166 H3N2 genomes from 2009, most from April
picture: http://magictour.free.fr/panflu/h3n2_t1.GIF
1145 H3s from 2008 or later
add 44 to the locations
picture: http://magictour.free.fr/panflu/h3_ts3a.GIF
the new Egypt/Iowa strain has 9 markers
(compared to Brisbane-like USA-viruses from 2008) in HA :
C318A,C483T,A522C,T615G,C660A,A682G,G1005A,C1053A, T1458C
nucleotide-enumeration starts with 1 in the coding area (ATG...)
while Perth/16 had:
G232A,T480A,A522C,T615A,T684C,T689G,C1548T
these translate to amino-acid(=protein) mutations :
K78E,K160N,T228A,S230I
if you take amino acid mutations that were neither in Brisbane
nor in Perth, then only T228A remains
original H3N2 had QQTII (226-230)
then came QQTVI (Brisbane)
also QQTVS (Perth)
now : QQAVI (Egypt)
But H3N2 usually doesn't oversummer in USA or come from Egypt.
So, what H3N2-viruses are prevalent in SE-Asea ?
Australia had some early H3N2 but now ****** dominates.
Singapore,China had both H3N2 and ****** in the last weeks.
The strain is unknown to me.
available full genomes from that new strain
some from east Asia, latest Nanjing, Jan.2010
130:>A/NY/3280/2009/05/03
131:>A/NY/3279/2009/05/03
132:>A/THA/CU-B657/2009/07/11
133:>A/AUS/19/2009/07/21
134 >A/CA/VRDL338/2009/05/18
135:>A/NY/3104/2009/04/29
136:>A/THA/CU-B4/2009/06/13
137:>A/Nanjing/01/2010/01/10
---------------------------------------------
mutations as compared with Brisbane:
about 70 differences to other average H3N2 from April 2009, USA
for a TMRCA of ~April 2008
earliest with
A232G(4) : A/Taiwan/4055/2009/01/19 , A111G,G182A,G232A,T480A,A522C,T615A,G1080A
C318A(4) : A/USA/AF1116/2008/01/23 , 318
A480T(4) : A/Kyoto/K106/2008/01/21 , 480
C483T(4) : A/Mbagathi/6906/2008/07/18 , 483
A615G(4) : A/Sendai/TU204/2008// , 615
C660A(4) : A/Aichi/32/2008/01/12 , 660
A682G(4) : A/Taiwan/F154/2009/05/04 , 318,483,615,660,682,1005,1053
G1005A(4) : A/NC/AF1531/2008/02/01 , 1005
C1053A(4) : A/Texas/AF1804/2008/02/25 , 1053
T1548C(4) : A/Boston/9/2008/02/27 , 1548
picture: http://magictour.free.fr/panflu/h3n2_t1.GIF
1145 H3s from 2008 or later
add 44 to the locations
picture: http://magictour.free.fr/panflu/h3_ts3a.GIF
the new Egypt/Iowa strain has 9 markers
(compared to Brisbane-like USA-viruses from 2008) in HA :
C318A,C483T,A522C,T615G,C660A,A682G,G1005A,C1053A, T1458C
nucleotide-enumeration starts with 1 in the coding area (ATG...)
while Perth/16 had:
G232A,T480A,A522C,T615A,T684C,T689G,C1548T
these translate to amino-acid(=protein) mutations :
K78E,K160N,T228A,S230I
if you take amino acid mutations that were neither in Brisbane
nor in Perth, then only T228A remains
original H3N2 had QQTII (226-230)
then came QQTVI (Brisbane)
also QQTVS (Perth)
now : QQAVI (Egypt)
But H3N2 usually doesn't oversummer in USA or come from Egypt.
So, what H3N2-viruses are prevalent in SE-Asea ?
Australia had some early H3N2 but now ****** dominates.
Singapore,China had both H3N2 and ****** in the last weeks.
The strain is unknown to me.
available full genomes from that new strain
some from east Asia, latest Nanjing, Jan.2010
130:>A/NY/3280/2009/05/03
131:>A/NY/3279/2009/05/03
132:>A/THA/CU-B657/2009/07/11
133:>A/AUS/19/2009/07/21
134 >A/CA/VRDL338/2009/05/18
135:>A/NY/3104/2009/04/29
136:>A/THA/CU-B4/2009/06/13
137:>A/Nanjing/01/2010/01/10
---------------------------------------------
mutations as compared with Brisbane:
Code:
>A/Perth/16/2009/04/07 (only segments 4,6 A46G(4),C60T(4),G232A(4),T480A(4),A522C(4),A565C(4),T615A(4),T684C(4),T689G(4),C729T(4),C903T(4),T1130G(4),G1197A(4),C1296T(4),C1548T(4),C1560A(4),A1578G(4) G27T(6),A288G(6),G429A(6),G439A(6),A643G(6),C891A(6),C935T(6),A1029G(6),A1044G(6),G1110A(6) >Index, average of the 166 genomes T228C(1),A708G(1),C735T(1),G873A(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),C1794T(1),G1920A(1),A2109G(1) A28C(2),C141T(2),A155G(2),A156G(2),C397T(2),T915C(2),A981G(2),C1051T(2),C1365T(2),C1726A(2),G1836A(2),G1953T(2),A2193G(2),C2200A(2) T153C(3),A303G(3),G456A(3),C561A(3),A1042G(3),A1060G(3),G1371A(3),T1680A(3),G1689A(3) A46G(4),C60T(4),G232A(4),T480A(4),A522C(4),A565C(4),T615A(4),C729T(4),C903T(4),T1130G(4),G1197A(4),C1296T(4),C1548T(4),C1560A(4),A1578G(4) G201A(5),G636A(5),G648A(5),G1348A(5),T1389C(5),C1488T(5) A288G(6),G429A(6),G439A(6),A643G(6),C891A(6),C935T(6),A1029G(6),A1044G(6),G1110A(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7),G591A(7),C685T(7) G331A(8),C634T(8),G703A(8), >A/NY/3280/2009/05/03 A187G(1),A303G(1),A708G(1),C735T(1),A861G(1),G873A(1),G906T(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),C397T(2),A405G(2),T915C(2),A981G(2),G1251A(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G813T(3),G1068A(3),A1226G(3),C1365T(3),G1371A(3),T1680G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5) T77C(6),T78C(6),T85C(6),A99G(6),A119G(6),A417G(6),G439A(6),C471T(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8) >A/NY/3279/2009/05/03 A187G(1),A303G(1),A708G(1),C735T(1),A861G(1),G873A(1),G906T(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),C397T(2),A405G(2),T915C(2),A981G(2),G1251A(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G813T(3),G1068A(3),A1226G(3),C1365T(3),G1371A(3),T1680G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5) T77C(6),T78C(6),T85C(6),A99G(6),A119G(6),A417G(6),G439A(6),C471T(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8) >A/THA/CU-B657/2009/07/11 A187G(1),A303G(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),A1180G(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),C397T(2),A405G(2),T915C(2),G924A(2),A981G(2),C1186T(2),G1251A(2),C1329T(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),A711G(3),G813T(3),G1068A(3),A1226G(3),C1365T(3),G1371A(3),T1680G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C732T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5),G1348A(5),T1389C(5),C1488T(5) A76C(6),A417G(6),G439A(6),C471T(6),C542A(6),A543C(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6),G1297A(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8) >A/AUS/19/2009/07/21 A187G(1),A303G(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),A1381G(1),G1678A(1),C1794T(1) G24A(2),A28C(2),A105G(2),A155G(2),A156G(2),G186A(2),A195G(2),C397T(2),A405G(2),G717A(2),A768G(2),T915C(2),A981G(2),G1251A(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G813T(3),G1068A(3),G1189A(3),A1226G(3),C1320T(3),C1365T(3),G1371A(3),T1680G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1458T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5) T77C(6),T78C(6),T85C(6),A119G(6),A417G(6),G439A(6),C471T(6),A643G(6),C935T(6),C978T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),A516G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),G729T(8),T731C(8),A735G(8) >A/CA/VRDL338/2009/05/18 A187G(1),A303G(1),C360T(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),C397T(2),A405G(2),T915C(2),A981G(2),G1251A(2),C1365T(2),T1533C(2),T1566C(2),G1707A(2),G1725A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),C1365T(3),G1371A(3),T1680G(3) A46G(4),C60T(4),A289G(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5),A855G(5) T77C(6),T78C(6),T85C(6),A119G(6),G439A(6),C471T(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7),T829C(7) G404A(8),A416G(8),G703A(8),A735G(8) >A/NY/3104/2009/04/29 A187G(1),A303G(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),C397T(2),A405G(2),A593G(2),T915C(2),A981G(2),G1251A(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G339A(3),G363A(3),G1068A(3),A1226G(3),C1365T(3),G1371A(3),T1437C(3),T1680G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),T228C(5),A300C(5),A306G(5),G648A(5) T77C(6),T78C(6),T85C(6),A119G(6),A417G(6),G439A(6),C471T(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8) >A/THA/CU-B4/2009/06/13 A187G(1),A303G(1),T619C(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1209A(1),G1221A(1),T1227C(1),A1381G(1),T1537C(1),G1599T(1),C1794T(1) A28C(2),A105G(2),A155G(2),A156G(2),A195G(2),T240C(2),C397T(2),A405G(2),C675T(2),G790A(2),T915C(2),A981G(2),C1051A(2),G1251A(2),C1365T(2),G1506A(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2193G(2),C2200A(2),A2234G(2) A18G(3),G69A(3),A96C(3),T153C(3),G339A(3),G363A(3),A1023G(3),G1068A(3),C1365T(3),G1371A(3),T1680G(3),A1932G(3) A46G(4),C60T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),C903T(4),G1005A(4),C1053A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G201A(5),A300C(5),A306G(5),G648A(5),A663G(5),A1386G(5) T77C(6),T78C(6),C84T(6),T85C(6),A119G(6),G439A(6),C471T(6),A643G(6),C935T(6),G1107A(6),G1110A(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8),A811G(8) >A/Nanjing/01/2010/01/10 A187G(1),A303G(1),A643G(1),A708G(1),C735T(1),A861G(1),G873A(1),G981C(1),G1026A(1),A1029G(1),A1058G(1),G1149A(1),G1176T(1),G1221A(1),T1227C(1),A1381G(1),C1794T(1),A2189G(1),A2243G(1) A28C(2),A39G(2),A95C(2),A105G(2),A155G(2),A156G(2),A195G(2),T384C(2),C397T(2),A405G(2),T915C(2),A981G(2),G1158A(2),G1251A(2),C1263T(2),C1365T(2),T1566C(2),G1707A(2),C1726A(2),G1759A(2),G2007A(2),A2031G(2),A2193G(2),C2200A(2),A2234G(2) A96C(3),T153C(3),G199A(3),G339A(3),G363A(3),T571C(3),C821T(3),T822A(3),A1065G(3),G1068A(3),G1134A(3),C1259T(3),C1365T(3),G1371A(3),T1680G(3),A2148T(3) A46G(4),C60T(4),A108C(4),C109T(4),C318A(4),C483T(4),A522C(4),A565C(4),T615G(4),C660A(4),A682G(4),C729T(4),A768G(4),C903T(4),G1005A(4),C1053A(4),G1058A(4),T1130G(4),G1197A(4),C1296T(4),C1560A(4),A1578G(4) G183A(5),G201A(5),A300C(5),A306G(5),G648A(5),G707A(5) T77C(6),T78C(6),T85C(6),A119G(6),A127G(6),A272G(6),G439A(6),G451A(6),C471T(6),C530T(6),A543G(6),A643G(6),A799G(6),C935T(6),G1107A(6),G1110A(6),A1116T(6),A1290G(6) T267C(7),C354T(7),A492G(7),G521A(7),C540T(7) G404A(8),A416G(8),G703A(8),A735G(8)
about 70 differences to other average H3N2 from April 2009, USA
for a TMRCA of ~April 2008
earliest with
A232G(4) : A/Taiwan/4055/2009/01/19 , A111G,G182A,G232A,T480A,A522C,T615A,G1080A
C318A(4) : A/USA/AF1116/2008/01/23 , 318
A480T(4) : A/Kyoto/K106/2008/01/21 , 480
C483T(4) : A/Mbagathi/6906/2008/07/18 , 483
A615G(4) : A/Sendai/TU204/2008// , 615
C660A(4) : A/Aichi/32/2008/01/12 , 660
A682G(4) : A/Taiwan/F154/2009/05/04 , 318,483,615,660,682,1005,1053
G1005A(4) : A/NC/AF1531/2008/02/01 , 1005
C1053A(4) : A/Texas/AF1804/2008/02/25 , 1053
T1548C(4) : A/Boston/9/2008/02/27 , 1548
Comment