summary, Jan.2013
-----------------------------
all current human H3N2 (except swinish H3N2v) goes back in all 8 segments to one ancester
from ~mid 2006 ("US-Index/2007" , one of the dominant strains in seasonal US-flu 2006/7)
similar to the "Brisbane" vax-strain.
Then we had the Perth-vax strain which was prevalent until Egypt/Iowa appeared
and is now no longer found.
then we had Egypt/Iowa which separated from Perth in most segments in ~2008,
was first seen in ~mid 2009 in Egypt,Kenya,Djibuti,Iowa and was dominant in ~2010
Egypt/Iowa has 63=10+13+7+15+3+9+3+3 mutations (as compared to US-Index/2007)
In NA,segment 6 we have a common ancestor from ~2009 with 7 mutations which later
reassorted with Egypt/Iowa to form the ancestor(~2010) of current human seasonal H3N2
("Egypt_Iowa+NA")
In genbank 2011 we see basically 2 strains that emerged from US-Index/2007:
1.) Index1/2011 = normal Egypt_Iowa+NA with meanwhile 106=14+18+14+22+10+16+7+5
mutations as compared to US-Index/2007, including all the 61 of Egypt_Iowa+NA.
2.) Index2/2011 = reassortant Egypt-Iowa+NA in segments 3,4,5,6,7 plus one other new virus
from ~2007, also a descendent of US-Index/2007.
It has 110=25+22+11+27+4+8+7+6 mutations as compared toi US-Index/2007 including
all the 35=7+15+3+7+3 Egyt_Iowa+NA mutations from segments 3,4,5,6,7 and also
2+6+0 of the 10+13+3 Egypt/Iowa mutations from segments 1,2,8. So it separated from the
forming Egypt/Iowa in ~2008.
--------------edit--------------
3.) Index3/2011 = A/Czech Republik/121/2012/03/06(H3N2) -like , see below
Now as of Jan.2013 we have segments 4,6,7 from 2 recent H3N2 viruses from USA at genbank:
A/Georgia/3058/2012/09/26 and A/Oklahoma/3059/2012/10/05
GA3058 is a direct descendent of Index2/2011 in segments 4,6,7 (and in the other 5 segments too ?)
It has those 27+8+7 mutations plus 9+10+5 further,others mutations for a total of
36+18+12=66 (as compared to US-Index/2007, as usual)
OK3059 is a completely different virus, it descends from Egypt_Iowa+NA, but not from Index1/2011
nor from Index2/2011. It has 34+20+7 mutations in segments 4,6,7 including the 15+7+3
from Egypt_Iowa+NA and further 2+4+0 from Index1/2011 to which it is therefore a bit more related
then to Index2/2011
================================================== ===============================
here the mentioned strains and their mutations:
Code:
21,>2007/02/06,14278,AUS,A/Brisbane/10/07 T735C(1),A1026G(1),G1029A(1),C1227T(1),T1794C(1) C28A(2),G156A(2),T397C(2),C915T(2),T1365C(2),G2193A(2) A1371G(3) G46A(4),T60C(4),T903C(4) A648G(5) T935C(6),A1110G(6) T354C(7),T540C(7) A703G(8) ------------------------------------------------------------ 9,>Index/Brisbane-like/2007 C652T(2),C2200A(2) G129A(3),C1353T(3),A1377C(3) A622G(4) T27A(5),T513C(5),T1440G(5) -------------------------------------------------------------- 8+8+8+12+5+7+5+2=55,>Index/Perth-like/2009 T228C(1),A708G(1),G873A(1),A1058G(1),G1149A(1),G1221A(1),G1920A(1),A2109G(1) C141T(2),A155G(2),A981G(2),C1051T(2),C1726A(2),G1836A(2),G1953T(2),C2200A(2) T153C(3),A303G(3),G456A(3),C561A(3),A1042G(3),A1060G(3),T1680A(3),G1689A(3) G232A(4),T480A(4),A522C(4),A565C(4),T615A(4),C729T(4),T1130G(4),G1197A(4) C1296T(4),C1548T(4),C1560A(4),A1578G(4) G201A(5),G636A(5),G1348A(5),T1389C(5),C1488T(5) A288G(6),G429A(6),G439A(6),A643G(6),C891A(6),A1029G(6),A1044G(6) T267C(7),A492G(7),G521A(7),G591A(7),C685T(7) G331A(8),C634T(8) ---------------------------------------------------------------- 10+13+7+15+3+9+3+3=63,>Index/2009/Egypt/Iowa A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1),G1149A(1) G1221A(1),A1381G(1) A105G(2),A155G(2),A195G(2),A405G(2),A981G(2),G1251A(2),T1566C(2),G1707A(2) C1726A(2),G1759A(2),G2007A(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),C1365T(3),T1680G(3) C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4) G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5) T77C(6),T78C(6),T85C(6),A119G(6),G439A(6),C471T(6),A643G(6),G1107A(6) A1290G(6) T267C(7),A492G(7),G521A(7) G404A(8),A416G(8),A735G(8) ------------------------------------------------------------------ 10+13+7+15+3+7+3+3=61,>Index/2009/Egypt_Iowa+NA A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1),G1149A(1) G1221A(1),A1381G(1) A105G(2),A155G(2),A195G(2),A405G(2),A981G(2),G1251A(2),T1566C(2),G1707A(2) C1726A(2),G1759A(2),G2007A(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),C1365T(3),T1680G(3) C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4) G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5) G439A(6),A643G(6),C837T(6),G1100A(6),A1106C(6),A1281T(6),A1390C(6) T267C(7),A492G(7),G521A(7) G404A(8),A416G(8),A735G(8) ------------------------------------------------------------------ vaccine strain A/Victoria/210/2009: P162S=P187S=C532T,I260M=I276M=A828G,R261Q=R277Q=G830A ----------------------------------------------------------------- 25+22+11+27+4+8+7+6=110,>Index2/2011-reassortedEI/2011 C19T(1),G204A(1),G243A(1),G348A(1),C444T(1),C588T(1),G661T(1),C666A(1) A708G(1),G763A(1),G846A(1),G878A(1),C966A(1),G981A(1),A1173C(1),G1284A(1) G1629A(1),T1636C(1),A1653G(1),G1678A(1),C1680T(1),T1746C(1),G2061A(1),T2142C(1) C2178A(1) T81C(2),A105G(2),A155G(2),C198A(2),G381A(2),T447C(2),A465G(2),G486A(2) C789T(2),G816A(2),T955C(2),A981G(2),G1082A(2),C1344T(2),C1726A(2),T1986C(2) G2124T(2),C2151A(2),C2200A(2),G2211A(2),A2214G(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),T408C(3),C489T(3),G1068A(3),C1293T(3) G1329A(3),C1365T(3),T1680G(3) A108G(4),G205A(4),T291C(4),C318A(4),T328C(4),C483T(4),A522C(4),A565C(4) T615G(4),C660A(4),A682G(4),C690T(4),C729T(4),A736G(4),A887C(4),G1005A(4) C1009A(4),C1053A(4),T1130G(4),A1131G(4),G1197A(4),C1296T(4),T1353C(4),A1518G(4) G1545A(4),C1560A(4),A1578G(4) G165T(5),G201A(5),A300C(5),A306G(5) G439A(6),A643G(6),C837T(6),G1100A(6),A1106C(6),C1113T(6),A1281T(6),A1390C(6) C207A(7),T267C(7),C276T(7),G315A(7),A492G(7),G521A(7),C546A(7) T6C(8),C150T(8),T386C(8),C429T(8),A747G(8),A796G(8) ----------------------------------------------------------------- 14+18+14+22+10+16+7+5=106,>Index1/2011-normalEIN/2011 C165T(1),A187G(1),A303G(1),A708G(1),A861G(1),G873A(1),G981C(1),A1058G(1) G1149A(1),G1221A(1),T1335C(1),A1381G(1),A1878G(1),T2235C(1) A105G(2),A155G(2),A195G(2),A405G(2),T447C(2),T772C(2),A981G(2),G1251A(2) C1344A(2),G1389A(2),T1566C(2),G1707A(2),C1726A(2),G1757A(2),G1759A(2),C1995A(2) G2007A(2),C2200A(2) A96C(3),T153C(3),G339A(3),G363A(3),G516A(3),A795G(3),G813T(3),A962G(3) A987G(3),G1068A(3),A1226G(3),C1365T(3),G1677A(3),T1680G(3) T9C(4),A190G(4),G219T(4),C318A(4),A323G(4),C483T(4),A522C(4),A565C(4) T615G(4),C660A(4),A682G(4),C729T(4),A983G(4),G1005A(4),C1053A(4),G1087A(4) T1130G(4),G1185A(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) C9T(5),G201A(5),A300C(5),A306G(5),C352A(5),T402C(5),G561A(5),G738A(5) C825T(5),A1281C(5) A165G(6),G267A(6),G439A(6),T609A(6),A643G(6),C666T(6),G732A(6),C837T(6) T936A(6),G1095A(6),G1100A(6),A1106C(6),A1116G(6),G1199A(6),A1281T(6),A1390C(6) T267C(7),T420C(7),A492G(7),G521A(7),A555T(7),A582G(7),A933G(7) C79A(8),G390A(8),G404A(8),A416G(8),A735G(8) ------------------------------------------------------------- 34+20+7=61,>A/Oklahoma/3059/2012,2012/10/05 C72T(4),A146G(4),G182A(4),C191T(4),C285T(4),C318A(4),A430G(4),C456T(4) A472G(4),A482G(4),C483T(4),G501A(4),A522C(4),A565C(4),T615G(4),G640T(4) C660A(4),A682G(4),G715A(4),C729T(4),T882G(4),A983G(4),G1005A(4),C1053A(4) G1087A(4),T1130G(4),A1195C(4),G1197A(4),C1254A(4),C1296A(4),A1524G(4),C1560A(4) A1578G(4),A1671G(4) A25T(6),C63T(6),T242C(6),G267A(6),A278G(6),T300C(6),G439A(6),C471T(6) A489G(6),A643G(6),C666T(6),G732A(6),G828A(6),C837T(6),G1095A(6),G1100A(6) A1106C(6),A1204G(6),A1281T(6),A1390C(6) G180A(7),G189T(7),T267C(7),A441G(7),C468T(7),A492G(7),G521A(7) ------------------------------------------------------------------- 36+18+12=66,>A/Georgia/3058/2012,2012/09/26 T9C(4),A33T(4),G39A(4),A52G(4),A70G(4),A108G(4),G205A(4),T291C(4) C318A(4),T328C(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4) C690T(4),C729T(4),A736G(4),G765A(4),A887C(4),T975C(4),G1005A(4),C1009A(4) C1053A(4),T1130G(4),A1131G(4),G1197A(4),C1296T(4),T1353C(4),C1509T(4),A1518G(4) G1545A(4),G1557A(4),C1560A(4),A1578G(4) G204A(6),T242C(6),C399T(6),G439A(6),A643G(6),C837T(6),C903T(6),T945G(6) A1016G(6),T1062C(6),G1100A(6),A1106C(6),C1113T(6),A1185G(6),A1204G(6),A1281T(6) T1326C(6),A1390C(6) C207A(7),T267C(7),C276T(7),G315A(7),G438A(7),C468T(7),A492G(7),G521A(7) C546A(7),G839A(7),C859T(7),C874T(7),
divide nucleotide-positions by 3 to get the amino-acid positions.
numbering the nucleotides of the coding region, other people often use
another numbering, e.g. substract 16 from the amino-acid positions to get the WHO numbering
mutations A<->G or C<->T at positions divisible by 3 are usually synonymous.
It would be useful to have a typical virus from the current outbreak with all 8 segments at genbank
-------------------------------------------------------------------------
there are currently 10 human HAs at genbank from June 2012 or later
3 are similar to GA3058 (Index2/2011,reassortant , 7 are similar to OK3059, new strain, now called "sgp11",
first seen in Singapore,July 2011 , see below
this could have led to reassortment between these 2
>A/Sao Paulo/49663/2012,2012/07/17
>A/Georgia/3058/2012,2012/09/26
>A/California/NHRC362744/2012,2012/11/06
>A/Guam/3049/2012,2012/08/08
>A/Guam/3050/2012,2012/06/15
>A/Guam/3057/2012,2012/08/24
>A/Japan/3060/2012,2012/10/17
>A/South Carolina/NHRC358725/2012,2012/08/24
>A/California/NHRC362154/2012,2012/10/25
>A/Oklahoma/3059/2012,2012/10/05
----------------------------------------------------------------------------
sgp11 HAs at genbank:
Code:
>A/Singapore/TT430/2011,2011/07/29 >A/Singapore/GP1490/2011,2011/09/08 >A/Singapore/GP1503/2011,2011/09/13 >A/Singapore/KK398/2011,2011/09/19 >A/Singapore/TT654/2011,2011/10/04 >A/Singapore/GP1575/2011,2011/10/06 >A/Singapore/TT662 /2011,2011/10/11 >A/Singapore/TT663/2011,2011/10/11 >A/Singapore/KK445/2011,2011/10/17 >A/Singapore/GP1655/2011,2011/10/20 >A/Singapore/H2011.808bC/2011,2011/10/22 >A/Singapore/GP1669/2011,2011/10/24 >A/Singapore/KK459/2011,2011/10/24 >A/Singapore/TT717/2011,2011/11/01 >A/Singapore/GP1703/2011,2011/11/03 >A/Singapore/KK482/2011,2011/11/08 >A/Singapore/KK505/2011,2011/11/17 >A/Singapore/GP1760/2011,2011/11/18 >A/Singapore/GP1810/2011,2011/12/01 >A/Singapore/KK535/2011,2011/12/05 >A/Singapore/GP1846/2011,2011/12/09 >A/Singapore/TT815/2011,2011/12/13 >A/Singapore/TT827/2011,2011/12/13 >A/Singapore/GP1905/2011,2011/12/21 >A/Singapore/TT837/2011,2011/12/22 >A/Singapore/TT879/2011,2011/12/30 >A/Korea/AF2784/2012,2012/01/19 >A/Korea/AF2785/2012,2012/01/20 >A/Korea/AF2781/2012,2012/01/24 >A/Kyrgyzstan/3056/2012,2012/01/26 >A/Novosibirsk/RII09/2012,2012/01/29 >A/Novosibirsk/155/2012,2012/01/29 >A/Tyumen/03/2012,2012/01/30 >A/Moscow/02/2012,2012/02/01 >A/Novosibirsk/RII08/2012,2012/02/02 >A/Novosibirsk/13/2012,2012/02/02 >A/Pavia/81/2012,2012/02/07 >A/Pavia/95/2012,2012/02/09 >A/Krasnoyarsk/10/2012,2012/02/09 >A/Korea/AF2857/2012,2012/02/13 >A/Japan/AF2846/2012,2012/02/14 >A/Kyrgyzstan/3053/2012,2012/02/18 >A/Novosibirsk/26k/2012,2012/02/19 >A/Novosibirsk/22/2012,2012/02/20 >A/Korea/AF2856/2012,2012/02/21 >A/Novosibirsk/RII14/2012,2012/02/24 >A/Novosibirsk/16/2012,2012/02/24 >A/North Carolina/AF2843/2012,2012/02/28 >A/Korea/2970/2012,2012/03/01 >A/Nevada/3001/2012,2012/03/03 >A/Illinois/AF2867/2012,2012/03/05 >A/Saint Petersburg/RII16/2012,2012/03/05 >A/Huzhou/1113/2012,2012/03/05 >A/New York/AF2868/2012,2012/03/06 >A/Czech Republic/121/2012,2012/03/06 >A/Novosibirsk/RII25/2012,2012/03/06 >A/Kaliningrad/RII02/2012,2012/03/07 >A/Kyrgyzstan/3051/2012,2012/03/12 >A/Ohio/3029/2012,2012/03/14 >A/Ohio/3027/2012,2012/03/14 >A/Novosibirsk/59d/2012,2012/03/14 >A/Ekaterinburg/RII06/2012,2012/03/20 >A/Japan/2974/2012,2012/03/21 >A/Kyrgyzstan/3048/2012,2012/03/22 >A/Ohio/2992/2012,2012/03/26 >A/Ohio/3015/2012,2012/04/23 >A/Ohio/3016/2012,2012/04/23 >A/Guam/3050/2012,2012/06/15 >A/Guam/3049/2012,2012/08/08 >A/South Carolina/NHRC358725/2012,2012/08/24 >A/Guam/3057/2012,2012/08/24 >A/Oklahoma/3059/2012,2012/10/05 >A/Japan/3060/2012,2012/10/17 >A/California/NHRC362154/2012,2012/10/25
we had this HA in Russia, i.e. Novosibirsk , Feb.Mar 2012 , several viruses are at genbank
with segments 4,5,6,7,8 - 1,2,3 missing.
There are many mutations in that strain, at least 12,6,6,5,3 more than in Index1/2011
from which it seems to descend. Almost double as many as I'd expect in 1 year.
so it seems that USA now has this strain: (from which only segments 4,5,6,7,8 are available)
-------edit--------no, we have one virus with these mutations and all 8 segments at genbank !
It's A/Czech Republik/121/2012/03/06(H3N2) it has 156=28+27+23+33+10+19+10+6
mutations , descends from Egypt_Iowa+NA but not from Index1/2011 nor Index2/2011
and is similar to OK3059 in segments 4,6,7
A/Novosibirsk/RII08/2012,2012/02/02
A/Novosibirsk/RII09/2012,2012/01/29
A/Novosibirsk/13/2012,2012/02/02
A/Novosibirsk/155/2012,2012/01/29
A/Kaliningrad/RII02/2012,2012/03/07
A/Krasnoyarsk/10/2012,2012/02/09
A/Novosibirsk/RII14/2012,2012/02/24
A/Novosibirsk/22/2012,2012/02/20
A/Novosibirsk/16/2012,2012/02/24
A/Novosibirsk/26k/2012,2012/02/19
A/Novosibirsk/RII25/2012,2012/03/06
A/Saint Petersburg/RII16/2012,2012/03/05
A/Saint Petersburg/RII50/2012,2012/04/10
A/Moscow/02/2012,2012/02/01
A/Ekaterinburg/RII06/2012,2012/03/20
A/Tyumen/03/2012,2012/01/30,H3N2
A/Novosibirsk/59d/2012,2012/03/14
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2013-01-25 : fludb uses the 5 available HAs for an antigenic analysis
A/Victoria/361/2011
A/Japan/3060/2012
A/Oklahoma/3059/2012
A/California/NHRC/362744/2012
A/California/NHRC/362154/2012
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