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gsgs
 Post subject: India sequences
PostPosted: Sat Oct 16, 2010 1:40 am 
Online
User avatar

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1773
Location: germany
repitition from March,2010:
---------------------------------

India:


Code:
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
   1 >A/******/index/2009/02/01      .......................... ............... ............ ............................................... ............ ........... ..... .....   
   2 >A/Delhi/2/2009/10/08           -------------------------- --------------- ------------ ------------......G---------------------------- ------------ ----------- ----- -----   
   5 >A/India/GWMH02/2009/10/        -------------------------- --------------- ------------ ------------------.....C..--------------------- ------------ ----------- ----- -----   
   3 >A/Pune/NIV10604/2009/09/       -------------------------- --------------- ------------ G...C..G............T.........T...G.......T..A. ------------ ----------- ----- -----   
   6 >A/Hyd/NIV51/2009/05/           .....CGC...........CA..... ......C........ AG.T........ ...A....G.....C...........................T.... .A.C...A.... GA.G....T.. ...TA ....A 
   4 >A/Pune/NIV6196/2009/08/        .CC.TCGCC.GC.............C ..GGACC..G....T ......TG.... G...C..........T..............T.TAGT......T.... TA.....A..AT GAGG..C..T. ..... A....   
  
   8 >A/Pune/NIV8489/2009/08/        ..................C..CGTA. T.........CTACT ..G......... .CC...................A....A..............T.... .A..CACATAA. .A.GT...... ..... ...A.   

   7 >A/Blore/NIV310/2009/07/        G..A.C.CCC..CAATT.......A. .T......C...... .....A..CT.. .........G.C..........A...................T.T.. .AG....A..AT .A.G....... .AA.. ..G..   
   9 >A/Pune/NIV6447/2009/08/        .................T.....TA. .......A..CT... ..G.G.....C. .CC...................A...................T.... .A.C...ATAA. GA.GT...... GAA.. ..G..   
  10 >A/Blore/NIV236/2009/06/        ...................C....A. ..............T ...........T ......................A...G.........A..G.AT...C .A.C...A.... GA.G.G.A..C .AA.. .GG..   
  11 >A/Pune/NIV9355/2009/08/        -------------------------- --------------- ------------ .CC...................A..G..........AA.G.AT...C ------------ ----------- ----- -----   
  12 >A/Pune/NIV10278/2009/09/       -------------------------- --------------- ------------ ......G......A........A..G.............G.AT...C ------------ ----------- ----- -----   
  13 >A/Mum/NIV9945/2009/09/         -------------------------- --------------- ------------ ......................A...............GGT.T.... ------------ ----------- ----- -----   
  14 >A/Mum/NIV5442/2009/08/         -------------------------- --------------- ------------ ......................A.....GC............T.... ------------ ----------- ----- -----   
  15 >A/Delhi/NIV3610/2009/08/       -------------------------- --------------- ------------ ............G...G.....A......C............TG... ------------ ----------- ----- -----   
  16 >A/Delhi/NIV3704/2009/09/       -------------------------- --------------- ------------ .....T....A.G....C....A........C.......G..T.... ------------ ----------- ----- -----   
  17 >A/India/GWMH05/2009//          -------------------------- --------------- ------------ ------------------.G..A...--------------------- ------------ ----------- ----- -----   
  18 >A/India/GWMH03/2009//          -------------------------- --------------- ------------ ------------------.G.GA...--------------------- ------------ ----------- ----- -----   
  19 >A/India/GWMH04/2009//          -------------------------- --------------- ------------ ------------------...GA.G.--------------------- ------------ ----------- ----- -----   
  20 >A/India/GWMH01/2009/10/        -------------------------- --------------- ------------ ------------------.G..A.G.--------------------- ------------ ----------- ----- -----   
  21 >A/Cancun-NY/Index/2009/04/15   ........................A. ............... ............ ......................A...................T.... .A.....A..A. .A.G....... .AA.. ..G..   
                                                                                                                                                                                    
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
.
.



.
.

reassortment in Pune/NIV8489
"Russian" mutations A1281G(4) and T1221C(6) in Blore/NIV236/2009/06 but not the others
Blore/NIV236 from June looks also reassorted, it lacks the Cancun G1248A(5) mutation,
same segment 5 as A/Hyd/NIV51 from May, which is pre-Cancun


(Russian is maybe not the correct name, it probably started earlier elsewhere)

2 A716G(4) mutations = D225G(H3) and both also have A1281G(4) !
But other similar sequences have 225D, so this looks like independent development
and not spread. But then, why are 716 and 1281 linked ? And 1281 is synonymous.


---------edit.----------
looks like recombination in HA : 8,9,11 have T11C and T30C , but these are near the start and
could be sequencing errors
then 10,11,12 have A1281G,G1403A and T1691C, although the latter is again near the end
where apparant errors are common

=============================================
table from 2010/05/24


Code:
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
   1 >A/Mexflu/index/2009/02/01            ............. ......... .. ......................... ........ ...... .. . 

pre-Cancun
   8 >A/Hyd/NIV51/2009/05/                 ...CGC...C... ...C..... G. .......................T. .ACA.... GA.G.. .. . 
  10 >A/Dhule/NIV9433/2009/08/             ------------- --------- -- G..C..T........T.G.....T. -------- ------ -- - 
   9 >A/Pune/NIV6196/2009/08/              .CTCGCC.....C GGAC....T .. G..C..T........TAG.....T. TA.A..AT GAGG.C .. .  segment 6 reassorted ?
  11 >A/Pune/NIV10604/2009/09/10           .CT.....AC..C GGA.C.C.T .. G..C...........T.G.....T. TA.A.... .AGG.C .. . 
  12 >A/Pune/NIV807/2009/07/               ------------- --------- -- G..C...........T.G.....T. -------- ------ -- - 
  13 >A/India/GWMH02/2009/10/              ------------- --------- -- -------......------------ -------- ------ -- - 
  14 >A/Mum/NIV968/2009/07/                ------------- --------- -- G..............TA......T. -------- ------ -- - 
  15 >A/Nsk/NIV10348/2009/09/07            G.T....CA.... ..A.....T G. G...........G..T.......T. .A.A.... .A.G.. .. . 

Cancun
   2 >A/Ytml/NIV9438/2009/08/28            G.......A..A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
   3 >A/Delhi/NIV57/2009/06/               ------------- --------- -- ..........A............T. -------- ------ -- - 
   4 >A/Mum/NIV9312/2009/08/               ------------- --------- -- ..........A.G..........T. -------- ------ -- - 
   5 >A/Pune/NIV10278/2009/09/             ------------- --------- -- ..........A.G........GATC -------- ------ -- - 
   6 >A/Pune/NIV9355/2009/08/              ------------- --------- -- .CC.......A.G.....A..GATC -------- ------ -- -  recombination in segment 4 ?
   7 >A/Blore/NIV236/2009/06/              .........C.A. ........T .. ..........A..G....A..GATC .ACA.... GA.G.. AA G 
  16 >A/Delhi/2/2009/10/08                 ------------- --------- -- ----....----------------- -------- ------ -- - 
  17 >A/Pune/NIV21123/2009/12/             ------------- --------- -- ..........A........A.G.T. -------- ------ -- - 
  18 >A/Mum/NIV9945/2009/09/               ------------- --------- -- ..........A..........G.T. -------- ------ -- - 
  19 >A/Delhi/NIV3704/2009/09/             ------------- --------- -- ....G.....A..........G.T. -------- ------ -- - 
  20 >A/Delhi/NIV3610/2009/08/             ------------- --------- -- ....G.....A...C........T. -------- ------ -- - 
  21 >A/Mum/NIV5442/2009/08/               ------------- --------- -- ..........A...C........T. -------- ------ -- - 
  22 >A/Blore/NIV1189/2009/08/             ------------- --------- -- ..........A............T. -------- ------ -- - 
  23 >A/Mum/NIV261/2009/06/                ------------- --------- -- ..........A............T. -------- ------ -- - 
  24 >A/Pune/NIV8489/2009/08/              ..........TA. .....C.TT .G .CC.......A............T. .A.ATAA. .A.GT. .. .  segments 7,8 reassorted ?
  25 >A/Pune/NIV6447/2009/08/              ..........TA. .....C.T. .G .CC.......A............T. .ACATAA. GA.GT. AA G 
  26 >A/Che/NIV658/2009/07/20              ...........A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
  27 >A/Jalna/NIV9436/2009/08/30           .......CA..A. ....C.C.. .. .....T....A..G.........T. .A.A..A. .A.G.. AA G 
  28 >A/Blore/NIV310/2009/07/              ...C.CC....A. ......... .. ..........A............T. .A.A..AT .A.G.. AA G 
  29 >A/swine/UP-India/IVRI01/2009/11/14   ------------- --------- -- .......A..--------------- -------- .A.--- AA - 
  30 >A/Pune/NIV21115/2009/12/             ------------- --------- -- .....T.A..A........AC..T. -------- ------ -- - 
  31 >A/Pune/NIV20007/2009/12/             ------------- --------- -- .....T....A........AC..T. -------- ------ -- - 
  32 >A/India/GWMH05/2009//                ------------- --------- -- -------.G.A..------------ -------- ------ -- - 
  33 >A/India/GWMH01/2009/10/              ------------- --------- -- -------.G.AG.------------ -------- ------ -- - 
  34 >A/India/GWMH04/2009//                ------------- --------- -- -------..GAG.------------ -------- ------ -- - 
  35 >A/India/GWMH03/2009//                ------------- --------- -- -------.GGA..------------ -------- ------ -- - 
  36 >A/Cancun-NY/Index/2009/04/15         ...........A. ......... .. ..........A............T. .A.A..A. .A.G.. AA G 
                                                                                                                     
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
                                                                                                                   .
.
 


.
.

_________________
no patents on genes, publish the GISAID sequences !
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 Profile  
 
gsgs
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 1:59 am 
Online
User avatar

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1773
Location: germany
mixin wrote:
> Concerning A/India/Srinagar/1/2010 H1N1, amino acid positions
> beginning with 331 >RQQKK; is this a new series of mutations
> we should be worrying about?

what enumeration,what segment ?
whas this emntioned somewhere ?
zero google-hits for that sequence
zero google hits for RQQKK and influenza

looks like HA-cleavage site
331*3=993 , close to the end of HA1

_________________
no patents on genes, publish the GISAID sequences !
Top
 Profile  
 
niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 2:39 am 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27279
Location: Pittsburgh, PA USA
gsgs wrote:
repitition from March,2010:
---------------------------------

India:


Code:
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
   1 >A/******/index/2009/02/01      .......................... ............... ............ ............................................... ............ ........... ..... .....   
   2 >A/Delhi/2/2009/10/08           -------------------------- --------------- ------------ ------------......G---------------------------- ------------ ----------- ----- -----   
   5 >A/India/GWMH02/2009/10/        -------------------------- --------------- ------------ ------------------.....C..--------------------- ------------ ----------- ----- -----   
   3 >A/Pune/NIV10604/2009/09/       -------------------------- --------------- ------------ G...C..G............T.........T...G.......T..A. ------------ ----------- ----- -----   
   6 >A/Hyd/NIV51/2009/05/           .....CGC...........CA..... ......C........ AG.T........ ...A....G.....C...........................T.... .A.C...A.... GA.G....T.. ...TA ....A 
   4 >A/Pune/NIV6196/2009/08/        .CC.TCGCC.GC.............C ..GGACC..G....T ......TG.... G...C..........T..............T.TAGT......T.... TA.....A..AT GAGG..C..T. ..... A....   
  
   8 >A/Pune/NIV8489/2009/08/        ..................C..CGTA. T.........CTACT ..G......... .CC...................A....A..............T.... .A..CACATAA. .A.GT...... ..... ...A.   

   7 >A/Blore/NIV310/2009/07/        G..A.C.CCC..CAATT.......A. .T......C...... .....A..CT.. .........G.C..........A...................T.T.. .AG....A..AT .A.G....... .AA.. ..G..   
   9 >A/Pune/NIV6447/2009/08/        .................T.....TA. .......A..CT... ..G.G.....C. .CC...................A...................T.... .A.C...ATAA. GA.GT...... GAA.. ..G..   
  10 >A/Blore/NIV236/2009/06/        ...................C....A. ..............T ...........T ......................A...G.........A..G.AT...C .A.C...A.... GA.G.G.A..C .AA.. .GG..   
  11 >A/Pune/NIV9355/2009/08/        -------------------------- --------------- ------------ .CC...................A..G..........AA.G.AT...C ------------ ----------- ----- -----   
  12 >A/Pune/NIV10278/2009/09/       -------------------------- --------------- ------------ ......G......A........A..G.............G.AT...C ------------ ----------- ----- -----   
  13 >A/Mum/NIV9945/2009/09/         -------------------------- --------------- ------------ ......................A...............GGT.T.... ------------ ----------- ----- -----   
  14 >A/Mum/NIV5442/2009/08/         -------------------------- --------------- ------------ ......................A.....GC............T.... ------------ ----------- ----- -----   
  15 >A/Delhi/NIV3610/2009/08/       -------------------------- --------------- ------------ ............G...G.....A......C............TG... ------------ ----------- ----- -----   
  16 >A/Delhi/NIV3704/2009/09/       -------------------------- --------------- ------------ .....T....A.G....C....A........C.......G..T.... ------------ ----------- ----- -----   
  17 >A/India/GWMH05/2009//          -------------------------- --------------- ------------ ------------------.G..A...--------------------- ------------ ----------- ----- -----   
  18 >A/India/GWMH03/2009//          -------------------------- --------------- ------------ ------------------.G.GA...--------------------- ------------ ----------- ----- -----   
  19 >A/India/GWMH04/2009//          -------------------------- --------------- ------------ ------------------...GA.G.--------------------- ------------ ----------- ----- -----   
  20 >A/India/GWMH01/2009/10/        -------------------------- --------------- ------------ ------------------.G..A.G.--------------------- ------------ ----------- ----- -----   
  21 >A/Cancun-NY/Index/2009/04/15   ........................A. ............... ............ ......................A...................T.... .A.....A..A. .A.G....... .AA.. ..G..   
                                                                                                                                                                                    
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
.
.



.
.

reassortment in Pune/NIV8489
"Russian" mutations A1281G(4) and T1221C(6) in Blore/NIV236/2009/06 but not the others
Blore/NIV236 from June looks also reassorted, it lacks the Cancun G1248A(5) mutation,
same segment 5 as A/Hyd/NIV51 from May, which is pre-Cancun


(Russian is maybe not the correct name, it probably started earlier elsewhere)

2 A716G(4) mutations = D225G(H3) and both also have A1281G(4) !
But other similar sequences have 225D, so this looks like independent development
and not spread. But then, why are 716 and 1281 linked ? And 1281 is synonymous.


---------edit.----------
looks like recombination in HA : 8,9,11 have T11C and T30C , but these are near the start and
could be sequencing errors
then 10,11,12 have A1281G,G1403A and T1691C, although the latter is again near the end
where apparant errors are common

=============================================
table from 2010/05/24


Code:
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
   1 >A/Mexflu/index/2009/02/01            ............. ......... .. ......................... ........ ...... .. . 

pre-Cancun
   8 >A/Hyd/NIV51/2009/05/                 ...CGC...C... ...C..... G. .......................T. .ACA.... GA.G.. .. . 
  10 >A/Dhule/NIV9433/2009/08/             ------------- --------- -- G..C..T........T.G.....T. -------- ------ -- - 
   9 >A/Pune/NIV6196/2009/08/              .CTCGCC.....C GGAC....T .. G..C..T........TAG.....T. TA.A..AT GAGG.C .. .  segment 6 reassorted ?
  11 >A/Pune/NIV10604/2009/09/10           .CT.....AC..C GGA.C.C.T .. G..C...........T.G.....T. TA.A.... .AGG.C .. . 
  12 >A/Pune/NIV807/2009/07/               ------------- --------- -- G..C...........T.G.....T. -------- ------ -- - 
  13 >A/India/GWMH02/2009/10/              ------------- --------- -- -------......------------ -------- ------ -- - 
  14 >A/Mum/NIV968/2009/07/                ------------- --------- -- G..............TA......T. -------- ------ -- - 
  15 >A/Nsk/NIV10348/2009/09/07            G.T....CA.... ..A.....T G. G...........G..T.......T. .A.A.... .A.G.. .. . 

Cancun
   2 >A/Ytml/NIV9438/2009/08/28            G.......A..A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
   3 >A/Delhi/NIV57/2009/06/               ------------- --------- -- ..........A............T. -------- ------ -- - 
   4 >A/Mum/NIV9312/2009/08/               ------------- --------- -- ..........A.G..........T. -------- ------ -- - 
   5 >A/Pune/NIV10278/2009/09/             ------------- --------- -- ..........A.G........GATC -------- ------ -- - 
   6 >A/Pune/NIV9355/2009/08/              ------------- --------- -- .CC.......A.G.....A..GATC -------- ------ -- -  recombination in segment 4 ?
   7 >A/Blore/NIV236/2009/06/              .........C.A. ........T .. ..........A..G....A..GATC .ACA.... GA.G.. AA G 
  16 >A/Delhi/2/2009/10/08                 ------------- --------- -- ----....----------------- -------- ------ -- - 
  17 >A/Pune/NIV21123/2009/12/             ------------- --------- -- ..........A........A.G.T. -------- ------ -- - 
  18 >A/Mum/NIV9945/2009/09/               ------------- --------- -- ..........A..........G.T. -------- ------ -- - 
  19 >A/Delhi/NIV3704/2009/09/             ------------- --------- -- ....G.....A..........G.T. -------- ------ -- - 
  20 >A/Delhi/NIV3610/2009/08/             ------------- --------- -- ....G.....A...C........T. -------- ------ -- - 
  21 >A/Mum/NIV5442/2009/08/               ------------- --------- -- ..........A...C........T. -------- ------ -- - 
  22 >A/Blore/NIV1189/2009/08/             ------------- --------- -- ..........A............T. -------- ------ -- - 
  23 >A/Mum/NIV261/2009/06/                ------------- --------- -- ..........A............T. -------- ------ -- - 
  24 >A/Pune/NIV8489/2009/08/              ..........TA. .....C.TT .G .CC.......A............T. .A.ATAA. .A.GT. .. .  segments 7,8 reassorted ?
  25 >A/Pune/NIV6447/2009/08/              ..........TA. .....C.T. .G .CC.......A............T. .ACATAA. GA.GT. AA G 
  26 >A/Che/NIV658/2009/07/20              ...........A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
  27 >A/Jalna/NIV9436/2009/08/30           .......CA..A. ....C.C.. .. .....T....A..G.........T. .A.A..A. .A.G.. AA G 
  28 >A/Blore/NIV310/2009/07/              ...C.CC....A. ......... .. ..........A............T. .A.A..AT .A.G.. AA G 
  29 >A/swine/UP-India/IVRI01/2009/11/14   ------------- --------- -- .......A..--------------- -------- .A.--- AA - 
  30 >A/Pune/NIV21115/2009/12/             ------------- --------- -- .....T.A..A........AC..T. -------- ------ -- - 
  31 >A/Pune/NIV20007/2009/12/             ------------- --------- -- .....T....A........AC..T. -------- ------ -- - 
  32 >A/India/GWMH05/2009//                ------------- --------- -- -------.G.A..------------ -------- ------ -- - 
  33 >A/India/GWMH01/2009/10/              ------------- --------- -- -------.G.AG.------------ -------- ------ -- - 
  34 >A/India/GWMH04/2009//                ------------- --------- -- -------..GAG.------------ -------- ------ -- - 
  35 >A/India/GWMH03/2009//                ------------- --------- -- -------.GGA..------------ -------- ------ -- - 
  36 >A/Cancun-NY/Index/2009/04/15         ...........A. ......... .. ..........A............T. .A.A..A. .A.G.. AA G 
                                                                                                                     
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
                                                                                                                   .
.
 


.
.

Please stop with the nonsense about sequencing errors. It was VERY old many years ago,

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niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 2:45 am 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27279
Location: Pittsburgh, PA USA
gsgs wrote:
repitition from March,2010:
---------------------------------

India:


Code:
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
   1 >A/******/index/2009/02/01      .......................... ............... ............ ............................................... ............ ........... ..... .....   
   2 >A/Delhi/2/2009/10/08           -------------------------- --------------- ------------ ------------......G---------------------------- ------------ ----------- ----- -----   
   5 >A/India/GWMH02/2009/10/        -------------------------- --------------- ------------ ------------------.....C..--------------------- ------------ ----------- ----- -----   
   3 >A/Pune/NIV10604/2009/09/       -------------------------- --------------- ------------ G...C..G............T.........T...G.......T..A. ------------ ----------- ----- -----   
   6 >A/Hyd/NIV51/2009/05/           .....CGC...........CA..... ......C........ AG.T........ ...A....G.....C...........................T.... .A.C...A.... GA.G....T.. ...TA ....A 
   4 >A/Pune/NIV6196/2009/08/        .CC.TCGCC.GC.............C ..GGACC..G....T ......TG.... G...C..........T..............T.TAGT......T.... TA.....A..AT GAGG..C..T. ..... A....   
  
   8 >A/Pune/NIV8489/2009/08/        ..................C..CGTA. T.........CTACT ..G......... .CC...................A....A..............T.... .A..CACATAA. .A.GT...... ..... ...A.   

   7 >A/Blore/NIV310/2009/07/        G..A.C.CCC..CAATT.......A. .T......C...... .....A..CT.. .........G.C..........A...................T.T.. .AG....A..AT .A.G....... .AA.. ..G..   
   9 >A/Pune/NIV6447/2009/08/        .................T.....TA. .......A..CT... ..G.G.....C. .CC...................A...................T.... .A.C...ATAA. GA.GT...... GAA.. ..G..   
  10 >A/Blore/NIV236/2009/06/        ...................C....A. ..............T ...........T ......................A...G.........A..G.AT...C .A.C...A.... GA.G.G.A..C .AA.. .GG..   
  11 >A/Pune/NIV9355/2009/08/        -------------------------- --------------- ------------ .CC...................A..G..........AA.G.AT...C ------------ ----------- ----- -----   
  12 >A/Pune/NIV10278/2009/09/       -------------------------- --------------- ------------ ......G......A........A..G.............G.AT...C ------------ ----------- ----- -----   
  13 >A/Mum/NIV9945/2009/09/         -------------------------- --------------- ------------ ......................A...............GGT.T.... ------------ ----------- ----- -----   
  14 >A/Mum/NIV5442/2009/08/         -------------------------- --------------- ------------ ......................A.....GC............T.... ------------ ----------- ----- -----   
  15 >A/Delhi/NIV3610/2009/08/       -------------------------- --------------- ------------ ............G...G.....A......C............TG... ------------ ----------- ----- -----   
  16 >A/Delhi/NIV3704/2009/09/       -------------------------- --------------- ------------ .....T....A.G....C....A........C.......G..T.... ------------ ----------- ----- -----   
  17 >A/India/GWMH05/2009//          -------------------------- --------------- ------------ ------------------.G..A...--------------------- ------------ ----------- ----- -----   
  18 >A/India/GWMH03/2009//          -------------------------- --------------- ------------ ------------------.G.GA...--------------------- ------------ ----------- ----- -----   
  19 >A/India/GWMH04/2009//          -------------------------- --------------- ------------ ------------------...GA.G.--------------------- ------------ ----------- ----- -----   
  20 >A/India/GWMH01/2009/10/        -------------------------- --------------- ------------ ------------------.G..A.G.--------------------- ------------ ----------- ----- -----   
  21 >A/Cancun-NY/Index/2009/04/15   ........................A. ............... ............ ......................A...................T.... .A.....A..A. .A.G....... .AA.. ..G..   
                                                                                                                                                                                    
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
.
.



.
.

reassortment in Pune/NIV8489
"Russian" mutations A1281G(4) and T1221C(6) in Blore/NIV236/2009/06 but not the others
Blore/NIV236 from June looks also reassorted, it lacks the Cancun G1248A(5) mutation,
same segment 5 as A/Hyd/NIV51 from May, which is pre-Cancun


(Russian is maybe not the correct name, it probably started earlier elsewhere)

2 A716G(4) mutations = D225G(H3) and both also have A1281G(4) !
But other similar sequences have 225D, so this looks like independent development
and not spread. But then, why are 716 and 1281 linked ? And 1281 is synonymous.


---------edit.----------
looks like recombination in HA : 8,9,11 have T11C and T30C , but these are near the start and
could be sequencing errors
then 10,11,12 have A1281G,G1403A and T1691C, although the latter is again near the end
where apparant errors are common

=============================================
table from 2010/05/24


Code:
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
   1 >A/Mexflu/index/2009/02/01            ............. ......... .. ......................... ........ ...... .. . 

pre-Cancun
   8 >A/Hyd/NIV51/2009/05/                 ...CGC...C... ...C..... G. .......................T. .ACA.... GA.G.. .. . 
  10 >A/Dhule/NIV9433/2009/08/             ------------- --------- -- G..C..T........T.G.....T. -------- ------ -- - 
   9 >A/Pune/NIV6196/2009/08/              .CTCGCC.....C GGAC....T .. G..C..T........TAG.....T. TA.A..AT GAGG.C .. .  segment 6 reassorted ?
  11 >A/Pune/NIV10604/2009/09/10           .CT.....AC..C GGA.C.C.T .. G..C...........T.G.....T. TA.A.... .AGG.C .. . 
  12 >A/Pune/NIV807/2009/07/               ------------- --------- -- G..C...........T.G.....T. -------- ------ -- - 
  13 >A/India/GWMH02/2009/10/              ------------- --------- -- -------......------------ -------- ------ -- - 
  14 >A/Mum/NIV968/2009/07/                ------------- --------- -- G..............TA......T. -------- ------ -- - 
  15 >A/Nsk/NIV10348/2009/09/07            G.T....CA.... ..A.....T G. G...........G..T.......T. .A.A.... .A.G.. .. . 

Cancun
   2 >A/Ytml/NIV9438/2009/08/28            G.......A..A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
   3 >A/Delhi/NIV57/2009/06/               ------------- --------- -- ..........A............T. -------- ------ -- - 
   4 >A/Mum/NIV9312/2009/08/               ------------- --------- -- ..........A.G..........T. -------- ------ -- - 
   5 >A/Pune/NIV10278/2009/09/             ------------- --------- -- ..........A.G........GATC -------- ------ -- - 
   6 >A/Pune/NIV9355/2009/08/              ------------- --------- -- .CC.......A.G.....A..GATC -------- ------ -- -  recombination in segment 4 ?
   7 >A/Blore/NIV236/2009/06/              .........C.A. ........T .. ..........A..G....A..GATC .ACA.... GA.G.. AA G 
  16 >A/Delhi/2/2009/10/08                 ------------- --------- -- ----....----------------- -------- ------ -- - 
  17 >A/Pune/NIV21123/2009/12/             ------------- --------- -- ..........A........A.G.T. -------- ------ -- - 
  18 >A/Mum/NIV9945/2009/09/               ------------- --------- -- ..........A..........G.T. -------- ------ -- - 
  19 >A/Delhi/NIV3704/2009/09/             ------------- --------- -- ....G.....A..........G.T. -------- ------ -- - 
  20 >A/Delhi/NIV3610/2009/08/             ------------- --------- -- ....G.....A...C........T. -------- ------ -- - 
  21 >A/Mum/NIV5442/2009/08/               ------------- --------- -- ..........A...C........T. -------- ------ -- - 
  22 >A/Blore/NIV1189/2009/08/             ------------- --------- -- ..........A............T. -------- ------ -- - 
  23 >A/Mum/NIV261/2009/06/                ------------- --------- -- ..........A............T. -------- ------ -- - 
  24 >A/Pune/NIV8489/2009/08/              ..........TA. .....C.TT .G .CC.......A............T. .A.ATAA. .A.GT. .. .  segments 7,8 reassorted ?
  25 >A/Pune/NIV6447/2009/08/              ..........TA. .....C.T. .G .CC.......A............T. .ACATAA. GA.GT. AA G 
  26 >A/Che/NIV658/2009/07/20              ...........A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
  27 >A/Jalna/NIV9436/2009/08/30           .......CA..A. ....C.C.. .. .....T....A..G.........T. .A.A..A. .A.G.. AA G 
  28 >A/Blore/NIV310/2009/07/              ...C.CC....A. ......... .. ..........A............T. .A.A..AT .A.G.. AA G 
  29 >A/swine/UP-India/IVRI01/2009/11/14   ------------- --------- -- .......A..--------------- -------- .A.--- AA - 
  30 >A/Pune/NIV21115/2009/12/             ------------- --------- -- .....T.A..A........AC..T. -------- ------ -- - 
  31 >A/Pune/NIV20007/2009/12/             ------------- --------- -- .....T....A........AC..T. -------- ------ -- - 
  32 >A/India/GWMH05/2009//                ------------- --------- -- -------.G.A..------------ -------- ------ -- - 
  33 >A/India/GWMH01/2009/10/              ------------- --------- -- -------.G.AG.------------ -------- ------ -- - 
  34 >A/India/GWMH04/2009//                ------------- --------- -- -------..GAG.------------ -------- ------ -- - 
  35 >A/India/GWMH03/2009//                ------------- --------- -- -------.GGA..------------ -------- ------ -- - 
  36 >A/Cancun-NY/Index/2009/04/15         ...........A. ......... .. ..........A............T. .A.A..A. .A.G.. AA G 
                                                                                                                     
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
                                                                                                                   .
.
 


.
.

Yes, your naming of polymorphisms is a joke. A1281G was in the Ukraine sequences, which also have clear time and space clustering of D225G and D225N (on MULTIPLE backgrounds).

D225G is widespread in H1 swine as well is earlier H1 human (including 1918). You really have no clue on polymorphism pedigrees and the relationship between swine and human sequences, even though pandemic H1N1 is SWINE.

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niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 2:52 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 27279
Location: Pittsburgh, PA USA
gsgs wrote:
mixin wrote:
> Concerning A/India/Srinagar/1/2010 H1N1, amino acid positions
> beginning with 331 >RQQKK; is this a new series of mutations
> we should be worrying about?

what enumeration,what segment ?
whas this emntioned somewhere ?
zero google-hits for that sequence
zero google hits for RQQKK and influenza

looks like HA-cleavage site
331*3=993 , close to the end of HA1

Try googling polybasic cleavage site (and then get a medical dictionary for polybasic - or read about highly pathogenic influenza H5N1).
Your lack of any understanding (at the most BASIC level, literally and figuratively) of influenza genetic remains profound (which has been the case for YEARS),

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niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 11:34 am 
Offline

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27279
Location: Pittsburgh, PA USA
gsgs wrote:
repitition from March,2010:
---------------------------------

India:


Code:
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
   1 >A/******/index/2009/02/01      .......................... ............... ............ ............................................... ............ ........... ..... .....   
   2 >A/Delhi/2/2009/10/08           -------------------------- --------------- ------------ ------------......G---------------------------- ------------ ----------- ----- -----   
   5 >A/India/GWMH02/2009/10/        -------------------------- --------------- ------------ ------------------.....C..--------------------- ------------ ----------- ----- -----   
   3 >A/Pune/NIV10604/2009/09/       -------------------------- --------------- ------------ G...C..G............T.........T...G.......T..A. ------------ ----------- ----- -----   
   6 >A/Hyd/NIV51/2009/05/           .....CGC...........CA..... ......C........ AG.T........ ...A....G.....C...........................T.... .A.C...A.... GA.G....T.. ...TA ....A 
   4 >A/Pune/NIV6196/2009/08/        .CC.TCGCC.GC.............C ..GGACC..G....T ......TG.... G...C..........T..............T.TAGT......T.... TA.....A..AT GAGG..C..T. ..... A....   
  
   8 >A/Pune/NIV8489/2009/08/        ..................C..CGTA. T.........CTACT ..G......... .CC...................A....A..............T.... .A..CACATAA. .A.GT...... ..... ...A.   

   7 >A/Blore/NIV310/2009/07/        G..A.C.CCC..CAATT.......A. .T......C...... .....A..CT.. .........G.C..........A...................T.T.. .AG....A..AT .A.G....... .AA.. ..G..   
   9 >A/Pune/NIV6447/2009/08/        .................T.....TA. .......A..CT... ..G.G.....C. .CC...................A...................T.... .A.C...ATAA. GA.GT...... GAA.. ..G..   
  10 >A/Blore/NIV236/2009/06/        ...................C....A. ..............T ...........T ......................A...G.........A..G.AT...C .A.C...A.... GA.G.G.A..C .AA.. .GG..   
  11 >A/Pune/NIV9355/2009/08/        -------------------------- --------------- ------------ .CC...................A..G..........AA.G.AT...C ------------ ----------- ----- -----   
  12 >A/Pune/NIV10278/2009/09/       -------------------------- --------------- ------------ ......G......A........A..G.............G.AT...C ------------ ----------- ----- -----   
  13 >A/Mum/NIV9945/2009/09/         -------------------------- --------------- ------------ ......................A...............GGT.T.... ------------ ----------- ----- -----   
  14 >A/Mum/NIV5442/2009/08/         -------------------------- --------------- ------------ ......................A.....GC............T.... ------------ ----------- ----- -----   
  15 >A/Delhi/NIV3610/2009/08/       -------------------------- --------------- ------------ ............G...G.....A......C............TG... ------------ ----------- ----- -----   
  16 >A/Delhi/NIV3704/2009/09/       -------------------------- --------------- ------------ .....T....A.G....C....A........C.......G..T.... ------------ ----------- ----- -----   
  17 >A/India/GWMH05/2009//          -------------------------- --------------- ------------ ------------------.G..A...--------------------- ------------ ----------- ----- -----   
  18 >A/India/GWMH03/2009//          -------------------------- --------------- ------------ ------------------.G.GA...--------------------- ------------ ----------- ----- -----   
  19 >A/India/GWMH04/2009//          -------------------------- --------------- ------------ ------------------...GA.G.--------------------- ------------ ----------- ----- -----   
  20 >A/India/GWMH01/2009/10/        -------------------------- --------------- ------------ ------------------.G..A.G.--------------------- ------------ ----------- ----- -----   
  21 >A/Cancun-NY/Index/2009/04/15   ........................A. ............... ............ ......................A...................T.... .A.....A..A. .A.G....... .AA.. ..G..   
                                                                                                                                                                                    
---Index-----------------------------ATGTCTATTTTGAGGCGATGGGACGT CCAAGATTAATCGTC CAACTCCCTGAA ATTGTCAACAGAAGAAATAAGCTAAAAGCAGTGGACGTAACGCAGGT CGAAATTGCGGA AGAACTACCAT AGGCG GAAGG   
-codon-position----------------------               1       1   21    1         2      2  1  12 1 1          1  2 1121221     1       21   2  1 1         1121 1 1        1 1 112   
                                     00000000000011111111111222 000000001111122 000000001111 00000000000000000000000000000000011111111111111 000000011111 00000000011 00000 00000   
                                     44688999999914444446899011 124566773455700 011345784578 00000111233344445555556667778999900111223444446 223699912223 03577779912 44668 01348   
                                     11168566777891223598124766 868706682713317 869451612946 01344789656713791145775781159233468056588003799 398966741445 81646680582 29099 89661   
                                     47278736258143231240207136 259339069923736 382533522010 41038262470875481901678426917403266781413384371 481469838589 86625631421 32062 28705   
.
.



.
.

reassortment in Pune/NIV8489
"Russian" mutations A1281G(4) and T1221C(6) in Blore/NIV236/2009/06 but not the others
Blore/NIV236 from June looks also reassorted, it lacks the Cancun G1248A(5) mutation,
same segment 5 as A/Hyd/NIV51 from May, which is pre-Cancun


(Russian is maybe not the correct name, it probably started earlier elsewhere)

2 A716G(4) mutations = D225G(H3) and both also have A1281G(4) !
But other similar sequences have 225D, so this looks like independent development
and not spread. But then, why are 716 and 1281 linked ? And 1281 is synonymous.


---------edit.----------
looks like recombination in HA : 8,9,11 have T11C and T30C , but these are near the start and
could be sequencing errors
then 10,11,12 have A1281G,G1403A and T1691C, although the latter is again near the end
where apparant errors are common

=============================================
table from 2010/05/24


Code:
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
   1 >A/Mexflu/index/2009/02/01            ............. ......... .. ......................... ........ ...... .. . 

pre-Cancun
   8 >A/Hyd/NIV51/2009/05/                 ...CGC...C... ...C..... G. .......................T. .ACA.... GA.G.. .. . 
  10 >A/Dhule/NIV9433/2009/08/             ------------- --------- -- G..C..T........T.G.....T. -------- ------ -- - 
   9 >A/Pune/NIV6196/2009/08/              .CTCGCC.....C GGAC....T .. G..C..T........TAG.....T. TA.A..AT GAGG.C .. .  segment 6 reassorted ?
  11 >A/Pune/NIV10604/2009/09/10           .CT.....AC..C GGA.C.C.T .. G..C...........T.G.....T. TA.A.... .AGG.C .. . 
  12 >A/Pune/NIV807/2009/07/               ------------- --------- -- G..C...........T.G.....T. -------- ------ -- - 
  13 >A/India/GWMH02/2009/10/              ------------- --------- -- -------......------------ -------- ------ -- - 
  14 >A/Mum/NIV968/2009/07/                ------------- --------- -- G..............TA......T. -------- ------ -- - 
  15 >A/Nsk/NIV10348/2009/09/07            G.T....CA.... ..A.....T G. G...........G..T.......T. .A.A.... .A.G.. .. . 

Cancun
   2 >A/Ytml/NIV9438/2009/08/28            G.......A..A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
   3 >A/Delhi/NIV57/2009/06/               ------------- --------- -- ..........A............T. -------- ------ -- - 
   4 >A/Mum/NIV9312/2009/08/               ------------- --------- -- ..........A.G..........T. -------- ------ -- - 
   5 >A/Pune/NIV10278/2009/09/             ------------- --------- -- ..........A.G........GATC -------- ------ -- - 
   6 >A/Pune/NIV9355/2009/08/              ------------- --------- -- .CC.......A.G.....A..GATC -------- ------ -- -  recombination in segment 4 ?
   7 >A/Blore/NIV236/2009/06/              .........C.A. ........T .. ..........A..G....A..GATC .ACA.... GA.G.. AA G 
  16 >A/Delhi/2/2009/10/08                 ------------- --------- -- ----....----------------- -------- ------ -- - 
  17 >A/Pune/NIV21123/2009/12/             ------------- --------- -- ..........A........A.G.T. -------- ------ -- - 
  18 >A/Mum/NIV9945/2009/09/               ------------- --------- -- ..........A..........G.T. -------- ------ -- - 
  19 >A/Delhi/NIV3704/2009/09/             ------------- --------- -- ....G.....A..........G.T. -------- ------ -- - 
  20 >A/Delhi/NIV3610/2009/08/             ------------- --------- -- ....G.....A...C........T. -------- ------ -- - 
  21 >A/Mum/NIV5442/2009/08/               ------------- --------- -- ..........A...C........T. -------- ------ -- - 
  22 >A/Blore/NIV1189/2009/08/             ------------- --------- -- ..........A............T. -------- ------ -- - 
  23 >A/Mum/NIV261/2009/06/                ------------- --------- -- ..........A............T. -------- ------ -- - 
  24 >A/Pune/NIV8489/2009/08/              ..........TA. .....C.TT .G .CC.......A............T. .A.ATAA. .A.GT. .. .  segments 7,8 reassorted ?
  25 >A/Pune/NIV6447/2009/08/              ..........TA. .....C.T. .G .CC.......A............T. .ACATAA. GA.GT. AA G 
  26 >A/Che/NIV658/2009/07/20              ...........A. ....C.C.. .. ..........A............T. .A.A..A. .A.G.. AA G 
  27 >A/Jalna/NIV9436/2009/08/30           .......CA..A. ....C.C.. .. .....T....A..G.........T. .A.A..A. .A.G.. AA G 
  28 >A/Blore/NIV310/2009/07/              ...C.CC....A. ......... .. ..........A............T. .A.A..AT .A.G.. AA G 
  29 >A/swine/UP-India/IVRI01/2009/11/14   ------------- --------- -- .......A..--------------- -------- .A.--- AA - 
  30 >A/Pune/NIV21115/2009/12/             ------------- --------- -- .....T.A..A........AC..T. -------- ------ -- - 
  31 >A/Pune/NIV20007/2009/12/             ------------- --------- -- .....T....A........AC..T. -------- ------ -- - 
  32 >A/India/GWMH05/2009//                ------------- --------- -- -------.G.A..------------ -------- ------ -- - 
  33 >A/India/GWMH01/2009/10/              ------------- --------- -- -------.G.AG.------------ -------- ------ -- - 
  34 >A/India/GWMH04/2009//                ------------- --------- -- -------..GAG.------------ -------- ------ -- - 
  35 >A/India/GWMH03/2009//                ------------- --------- -- -------.GGA..------------ -------- ------ -- - 
  36 >A/Cancun-NY/Index/2009/04/15         ...........A. ......... .. ..........A............T. .A.A..A. .A.G.. AA G 
                                                                                                                     
---Index-----------------------------------CTCTATTAGGCGT AAGTTTTCC AA ATTTACAGACTAAAAGGAGGTAGCT CGAGCGGA AGAACA GG A 
-codon-position----------------------------2         1      1         12      211122  1  1  212  11      1121      1 
                                           0000000111222 000011112 00 0000000000000000111111111 00011111 000000 00 0 
                                           0489999666011 456755550 11 0000444555667799001112446 22612223 035777 46 3 
                                           3185667568766 870601137 69 0134189357581123685798009 39941445 816468 90 6 
                                           5787362950136 933092536 82 4108738117826940668111381 48438589 866253 20 7 
                                                                                                                   .
.
 


.
.

Here is the GISAID pedigree for T30C, which has been identified by MANY labs (including the CDC) and frequently is in multile sequences from the same geographic region (like India, Singapore, Guangdong).

You CONTINUE to post UTTER nonsense:

EPI287008 A/Ghana/FS-10-4009/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280308 A/Santiago/14851/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278909 A/Puerto Montt/11868/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276298 A/ENG/707/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273917 A/Puerto Montt/12498/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273914 A/Castro/12274/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273911 A/Puerto Montt/11868/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI266480 A/Guangdong/1240/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI266111 A/Guangdong-Zhenjiang/SWL176/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI266103 A/Guangdong-Wujiang/SWL51/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263507 A/Singapore/ON2400/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263463 A/Singapore/KK081/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263458 A/Singapore/KK066/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263445 A/Singapore/GP737/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263440 A/Singapore/GP562/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257984 A/Guangxi-Longan/SWL1979/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257740 A/Fujian-Gulou/SWL1257/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257384 A/Chongqing-Yongchuan/SWL5226/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257284 A/Fujian-Gulou/SWL11875/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257280 A/Fujian-Gulou/SWL11954/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257276 A/Fujian-Gulou/SWL11951/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257264 A/Hebei-Yuhua/SWL1442/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256502 A/Guangdong-Luohu/SWL1808/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256478 A/Guangdong/SWL36/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256426 A/Guangdong-Futian/SWL1562/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256422 A/Guangdong-Futian/SWL1559/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256418 A/Guangdong-Luohu/SWL1755/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256374 A/Beijing-Huairou/SWL11005/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256366 A/Shanxi-Yuci/SWL352/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256346 A/Beijing-Huairou/SWL11032/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256166 A/Guangdong-Luohu/SWL1712/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256106 A/Beijing-Huairou/SWL1856/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI253751 A/Berlin/88/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI253709 A/Bayern/75/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247095 A/Pune/NIV9355/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247090 A/Pune/NIV8489/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247082 A/Pune/NIV6447/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI246391 A/Germany-BY/74/09 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI245468 A/Pensacola/INS40/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI241774 A/Sulaimani/05/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI232918 A/India/8489/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI183370 A/Paris/2650/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI177573 A/swine/Hong Kong/9656/2001 (A/H1N1) segment 4 (HA) 52.8 0.00000

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gsgs
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 12:18 pm 
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Location: germany
do those have C at position 11 and 30 ?


OK, from your lists I get 5 with 11C and 30C:
------------------------------------------------------------------
A/Guangdong/SWL36/2009 (A/H1N1 swl)
A/Pune/NIV9355/2009 (A/H1N1 swl)
A/Pune/NIV8489/2009 (A/H1N1 swl)
A/Pune/NIV6447/2009 (A/H1N1 swl)
A/India/8489/2009 (A/H1N1 swl)
------------------------------------------------------

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Last edited by gsgs on Sat Oct 16, 2010 12:30 pm, edited 1 time in total.

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niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 12:24 pm 
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Posts: 27279
Location: Pittsburgh, PA USA
gsgs wrote:
do those have C at position 11 and 30 ?

The sequences from India (in bold) have C at positions 11 and 30.

T11C pedigree

EPI280347 A/Kenya/3863/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278374 A/Ghana/FS-09-1183/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277641 A/Bishkek/WR0881T/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271323 A/Brussels/INS243/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256478 A/Guangdong/SWL36/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI255807 A/Thailand/THB0405/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247095 A/Pune/NIV9355/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247090 A/Pune/NIV8489/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247082 A/Pune/NIV6447/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI245755 A/ENG/92900391/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI232996 A/SAPPORO/464/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI232918 A/India/8489/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI218111 A/New York/4567/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI212697 A/New York/3463/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI255235 A/Ghana/N12975/2009 (A/H1N1 swl) segment 4 (HA) 49.1 0.00000

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gsgs
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 12:41 pm 
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India/8489 is the same as Pune/8489 ?

A/Guangdong/SWL36/2009
would be interesting

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niman
 Post subject: Re: India sequences
PostPosted: Sat Oct 16, 2010 1:01 pm 
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And why would that be? India is already compelling.

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