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hard to follow the thread with so long posts of data
so, we have "T1194A"
which you claim is nonsynonymous chnages and also in H1N1pdm09
as well as in e.g. A/Ck/Egypt/1119AF/2011
I may still post my opinion here, or not ?
Time will tell who is right, who understands this better.
I offered you bets in the past but you refused.
What you claim that I don't understand well is however the
common opinion of most experts, agreed ?
In your examples of recombination the recombined strain didn't spread, died out.
So those recombinations, even if they are real and not errors, don't change the
flu-evolution.
N14604 are G87A, A226G, G332A, T900C, A996G. These polymorphisms define the new subclade that evolved from N14604.
2.2.1 G , deletion
2.2.1 F common in 2008,2009 fading in 2011
new subclade (221G?) evolved from A/Egypt/N14604/2009
earlier version has T59C, G81A, G87A, G332A, T900C, A996G, T1194A and a subset
also has A226G. 6 of these 8 are found in H1N1pdm09 and 4 of those 6 are non-synonymous.
found "somewhere" in mexflu or in the index ?
-----------------
I'll post the 33 mutations defining the 2011-index-egypt-NA ...
...---------------------------...
>A/Ck/Egypt/1113/2011/01/11,JQ983350,35-1365,
A54G,T59C,G81A,G87A,C130T,C137A,C142T,T213C,A226G,C276T,
A297G,C309T,T315C,G332A,G360A,G402A,T405C,G417A,G441A,C670A,
A743G,(A777G),A780G,G783A,C894A,T900C,A996G,C1016T,T1128C,G1164A,
T1194A,G1320A,T1341G,A1348G
(new are : G87A,A226G,T900C,A996G,T1194A,)
-------------------------------------
>A/Egypt/N14604/2009/12/19,CY062461,1-1410,
already had:
A54G,T59C,G81A,C130T,C137A,C142T,T213C,C276T,A297G,C309T,
T315C,G332A,G360A,G402A,T405C,G417A,G441A,C670A,A743G,A780G,
G783A,C894A,C1016T,T1128C,G1164A,G1320A,T1341G,A1348G,G1410A
(those divisible by 3 and A<-->G or C<-->T are likely synonymous)
...-----------------------------------...
out of those 5 new mutations
G87A,A226G,T900C,A996G,T1194A,
G87A and A226G are in the mexflu-index while T900C,A996G,T1194A are not.
It seems that you claim T1194A and maybe others were developed
subsequently in (widespread) mexflu strains. I'll check ...
-------------------------------------
what I have in mexflu NA , April 2011,genbank :
Y >A/New York/3351,2009/05/06
C >A/Canada-ON/RV2888,2009/08/29
C >A/Catalonia/S1333,2009/09/01
C >A/Catalonia/S1331,2009/09/03
C >A/New York/6214,2009/11/16
C >A/New York/6546,2009/11/23
C >A/New York/6810,2009/11/25
C >A/Bishkek/WR0881T,2009/12/02
C >A/Mexico/InDRE1945/2011/03/(H1N1)
C >A/Mexico/InDRE1946/2011/03/22(H1N1)
C >A/Mexico/InDRE1947/2011/03/23(H1N1)
900 mxnae 11 -:78 C:10 T:4567 Y:1
G >A/Chile/3220,2009/06/30
G >A/Texas/42303371,2009/06/30
G >A/California/VRDL39,2009/07/09
G >A/UAE/F06,2009/10/02
G >A/Kenya/0052,2009/10/26
G >A/New York/0352,2009/12/27
996 mxnae 6 -:98 A:4552 G:6
...
1194 mxnae 309 -:286 A:307 G:4061 T:2
original mexflu had G at 1194, A developed in 2009 in California,Texas
-----------------------------
update with actual genbank (June 2012) :
900 mxnaf 17 -:180 C:16 T:6853 Y:1
996 mxnaf 9 -:215 A:6826 C:1 G:7 T:1
1194 mxnaf 398 -:498 A:395 G:6154 T:3
Y >2009/05/06,A/New York/3351/2009,CY041816,USA,H1N1
C >2009/06/09,A/Shenzhen/54/2009,CY095825,China,H1N1
C >2009/08/29,A/Canada-ON/RV2888/2009,HQ239981,Canada,H1N1
C >2009/09/01,A/Catalonia/S1333/2009,CY049016,Spain,H1N1
C >2009/09/03,A/Catalonia/S1331/2009,CY049013,Spain,H1N1
C >2009/11/16,A/New York/6214/2009,CY056677,USA,H1N1
C >2009/11/23,A/New York/6546/2009,CY056733,USA,H1N1
C >2009/11/25,A/New York/6810/2009,CY056821,USA,H1N1
C >2009/12/02,A/Bishkek/WR0881T/2009,CY071436,Kyrgyzstan,H1N1
C >2010/12/24,A/District of Columbia/WRAIR0307/2010,CY097823,USA,H1N1
C >2010/12/25,A/Ecuador/IEC00027/2010,CY090053,Ecuador,H1N1
C >2010/12/26,A/District of Columbia/WRAIR0303/2010,CY097799,USA,H1N1
C >2011/01/04,A/Ecuador/IEC00043/2011,CY090056,Ecuador,H1N1
C >2011/02/10,A/swine/MN/25618/2011,JN193423,USA,H1N1
C >2011/03/,A/Mexico/InDRE1945/2011,CY089388,Mexico,H1N1
C >2011/03/22,A/Mexico/InDRE1946/2011,CY089390,Mexico,H1N1
C >2011/03/23,A/Mexico/InDRE1947/2011,CY089392,Mexico,H1N1
900 mxnaf 17 -:180 C:16 T:6853 Y:1
G >2009/06/30,A/Chile/3220/2009,CY075301,Chile,H1N1
G >2009/06/30,A/Texas/42303371/2009,CY052204,USA,H1N1
G >2009/07/09,A/California/VRDL39/2009,CY054901,USA,H1N1
G >2009/08/,A/Eastern India/107/2009,GU983247,India,H1N1
C >2009/08/09,A/Malaysia/2089888/2009,CY119420,Malaysia,H1N1
G >2009/10/02,A/UAE/F06/2009,CY052361,United Arab Emirates,H1N1
T >2009/10/15,A/Taiwan/7855/2009,HM072406,Taiwan,H1N1
G >2009/10/26,A/Kenya/0052/2009,HQ214286,Kenya,H1N1
G >2009/12/27,A/New York/0352/2009,CY062044,USA,H1N1
996 mxnaf 9 -:215 A:6826 C:1 G:7 T:1
A >2009/06/15,A/California/VRDL12/2009,CY055457,USA,H1N1
...
A >2010/07/20,A/Khon Kaen/INS459/2010,CY096180,Thailand,H1N1
A >2010/08/12,A/Bangkok/INS482/2010,CY096332,Thailand,H1N1
A >2010/08/25,A/Bangkok/INS501/2010,CY096436,Thailand,H1N1
A >2010/09/,A/swine/Thailand/CU-RP1/2010,CY089812,Thailand,H1N1
A >2010/09/,A/swine/Thailand/CU-RP3/2010,CY089819,Thailand,H1N1
A >2010/09/01,A/Bangkok/INS511/2010,CY096492,Thailand,H1N1
A >2010/09/13,A/Thailand/CU-H2417/2010,CY088832,Thailand,H1N1
A >2010/11/10,A/Sydney/DD3-33/2010,CY098189,Australia,mixed,N1
A >2011/02/16,A/swine/Illinois/A01049574/2011,JQ398761,USA,H1N1
A >2011/02/16,A/swine/Illinois/A01049575/2011,JQ398762,USA,H1N1
A >2011/03/10,A/swine/Illinois/A01049673/2011,JQ398763,USA,H1N1
1194 mxnaf 398 -:498 A:395 G:6154 T:3
_________________
no patents on genes, publish the GISAID sequences !
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