Announcement

Collapse
No announcement yet.

new strain of H3N2

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • new strain of H3N2

    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:


    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
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    Re: new strain of H3N2

    Thank you Gs.

    Comment


    • #3
      Re: new strain of H3N2

      nucleotide-differences:

      Code:
                                                   1   2   3   PB2 PB1  PA  HA  NP  NA   M  NS
      --------------------------------------------------------------------------------------------------
        1 >A/Index/Egypt-Iowa-like/2010(H3N2)      0  70  68    26  38  34  50  26  49  16  31    35#   46   13138   5606      1:>A/Index/Egypt-Iowa-like/2010(H3N2)   
        2 >A/Index/Brisbane-like/2007(H3N2)       70   0  62    26  30  32  56  31  37  27  19    33#   44   13138   5611      2:>A/Index/Brisbane-like/2007(H3N2)     
        3 >A/Index/Perth-like/2009(H3N2)          68  62   0    23  30  35  45  31  44  23  27    32#   43   13138   5618      3:>A/Index/Perth-like/2009(H3N2)        
      -------------------------------------------------------------------------------------------------------------
                                                   1   2   3    25  32  33  50  29  43  22  25
      
                                                 0000000111112 00000001111111122 0000000011111111 0000000000011111111 0000001111 00000000001111 00000 00000 
                                                 1237889012391 11114690257778902 0113334500033366 2344556666700112555 0233563344 00012444680012 24556 34467 
                                                 8200678542820 04590585560253503 9250365646656788 3188261268205399467 2000134848 77818237492409 69298 30133 
                                                 7838131891109 51555211167696374 6933936120835709 2803255202953076808 7106368908 78598991319470 72115 14645 
      -codon-position----------------------------1      2  1     2  1 1   11   2         11       1    1 1 1   2            1    2 12  1 1        2 1 1221  
      ---Index-----------------------------------ATAAAGGAGGAGA ACAAATACGTGCGGGGA AATAGGGCAAGTCCTG GCTCAATGCACGCTGCCCA AGAACGGTGC TTTAAGGCACAAGA TAGGC GGACA 
         1 >A/Index/Egypt-Iowa-like/2010(H3N2)   G.GGGACGAAG.. G.GGGCG.ACAAA..AG CGC.AA....ACTAG. .A.TCCGAAGTAAGAT.AG TACGT...T. CCCG..ATG...AG CGA.. .AG.G
         2 >A/Index/Brisbane-like/2007(H3N2)     ............. ................. ................ ................... .......... .............. ..... .....
         3 >A/Index/Perth-like/2009(H3N2)        .C.G.A.GAA.AG .TG..CGT...A.AT.. .GCG..AAGG.C.AAA A.A.CCAA..T..GATTAG TA..TAACTT ....GAA.GAGG.. CGAAT A..T.

      amino-acid differences:

      Code:
                                          000 000000000 00 00000000 00 0000 00 000000 
                                          034 055777777 33 01112223 44 0012 12 111223 
                                          656 578456779 45 76780027 58 2441 75 133131 
                                          331 267582492 84 80495887 00 6075 43 159219 
                                          --- --------- -- -------- -- ---- -- ------ 
                                          IKI KLAK}ETRN II ENKKNVTI GE IYDI R} VSDP}K 
      >A/Index/Egypt-Iowa-like/2010(H3N2) VRV RITR}G.GS .. ..NQKIAR .D TCNV K} .NG.}R 
      >A/Index/Brisbane-like/2007(H3N2)   ... ....}.... .. ........ .. .... .} ....}. 
      >A/Index/Perth-like/2009(H3N2)      .R. RI..}.IG. VV KKNQKI.R SD ..NV K} M..S}.

      you can see, it's a mixture of Brisbane and Perth.
      It probably did split from Brisbane in spring 2008
      but stayed undetected.
      Now we had it in Nanjing,Thailand,Egypt,Iowa(?).

      amino-acid differences in HA to Perth : K78E,K160N,T228A,

      I uploaded the 3 calculated/estimated index-(ancestor)sequences here:

      they have a few changes to the actual Brisbane and Perth (of which only HA,NA are public)
      sequences since those were not the direct origins of a new strain but only close.
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment

      Working...
      X