,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       23     23 ,     23     23     113:>KF041894,A/Para/122805/2013,2013/04/15,Brazil,H1N1,Human,4              
 114 >KF151219,A/Sao Paulo/28683/2013,2013/04/15,Brazil,H1N1,Human,4          ...C.............T.........A.........C......C...G.....C.......A....G.......A.......GA..G....C.C...A.A..G......G.ATT.....A.C.....       24     24 ,     24     24     114:>KF151219,A/Sao Paulo/28683/2013,2013/04/15,Brazil,H1N1,Human,4          
 115 >KF151220,A/Sao Paulo/29229/2013,2013/04/15,Brazil,H1N1,Human,4          ...C.............T.........A.........C......C...G.....C.......A............A.......GA..G....C.C...A.A..G......G.ATT.....A.C.....       23     23 ,     23     23     115:>KF151220,A/Sao Paulo/29229/2013,2013/04/15,Brazil,H1N1,Human,4          
 119 >CY147209,A/Alabama/3317/2013,2013/04/19,USA,H1N1,Human,4                .................T.........A.........C......C...G.....C.......A............A.A.....G...G....C.C...A.A..G...C..G.AT..C...A.C.....       26     23 ,     26     23     119:>CY147209,A/Alabama/3317/2013,2013/04/19,USA,H1N1,Human,4                
 120 >KF151221,A/Sao Paulo/12-7118/2013,2013/04/27,Brazil,H1N1,Human,4        .................T.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C..AA.A..G......G.AT......A.C.....       23     23 ,     23     23     120:>KF151221,A/Sao Paulo/12-7118/2013,2013/04/27,Brazil,H1N1,Human,4        
 129 >KF648221,A/Wisconsin/09/2013,2013/05/24,USA,H1N1,Human,4                .................T.......A.A.........C......C...G.....C.......A............A.......GT..G....C.C...A.A..G......G.AT......A.C.....       25     22 ,     25     22     129:>KF648221,A/Wisconsin/09/2013,2013/05/24,USA,H1N1,Human,4                
 132 >KF648022,A/Florida/18/2013,2013/06/15,USA,H1N1,Human,4                  .................T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT.A....A.C.....       23     21 ,     23     21     132:>KF648022,A/Florida/18/2013,2013/06/15,USA,H1N1,Human,4                  
 133 >KF647939,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4                  ........T........T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT......A.C.....       21     21 ,     21     21     133:>KF647939,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4                  
 134 >KF647949,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4                  ........T........T.........A.........C......C...G.....C.......A....G.......A.......G...G....C.C...A.A..G......G.AT......A.C.....       22     22 ,     22     22     134:>KF647949,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4                  
 136 >KF647985,A/Kentucky/05/2013,2013/06/27,USA,H1N1,Human,4                 .................T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G.T....G.AT......A.C.....       23     21 ,     23     21     136:>KF647985,A/Kentucky/05/2013,2013/06/27,USA,H1N1,Human,4                 
 138 >KF647957,A/Florida/19/2013,2013/07/02,USA,H1N1,Human,4                  .................T.........A.........C......C...G.....C.......A............A.......G..TG....C.C...A.A..G......G.AT......A.C.....       21     21 ,     21     21     138:>KF647957,A/Florida/19/2013,2013/07/02,USA,H1N1,Human,4                  
 139 >KF648044,A/Indiana/12/2013,2013/07/03,USA,H1N1,Human,4                  ............T....T.........A.........C......C...G.C...C.......A............A.......G...G....C.C...A.A..G.....TG.AT......A.C.....       23     23 ,     23     23     139:>KF648044,A/Indiana/12/2013,2013/07/03,USA,H1N1,Human,4                  
 140 >KF648018,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       23     23 ,     23     23     140:>KF648018,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4              
 141 >KF648021,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4              ................TT.........A.........C.G....C...G.....C.....M.A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       25     24 ,     25     24     141:>KF648021,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4              
 143 >KF648015,A/South Carolina/01/2013,2013/07/10,USA,H1N1,Human,4           .................T.........A.........C.G....C...G.....C.......A.......T....A.......G...G....C.C...A.A..G......G.AT......A.C.....       24     22 ,     24     22     143:>KF648015,A/South Carolina/01/2013,2013/07/10,USA,H1N1,Human,4           
 145 >KF648052,A/Indiana/20/2013,2013/07/15,USA,H1N1,Human,4                  ............T....T.........A.........C......C...G.C...C.......A............A.......G...G....C.C...A.A..G.....TG.AT......A.C.....       23     23 ,     23     23     145:>KF648052,A/Indiana/20/2013,2013/07/15,USA,H1N1,Human,4                  
 146 >KF648129,A/Texas/13/2013,2013/07/21,USA,H1N1,Human,4                    .................T.........A.........C......C...GC....C.......A.A..........A.......G...G....C.C...A.A..G......G.AT......A.C...A.       25     23 ,     25     23     146:>KF648129,A/Texas/13/2013,2013/07/21,USA,H1N1,Human,4                    
 147 >KF648085,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4                   ...............T.T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.AACG......G.AT.....TA.C.....       24     24 ,     24     24     147:>KF648085,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4                   
 148 >KF648120,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4                   ...............T.T.........A.........C......C...G..Y..C.....M.A............A.......G...G....C.C...A.AACG......G.AT.....TA.C.....       26     26 ,     26     26     148:>KF648120,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4                   
 150 >KF648080,A/North Carolina/08/2013,2013/07/24,USA,H1N1,Human,4           ...............T.T.........A.........C......C...G.....C.......A...A........A.......G...G....C.C...A.A.CG......G.AT.....TA.C.....       25     24 ,     25     24     150:>KF648080,A/North Carolina/08/2013,2013/07/24,USA,H1N1,Human,4           
 152 >KF648118,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4                ...........G.....T.........A.........C......C...G.....C.......A............A...A...G...G....C.C...A.A..G......G.AT....A.A.C.....       23     23 ,     23     23     152:>KF648118,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4                
 153 >KF648128,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4                ...........G.....T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT....A.A.C.....       22     22 ,     22     22     153:>KF648128,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4                
 154 >KF648169,A/California/24/2013,2013/08/08,USA,H1N1,Human,4               .................T.........A.........C......C...G.....C.......A............A.......G...G....C.C...A.A..G......G.AT......A.C.....       21     20 ,     21     20     154:>KF648169,A/California/24/2013,2013/08/08,USA,H1N1,Human,4               
 156 >KF648172,A/Texas/15/2013,2013/08/15,USA,H1N1,Human,4                    ......A..........TA........A.........C......C...G.....C.......A...........TA..T....G...G....C.C...A.A..G......G.AT......A.C.....       28     24 ,     28     24     156:>KF648172,A/Texas/15/2013,2013/08/15,USA,H1N1,Human,4                    
                                                                                                                                                                                                               
---Index----------------------------------------------------------------------CGCTTCGCGCGAGTACGCGTTGTGAGAGAGAGATCGTTGAGACCAAACATTTCTGGTAGTCGTGGAGAGACGGACGGGCGTATAGTCAATGATCTGGGGAGGTAACATCCAGGCCGAGGCGGTTCAGT 
-codon-position---------------------------------------------------------------211 121   1 1   1 2 11 1  11  12      1 2   12     12 21 22 1112  12  11   121 1 1 1      1        11   21  2  121 2 1  1   1    
                                                                              00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111 
                                                                              00000001111112222233333333333333344444455555555555555666666666666677777777788888888899999000000011111112222333334444555555666666 
                                                                              01233444569991466700001111346788912566711123334478999000012224567911224557713667788903468112445822567793445056890019122346567888 
                                                                              86204134950236018323472358703589943025205657890398489357910120855056698194776571908803561126176025851310494522663866224963388036

and when centered to the new 2013f-USA-H1-index:

Code:

                                                            0000000000000000000000000000000001111111111111111111 
                                                            0000001112223334555555667777788990011123333444555556 
                                                            3334475996660190113369021123416091617942689129022365 
                                                            0473789231782808065884725608875067863197206627624933 
-codon-position--------------------------------------------- 1112   1  12     111 1112  111       11  1    1     
---Index----------------------------------------------------TTGGAGGAGCAGGGGGAAACGTGCGAATCAGGCGGTGTCTCGGCCGCGGCGC 
   1 >Index-H1N1-USA-2013f/                                 .................................................... 
   2 >A/******/index/2009/02/01                             ...................A.........G.....................T 
   3 >CY147203,A/California/3311/2013,2013/01/29,USA        ...................AA........G.....................T 
   4 >KC891213,A/Washington/34/2012,2012/07/30,USA          ...................A.........GA...............A....T 
   5 >KF280751,A/India/P132194/2013,2013/02/18,India        .............A...............G...................... 
   6 >KF648221,A/Wisconsin/09/2013,2013/05/24,USA           .............A.................T.................... 
   7 >KF151218,A/Sao Paulo/3-13108/2013,2013/04/13,Brazil   ................G...........T....................... 
   8 >KF648015,A/South Carolina/01/2013,2013/07/10,USA      ................G...........T....................... 
   9 >KF041893,A/Para/122687/2013,2013/04/09,Brazil         ...........T....G...........T....................... 
  10 >KF648021,A/Connecticut/02/2013,2013/07/06,USA         ...........T....G......M....T....................... 
  11 >KF648018,A/Connecticut/02/2013,2013/07/06,USA         ...........T....G...........T....................... 
  12 >KF041892,A/Para/122686/2013,2013/04/09,Brazil         ...........T....G...........T........A.............. 
  13 >KF041891,A/Para/122682/2013,2013/04/09,Brazil         ...........T....G...........T....................... 
  14 >KF041894,A/Para/122805/2013,2013/04/15,Brazil         ...........T....G...........T....................... 
  15 >KF151221,A/Sao Paulo/12-7118/2013,2013/04/27,Brazil   ................G...........T....................... 
  16 >KF142475,A/Sao Paulo/15835/2013,2013/03/10,Brazil     ................G...........T....................... 
  17 >KF648022,A/Florida/18/2013,2013/06/15,USA             .................................................... 
  18 >CY147209,A/Alabama/3317/2013,2013/04/19,USA           ....C.........................A..................... 
  19 >CY163496,A/Texas/3508/2013                            ....CA......A..A.....................C.............. 
  20 >CY163483,A/Arkansas/3495/2013                         ....CA.........A.....................C....A......... 
  21 >CY163475,A/Florida/3487/2013                          .....A.........A.....................C.............. 
  22 >CY163494,A/Alaska/3506/2013                           ................................A....C.............. 
  23 >KF151216,A/Sao Paulo/28426/2013,2013/04/11,Brazil     .A...................................C.............. 
  24 >KF648080,A/North Carolina/08/2013,2013/07/24,USA      .........T..............A............C...........T.. 
  25 >KF648120,A/Nevada/06/2013,2013/07/23,USA              .........T.............M............AC...........T.. 
  26 >KF648085,A/Nevada/06/2013,2013/07/23,USA              .........T..........................AC...........T.. 
  27 >CY163474,A/Virginia/3486/2013                         C.............A.................AA..A..C............ 
  28 >CY163500,A/Texas/3512/2013                            C.............A..................A..A.TC..........A. 
  29 >CY163501,A/Texas/3513/2013                            C.............A..................A..A.TC............ 
  30 >CY163493,A/California/3505/2013                       C.............A..................A..A.TC............ 
  31 >CY163468,A/Oklahoma/3480/2013                         C.............A..................A..A.TC............ 
  32 >KF648036,A/New Jersey/04/2013,2013/03/19,USA          C................................................... 
  33 >KF151220,A/Sao Paulo/29229/2013,2013/04/15,Brazil     C..............................A...........T........ 
  34 >KF151219,A/Sao Paulo/28683/2013,2013/04/15,Brazil     C........................G.....A...........T........ 
  35 >KF647949,A/Florida/16/2013,2013/06/19,USA             ......T..................G.......................... 
  36 >KF647939,A/Florida/16/2013,2013/06/19,USA             ......T............................................. 
  37 >KF648172,A/Texas/15/2013,2013/08/15,USA               ...A........A................................A...... 
  38 >CY163506,A/Mississippi/3518/2013                      ...A........................................A....... 
  39 >CY163472,A/Alabama/3484/2013                          ...A........................................A....... 
  40 >KF648169,A/California/24/2013,2013/08/08,USA          ..A................................................. 
  41 >CY163490,A/Florida/3502/2013                          ..A................................................. 
  42 >CY163482,A/California/3494/2013                       ..A..............G........................A...A..... 
  43 >CY163465,A/Mississippi/3477/2013                      .................G...C............................A. 
  44 >CY163499,A/Mississippi/3511/2013                      .....................C............................A. 
  45 >CY163508,A/Texas/3520/2013                            .C.......AG..........C.....C......................A. 
  46 >CY163498,A/Texas/3510/2013                            .C........G..........C.....C......................A. 
  47 >CY163487,A/Louisiana/3499/2013                        .C........G..........C.....C......................A. 
  48 >CY163484,A/Arkansas/3496/2013                         .C........G..........C.....C......................A. 
  49 >CY163503,A/Texas/3515/2013                            .....................C.....C......................A. 
  50 >CY163507,A/Florida/3519/2013                          .....................C.....C......................A. 
  51 >CY163473,A/Florida/3485/2013                          .....................C............A................. 
  52 >CY163486,A/North Carolina/3498/2013                   .....................C............A................. 
  53 >CY163469,A/Colorado/3481/2013                         .....................C............A................. 
  54 >CY163489,A/Florida/3501/2013                          .....................C............A................. 
  55 >CY163480,A/Florida/3492/2013                          .....................C............A................. 
  56 >CY163485,A/North Carolina/3497/2013                   .....................C............A......A.......... 
  57 >CY163477,A/Mississippi/3489/2013                      .....................C............A................. 
  58 >CY163491,A/Georgia/3503/2013                          .....................C............A................. 
  59 >CY163488,A/Colorado/3500/2013                         .....................C............A................. 
  60 >CY163471,A/Florida/3483/2013                          ............A........C....G.......A................. 
  61 >CY163479,A/California/3491/2013                       ............A........C....G.......A................. 
  62 >CY163481,A/South Dakota/3493/2013                     ..................C..CA...........A................. 
  63 >CY163476,A/Arkansas/3488/2013                         ..................C..CA...........A................. 
  64 >CY163497,A/Texas/3509/2013                            .....................C............AC.........A...... 
  65 >CY163478,A/Utah/3490/2013                             .....................C............AC................ 
  66 >CY163502,A/Colorado/3514/2013                         .....................C............AC................ 
  67 >CY163492,A/Georgia/3504/2013                          ....................AC............AC................ 
  68 >CY163467,A/Florida/3479/2013                          .....................C.............................. 
  69 >KF648052,A/Indiana/20/2013,2013/07/15,USA             ........T............C..................T........... 
  70 >KF648044,A/Indiana/12/2013,2013/07/03,USA             ........T............C..................T........... 
  71 >CY163504,A/Louisiana/3516/2013                        .................................................... 
  72 >CY163466,A/Georgia/3478/2013                          .................................................... 
  73 >CY163470,A/Ohio/3482/2013                             .................................................... 
  74 >KF647985,A/Kentucky/05/2013,2013/06/27,USA            ......................................T............. 
  75 >KF647957,A/Florida/19/2013,2013/07/02,USA             .................................................... 
  76 >CY163505,A/South Dakota/3517/2013                     .........................................A.......... 
  77 >KF648164,A/Louisiana/05/2013,2013/04/11,USA           ...............................................A.... 
  78 >KF648196,A/North Carolina/07/2013,2013/04/09,USA      ...............................................A.... 
  79 >KF648128,A/Wisconsin/12/2013,2013/08/04,USA           .......G........................................A... 
  80 >KF648118,A/Wisconsin/12/2013,2013/08/04,USA           .......G........................................A... 
  81 >KF280743,A/India/P131845/2013,2013/02/15,India        ........................A........................... 
                                                                                                                 
---Index----------------------------------------------------TTGGAGGAGCAGGGGGAAACGTGCGAATCAGGCGGTGTCTCGGCCGCGGCGC 
-codon-position--------------------------------------------- 1112   1  12     111 1112  111       11  1    1     
                                                            0000000000000000000000000000000001111111111111111111 
                                                            0000001112223334555555667777788990011123333444555556 
                                                            3334475996660190113369021123416091617942689129022365 
                                                            0473789231782808065884725608875067863197206627624933

**gsgs** · August 22, 2014, 07:59 AM

Re: Sequences at Genbank!

update 2014 , accumulation of mutations over time

I assume that most pixels=genomes that fall outside the corridor
have sequencing errors

the 2014 genomes (Helsinki) are reassorted, thet got a new old segment 3 (PA) from ~2010,
still the India/UK strain

earliest from that strain is TN/F1024A/2010/02/04,2f with 64 mutations --> the date could be wrong

this one : http://www.ncbi.nlm.nih.gov/nuccore/KF560214
Helsinki from 2013
is very similar to the CA/07 vaccine strain

Attached Files

**gsgs** · September 2, 2014, 10:30 AM

Re: Sequences at Genbank!

delete

**gsgs** · March 20, 2015, 03:53 PM

http://magictour.free.fr/MEXFLUG5.GIF

high mutation rate, human H3N2 currently has ~150 mutations in 5 years

**Emily** · March 20, 2015, 05:32 PM

Thanks, gsgs. So it is pH1N1 at 200 vs H3N2 at 150.

**gsgs** · June 29, 2016, 02:56 AM

https://www.sciencedaily.com/releases/2016/06/160627160935.htm

> originated in pigs from a very small region in central Mexico

Mount Siani, journal eLife, Adolfo Garc?a-Sastre, Irene and Dr. Arthur M. Fishberg

Researchers used state-of-the-art genetic analysis to identify the precise location and the
main molecular transformations

circulated for more than 10 years in pigs in Mexico before jumping into humans.

swine Mexican isolates found in this study.

obtained 58 whole-genome sequences from influenza A viruses collected in the Mexican pigs
and found viral sequences previously not known to exist in Mexico or in any other part of the world.

the parent strains still exist in the pigs there today.

Journal Reference:
1.Ignacio Mean, Martha I Nelson, Francisco Quezada-Monroy, Jayeeta Dutta,
Refugio Cortes-Fern?ndez, J Horacio Lara-Puente, Felipa Castro-Peralta,
Luis F Cunha, N?dia Sequeira Trov?o, Bernardo Lozano-Dubernard,
Andrew Rambaut, Harm van Bakel, Adolfo Garc?a-Sastre. Origins of the
2009 H1N1 influenza pandemic in swine in Mexico. eLife, 2016; 5 DOI: 10.7554/eLife.16777

--------------------------------------------------------
Cite This Page:
MLAAPAChicago The Mount Sinai Hospital / Mount Sinai School of Medicine.
"2009 swine flu pandemic originated in Mexico, researchers discover."
ScienceDaily. ScienceDaily, 27 June 2016.
<www.sciencedaily.com/releases/2016/06/160627160935.htm>.

40-pages .pdf here: https://elifesciences.org/content/5/e16777-download.pdf

[this should have been done in 2009 ]

**gsgs** · June 29, 2016, 03:52 AM

lack of any complete swIAV genomes from Mexico?s large swine populations
at the start of the pandemic,

the majority of swIAVs in previous analyses were collected in northern and eastern Mexico,
and no studies to date have included viruses from major swine-producing states in central Mexico,

samples from Sonora,Yucatan,Puebla,Jalisco,Guanajuato,Aguascali entes

(sequence accession numbers are available in the Dryad data repository under DOI: 10.5061/dryad.m550m)

viral introductions from US and European swine into Mexico have occurred periodically for
at least two decades

live swine imports into Mexico also were reported from several European countries during the
late 1990s, including the United Kingdom and Denmark

"genotype 1"

Guanajuato most closely to pdmH1N1 in PB2, PB1, H1,N1,NP
Jalisco in PA,MP,NP

highest in Mexico City (0.81), consistent with an origin of the pandemic outbreak in Mexico?s capital city

2010 (1), 2011 (6), 2012 (34), 2013 (14), 2014 (3)
All samples came from large commercial facilities

GenBank accession numbers of the 58 genomes are available in the Dryad data repository
under DOI: 10.5061/dryad.m550m

A large number of whole-genome sequences from swIAVs in European swine were published
by Watson et al., (Watson et al., 2015) after we completed our analysis.

We excluded nine triple reassortant Mexican swIAVs (e.g., A/swine/Mexico/Mex19/2010(H1N1),
Figure 3--figure supplement 1) that had shorter branch lengths than expected given their year of
sampling, an indication of possible errors in sequencing or assembly.

Figure 2. 12 genotypes in Mexican swine herds during 2010-2014.

I didn't find anything at "datadryad"
However, when the sequences are uploaded to genbank, I'll probably notice that.

Announcement

Sequences at Genbank!

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