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3 BP Deletion in Donkey H5N1

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Mon Apr 19, 2010 1:33 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

is there a list of profiles or pairwise distances in profiles ?

> This combination leaves no doubt that the 3 BP deletion was acquired via recombination.

I think most people have lots of doubt here.

all H5N1 in Egypt is Qinghai, how should Shanxi-polymorphisms come to Egypt

I'm currently not so happy with the grouping algorithm

here is another grouping, which seems to be better for small files:

Code:

                                             00000000000000000000000000000000000000000000000000000011111111111111111111111111111111 
                                             00000112222223344444555555555666666666777777888888999900000011222233333444444445555666 
                                             23499371224462905669000145678001566789113567246678338901115639355848899003456792679015 
                                             77503856250911979892018292838128136679162184292795362964680577323716958781054741359548 
-codon-position------------------------------ 1    1        2  1 2 12  1  12    1   2 1    1     1 1 21     12       1    1       2 
---Index-------------------------------------ACAGGAGTTACTCCCGCATATCGACCGGTGCCGACGATGGCTCGGTGCGACTGCAAGGATGCTAAGCGCCCACGTGCGAGAAGTAT 
   1 >A/Ck/Egypt/06553-NLQP,2006/03/21       ......................................................................................        0      0 ,      0      0       1:>A/Ck/Egypt/06553-NLQP,2006/03/21       
   2 >A/Ck/Egypt/092-NLQP,2009/01            ......A.C..C.T.A....C......A...T..............A..G...............................G....       11     11 ,     11     11       2:>A/Ck/Egypt/092-NLQP,2009/01            
   3 >A/Gs/Egypt/0910sm-NLQP,2009/01         ......A.C..C.T.A....C......A...T..............A..G...............................G....       12     11 ,     12     11       3:>A/Gs/Egypt/0910sm-NLQP,2009/01         
   4 >A/Dk/Egypt/0821S-NLQP,2008/08/25       ......A.C..C.T.A....C......A...T..............A..G...............................G....       17     11 ,     12     11       4:>A/Dk/Egypt/0821S-NLQP,2008/08/25       
   5 >A/Dk/Egypt/09332sm-NLQP,2009/05        ....A.A.CC.C.T.A....C......A...T.................G.........................A.....G...-       23     14 ,     15     13       5:>A/Dk/Egypt/09332sm-NLQP,2009/05        
   6 >A/Ck/Egypt/0945-NLQP,2009/03           ......A.C..C.T.A....C......A...T.................G...........T......T.........G..G....       13     13 ,     13     13       6:>A/Ck/Egypt/0945-NLQP,2009/03           
   7 >A/Egypt/N03228,2009/03/30              ..G...A.C..C.T.A.G..C...A..A...T......AA.......T.G.C................T..........T.G....       19     19 ,     19     19       7:>A/Egypt/N03228,2009/03/30              
   8 >A/Egypt/N03272,2009/04/01              ..G...A.C..C.T.A.G..C...A..A...T......A........T.G.C................T..........T.G....       19     18 ,     19     18       8:>A/Egypt/N03272,2009/04/01              
   9 >A/Egypt/N02407,2009/03/09              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       16     13 ,     16     13       9:>A/Egypt/N02407,2009/03/09              
  10 >A/Egypt/N04395,2009/05/13              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       13     13 ,     13     13      10:>A/Egypt/N04395,2009/05/13              
  11 >A/Egypt/N04396,2009/05/17              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       16     13 ,     16     13      11:>A/Egypt/N04396,2009/05/17              
  12 >A/Egypt/N03439,2009/04/18              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       13     13 ,     13     13      12:>A/Egypt/N03439,2009/04/18              
  13 >A/Gs/Egypt/09324sm-NLQP,2009/04        ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       14     13 ,     14     13      13:>A/Gs/Egypt/09324sm-NLQP,2009/04        
  14 >A/Egypt/N02039,2009/03/03              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       14     13 ,     14     13      14:>A/Egypt/N02039,2009/03/03              
  15 >A/Dk/Egypt/0918-NLQP,2009/02           ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       13     13 ,     13     13      15:>A/Dk/Egypt/0918-NLQP,2009/02           
  16 >A/Egypt/N01310,2009/02/28              ..G...A.C..C.T.A....C......A...T......A..........G..................T............G....       14     13 ,     14     13      16:>A/Egypt/N01310,2009/02/28              
  17 >A/Ck/Egypt/0987alb-NLQP,2009/05/12     G.G...A.C..C.T.A....C......A...T......A..........G....G.............T............G....       18     15 ,     15     15      17:>A/Ck/Egypt/0987alb-NLQP,2009/05/12     
  18 >A/Ck/Egypt/0987-NLQP,2009/05/12        ..G...A.C..C.T.A....C......A...T......A..........G....G.............T............G....       16     14 ,     16     14      18:>A/Ck/Egypt/0987-NLQP,2009/05/12        
  19 >A/Dk/Egypt/09274sm-NLQP,2009/04        ..G...A.C..C.T.A....C......A...T......A..........G..................T....A.......G....       23     14 ,     16     14      19:>A/Dk/Egypt/09274sm-NLQP,2009/04        
  20 >A/Ck/Egypt/09485s-NLQP,2009/05         ..G...A.C..C.T.A....C.A....A...T......A..........G..................T............G...-       22     15 ,     14     14      20:>A/Ck/Egypt/09485s-NLQP,2009/05         
  21 >A/Egypt/N00605,2009/02/03              ......A.C..C.T.A....C.A....A...T.............C...G..................T............G....       14     13 ,     14     13      21:>A/Egypt/N00605,2009/02/03              
  22 >A/Egypt/N03438,2009/04/16              ......A.C..C.T.A....C......A...T.................G..................T............G....       15     11 ,     15     11      22:>A/Egypt/N03438,2009/04/16              
  23 >A/Ck/Egypt/0894-NLQP,2008/11/27        ......A.C..C.T.A....C......A...T.................G..................T............G....       11     11 ,     11     11      23:>A/Ck/Egypt/0894-NLQP,2008/11/27        
  24 >A/Dk/Egypt/0972-NLQP,2009/04           ......A.C..C.T.A....C......A...T.................G..................T............G....       13     11 ,     13     11      24:>A/Dk/Egypt/0972-NLQP,2009/04           
  25 >A/Dk/Egypt/093-NLQP,2009/01            ......A.C..CTT.A..C.C......A...T.................G...............................G...-       20     13 ,     12     12      25:>A/Dk/Egypt/093-NLQP,2009/01            
  26 >A/Egypt/N00001,2009/01/11              ......A.C..CTT.A..C.C......A...T.................G...............................G....       14     12 ,     14     12      26:>A/Egypt/N00001,2009/01/11              
  27 >A/Gs/Egypt/0929-NLQP,2009/02           ...A..A.C..C.T......C......A...T.................G...............................G....       11     10 ,     11     10      27:>A/Gs/Egypt/0929-NLQP,2009/02           
  28 >A/Dk/Egypt/0967smf-NLQP,2009/02        ......A.C..C.T.A....C......A...T.................G...............................G....       16     10 ,     13     10      28:>A/Dk/Egypt/0967smf-NLQP,2009/02        
  29 >A/Gs/Egypt/09102smf-NLQP,2009/03       -.....A.C..C.T.A....C......A...T................AG...............................G....       21     12 ,     16     11      29:>A/Gs/Egypt/09102smf-NLQP,2009/03       
  30 >A/Ck/Egypt/0896-NLQP,2008/12/24        ......ACC..C.T.A....C.....AA...T................AG........G......................G....       15     14 ,     15     14      30:>A/Ck/Egypt/0896-NLQP,2008/12/24        
  31 >A/Dk/Egypt/09315s-NLQP,2009/04         --....ACC..C.T.AT...C.....AA...T.................G...T...............T...........G....       25     17 ,     19     15      31:>A/Dk/Egypt/09315s-NLQP,2009/04         
  32 >A/Dk/Egypt/0926-NLQP,2009/02           ......A....C.T.A....C......A...T...........A.....G...............................G...C       14     11 ,     14     11      32:>A/Dk/Egypt/0926-NLQP,2009/02           
  33 >A/Egypt/2629-NAMRU3,2007/              ---...A......T.A....C......A...T.................G...............................G....       17     11 ,      8      8      33:>A/Egypt/2629-NAMRU3,2007/              
  34 >A/Egypt/2621-NAMRU3,2007/              ......A......T.A....C......A...T.................G...............................G....        8      8 ,      8      8      34:>A/Egypt/2621-NAMRU3,2007/              
  35 >A/Egypt/0636-NAMRU3,2007/01            ......A......T.A....C......A.....................G......................T........G....       10      8 ,     10      8      35:>A/Egypt/0636-NAMRU3,2007/01            
  36 >A/Ck/Egypt/9400NAMRU3-CLEVB211,2007/   ....A.A......T.A....C.....................T......G...............................G....       15      8 ,     15      8      36:>A/Ck/Egypt/9400NAMRU3-CLEVB211,2007/   
  37 >A/Egypt/1394-NAMRU3,2007/              ...A..A......T.A....C..................R.........G...............................G...C       12      9 ,     12      9      37:>A/Egypt/1394-NAMRU3,2007/              
  38 >A/Egypt/2289-NAMRU3,2008/03/02         ---...A...T..T.A....C..................T.........G.....G...........A........TA...G....       22     15 ,     13     12      38:>A/Egypt/2289-NAMRU3,2008/03/02         
  39 >A/Egypt/2546-NAMRU3,2008/03/08         ---...A...T..T.A....C..................A.........G.....G...........A........T...GG....       24     15 ,     15     12      39:>A/Egypt/2546-NAMRU3,2008/03/08         
  40 >A/Ck/Egypt/0847-NLQP,2008/01/18        ......A......T.A....C............................G............................G..G....       15      7 ,     15      7      40:>A/Ck/Egypt/0847-NLQP,2008/01/18        
  41 >A/Egypt/2631-NAMRU3,2007/              ---...A.....TT.A....C............................G....................T..........G....       18     11 ,      9      8      41:>A/Egypt/2631-NAMRU3,2007/              
  42 >A/Ck/Egypt/R2,2007/01/01               ......A......T.A....C....T..................A....G....................T..........G....       18      9 ,     18      9      42:>A/Ck/Egypt/R2,2007/01/01               
  43 >A/Dk/Egypt/R5,2007/02/20               ......A......T.A....C............G...............G....................T..........G....       11      8 ,     11      8      43:>A/Dk/Egypt/R5,2007/02/20               
  44 >A/Gs/Egypt/R4,2007/02/01               ......A......T.A...GC...................T........GT......A....A.......T.........GG....       15     13 ,     15     13      44:>A/Gs/Egypt/R4,2007/02/01               
  45 >A/Ck/Egypt/R3,2007/02/01               ......A......T.A...GC............G......T........GT...........A..................G....       12     11 ,     12     11      45:>A/Ck/Egypt/R3,2007/02/01               
  46 >A/Ck/Egypt/R6,2007/02/26               .G....A......T.A....C..........T.GT.........A....GT......A............................       24     12 ,     24     12      46:>A/Ck/Egypt/R6,2007/02/26               
  47 >A/Dk/Egypt/09349S-NLQP,2009/04         -----.A....C.T.A....C......A...TA...T....C.......G..A............A...........A...G....       39     20 ,     18     15      47:>A/Dk/Egypt/09349S-NLQP,2009/04         
  48 >A/Egypt/N04394,2009/05/11              ......A....C.T.A....C......A...TA...T....C.A.....G..A............A...............G....       19     15 ,     19     15      48:>A/Egypt/N04394,2009/05/11              
  49 >A/Egypt/N02752,2009/03/24              ......A....C.T.A....C......A...T...A.....CT......G...A.....CT..........GT........G....       19     17 ,     19     17      49:>A/Egypt/N02752,2009/03/24              
  50 >A/Egypt/N00606,2009/02/07              ......A......T.A.G..C......A...T...A.............G...A.....CT..........GT........GT...       18     16 ,     18     16      50:>A/Egypt/N00606,2009/02/07              
  51 >A/Dk/Egypt/093L-NLQP,2009/02           ......A......T.AT...C....T.A...T...A.............G...A.....CT..........GTA.......GT.G.       20     19 ,     20     19      51:>A/Dk/Egypt/093L-NLQP,2009/02           
  52 >A/Ck/Egypt/092L-NLQP,2009/02           ......A..G...T.A....C....T.A...T...A.............G...A.....CT..........GTA.......GT.G.       19     19 ,     19     19      52:>A/Ck/Egypt/092L-NLQP,2009/02           
  53 >A/Dk/Egypt/0912-NLQP,2009/02           ......A..G...T.A....C....T.A...T...A.............G...A.....CT..........GTA.......GT.G.       19     19 ,     19     19      53:>A/Dk/Egypt/0912-NLQP,2009/02           
  54 >A/Dk/Egypt/0930smL-NLQP,2009/02        ......A......T.A....C......A...T...A.............G...A.....CT........T.GT........G....       20     15 ,     20     15      54:>A/Dk/Egypt/0930smL-NLQP,2009/02        
  55 >A/Egypt/N05056,2009/06/06              .....GA......T.A....C......A...T...A.C...........G...A.....CT..........GT........G....       22     16 ,     22     16      55:>A/Egypt/N05056,2009/06/06              
  56 >A/Dk/Egypt/0970-NLQP,2009/04           .....GA......T.A....C.A....A...T...A.C.......C...G...A.....CT..........GT........G....       20     18 ,     20     18      56:>A/Dk/Egypt/0970-NLQP,2009/04           
  57 >A/Egypt/N03450,2009/04/19              ......A......T.A....CAA....A.A.T...A.............G.C.A..A..CT..........GT........G....       21     19 ,     21     19      57:>A/Egypt/N03450,2009/04/19              
  58 >A/Egypt/N04527,2009/05/18              ......A......T.A....CA.....A.A.T...A.............G.C.A..A..CT..........GT........G....       19     18 ,     19     18      58:>A/Egypt/N04527,2009/05/18              
  59 >A/Dk/Egypt/0969smL-NLQP,2009/05        ......A......T.A....CA.....ACA.T...A.............G...A..A..CTT.........GT........G....       19     19 ,     19     19      59:>A/Dk/Egypt/0969smL-NLQP,2009/05        
  60 >A/equine/Egypt/av1,2009/03/24          ......A.C..C.T.A....C......ACA.T.GT..............G................T..............G....       21     15 ,     21     15      60:>A/equine/Egypt/av1,2009/03/24          
  61 >A/Dk/Egypt/0945smf-NLQP,2009/02        -.....A.C..C.T.A....C......A.A.T.................G................T..............G...-       25     14 ,     13     12      61:>A/Dk/Egypt/0945smf-NLQP,2009/02        
  62 >A/Ck/Egypt/0910-NLQP,2009/01           G.....A....C.T.A....C......A...T.................GT..............................G.C..       14     12 ,     14     12      62:>A/Ck/Egypt/0910-NLQP,2009/01           
  63 >A/Ck/Egypt/0915-NLQP,2009/02           G.....A....C.T.A....C......A...T.G...............GT.......G................A.....G.C..       17     15 ,     17     15      63:>A/Ck/Egypt/0915-NLQP,2009/02           
  64 >A/Gs/Egypt/0912smg-NLQP,2009/02        G.....A....C.T.A....C......A...T.................GT........................A.....G.C..       17     13 ,     17     13      64:>A/Gs/Egypt/0912smg-NLQP,2009/02        
  65 >A/Ck/Egypt/093smg-NLQP,2009/01         G.....A....C.T.A....C......A...T.................GT.................T......A.....G.C..       17     14 ,     17     14      65:>A/Ck/Egypt/093smg-NLQP,2009/01         
  66 >A/Egypt/N00585,2009/01/23              .A....A....C.TTA....C.A....A...T.................G...............................G....       14     12 ,     14     12      66:>A/Egypt/N00585,2009/01/23              
  67 >A/Ck/Egypt/0920-NLQP,2009/02           .A....A....C.TTA....C.A....A...T.................G...............................G....       15     12 ,     15     12      67:>A/Ck/Egypt/0920-NLQP,2009/02           
  68 >A/Dk/Egypt/09339S-NLQP,2009/04         --....A.C..C.T.A....C.A....A..AT.................G.C...........GC.........C......G....       23     18 ,     17     16      68:>A/Dk/Egypt/09339S-NLQP,2009/04         
  69 >A/Egypt/N04316,2009/05/09              ......A.C..C.T.A....C.A....A..AT.................G.............GC.........C......G....       16     15 ,     16     15      69:>A/Egypt/N04316,2009/05/09              
  70 >A/Egypt/N02563,2009/03/14              ......A.C..C.T.A....C.A....A..AT.................G...........T.GC.........C......G....       17     16 ,     17     16      70:>A/Egypt/N02563,2009/03/14              
  71 >A/Egypt/N04823,2009/05/25              ......A.C..C.T.A....C.AG...A...T..............A..G...............................G....       15     13 ,     15     13      71:>A/Egypt/N04823,2009/05/25              
  72 >A/Dk/Egypt/0990SM-NLQP,2009/02         ......A.C..C.T.A....C.AG...A...T..............A..G...............................G....       14     13 ,     14     13      72:>A/Dk/Egypt/0990SM-NLQP,2009/02         
  73 >A/Dk/Egypt/09238sm-NLQP,2009/03        ......A.C..C.T.A....C....T.A...T..............A..G...............................G....       15     12 ,     15     12      73:>A/Dk/Egypt/09238sm-NLQP,2009/03        
                                                                                                                                    
---Index-------------------------------------ACAGGAGTTACTCCCGCATATCGACCGGTGCCGACGATGGCTCGGTGCGACTGCAAGGATGCTAAGCGCCCACGTGCGAGAAGTAT 
-codon-position------------------------------ 1    1        2  1 2 12  1  12    1   2 1    1     1 1 21     12       1    1       2 
                                             00000000000000000000000000000000000000000000000000000011111111111111111111111111111111 
                                             00000112222223344444555555555666666666777777888888999900000011222233333444444445555666 
                                             23499371224462905669000145678001566789113567246678338901115639355848899003456792679015 
                                             77503856250911979892018292838128136679162184292795362964680577323716958781054741359548

Since this thread is on the H5N1 donkey sequence, it is worth going through that sequence to demonstrate additional examples of recombination.
The above rearranged table now has the donkey sequence on row 60. As noted yesterday, the doney sequence has a “triple” that is also found in the duck sequence which is now on line 59. The “triple” is really a “quadruple”, because 4 polymorphisms in a row match in rows 59 and 60, even though the two sequences are quite distinct. The quadruple is G573A, T588C, G601A, and C618T. The outside markers, G573A and C618T are fairly widespread, but T588C and G601A are quite rare.
T588C is only found in the two sequences on lines 59 and 60. Not only isn’t it in other H5N1 sequences with the 3BP deletion, but it is not in any other H5N1 in Egypt, or even any clade 2.2 sequence at Genbank. It is in only one other sequence at Genbank, a 2004 H5N1 isolate from Guangdong, China. Because it is on two different backgrounds in Egypt, it arose by independent events. It either jumped from one sequence to the other via recombination, or is a coincidental copy error. The fact that it is so rare, yet is found in the same 3 BP deletion sub-clade in isolates collected on March 24 and May in 2009 at relatively close locations (Beni Suef and Sohag), makes the coincidence argument EXTREMELY unlikely.
However, when combined with the adjacent change , G601A, the coincidental random error explanation moves into the CDC/WHO/GSGS "hopes and dreams" category because G601A is also exceedingly rare and is only found in the 5 isolates on lines 57-62, but clearly falls into two distinct groups. One group includes the duck sequence on line 59 as well as the two human sequences on lines 57 and 58. The two human sequences where both from young children (4M) who lived in Sohag. The collections were on Apr 19, 2009 and May 18, 2009. The duck isolate was also from Sohag and also collected in May, 2009.
The other group includes the donkey sequence from Beni Suef, as well as a duck sequence collected in Feb in Fayoum, which is adjacent to Beni Suef,
Thus, once again a VERY rare polymorphism is found in 5 sequences which represent two distinct backgrounds collected over the same time frame (Feb-May 2009) in the same general area (Fayoum, Beni Suef, Sohag), which are do to two independent events, recombination between co-circulating H5N1’s which include the two sequences positive for T588C, which are also positive for G610A, or random error coincidences.
The matching of these two adjacent polymorphisms in the same two sub-clades is well into the “too many coincidences” category to support the “random mutation” fantasy.
Moreover, a bit further down is a “triple” (C618T, C651G, A663T) which is in the donkey sequence on line 60, as well as the chicken sequence on line 46, which is another background, but also from Beni Suef, providing more support for recombination and less support for more random coincidences.

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Mon Apr 19, 2010 11:57 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Stockholm wrote:

rml wrote:

gsgs and niman, thank you for this conversation which has turned into a learning experience. Thank you for both the questions and for sharing of knowledge. It takes time to explain things - and that is appreciated.

I do agree! Dr Niman, I really appreciate your patience and your willingness to explain "elegant evolution" in detail! :hello:

And thanks gsgs for your replies and your questions :hello:

This scientific dispute is really a learning experience!

There is quite a bit of info in the table, and the examples of recombination are quite clear. This is also obvious on phylogenetic analysis, which also groups like sequences, but placed widely divergent sub-clades at very different positions.
The donkey H5N1 is a clear recombinant drawing from other 3 BP deletion sequences to acquire new polymorphisms.

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Thu Apr 22, 2010 9:20 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

> This combination leaves no doubt that the 3 BP deletion was acquired via recombination.

I think most people have lots of doubt here.

all H5N1 in Egypt is Qinghai, how should Shanxi-polymorphisms come to Egypt

Movement of H5N1 polymorphisms from location to location is linked to migratory birds, so there is no problems with polymorphisms getting to Egypt from Shanxi, Hunan, or the other Asia locations (and I believe these other examples will be released at Genbank shortly).

All three of the geographic locations have the same 3 BP deletion (125del using H3 numbering). Moreover, all 125del sequences in Egypt have I147T (T500C in table), which is only in the 125del sequences. Moreover, all 125del sequence in this other subclade also have I147T, so there is little doubt that this quadruple was acquired by recombination. The 125del/I147T represents a quadruple, which is a match in the three deleted positions, plus the adjacent position encoding for I147T. Moreover, the unpublished quadruple is on two different backgrounds, demonstrating additional recombination within that clade.

Too much data coming out. Random mutations are only viable in the absence of data. The paradigm (which is the basis or WHO and CDC policy) is now in its death throes.

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gsgs

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 4:54 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1784
Location: germany

do you have some databases that you can share ?

e.g. viruses with deletions from Africa+China

aren't you also downloading the sequences from genbank,
filtered by criteria from their search-page ?

just curious

I'm actually getting all H5N1-HAs (n=3229) since 1996, then sorting,aligning,
correcting errors, unifying names, filtering other (LP)-types etc.

that takes me hours each time. It yould be useful to share these
improved databases

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 6:36 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

I am just pulling matches out of the Genbank database.

Sequences with T500C (T147I) at Genbank are

gb|GU811746.1| Influenza A virus (A/duck/Egypt/0969smL-NLQP/2... 34.2 3.1
gb|GU811743.1| Influenza A virus (A/goose/Egypt/0912smg-NLQP/... 34.2 3.1
gb|GU811742.1| Influenza A virus (A/chicken/Egypt/093smg-NLQP... 34.2 3.1
gb|GU811741.1| Influenza A virus (A/goose/Egypt/09102smf-NLQP... 34.2 3.1
gb|GU811740.1| Influenza A virus (A/duck/Egypt/0967smf-NLQP/2... 34.2 3.1
gb|GU811739.1| Influenza A virus (A/duck/Egypt/0945smf-NLQP/2... 34.2 3.1
gb|GU811738.1| Influenza A virus (A/duck/Egypt/09332sm-NLQP/2... 34.2 3.1
gb|GU811737.1| Influenza A virus (A/goose/Egypt/09324sm-NLQP/... 34.2 3.1
gb|GU811736.1| Influenza A virus (A/duck/Egypt/09274sm-NLQP/2... 34.2 3.1
gb|GU811735.1| Influenza A virus (A/duck/Egypt/09238sm-NLQP/2... 34.2 3.1
gb|GU811731.1| Influenza A virus (A/goose/Egypt/0910sm-NLQP/2... 34.2 3.1
gb|GU811729.1| Influenza A virus (A/chicken/Egypt/09485s-NLQP... 34.2 3.1
gb|GU811728.1| Influenza A virus (A/duck/Egypt/09315s-NLQP/20... 34.2 3.1
gb|GU811725.1| Influenza A virus (A/chicken/Egypt/092L-NLQP/2... 34.2 3.1
gb|GU811723.1| Influenza A virus (A/duck/Egypt/0970-NLQP/2009... 34.2 3.1
gb|GU811720.1| Influenza A virus (A/chicken/Egypt/0945-NLQP/2... 34.2 3.1
gb|GU811719.1| Influenza A virus (A/chicken/Egypt/0915-NLQP/2... 34.2 3.1
gb|GU811718.1| Influenza A virus (A/duck/Egypt/0912-NLQP/2009... 34.2 3.1
gb|GU811717.1| Influenza A virus (A/chicken/Egypt/0910-NLQP/2... 34.2 3.1
gb|GU366078.1| Influenza A virus (A/chicken/Egypt/0987-NLQP/2... 34.2 3.1
gb|GU370127.1| Influenza A virus (A/chicken/Egypt/0987alb-NLQ... 34.2 3.1
gb|EU195408.1| Influenza A virus (A/mallard/Huadong/hn/2005(H... 34.2 3.1
gb|GU002704.1| Influenza A virus (A/duck/Egypt/09339S-NLQP/20... 34.2 3.1
gb|GU002700.1| Influenza A virus (A/chicken/Egypt/0920-NLQP/2... 34.2 3.1
gb|GU002699.1| Influenza A virus (A/duck/Egypt/093-NLQP/2009(... 34.2 3.1
gb|GU002696.1| Influenza A virus (A/duck/Egypt/0990SM-NLQP/20... 34.2 3.1
gb|GU002691.1| Influenza A virus (A/duck/Egypt/09349S-NLQP/20... 34.2 3.1
gb|GU002685.1| Influenza A virus (A/duck/Egypt/093L-NLQP/2009... 34.2 3.1
gb|GU002682.1| Influenza A virus (A/duck/Egypt/0972-NLQP/2009... 34.2 3.1
gb|GU002677.1| Influenza A virus (A/goose/Egypt/0929-NLQP/200... 34.2 3.1
gb|GU002676.1| Influenza A virus (A/duck/Egypt/0926-NLQP/2009... 34.2 3.1
gb|GU002674.1| Influenza A virus (A/duck/Egypt/0918-NLQP/2009... 34.2 3.1
gb|GU002672.1| Influenza A virus (A/chicken/Egypt/092-NLQP/20... 34.2 3.1
gb|CY041955.1| Influenza A virus (A/Egypt/N05056/2009(H5N1)) ... 34.2 3.1
gb|CY041951.1| Influenza A virus (A/Egypt/N04823/2009(H5N1)) ... 34.2 3.1
gb|CY041947.1| Influenza A virus (A/Egypt/N04527/2009(H5N1)) ... 34.2 3.1
gb|CY041943.1| Influenza A virus (A/Egypt/N04396/2009(H5N1)) ... 34.2 3.1
gb|CY041941.1| Influenza A virus (A/Egypt/N04395/2009(H5N1)) ... 34.2 3.1
gb|CY041940.1| Influenza A virus (A/Egypt/N04394/2009(H5N1)) ... 34.2 3.1
gb|CY041938.1| Influenza A virus (A/Egypt/N04316/2009(H5N1)) ... 34.2 3.1
gb|CY041936.1| Influenza A virus (A/Egypt/N03450/2009(H5N1)) ... 34.2 3.1
gb|CY041934.1| Influenza A virus (A/Egypt/N03439/2009(H5N1)) ... 34.2 3.1
gb|CY041932.1| Influenza A virus (A/Egypt/N03438/2009(H5N1)) ... 34.2 3.1
gb|CY041928.1| Influenza A virus (A/Egypt/N03272/2009(H5N1)) ... 34.2 3.1
gb|CY041926.1| Influenza A virus (A/Egypt/N03228/2009(H5N1)) ... 34.2 3.1
gb|CY041924.1| Influenza A virus (A/Egypt/N02752/2009(H5N1)) ... 34.2 3.1
gb|CY041922.1| Influenza A virus (A/Egypt/N02563/2009(H5N1)) ... 34.2 3.1
gb|CY041920.1| Influenza A virus (A/Egypt/N02407/2009(H5N1)) ... 34.2 3.1
gb|CY041918.1| Influenza A virus (A/Egypt/N02039/2009(H5N1)) ... 34.2 3.1
gb|CY041916.1| Influenza A virus (A/Egypt/N01310/2009(H5N1)) ... 34.2 3.1
gb|CY041914.1| Influenza A virus (A/Egypt/N00606/2009(H5N1)) ... 34.2 3.1
gb|CY041912.1| Influenza A virus (A/Egypt/N00605/2009(H5N1)) ... 34.2 3.1
gb|CY041910.1| Influenza A virus (A/Egypt/N00585/2009(H5N1)) ... 34.2 3.1
gb|CY041908.1| Influenza A virus (A/Egypt/N00001/2009(H5N1)) ... 34.2 3.1
gb|GQ184243.1| Influenza A virus (A/duck/Egypt/0821S-NLQP/200... 34.2 3.1
gb|GQ184242.1| Influenza A virus (A/chicken/Egypt/0896-NLQP/2... 34.2 3.1
gb|GQ184241.1| Influenza A virus (A/chicken/Egypt/0894-NLQP/2... 34.2 3.1
gb|GQ184228.1| Influenza A virus (A/chicken/Egypt/0847-NLQP/2... 34.2 3.1
gb|FJ842486.1| Influenza A virus (A/chicken/Vietnam/NCVD-swab... 34.2 3.1
gb|FJ784842.1| Influenza A virus (A/chicken/Anhui/1089/2007(H... 34.2 3.1
gb|FJ226059.1| Influenza A virus (A/Egypt/2546-NAMRU3/2008(H5... 34.2 3.1
gb|FJ226057.1| Influenza A virus (A/Egypt/2289-NAMRU3/2008(H5... 34.2 3.1
gb|EU371922.1| Influenza A virus (A/chicken/Egypt/9400NAMRU3-... 34.2 3.1
gb|EU122394.1| Influenza A virus (A/Viet Nam/1203/2004(H5N1))... 34.2 3.1
gb|EU183332.1| Influenza A virus (A/chicken/Egypt/R6/2007(H5N... 34.2 3.1
gb|EU183331.1| Influenza A virus (A/duck/Egypt/R5/2007(H5N1))... 34.2 3.1
gb|EU183328.1| Influenza A virus (A/chicken/Egypt/R2/2007(H5N... 34.2 3.1
gb|EU095025.1| Influenza A virus (A/Egypt/2629-NAMRU3/2007(H5... 34.2 3.1
gb|EF535826.1| Influenza A virus (A/Egypt/2621-NAMRU3/2007(H5... 34.2 3.1
gb|EF535817.1| Influenza A virus (A/Egypt/1394-NAMRU3/2007(H5... 34.2 3.1
gb|EF382359.1| Influenza A virus (A/Egypt/0636-NAMRU3/2007(H5... 34.2 3.1
gb|CY017646.1| Influenza A virus (A/Indonesia/CDC938E/2006(H5... 34.2 3.1
gb|CY017638.1| Influenza A virus (A/Indonesia/CDC938/2006(H5N... 34.2 3.1
gb|AY585363.1| Influenza A virus (A/duck/Guangxi/07/1999(H5N1... 34.2 3.1

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 6:45 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

All of the H5N1 in Egypt is clade 2.2 (Qinghai strain).
The unbulished sequences are from another clade. They also have 125del and I147T.
The sequences from clade 7 (below) have 125del but not I147T

gb|DQ914814.3| Influenza A virus (A/chicken/Shanxi/2/2006(H5N... 36.2 0.79
gb|DQ993057.1| Influenza A virus (A/chicken/Hunan/2292/2006(H... 36.2 0.79
gb|DQ993056.1| Influenza A virus (A/chicken/Hunan/2246/2006(H... 36.2 0.79

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 7:09 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Stockholm wrote:

rml wrote:

I do agree! Dr Niman, I really appreciate your patience and your willingness to explain "elegant evolution" in detail! :hello:

And thanks gsgs for your replies and your questions :hello:

This scientific dispute is really a learning experience!

At this point it is probably worth reviewing why the 3 BP deletion (125del) provides such compelling evidence for recombination. In the table of the Egyptian isolates with 125del, there are several other markers that are in all isolates. These markers define the sub-clade and were there first (which is why they are in all). The changes in a subset were added subsequently to the creation of that background. These additions can either be due to recombination, which are changes found in other flu sequences, or copy errors. However, the finding of the same change on multiple backgrounds requires the same error repeated again and again, and when these chnages are clustered in time and space, coincidental errors become increasingly likley.

That is why WHO/CDC put out their D225G announcement in December, 2009. They knew that after December, there claim that D225G did not cluster in time, space, or phylogeny would be invalidated by the Ukraine and Russian data. They also knew it was invalidated by the Duke death cluster, which they are claiming is (their) lab error. Now data is coming out showing that D225G is commonly found in mixtures with wild type, D225N, or both, but the WHO/CDC have not isssued an update to show that their propaganda piece was demonstrably false on all main points. This is "random mutations" in its death throes, and WHO/CDC putting out utter nonsense to try to support the basic tenet.

The 3 BP deletion is another nail in their coffin. The deletion represents three changes in a row (or a triple). The sequences in the table all have the deletion, but those sequences are part of a larger set of H5N1 sequences in Egypt, which have markers for Egyptian clade 2.2. Moreover, there are additional markers that distinguish clade 2.2 from clade 7 and the unplublished sequences. Thus, the 3 BP deletion in the table is appended onto the Egyptian H5N1 genetic background. In Egypt there is no lab error because there are now more than 70 such sequence generated by multiple labs. The deletion is in human H5N1, avian H5N1, and donkey H5N1, each set done by a different lab. It was first identified by NAMRU-3 in human cases in early 2007.

The same deletion is found in three clade 7 sequences (in Shanxi and Hunan). Clade 7 is very different from clade 2.2, so again the "triple" is on two very different backgrounds, and coming up with the same three changes (deletions) via copy error is difficult.

However, the unpublished sequences on yet another H5N1 background are the clincher, because not only is 125del present, but so is the adjacent change, I147T. This match is in the "beyond statistics" category, as well as the lab error category (the sequences are by another lab in another country, yet matches 125del and I147T), so the deniers have run out of hand waving explanations.

The only question is how long the WHO and CDC can keep "random mutations" alive. The increasing data ensures their failure, and that's when its time to look into who kept the nonsense alive, how many papers and grants they rejected, and how they endangered the world's health.

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gsgs

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 8:30 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1784
Location: germany

I found

A/Shangxi/2/2006
A/Hunan/2246/2006
A/Hunan/2292/2006

from Asia with the deletion. None else.

Database with H5N1-HAs :
http://magictour.free.fr/seq/H5N1(4).GZ
3211 HAs , 18 deleted with obviously unrelated H5

Code:


                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111 
                                              0000000001111111222222222222222333333444444444444444455555555555555555555555556666666666666667777777777777777888888888889999999999000000000000001122222333344444444455566666 
                                              2333468992333567001223445666999122399011235556666668900001112333334444567889990011113566778890011233556666779023345667890033388999001111223355662403559489901134568926700126 
                                              7147514030258087466257098178569118619778484691567890201480243234672379283281591214683136461792516325010258142225792279546903627069674568474836585006560492810143870746828761 
-codon-position------------------------------- 111 1           2         11222 1 1 2 11 1  2 12 1  2  1 21112 2 2 1  1    1212221     21      2    11      1 1   1         1    12 121112         12       1    1        2 
---Index--------------------------------------AGACAAGGGCCCAAATAGTCAGCCCCGCATAATACCCAAGGACACAAAGATTACCAGCAGAAGAGTATACCGATTAGCGCCGCTTGACTGAATGAGGGCTATGAACTGTAGAATGGCGGACCCCTGTTGCAGAGGGAAAGATTTCGCTAAGCGCCCACGTGCGAGAGGTACT 
   1 >A/Egypt/2629-NAMRU3,2007//              -----..............T...T....................................................................................................................................................       14      7 ,      2      2       1:>A/Egypt/2629-NAMRU3,2007//              
   2 >A/Egypt/2621-NAMRU3,2007//              ...................T...T....................................................................................................................................................        2      2 ,      2      2       2:>A/Egypt/2621-NAMRU3,2007//              
   3 >A/Ck/Egypt/0894-NLQP,2008/11/27         .........................................................................................................................................................T..................        1      1 ,      1      1       3:>A/Ck/Egypt/0894-NLQP,2008/11/27         
   4 >A/Egypt/N03439,2009/04/18               ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       4:>A/Egypt/N03439,2009/04/18               
   5 >A/Egypt/N04395,2009/05/13               ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       5:>A/Egypt/N04395,2009/05/13               
   6 >A/Dk/Egypt/0918-NLQP,2009/02/           ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       6:>A/Dk/Egypt/0918-NLQP,2009/02/           
   7 >A/Egypt/N01310,2009/02/28               ....G..........................................................................................A.........................................................T..................        4      3 ,      4      3       7:>A/Egypt/N01310,2009/02/28               
   8 >A/Egypt/N02039,2009/03/03               ....G..........................................................................................A.........................................................T..................        4      3 ,      4      3       8:>A/Egypt/N02039,2009/03/03               
   9 >A/Gs/Egypt/09324sm-NLQP,2009/04/        ....G..........................................................................................A.........................................................T..................        5      3 ,      4      3       9:>A/Gs/Egypt/09324sm-NLQP,2009/04/        
  10 >A/Ck/Egypt/09485s-NLQP,2009/05/         ....G...................................................A......................................A.........................................................T.................-       13      5 ,      4      4      10:>A/Ck/Egypt/09485s-NLQP,2009/05/         
  11 >A/Ck/Egypt/0987alb-NLQP,2009/05/12      G...G..........................................................................................A..................................G......................T..................        9      5 ,      5      5      11:>A/Ck/Egypt/0987alb-NLQP,2009/05/12      
  12 >A/Ck/Egypt/0987-NLQP,2009/05/12         ....G..........................................................................................A..................................G......................T..................        6      4 ,      6      4      12:>A/Ck/Egypt/0987-NLQP,2009/05/12         
  13 >A/Dk/Egypt/09274sm-NLQP,2009/04/        ....G..........................................................................................A.........................................................T....A.............       14      4 ,      6      4      13:>A/Dk/Egypt/09274sm-NLQP,2009/04/        
  14 >A/Egypt/N02407,2009/03/09               ....G..........................................................................................A.........................................................T..................        6      3 ,      6      3      14:>A/Egypt/N02407,2009/03/09               
  15 >A/Egypt/N04396,2009/05/17               ....G..........................................................................................A.........................................................T..................        6      3 ,      6      3      15:>A/Egypt/N04396,2009/05/17               
  16 >A/Ck/Egypt/092-NLQP,2009/01/            ...................................................................................................................A........................................................        1      1 ,      1      1      16:>A/Ck/Egypt/092-NLQP,2009/01/            
  17 >A/Gs/Egypt/0910sm-NLQP,2009/01/         ...................................................................................................................A........................................................        3      1 ,      2      1      17:>A/Gs/Egypt/0910sm-NLQP,2009/01/         
  18 >A/Dk/Egypt/0821S-NLQP,2008/08/25        ...................................................................................................................A........................................................        8      1 ,      2      1      18:>A/Dk/Egypt/0821S-NLQP,2008/08/25        
  19 >A/Dk/Egypt/093-NLQP,2009/01/            .........................T........................C........................................................................................................................-       11      3 ,      2      2      19:>A/Dk/Egypt/093-NLQP,2009/01/            
  20 >A/Egypt/N00001,2009/01/11               .........................T........................C.........................................................................................................................        4      2 ,      4      2      20:>A/Egypt/N00001,2009/01/11               
  21 >A/Dk/Egypt/0972-NLQP,2009/04/           .........................................................................................................................................................T..................        3      1 ,      3      1      21:>A/Dk/Egypt/0972-NLQP,2009/04/           
  22 >A/Ck/Egypt/0945-NLQP,2009/03/           ..................................................................................................................................................T......T.........G........        4      3 ,      3      3      22:>A/Ck/Egypt/0945-NLQP,2009/03/           
  23 >A/Egypt/N00605,2009/02/03               ........................................................A........................................................C.......................................T..................        4      3 ,      4      3      23:>A/Egypt/N00605,2009/02/03               
  24 >A/Dk/Egypt/0990SM-NLQP,2009/02/         ........................................................A.G........................................................A........................................................        5      3 ,      4      3      24:>A/Dk/Egypt/0990SM-NLQP,2009/02/         
  25 >A/Egypt/N04823,2009/05/25               ........................................................A.G........................................................A........................................................        5      3 ,      5      3      25:>A/Egypt/N04823,2009/05/25               
  26 >A/Dk/Egypt/09238sm-NLQP,2009/03/        ..........T.....................................T.....................T............................................A........................................................        6      4 ,      5      4      26:>A/Dk/Egypt/09238sm-NLQP,2009/03/        
  27 >A/Dk/Egypt/0967smf-NLQP,2009/02/        ............................................................................................................................................................................        7      0 ,      3      0      27:>A/Dk/Egypt/0967smf-NLQP,2009/02/        
  28 >A/Gs/Egypt/0929-NLQP,2009/02/           .......A.............................G......................................................................................................................................        4      2 ,      3      2      28:>A/Gs/Egypt/0929-NLQP,2009/02/           
  29 >A/Dk/Egypt/0945smf-NLQP,2009/02/        -.............................................................................A........................................................................T...................-       16      4 ,      3      2      29:>A/Dk/Egypt/0945smf-NLQP,2009/02/        
  30 >A/Ck/Egypt/0896-NLQP,2008/12/24         ..................C....................................................A.............................................A......................G...............................        5      4 ,      5      4      30:>A/Ck/Egypt/0896-NLQP,2008/12/24         
  31 >A/Gs/Egypt/09102smf-NLQP,2009/03/       ---..G...............................................................................................................A......................................................       14      5 ,      6      2      31:>A/Gs/Egypt/09102smf-NLQP,2009/03/       
  32 >A/Dk/Egypt/09332sm-NLQP,2009/05/        ........A...........C...........................................................................................................................................A..........-       14      4 ,      5      3      32:>A/Dk/Egypt/09332sm-NLQP,2009/05/        
  33 >A/Egypt/N00585,2009/01/23               ...A...............T................T...................A.....................................................................................G.............................        6      5 ,      6      5      33:>A/Egypt/N00585,2009/01/23               
  34 >A/Ck/Egypt/0920-NLQP,2009/02/           ...A...............T................T...................A...................................................................................................................        7      4 ,      7      4      34:>A/Ck/Egypt/0920-NLQP,2009/02/           
  35 >A/Egypt/N04316,2009/05/09               ........................................................A......................A....................................................................GC.........C............        6      5 ,      6      5      35:>A/Egypt/N04316,2009/05/09               
  36 >A/Egypt/N02563,2009/03/14               ........................................................A......................A..................................................................T.GC.........C............        7      6 ,      7      6      36:>A/Egypt/N02563,2009/03/14               
  37 >A/Dk/Egypt/09339S-NLQP,2009/04/         ----....................................................A......................A............................................C.......................GC.........C............       15     10 ,      7      6      37:>A/Dk/Egypt/09339S-NLQP,2009/04/         
  38 >A/Egypt/N03438,2009/04/16               .........................................................................................................................................................T..................        5      1 ,      5      1      38:>A/Egypt/N03438,2009/04/16               
  39 >A/Ck/Egypt/0910-NLQP,2009/01/           G..................T.......................................................................................................T............................................C...        7      4 ,      6      4      39:>A/Ck/Egypt/0910-NLQP,2009/01/           
  40 >A/Ck/Egypt/0915-NLQP,2009/02/           G..................T..................................................................G....................................T.........A......G...................A.......C...       10      8 ,      9      8      40:>A/Ck/Egypt/0915-NLQP,2009/02/           
  41 >A/Ck/Egypt/093smg-NLQP,2009/01/         G..................T.........G.............................................................................................T.............................T......A.......C...       10      7 ,      9      7      41:>A/Ck/Egypt/093smg-NLQP,2009/01/         
  42 >A/Gs/Egypt/0912smg-NLQP,2009/02/        G..................T.......................................................................................................T....................................A.......C...       10      5 ,      9      5      42:>A/Gs/Egypt/0912smg-NLQP,2009/02/        
  43 >A/Dk/Egypt/0926-NLQP,2009/02/           ...................T.......................................................................................A...............................................................C        6      3 ,      6      3      43:>A/Dk/Egypt/0926-NLQP,2009/02/           
  44 >A/Egypt/2631-NAMRU3,2007//              -----..............T...T.T..............................................G..........C.......................................................................T................       19     11 ,      7      6      44:>A/Egypt/2631-NAMRU3,2007//              
  45 >A/Dk/Egypt/R5,2007/02/20                ...................T...T................................................G..........C..G....................................................................T................        9      6 ,      9      6      45:>A/Dk/Egypt/R5,2007/02/20                
  46 >A/Ck/Egypt/R3,2007/02/01                ...................T...T............................G...................G..........C..G...........T........................T.......................A........................       10      9 ,     10      9      46:>A/Ck/Egypt/R3,2007/02/01                
  47 >A/Gs/Egypt/R4,2007/02/01                ...................T...T............................G...................G..........C..............T........................T...........A...........A.......T.........G......       13     11 ,     13     11      47:>A/Gs/Egypt/R4,2007/02/01                
  48 >A/Egypt/0636-NAMRU3,2007/01/            ...................T...T...........................................................C.........................................................................T..............        6      4 ,      6      4      48:>A/Egypt/0636-NAMRU3,2007/01/            
  49 >A/Egypt/1394-NAMRU3,2007//              .......A...........T...T................................................G.......S..C............R..........................................................................C       11      8 ,     11      8      49:>A/Egypt/1394-NAMRU3,2007//              
  50 >A/Egypt/2289-NAMRU3,2008/03/02          -----..............T..TT................................................G..........C............T...................................G...................A........TA.........       23     15 ,     11     10      50:>A/Egypt/2289-NAMRU3,2008/03/02          
  51 >A/Egypt/2546-NAMRU3,2008/03/08          -----..............T..TT................................................G..........C............A...................................G...................A........T...G......       25     15 ,     13     10      51:>A/Egypt/2546-NAMRU3,2008/03/08          
  52 >A/Ck/Egypt/0847-NLQP,2008/01/18         ...................T...T................................................G........A.C...............................................................................G........       13      6 ,     13      6      52:>A/Ck/Egypt/0847-NLQP,2008/01/18         
  53 >A/Ck/Egypt/9400NAMRU3-CLEVB211,2007//   ........A..........T...T...........A....................................G..........C.....................T................................................................T.       13      8 ,     13      8      53:>A/Ck/Egypt/9400NAMRU3-CLEVB211,2007//   
  54 >A/Egypt/N02752,2009/03/24               ...................T.....................................................................A...........C...T.......................A.............C.T..........GT..............       11      9 ,     11      9      54:>A/Egypt/N02752,2009/03/24               
  55 >A/Egypt/N00606,2009/02/07               ...................T...T.........................G.......................................A.......................................A.............C.T..........GT.........T....       12     10 ,     12     10      55:>A/Egypt/N00606,2009/02/07               
  56 >A/Dk/Egypt/0912-NLQP,2009/02/           ...................TG..T..............................................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     13     13      56:>A/Dk/Egypt/0912-NLQP,2009/02/           
  57 >A/Ck/Egypt/092L-NLQP,2009/02/           ...................TG..T..............................................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     13     13      57:>A/Ck/Egypt/092L-NLQP,2009/02/           
  58 >A/Dk/Egypt/093L-NLQP,2009/02/           ...................T...T....................T.........................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     14     13      58:>A/Dk/Egypt/093L-NLQP,2009/02/           
  59 >A/Egypt/N04527,2009/05/18               ...................T...T..............................A.......................A..........A..................................C....A....A........C.T..........GT..............       13     12 ,     13     12      59:>A/Egypt/N04527,2009/05/18               
  60 >A/Egypt/N03450,2009/04/19               ...................T...T..............................A.A.....................A..........A..................................C....A....A........C.T..........GT..............       15     13 ,     15     13      60:>A/Egypt/N03450,2009/04/19               
  61 >A/Dk/Egypt/0969smL-NLQP,2009/05/        ...................T...T..............................A...................C...A..........A.......................................A....A........C.TT.........GT..............       14     13 ,     13     13      61:>A/Dk/Egypt/0969smL-NLQP,2009/05/        
  62 >A/Dk/Egypt/0930smL-NLQP,2009/02/        ...................T...T.................................................................AC......................................A.............CTT........T.GT..............       15     11 ,     14     11      62:>A/Dk/Egypt/0930smL-NLQP,2009/02/        
  63 >A/Dk/Egypt/0970-NLQP,2009/04/           ............G......T...T................................A................................A..C....................C...............A.............C.T..........GT..............       15     12 ,     14     12      63:>A/Dk/Egypt/0970-NLQP,2009/04/           
  64 >A/Egypt/N05056,2009/06/06               ............G......T...T.................................................................A..C....................................A.............C.T..........GT..............       16     10 ,     16     10      64:>A/Egypt/N05056,2009/06/06               
  65 >A/Dk/Egypt/09349S-NLQP,2009/04/         ----------.........T.................................................................A.....T.........C......C................A........................A...........A.........       34     18 ,     10      8      65:>A/Dk/Egypt/09349S-NLQP,2009/04/         
  66 >A/Egypt/N04394,2009/05/11               ...................T.................................................................A.....T.........C.....A.................A........................A.....................       11      7 ,     11      7      66:>A/Egypt/N04394,2009/05/11               
  67 >A/Egypt/N03228,2009/03/30               ....G............................................G...................A.........................AA...................T.......C............................T..........T.......        9      9 ,      9      9      67:>A/Egypt/N03228,2009/03/30               
  68 >A/Egypt/N03272,2009/04/01               ....G............................................G...................A.........................A....................T.......C............................T..........T.......        9      8 ,      9      8      68:>A/Egypt/N03272,2009/04/01               
  69 >A/Dk/Egypt/09315s-NLQP,2009/04/         ----..............C.........................T.................A........A.........................................................T........................T.................       18     10 ,      9      6      69:>A/Dk/Egypt/09315s-NLQP,2009/04/         
  70 >A/equine/Egypt/av1,2009/03/24           ..........................................................................C...A.......GT...............................................................T....................       11      5 ,     11      5      70:>A/equine/Egypt/av1,2009/03/24           
  71 >A/Ck/Egypt/R2,2007/01/01                ...................T...T..............................................T.G..........C..........................A............................................T................       16      7 ,     16      7      71:>A/Ck/Egypt/R2,2007/01/01                
  72 >A/Ck/Egypt/R6,2007/02/26                ...G..A............T...T................................................G.............GT......................A............T...........A..............................A.....       22     11 ,     22     11      72:>A/Ck/Egypt/R6,2007/02/26                
  73 >A/Ck/Shanxi/2,2006//                    .AG..GA..TTT.GGCGA.T.A.TT..TGCGGCGTA.GCA.GTCTTG.AGCC.T..AT.ACGTGACCC....G..C.AA.TAACCA......CAG..A.CGC.TCTCT.T.GG.A...AGTTA...CGA.GC.A..GGGA.CG.TA.C.......A..........A...TC      118    100 ,    118    100      73:>A/Ck/Shanxi/2,2006//                    
  74 >A/Ck/Hunan/2246,2006//                  ----.G...TTT.GGCGA.T.A.TT.ATGCGGCGTA.GCAAGTCTTGGAGCC.T.GAT.ACGTGACCCG...GC.CAA.ATAACCA..C...CAG..A.CGCACCTCTCT.GG.A...AGTTA...CGA.GC.A..GGGA.CG-----------------------------      200    133 ,    100    100      74:>A/Ck/Hunan/2246,2006//                  
  75 >A/Ck/Hunan/2292,2006//                  .AG..G...TTT.GGCGA.T.A.TT.ATGCGGCGTA.GCAAGTCTTGGAGCC.T.GAT.ACGTGACCCG...GC.CAA.ATAACC...C.C.CAG..A.CGCATCTCTCT.GG.A...AGTTA...CGA.GC.A..GGGA.CG.----------------------------      193    130 ,    102    102      75:>A/Ck/Hunan/2292,2006//                  
                                                                                                                                                                                                                           
---Index--------------------------------------AGACAAGGGCCCAAATAGTCAGCCCCGCATAATACCCAAGGACACAAAGATTACCAGCAGAAGAGTATACCGATTAGCGCCGCTTGACTGAATGAGGGCTATGAACTGTAGAATGGCGGACCCCTGTTGCAGAGGGAAAGATTTCGCTAAGCGCCCACGTGCGAGAGGTACT 
-codon-position------------------------------- 111 1           2         11222 1 1 2 11 1  2 12 1  2  1 21112 2 2 1  1    1212221     21      2    11      1 1   1         1    12 121112         12       1    1        2 
                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111 
                                              0000000001111111222222222222222333333444444444444444455555555555555555555555556666666666666667777777777777777888888888889999999999000000000000001122222333344444444455566666 
                                              2333468992333567001223445666999122399011235556666668900001112333334444567889990011113566778890011233556666779023345667890033388999001111223355662403559489901134568926700126 
                                              7147514030258087466257098178569118619778484691567890201480243234672379283281591214683136461792516325010258142225792279546903627069674568474836585006560492810143870746828761

_________________
no patents on genes, publish the GISAID sequences !

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gsgs

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 8:42 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1784
Location: germany

differences

Code:

>A/Egypt/2621-NAMRU3,2007//
>A/Ck/Shanxi/2,2006//
..............................o..o.......................... 2 
o......................o...................................o 3 
...........o..o..............o.................o........o... 5 
.......................o.o..............................o... 3 
.................o.........o..........................oo..o. 5 
..........o.........o......o.......o........................ 4 
..............................o...............o.........oo.. 4 
.........-----...o...............o.o..o.o...o.ooo..........o 10 
......o............o.......o.o...o........o........ooo.oo... 11 
.oo.............................o.................o..o....o. 6 
o........oo..o.o.o..............o.................o......... 8 
......................................o..o..o............... 3 
..o...........o..............oo..........o..o..o..o..o...... 9 
.....................o................................o.o... 3 
...........o................................o........o...... 3 
.....o..o....................o.............................. 3 
..........................o..o.....o.........oo.......o..... 6 
---o..o......o...o.................o........o............... 6 
............................................o..............o 2 
..........................................o................. 1 
...................................o........................ 1 
..........................o........o........................ 2 
.....o...................................................... 1 
....................o...........o..........................o 3 
.......................o....o.............................o. 3 
..........................................o....o............ 2 
.................o.....o.o.................................. 3 
.....o.........o........................o................... 3 
............................o.-- 116 

 116 ( 1702 )

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

_________________
no patents on genes, publish the GISAID sequences !

Last edited by gsgs on Fri Apr 23, 2010 9:45 am, edited 1 time in total.

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niman

Post subject: Re: 3 BP Deletion in Donkey H5N1

Posted: Fri Apr 23, 2010 9:07 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

Code:


                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111 
                                              0000000001111111222222222222222333333444444444444444455555555555555555555555556666666666666667777777777777777888888888889999999999000000000000001122222333344444444455566666 
                                              2333468992333567001223445666999122399011235556666668900001112333334444567889990011113566778890011233556666779023345667890033388999001111223355662403559489901134568926700126 
                                              7147514030258087466257098178569118619778484691567890201480243234672379283281591214683136461792516325010258142225792279546903627069674568474836585006560492810143870746828761 
-codon-position------------------------------- 111 1           2         11222 1 1 2 11 1  2 12 1  2  1 21112 2 2 1  1    1212221     21      2    11      1 1   1         1    12 121112         12       1    1        2 
---Index--------------------------------------AGACAAGGGCCCAAATAGTCAGCCCCGCATAATACCCAAGGACACAAAGATTACCAGCAGAAGAGTATACCGATTAGCGCCGCTTGACTGAATGAGGGCTATGAACTGTAGAATGGCGGACCCCTGTTGCAGAGGGAAAGATTTCGCTAAGCGCCCACGTGCGAGAGGTACT 
   1 >A/Egypt/2629-NAMRU3,2007//              -----..............T...T....................................................................................................................................................       14      7 ,      2      2       1:>A/Egypt/2629-NAMRU3,2007//              
   2 >A/Egypt/2621-NAMRU3,2007//              ...................T...T....................................................................................................................................................        2      2 ,      2      2       2:>A/Egypt/2621-NAMRU3,2007//              
   3 >A/Ck/Egypt/0894-NLQP,2008/11/27         .........................................................................................................................................................T..................        1      1 ,      1      1       3:>A/Ck/Egypt/0894-NLQP,2008/11/27         
   4 >A/Egypt/N03439,2009/04/18               ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       4:>A/Egypt/N03439,2009/04/18               
   5 >A/Egypt/N04395,2009/05/13               ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       5:>A/Egypt/N04395,2009/05/13               
   6 >A/Dk/Egypt/0918-NLQP,2009/02/           ....G..........................................................................................A.........................................................T..................        3      3 ,      3      3       6:>A/Dk/Egypt/0918-NLQP,2009/02/           
   7 >A/Egypt/N01310,2009/02/28               ....G..........................................................................................A.........................................................T..................        4      3 ,      4      3       7:>A/Egypt/N01310,2009/02/28               
   8 >A/Egypt/N02039,2009/03/03               ....G..........................................................................................A.........................................................T..................        4      3 ,      4      3       8:>A/Egypt/N02039,2009/03/03               
   9 >A/Gs/Egypt/09324sm-NLQP,2009/04/        ....G..........................................................................................A.........................................................T..................        5      3 ,      4      3       9:>A/Gs/Egypt/09324sm-NLQP,2009/04/        
  10 >A/Ck/Egypt/09485s-NLQP,2009/05/         ....G...................................................A......................................A.........................................................T.................-       13      5 ,      4      4      10:>A/Ck/Egypt/09485s-NLQP,2009/05/         
  11 >A/Ck/Egypt/0987alb-NLQP,2009/05/12      G...G..........................................................................................A..................................G......................T..................        9      5 ,      5      5      11:>A/Ck/Egypt/0987alb-NLQP,2009/05/12      
  12 >A/Ck/Egypt/0987-NLQP,2009/05/12         ....G..........................................................................................A..................................G......................T..................        6      4 ,      6      4      12:>A/Ck/Egypt/0987-NLQP,2009/05/12         
  13 >A/Dk/Egypt/09274sm-NLQP,2009/04/        ....G..........................................................................................A.........................................................T....A.............       14      4 ,      6      4      13:>A/Dk/Egypt/09274sm-NLQP,2009/04/        
  14 >A/Egypt/N02407,2009/03/09               ....G..........................................................................................A.........................................................T..................        6      3 ,      6      3      14:>A/Egypt/N02407,2009/03/09               
  15 >A/Egypt/N04396,2009/05/17               ....G..........................................................................................A.........................................................T..................        6      3 ,      6      3      15:>A/Egypt/N04396,2009/05/17               
  16 >A/Ck/Egypt/092-NLQP,2009/01/            ...................................................................................................................A........................................................        1      1 ,      1      1      16:>A/Ck/Egypt/092-NLQP,2009/01/            
  17 >A/Gs/Egypt/0910sm-NLQP,2009/01/         ...................................................................................................................A........................................................        3      1 ,      2      1      17:>A/Gs/Egypt/0910sm-NLQP,2009/01/         
  18 >A/Dk/Egypt/0821S-NLQP,2008/08/25        ...................................................................................................................A........................................................        8      1 ,      2      1      18:>A/Dk/Egypt/0821S-NLQP,2008/08/25        
  19 >A/Dk/Egypt/093-NLQP,2009/01/            .........................T........................C........................................................................................................................-       11      3 ,      2      2      19:>A/Dk/Egypt/093-NLQP,2009/01/            
  20 >A/Egypt/N00001,2009/01/11               .........................T........................C.........................................................................................................................        4      2 ,      4      2      20:>A/Egypt/N00001,2009/01/11               
  21 >A/Dk/Egypt/0972-NLQP,2009/04/           .........................................................................................................................................................T..................        3      1 ,      3      1      21:>A/Dk/Egypt/0972-NLQP,2009/04/           
  22 >A/Ck/Egypt/0945-NLQP,2009/03/           ..................................................................................................................................................T......T.........G........        4      3 ,      3      3      22:>A/Ck/Egypt/0945-NLQP,2009/03/           
  23 >A/Egypt/N00605,2009/02/03               ........................................................A........................................................C.......................................T..................        4      3 ,      4      3      23:>A/Egypt/N00605,2009/02/03               
  24 >A/Dk/Egypt/0990SM-NLQP,2009/02/         ........................................................A.G........................................................A........................................................        5      3 ,      4      3      24:>A/Dk/Egypt/0990SM-NLQP,2009/02/         
  25 >A/Egypt/N04823,2009/05/25               ........................................................A.G........................................................A........................................................        5      3 ,      5      3      25:>A/Egypt/N04823,2009/05/25               
  26 >A/Dk/Egypt/09238sm-NLQP,2009/03/        ..........T.....................................T.....................T............................................A........................................................        6      4 ,      5      4      26:>A/Dk/Egypt/09238sm-NLQP,2009/03/        
  27 >A/Dk/Egypt/0967smf-NLQP,2009/02/        ............................................................................................................................................................................        7      0 ,      3      0      27:>A/Dk/Egypt/0967smf-NLQP,2009/02/        
  28 >A/Gs/Egypt/0929-NLQP,2009/02/           .......A.............................G......................................................................................................................................        4      2 ,      3      2      28:>A/Gs/Egypt/0929-NLQP,2009/02/           
  29 >A/Dk/Egypt/0945smf-NLQP,2009/02/        -.............................................................................A........................................................................T...................-       16      4 ,      3      2      29:>A/Dk/Egypt/0945smf-NLQP,2009/02/        
  30 >A/Ck/Egypt/0896-NLQP,2008/12/24         ..................C....................................................A.............................................A......................G...............................        5      4 ,      5      4      30:>A/Ck/Egypt/0896-NLQP,2008/12/24         
  31 >A/Gs/Egypt/09102smf-NLQP,2009/03/       ---..G...............................................................................................................A......................................................       14      5 ,      6      2      31:>A/Gs/Egypt/09102smf-NLQP,2009/03/       
  32 >A/Dk/Egypt/09332sm-NLQP,2009/05/        ........A...........C...........................................................................................................................................A..........-       14      4 ,      5      3      32:>A/Dk/Egypt/09332sm-NLQP,2009/05/        
  33 >A/Egypt/N00585,2009/01/23               ...A...............T................T...................A.....................................................................................G.............................        6      5 ,      6      5      33:>A/Egypt/N00585,2009/01/23               
  34 >A/Ck/Egypt/0920-NLQP,2009/02/           ...A...............T................T...................A...................................................................................................................        7      4 ,      7      4      34:>A/Ck/Egypt/0920-NLQP,2009/02/           
  35 >A/Egypt/N04316,2009/05/09               ........................................................A......................A....................................................................GC.........C............        6      5 ,      6      5      35:>A/Egypt/N04316,2009/05/09               
  36 >A/Egypt/N02563,2009/03/14               ........................................................A......................A..................................................................T.GC.........C............        7      6 ,      7      6      36:>A/Egypt/N02563,2009/03/14               
  37 >A/Dk/Egypt/09339S-NLQP,2009/04/         ----....................................................A......................A............................................C.......................GC.........C............       15     10 ,      7      6      37:>A/Dk/Egypt/09339S-NLQP,2009/04/         
  38 >A/Egypt/N03438,2009/04/16               .........................................................................................................................................................T..................        5      1 ,      5      1      38:>A/Egypt/N03438,2009/04/16               
  39 >A/Ck/Egypt/0910-NLQP,2009/01/           G..................T.......................................................................................................T............................................C...        7      4 ,      6      4      39:>A/Ck/Egypt/0910-NLQP,2009/01/           
  40 >A/Ck/Egypt/0915-NLQP,2009/02/           G..................T..................................................................G....................................T.........A......G...................A.......C...       10      8 ,      9      8      40:>A/Ck/Egypt/0915-NLQP,2009/02/           
  41 >A/Ck/Egypt/093smg-NLQP,2009/01/         G..................T.........G.............................................................................................T.............................T......A.......C...       10      7 ,      9      7      41:>A/Ck/Egypt/093smg-NLQP,2009/01/         
  42 >A/Gs/Egypt/0912smg-NLQP,2009/02/        G..................T.......................................................................................................T....................................A.......C...       10      5 ,      9      5      42:>A/Gs/Egypt/0912smg-NLQP,2009/02/        
  43 >A/Dk/Egypt/0926-NLQP,2009/02/           ...................T.......................................................................................A...............................................................C        6      3 ,      6      3      43:>A/Dk/Egypt/0926-NLQP,2009/02/           
  44 >A/Egypt/2631-NAMRU3,2007//              -----..............T...T.T..............................................G..........C.......................................................................T................       19     11 ,      7      6      44:>A/Egypt/2631-NAMRU3,2007//              
  45 >A/Dk/Egypt/R5,2007/02/20                ...................T...T................................................G..........C..G....................................................................T................        9      6 ,      9      6      45:>A/Dk/Egypt/R5,2007/02/20                
  46 >A/Ck/Egypt/R3,2007/02/01                ...................T...T............................G...................G..........C..G...........T........................T.......................A........................       10      9 ,     10      9      46:>A/Ck/Egypt/R3,2007/02/01                
  47 >A/Gs/Egypt/R4,2007/02/01                ...................T...T............................G...................G..........C..............T........................T...........A...........A.......T.........G......       13     11 ,     13     11      47:>A/Gs/Egypt/R4,2007/02/01                
  48 >A/Egypt/0636-NAMRU3,2007/01/            ...................T...T...........................................................C.........................................................................T..............        6      4 ,      6      4      48:>A/Egypt/0636-NAMRU3,2007/01/            
  49 >A/Egypt/1394-NAMRU3,2007//              .......A...........T...T................................................G.......S..C............R..........................................................................C       11      8 ,     11      8      49:>A/Egypt/1394-NAMRU3,2007//              
  50 >A/Egypt/2289-NAMRU3,2008/03/02          -----..............T..TT................................................G..........C............T...................................G...................A........TA.........       23     15 ,     11     10      50:>A/Egypt/2289-NAMRU3,2008/03/02          
  51 >A/Egypt/2546-NAMRU3,2008/03/08          -----..............T..TT................................................G..........C............A...................................G...................A........T...G......       25     15 ,     13     10      51:>A/Egypt/2546-NAMRU3,2008/03/08          
  52 >A/Ck/Egypt/0847-NLQP,2008/01/18         ...................T...T................................................G........A.C...............................................................................G........       13      6 ,     13      6      52:>A/Ck/Egypt/0847-NLQP,2008/01/18         
  53 >A/Ck/Egypt/9400NAMRU3-CLEVB211,2007//   ........A..........T...T...........A....................................G..........C.....................T................................................................T.       13      8 ,     13      8      53:>A/Ck/Egypt/9400NAMRU3-CLEVB211,2007//   
  54 >A/Egypt/N02752,2009/03/24               ...................T.....................................................................A...........C...T.......................A.............C.T..........GT..............       11      9 ,     11      9      54:>A/Egypt/N02752,2009/03/24               
  55 >A/Egypt/N00606,2009/02/07               ...................T...T.........................G.......................................A.......................................A.............C.T..........GT.........T....       12     10 ,     12     10      55:>A/Egypt/N00606,2009/02/07               
  56 >A/Dk/Egypt/0912-NLQP,2009/02/           ...................TG..T..............................................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     13     13      56:>A/Dk/Egypt/0912-NLQP,2009/02/           
  57 >A/Ck/Egypt/092L-NLQP,2009/02/           ...................TG..T..............................................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     13     13      57:>A/Ck/Egypt/092L-NLQP,2009/02/           
  58 >A/Dk/Egypt/093L-NLQP,2009/02/           ...................T...T....................T.........................T..................A.......................................A.............C.T..........GTA........T.G..       14     13 ,     14     13      58:>A/Dk/Egypt/093L-NLQP,2009/02/           
  59 >A/Egypt/N04527,2009/05/18               ...................T...T..............................A.......................A..........A..................................C....A....A........C.T..........GT..............       13     12 ,     13     12      59:>A/Egypt/N04527,2009/05/18               
  60 >A/Egypt/N03450,2009/04/19               ...................T...T..............................A.A.....................A..........A..................................C....A....A........C.T..........GT..............       15     13 ,     15     13      60:>A/Egypt/N03450,2009/04/19               
  61 >A/Dk/Egypt/0969smL-NLQP,2009/05/        ...................T...T..............................A...................C...A..........A.......................................A....A........C.TT.........GT..............       14     13 ,     13     13      61:>A/Dk/Egypt/0969smL-NLQP,2009/05/        
  62 >A/Dk/Egypt/0930smL-NLQP,2009/02/        ...................T...T.................................................................AC......................................A.............CTT........T.GT..............       15     11 ,     14     11      62:>A/Dk/Egypt/0930smL-NLQP,2009/02/        
  63 >A/Dk/Egypt/0970-NLQP,2009/04/           ............G......T...T................................A................................A..C....................C...............A.............C.T..........GT..............       15     12 ,     14     12      63:>A/Dk/Egypt/0970-NLQP,2009/04/           
  64 >A/Egypt/N05056,2009/06/06               ............G......T...T.................................................................A..C....................................A.............C.T..........GT..............       16     10 ,     16     10      64:>A/Egypt/N05056,2009/06/06               
  65 >A/Dk/Egypt/09349S-NLQP,2009/04/         ----------.........T.................................................................A.....T.........C......C................A........................A...........A.........       34     18 ,     10      8      65:>A/Dk/Egypt/09349S-NLQP,2009/04/         
  66 >A/Egypt/N04394,2009/05/11               ...................T.................................................................A.....T.........C.....A.................A........................A.....................       11      7 ,     11      7      66:>A/Egypt/N04394,2009/05/11               
  67 >A/Egypt/N03228,2009/03/30               ....G............................................G...................A.........................AA...................T.......C............................T..........T.......        9      9 ,      9      9      67:>A/Egypt/N03228,2009/03/30               
  68 >A/Egypt/N03272,2009/04/01               ....G............................................G...................A.........................A....................T.......C............................T..........T.......        9      8 ,      9      8      68:>A/Egypt/N03272,2009/04/01               
  69 >A/Dk/Egypt/09315s-NLQP,2009/04/         ----..............C.........................T.................A........A.........................................................T........................T.................       18     10 ,      9      6      69:>A/Dk/Egypt/09315s-NLQP,2009/04/         
  70 >A/equine/Egypt/av1,2009/03/24           ..........................................................................C...A.......GT...............................................................T....................       11      5 ,     11      5      70:>A/equine/Egypt/av1,2009/03/24           
  71 >A/Ck/Egypt/R2,2007/01/01                ...................T...T..............................................T.G..........C..........................A............................................T................       16      7 ,     16      7      71:>A/Ck/Egypt/R2,2007/01/01                
  72 >A/Ck/Egypt/R6,2007/02/26                ...G..A............T...T................................................G.............GT......................A............T...........A..............................A.....       22     11 ,     22     11      72:>A/Ck/Egypt/R6,2007/02/26                
  73 >A/Ck/Shanxi/2,2006//                    .AG..GA..TTT.GGCGA.T.A.TT..TGCGGCGTA.GCA.GTCTTG.AGCC.T..AT.ACGTGACCC....G..C.AA.TAACCA......CAG..A.CGC.TCTCT.T.GG.A...AGTTA...CGA.GC.A..GGGA.CG.TA.C.......A..........A...TC      118    100 ,    118    100      73:>A/Ck/Shanxi/2,2006//                    
  74 >A/Ck/Hunan/2246,2006//                  ----.G...TTT.GGCGA.T.A.TT.ATGCGGCGTA.GCAAGTCTTGGAGCC.T.GAT.ACGTGACCCG...GC.CAA.ATAACCA..C...CAG..A.CGCACCTCTCT.GG.A...AGTTA...CGA.GC.A..GGGA.CG-----------------------------      200    133 ,    100    100      74:>A/Ck/Hunan/2246,2006//                  
  75 >A/Ck/Hunan/2292,2006//                  .AG..G...TTT.GGCGA.T.A.TT.ATGCGGCGTA.GCAAGTCTTGGAGCC.T.GAT.ACGTGACCCG...GC.CAA.ATAACC...C.C.CAG..A.CGCATCTCTCT.GG.A...AGTTA...CGA.GC.A..GGGA.CG.----------------------------      193    130 ,    102    102      75:>A/Ck/Hunan/2292,2006//                  
                                                                                                                                                                                                                           
---Index--------------------------------------AGACAAGGGCCCAAATAGTCAGCCCCGCATAATACCCAAGGACACAAAGATTACCAGCAGAAGAGTATACCGATTAGCGCCGCTTGACTGAATGAGGGCTATGAACTGTAGAATGGCGGACCCCTGTTGCAGAGGGAAAGATTTCGCTAAGCGCCCACGTGCGAGAGGTACT 
-codon-position------------------------------- 111 1           2         11222 1 1 2 11 1  2 12 1  2  1 21112 2 2 1  1    1212221     21      2    11      1 1   1         1    12 121112         12       1    1        2 
                                              0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111 
                                              0000000001111111222222222222222333333444444444444444455555555555555555555555556666666666666667777777777777777888888888889999999999000000000000001122222333344444444455566666 
                                              2333468992333567001223445666999122399011235556666668900001112333334444567889990011113566778890011233556666779023345667890033388999001111223355662403559489901134568926700126 
                                              7147514030258087466257098178569118619778484691567890201480243234672379283281591214683136461792516325010258142225792279546903627069674568474836585006560492810143870746828761

Yes, those are three posted
viewtopic.php?f=5&t=5218&start=95
and discussed in many prior commentaries
http://www.recombinomics.com/News/02240 ... anges.html
Shanxi and Hunan sequences are clade 7, which is VERY different than clade 2.2 (in Egypt). The additional unpublished sequences with 125del and I147T are not at Genabnk yet, because they are still unpublished. The new sequences are not clade 2.2 and not clade 7, but have 125del and I147T.

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