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gsgs
 Post subject: recombinations
PostPosted: Sat Dec 25, 2010 8:52 am 
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Posts: 1806
Location: germany
American and Eurasian avian flu recombined in PB2
of A/mallard/Sweden/49/02(H5N9),2002//


Code:
>A/mallard/Sweden/46/02(H4N3),2002/11/14
>A/mallard/Sweden/49/02(H5N9),2002//
............................................................ 0 
............................................................ 0 
...........o................................................ 1 
............................................................ 0 
.....o........o............................................. 2 
.............o.....o............o....................o...... 4 
........o...........................o....................... 2 
.................o.......................................... 1 
.............................o.............................. 1 
....................o.....................o....o............ 3 
............................................................ 0 
................................o........................... 1 
...................................o........................ 1 
.........................................o........o......... 2 
.....o.......................o.............................. 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
....................o.......................o............... 2 
...........................o.........................o...... 2 
..o.....o..............o........o..o.....o..o.....oo....o... 10 
.....o..o..o...........o..o..o............o.......o......... 8 
........o...o.o..o................................o.....o... 6 
.....o.....o..o...........o..o..o........o..o..o...o.o...... 11 
.....o........o........o........o...o.o..o..o..o.....o.....o 11 
..o..o..o..o........oo..........o..o..............o..o.....o 11 
.....o...o.o.....o.....o..o..o.....o..o..o...........o...... 11 
.....o..o..o.....o..o..o..o.....o.....o..o.............o.... 11 
..o...........o..o..o..o......o....o..............o........o 9 
..o..oo....o........o........o..o..o.....o..o........o...... 11 
...........o........o..o..............o...........o..o..o..o 8 
.....o..o..............o...........o.....o..o..o........o..o 9 
..o..o.................o..o........o.....o........o..o...... 8 
..o...........o.....o..o..o..o.................o............ 7 
..o..o.....o........o.....o..oo..........o..o...o..........o 11 
.....o........o.................o..oo.............o..o..o... 8 
............o.o..o.......................................... 3 
............................................................ 0 
-- 177 


 177 ( 2280 )+ 177 ( 2280 )
.


.

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

Code:

>A/mallard/Sweden/49/02(H5N9),2002//
>A/blue-winged teal/Minnesota/Sg-00226/06(H3N8),2006/09/30
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
------------------------------------------------------------ 0 
-------------------------------.o........o..o...........o... 4 
............................................................ 0 
...........o...................................o............ 2 
............................................................ 0 
..................................................o......... 1 
............................................................ 0 
..........................o...o..........o..o...........o... 5 
.........o.o..o...o......................................... 4 
.......................................................o...o 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
........o................................................... 1 
............................................................ 0 
.......................o.................................... 1 
............................................................ 0 
-- 20 


 20 ( 1109 )+ 20 ( 1109 )
.

.

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Last edited by gsgs on Sat Dec 25, 2010 11:24 pm, edited 1 time in total.

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gsgs
 Post subject: Re: recombinations
PostPosted: Sat Dec 25, 2010 9:14 am 
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Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1806
Location: germany
Swedish sequence, but sampled in USA, which is unusual for Swedish sequences.
No such recombination of American and Eurasian PB2 in any of the
numerous Swedish sequences sampled in Sweden or Netherlands



Southeast Poultry Research Laboratory, USDA
Agriculture Research Service, 934 College Station Rd, Athens, GA
30605, USA

/note="passaged in allantoic fluid"

http://www.ncbi.nlm.nih.gov/nuccore/GU052875?

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gsgs
 Post subject: Re: recombinations
PostPosted: Wed Apr 20, 2011 12:40 am 
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Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1806
Location: germany
Code:
>A/Mexflu/index/2009/02/01
>A/swine/Thailand/CU-RP1/2010,2010/09/
......................................o..o.oo.oo............ 6 
................oo...o...............oo.....oo......o.....oo 10 
o.ooo..oo...........oo.....o................................ 9 
o............................o.............................. 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.........................................................o.. 1 
.........................................................o.. 1 
.............................o.............................. 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
..............................o............................. 1 
............................................................ 0 
............................................................ 0 
...............................................o............ 1 
...........................o.....................o.......... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.....................-- 34 


 34 ( 1701 )+ 34 ( 1701 )
.
.

.
.



Code:
>A/swine/Thailand/CU-DP83/2010,2010/12/
>A/swine/Thailand/CU-PL63/2010,2010/11/
------------------------------------------------------------ 0 
------...................................................... 0 
.......................o.......................o............ 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
..........................o................................. 1 
...................................o........................ 1 
......................o..................................... 1 
....o...............o..................o.................o.. 4 
..........................................................o. 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
........o................................................... 1 
......................o.................................o... 2 
........o................................................... 1 
............................................................ 0 
............................................................ 0 
...................................o..................------ 1 
----------------------- 15 


 15 ( 1608 )+ 15 ( 1608 )

.
.

.
.

Code:
                                               000000000000000000000000000000011111111111111111111111111 
                                               001112444444555555566666789999900000001334444466666666666 
                                               024681114799013467902459132357901458897260033457788999999 
                                               484810787505260833851080901054652760681983807965789134579 
-codon-position--------------------------------11  1  1 11 1 222 12 11 22  12  1     1  212   1 2 212 21 
---Index---------------------------------------ATCGCTATAAAACAATACTGTGTAAACGAACGGCTGACGGTGCTCACTTGATTGTTT 
   1 >A/Mexflu/index/2009/02/01                .........................................................        0      0 ,      0      0       1:>A/Mexflu/index/2009/02/01                
   2 >A/swine/Thailand/CU-RP3/2010,2010/09/    .C..TC.........G..A...AG......TAA.....A.C.TC..-----------       25     25 ,     14     14       2:>A/swine/Thailand/CU-RP3/2010,2010/09/    
   3 >A/swine/Thailand/CU-DP83/2010,2010/12/   G.T................C.AA.GG.T.......AG....AT.TGT----------       25     25 ,     15     15       3:>A/swine/Thailand/CU-DP83/2010,2010/12/   
   4 >A/Thailand/SN_0116/2010,2010/10/         ------........C..T.C.AA..--------------------------------       43     43 ,      5      5       4:>A/Thailand/SN_0116/2010,2010/10/         
   5 >A/swine/Thailand/CU-PL63/2010,2010/11/   --.A....G....G..G...C....G.T.......AG..A..T....CCTCAATCCC       23     23 ,     21     21       5:>A/swine/Thailand/CU-PL63/2010,2010/11/   
   6 >A/swine/Thailand/CU-PL65/2010,2010/11/   ...A..TGGGTTT...G...C...G.T.GG...AC..TAA..T..............       20     20 ,     20     20       6:>A/swine/Thailand/CU-PL65/2010,2010/11/   


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gsgs
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 10:57 am 
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Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1806
Location: germany
http://evol.mcmaster.ca/~weilong/PDFs/HaoGene2011.pdf

A/Sw/HK/NS1809/2009(H1N1)
A/Sw/HK/NS1810/2009(H1N1)


Attachments:
reco2.jpg
reco2.jpg [ 30.8 KiB | Viewed 1202 times ]

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gsgs
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 11:43 am 
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Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1806
Location: germany
I don't see it yet (haven't read the paper)


Code:
                                       000000000000000111111111222222 001111 000000011111122 00000001111 0000111111 00000000011 000000 0000000 
                                       000123345555679001113457000111 130167 024679924667900 44666670124 0029012223 01357789923 445567 2233556 
                                       009770312569914243785106246368 639284 504771547141167 33005811480 6696544455 38172492423 595902 5556572 
                                       899136645141415044398393131737 803933 191670780316130 34578774918 0989035876 99613275518 925409 2447846 
-codon-position------------------------2        2  1      12  22  1     11    2 1 1   2   2  12211     1   1          11 1 1            2 1 12 
---Index-------------------------------GAGTATTAACGATGAACCGGCGGCCAGCGG GACGCT GCCCACGAGACGCAC TCGGTGTCGAC GAGTGGGGTG CTGCAAGAATT GGGGGA ACAAAGA 
   1 >A/Mexflu/index/2009/02/01        .............................. ...... ............... ........... .......... ........... ...... ....... 
   2 >A/Sw/HK/2995/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   3 >A/Sw/HK/2885/2009(H1N1/12/17     .....C.....G...TY...TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   4 >A/Sw/HK/2974/2009(H1N1/12/17     .....CC...AG...T....TAA.AGATAA ....T. A.ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   5 >A/Sw/HK/2886/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   6 >A/Sw/HK/2894/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....TC ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   7 >A/Sw/HK/NS1809/2009(H1N1/12/03   --AC...............A...T....A. TG.... .T...T...GT.... C.AAA.CTA.T .TACAA.A.. ..AT.G..G.C .A..AG .TGG.A. 
   8 >A/Sw/HK/NS1810/2009(H1N1/12/03   --AC...............A...T....A. TG.... .T...T...GT.... CTA.A.CTA.T .TACAA.A.. ..AT.G..G.C .A..AG .TGG.A. 
   9 >A/Sw/HK/NS1583/2009(H1N1/10/22   AG..C..GGT..CAG..TA.........A. ..AA.. ......AGA..A.G. ....AA....T A.A..A.A.A T.A..G..... .A.AA. ...G..G 
  10 >A/Sw/HK/2299/2009(H1N1/10/22     --..C..GGT..CAG..TA.........A. ..AA.. ......AGA..A.G. ....AA....T A.A..A.A.A T.A..G..... .A.AA. ...G..G 
.


.

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no patents on genes, publish the GISAID sequences !


Last edited by gsgs on Thu May 12, 2011 12:13 pm, edited 1 time in total.

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niman
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 11:48 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28221
Location: Pittsburgh, PA USA
gsgs wrote:
I don't see it yet (haven't read the paper)


Code:
                                       000000000000000111111111222222 001111 000000011111122 00000001111 0000111111 00000000011 000000 0000000 
                                       000123345555679001113457000111 130167 024679924667900 44666670124 0029012223 01357789923 445567 2233556 
                                       009770312569914243785106246368 639284 504771547141167 33005811480 6696544455 38172492423 595902 5556572 
                                       899136645141415044398393131737 803933 191670780316130 34578774918 0989035876 99613275518 925409 2447846 
-codon-position------------------------2        2  1      12  22  1     11    2 1 1   2   2  12211     1   1          11 1 1            2 1 12 
---Index-------------------------------GAGTATTAACGATGAACCGGCGGCCAGCGG GACGCT GCCCACGAGACGCAC TCGGTGTCGAC GAGTGGGGTG CTGCAAGAATT GGGGGA ACAAAGA 
   1 >A/Mexflu/index/2009/02/01        .............................. ...... ............... ........... .......... ........... ...... ....... 
   2 >A/Sw/HK/2995/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   3 >A/Sw/HK/2885/2009(H1N1/12/17     .....C.....G...TY...TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   4 >A/Sw/HK/2974/2009(H1N1/12/17     .....CC...AG...T....TAA.AGATAA ....T. A.ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   5 >A/Sw/HK/2886/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....T. ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   6 >A/Sw/HK/2894/2009(H1N1/12/17     .....C.....G...T....TAA.A.ATAA ....TC ..ATG.......T.T ....A....GT ..A..AAAC. .CA.GGAG.C. AAA.A. G..GG.. 
   7 >A/Sw/HK/NS1809/2009(H1N1/12/03   --AC...............A...T....A. TG.... .T...T...GT.... C.AAA.CTA.T .TACAA.A.. ..AT.G..G.C .A..AG .TGG.A. 
   8 >A/Sw/HK/NS1810/2009(H1N1/12/03   --AC...............A...T....A. TG.... .T...T...GT.... CTA.A.CTA.T .TACAA.A.. ..AT.G..G.C .A..AG .TGG.A. 
   9 >A/Sw/HK/NS1583/2009(H1N1/10/22   AG..C..GGT..CAG..TA.........A. ..AA.. ......AGA..A.G. ....AA....T A.A..A.A.A T.A..G..... .A.AA. ...G..G 
  10 >A/Sw/HK/2299/2009(H1N1/10/22     --..C..GGT..CAG..TA.........A. ..AA.. ......AGA..A.G. ....AA....T A.A..A.A.A T.A..G..... .A.AA. ...G..G







No surpise. You couldn't find the NA recombination with a 10 billion p value.

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gsgs
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 12:11 pm 
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Posts: 1806
Location: germany
actually, it's in PB2 (they claim)

http://evol.mcmaster.ca/~weilong/PDFs/HaoGene2011.pdf

claimed recombination in swine with pH1N1=***


PB2 , breakpoint 1197


1583+2886-->1809



Code:

>A/Sw/HK/NS1809/2009(H1N1/12/03
>A/Sw/HK/NS1583/2009(H1N1/10/22
---------................................................... 0 
......................................o..................... 1 
..................................................o......... 1 
............................................................ 0 
................................o........................... 1 
............................................................ 0 
.....................................................o...... 1 
............................................................ 0 
............................................o............... 1 
..........o................................................. 1 
............................................................ 0 
.................................o................o......... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................o............... 1 
............................................................ 0 
............................................................ 0 
.....................................................o...... 1 
................................o...............o........... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
......................o..................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 13 


 13 ( 2271 )+ 4 ( 2274 )+ 9 ( 2151 )+ 7 ( 1701 )+ 5 ( 1485 )+ 4 ( 1410 )+ 2 ( 982 )+ 4 ( 838 )+ 48 ( 13112 )



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niman
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 12:23 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28221
Location: Pittsburgh, PA USA
gsgs wrote:
actually, it's in PB2 (they claim)

http://evol.mcmaster.ca/~weilong/PDFs/HaoGene2011.pdf

claimed recombination in swine with pH1N1=***


PB2 , breakpoint 1197


1583+2886-->1809



Code:

>A/Sw/HK/NS1809/2009(H1N1/12/03
>A/Sw/HK/NS1583/2009(H1N1/10/22
---------................................................... 0 
......................................o..................... 1 
..................................................o......... 1 
............................................................ 0 
................................o........................... 1 
............................................................ 0 
.....................................................o...... 1 
............................................................ 0 
............................................o............... 1 
..........o................................................. 1 
............................................................ 0 
.................................o................o......... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................o............... 1 
............................................................ 0 
............................................................ 0 
.....................................................o...... 1 
................................o...............o........... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
......................o..................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 13 


 13 ( 2271 )+ 4 ( 2274 )+ 9 ( 2151 )+ 7 ( 1701 )+ 5 ( 1485 )+ 4 ( 1410 )+ 2 ( 982 )+ 4 ( 838 )+ 48 ( 13112 )



It is pretty easy to see the clustering in the 5' half of the gene.
Once homologous recombination is acknowledged for long stretches (like 1/2 of the gene) it becomes a VERY slippery slope to deny exchanges of single nucleotides, which is VERY common among co-circulating sub-clades that are VERY closley related, like the current exchanges (S165N and A189T) between the S188T sub-clade and Chihuahua in the US in 2011.

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gsgs
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 12:34 pm 
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Posts: 1806
Location: germany
We have one substrain with 3 markers in the first half of PB2 and 8 markers in the 2nd half.
Then we have another substrain with 11 markers in the first half and one marker in the 2nd.
This is quite unusual.
Now we have a 3rd substrain (the claimed recombination) with only 3 markers in the 1st half
and 2 markers in the 2nd.
All from late 2009, so the first 2 have quite many markers and the 3rd has a normal number.

BUT this doesn't indicate recombination.
Markers won't "eradicate" each other by recombination.

Could it be that they made a silly mistake ??!?

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niman
 Post subject: Re: recombinations
PostPosted: Thu May 12, 2011 12:52 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28221
Location: Pittsburgh, PA USA
gsgs wrote:
We have one substrain with 3 markers in the first half of PB2 and 8 markers in the 2nd half.
Then we have another substrain with 11 markers in the first half and one marker in the 2nd.
This is quite unusual.
Now we have a 3rd substrain (the claimed recombination) with only 3 markers in the 1st half
and 2 markers in the 2nd.
All from late 2009, so the first 2 have quite many markers and the 3rd has a normal number.

BUT this doesn't indicate recombination.
Markers won't "eradicate" each other by recombination.

Could it be that they made a silly mistake ??!?

Please. You remain clueless. Recombination with wild type "erases" markers. You lack an understanding of recombination at the most BASIC level.

Your posts are "silly mistakes" which are only viable in your parallel universe.

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