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recombination and preserved regions in swine-flu

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  • recombination and preserved regions in swine-flu

    taking all 96 full swine genomes from genbank
    and examining for segments with unusually few mutations
    I get the table below. Groups are formed
    and separated by a blank line manually:


    columns are:
    measure of "strangeness"
    years apart
    segment
    nucleotide differences in 1/100 % for segment 1
    nucleotide differences in 1/100 % for segment 2
    nucleotide differences in 1/100 % for segment 3
    nucleotide differences in 1/100 % for segment 4
    nucleotide differences in 1/100 % for segment 5
    nucleotide differences in 1/100 % for segment 6
    nucleotide differences in 1/100 % for segment 7
    nucleotide differences in 1/100 % for segment 8
    No. of first sequence
    No. of second sequence
    name of first sequence
    name of second sequence

    Code:
    -------------------------------------------------------------------
    involving A/swine/31(H1N1)
       72Y s3 1174 1038 0560 1369 1135 1271 0780 1239       52  7 A/swine/Alberta/56626/03(H1N1)   A/Swine/31(H1N1)
    75 57Y s7 1100 1074 1059 1318 1116 1078 0683 0970       49  7 A/swine/Wisconsin/1915/1988(H1N1)   A/Swine/31(H1N1)
    74 57Y s7 1100 1065 1043 1284 0991 1081 0673 0912       50  7 A/swine/Iowa/17672/1988(H1N1)   A/Swine/31(H1N1)
    73 72Y s7 1495 1650 1417 3517 1295 1734 1000 1347       89  7 A/swine/Shandong/2/03(H5N1)   A/Swine/31(H1N1)
    73 57Y s7 1108 1061 1051 1307 1005 1095 0653 0959       47  7 A/swine/Iowa/31483/1988(H1N1)   A/Swine/31(H1N1)
    73 56Y s7 1078 1043 1052 1307 1063 1039 0643 0970       48  7 A/swine/Kansas/3228/1987(H1N1)   A/Swine/31(H1N1)
    72 74Y s7 1556 1681 1453 4290 1458 4819 1000 1451       95  7 A/swine/Guangxi/58/2005(H9N2)   A/Swine/31(H1N1)
    72 73Y s7 1513 1715 1431 3465 1328 1727 0979 1111       90  7 A/swine/Guangxi/wz/2004(H5N1)   A/Swine/31(H1N1)
    72 72Y s7 1333 1836 1313 1775 1328 4700 0981 1455       76  7 A/swine/Ontario/52156/03(H1N2)   A/Swine/31(H1N1)
    71 73Y s7 1223 1776 1185 1457 1130 1418 0966 1229       54  7 A/swine/Ontario/23866/04(H1N1)   A/Swine/31(H1N1)
    70 73Y s7 1556 1689 1447 4149 1451 4744 0939 1219       96  7 A/swine/Korea/S452/2004(H9N2)   A/Swine/31(H1N1)
    70 56Y s7 1112 1039 1059 1307 1050 1137 0604 0970       44  7 A/swine/Iowa/1/1987(H1N1)   A/Swine/31(H1N1)
    69 73Y s7 1065 1800 1123 1791 1259 4674 0930 1181       75  7 A/swine/Ontario/55383/04(H1N2)   A/Swine/31(H1N1)
    69 68Y s7 1275 1797 1524 4792 1087 4664 0789 1137       62  7 A/Swine/Iowa/569/99 (H3N2)   A/Swine/31(H1N1)
    69 60Y s7 1156 1087 1089 1399 1015 1143 0663 0920       51  7 A/swine/Maryland/23239/1991(H1N1)   A/Swine/31(H1N1)
    68 73Y s7 1054 1791 1020 1801 1229 4659 0885 1187       74  7 A/swine/Ontario/48235/04(H1N2)   A/Swine/31(H1N1)
    68 72Y s7 1290 1772 1070 1516 1155 1354 0882 1263       55  7 A/swine/Ontario/53518/03(H1N1)   A/Swine/31(H1N1)
    68 68Y s7 1297 1777 1486 1579 1098 4646 0778 1076       71  7 A/Swine/Indiana/9K035/99 (H1N2)   A/Swine/31(H1N1)
    68 68Y s7 1275 1797 1524 4795 1093 4642 0769 1088       63  7 A/Swine/Minnesota/593/99 (H3N2)   A/Swine/31(H1N1)
    68 68Y s7 1275 1797 1524 4789 1080 4642 0770 1122       61  7 A/Swine/Iowa/533/99 (H3N2)   A/Swine/31(H1N1)
    67 71Y s7 1322 1794 1514 1653 1196 4634 0840 1152       70  7 A/Swine/Korea/CY02/02(H1N2)   A/Swine/31(H1N1)
    67 67Y s7 1275 1797 1524 4789 1236 4649 0751 1097       64  7 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/31(H1N1)
    64 75Y s7 1346 1800 1551 4768 1201 1389 0824 1247       60  7 A/swine/Korea/CN22/2006(H3N1)   A/Swine/31(H1N1)
    64 75Y s7 1341 1800 1551 4768 1201 1408 0824 1247       59  7 A/swine/Korea/PZ72-1/2006(H3N1)   A/Swine/31(H1N1)
    64 73Y s7 1395 1776 1538 4768 1163 1347 0795 1226       58  7 A/swine/Minnesota/00395/2004(H3N1)   A/Swine/31(H1N1)
    64 73Y s7 1327 1754 1512 4839 1178 1375 0799 1149       57  7 A/swine/MI/PU243/04 (H3N1)   A/Swine/31(H1N1)
    64 72Y s7 1322 1773 1472 4809 1170 4710 0801 1167       65  7 A/swine/North Carolina/2003(H3N2)   A/Swine/31(H1N1)
    64 71Y s7 1342 1578 1469 2092 1362 1425 0773 2915       7  4 A/Swine/31(H1N1)   A/swine/Saskatchewan/18789/02(H1N1)
    63 75Y s7 1340 1789 1545 1645 1145 4658 0810 1207       72  7 A/swine/Guangxi/13/2006(H1N2)   A/Swine/31(H1N1)
    63 74Y s7 1350 1745 1538 4797 1194 4686 0794 1157       66  7 A/swine/Manitoba/12707/2005(H3N2)   A/Swine/31(H1N1)
    63 74Y s7 1324 1763 1543 4821 1201 4678 0794 1169       69  7 A/swine/British Columbia/28103/2005(H3N2)   A/Swine/31(H1N1)
    63 74Y s7 1324 1750 1524 4785 1188 4671 0794 1157       68  7 A/swine/Ontario/33853/2005(H3N2)   A/Swine/31(H1N1)
    63 74Y s7 1324 1745 1515 4785 1188 4693 0794 1169       67  7 A/swine/Alberta/14722/2005(H3N2)   A/Swine/31(H1N1)
    63 73Y s7 1318 1759 1485 4851 1184 1347 0769 1173       56  7 A/swine/IN/PU542/04 (H3N1)   A/Swine/31(H1N1)
    62 72Y s7 1276 1316 1018 1399 1189 1326 0750 1085       53  7 A/swine/Ontario/57561/03(H1N1)   A/Swine/31(H1N1)
       73Y s7 1301 1285 1231 1545 1158 4838 0799 1056       73  7 A/swine/Zhejiang/1/2004(H1N2)   A/Swine/31(H1N1)
       73Y s7 1093 1003 0963 1556 0989 1270 0799 1022       7  5 A/Swine/31(H1N1)   A/swine/Tianjin/01/04(H1N1)
       75Y s7 1115 0990 1008 1556 0983 1281 0729 1010       7  6 A/Swine/31(H1N1)   A/swine/Henan/01/06(H1N1)
    76 73Y s8 1478 1681 1453 3465 1438 1697 1186 1078       92  7 A/swine/Anhui/ca/2004(H5N1)   A/Swine/31(H1N1)
    71 68Y s8 1227 1563 1476 4967 1345 5014 0840 0847       7  1 A/Swine/31(H1N1)   A/Swine/Ontario/01911-1/99 (H4N6)
    69 70Y s8 1293 1649 1492 4720 1389 4814 0743 0883       7  2 A/Swine/31(H1N1)   A/swine/Ontario/K01477/01(H3N3)
    69 70Y s8 1289 1657 1487 4720 1389 4807 0723 0883       7  3 A/Swine/31(H1N1)   A/swine/Ontario/42729A/01(H3N3)
    
    involving swine from 1975-1981:
    72 27Y s1 0201 1901 0365 2166 0758 4630 0616 0781       75  12 A/swine/Ontario/55383/04(H1N2)   A/swine/Tennessee/25/77(H1N1)
    
    74 23Y s2 0631 0169 0706 0564 0474 0563 0397 0703       52  35 A/swine/Alberta/56626/03(H1N1)   A/swine/Wisconsin/629/1980(H1N1)
    74 23Y s2 0626 0169 0699 0570 0474 0563 0397 0691       52  36 A/swine/Alberta/56626/03(H1N1)   A/swine/Wisconsin/661/1980(H1N1)
    73 23Y s2 0626 0165 0699 0564 0467 0563 0397 0727       52  37 A/swine/Alberta/56626/03(H1N1)   A/swine/Wisconsin/641/1980(H1N1)
    69 23Y s2 0613 0147 0693 0611 0474 0571 0397 0727       52  38 A/swine/Alberta/56626/03(H1N1)   A/swine/Wisconsin/8/1980(H1N1)
    76 27Y s2 0617 0221 0662 0658 0567 0557 0437 0774       52  28 A/swine/Alberta/56626/03(H1N1)   A/swine/Kentucky/1/1976(H1N1)
    57 22Y s2 0626 0100 0731 0558 0501 0584 0427 0560       52  41 A/swine/Alberta/56626/03(H1N1)   A/swine/Ontario/7/1981(H1N1)
    56 22Y s2 0619 0095 0726 0552 0507 0577 0417 0584       52  40 A/swine/Alberta/56626/03(H1N1)   A/swine/Ontario/1/1981(H1N1)
    55 23Y s2 0604 0095 0740 0552 0501 0591 0407 0548       52  42 A/swine/Alberta/56626/03(H1N1)   A/swine/Wisconsin/11/1980(H1N1)
    55 22Y s2 0622 0091 0731 0558 0507 0591 0417 0560       52  43 A/swine/Alberta/56626/03(H1N1)   A/swine/Ontario/4/1981(H1N1)
    
    76 28Y s3 0294 1872 0229 2169 0748 4604 0529 0736       74  17 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/3/1976(H1N1)
    76 28Y s3 0294 1872 0229 2169 0748 4604 0529 0736       74  16 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/7/1976(H1N1)
    75 28Y s3 0307 1861 0225 2186 0768 4596 0529 0783       74  18 A/swine/Ontario/48235/04(H1N2)   A/swine/Iowa/1/1976(H1N1)
    75 28Y s3 0294 1872 0225 2145 0761 4618 0631 0724       74  15 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/19/1976(H1N1)
    75 26Y s3 0346 1928 0202 2163 0768 4655 0498 0676       74  29 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/11/1978(H1N1)
    74 33Y s3 0476 1902 0275 2087 0794 4731 0560 0712       74  9 A/swine/Ontario/48235/04(H1N2)   A/swine/Wisconsin/1/1971(H1N1)
    72 27Y s3 0337 1925 0202 2151 0768 4655 0519 0760       74  31 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/65/1977(H1N1)
    72 27Y s3 0337 1924 0202 2151 0768 4655 0519 0760       74  30 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/64/1977(H1N1)
    67 27Y s3 0286 1863 0179 2169 0721 4647 0529 0748       74  13 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/79/1977(H1N1)
    66 27Y s3 0281 1876 0174 2151 0721 4604 0621 0748       74  14 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/62/1977(H1N1)
    62 27Y s3 0207 1869 0156 2163 0714 4616 0600 0783       74  12 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/25/77(H1N1)
    
    pairs less than 3 years apart
    75 00Y s3 0017 0013 0004 0017 0006 0014 0010 0023       41  40 A/swine/Ontario/7/1981(H1N1)   A/swine/Ontario/1/1981(H1N1)
    74 01Y s3 0021 0200 0009 0022 0026 0021 0191 0198       28  27 A/swine/Kentucky/1/1976(H1N1)   A/swine/Tennessee/10/1977(H1N1)
    
    65 02Y s8 0029 0012 0206 0016 0031 0028 0165 0011       6  5 A/swine/Henan/01/06(H1N1)   A/swine/Tianjin/01/04(H1N1)
    
    62 02Y s7 0315 0321 0334 0388 0046 0092 0010 0107       68  65 A/swine/Ontario/33853/2005(H3N2)   A/swine/North Carolina/2003(H3N2)
    62 02Y s7 0315 0307 0344 0470 0060 0078 0010 0119       69  65 A/swine/British Columbia/28103/2005(H3N2)   A/swine/North Carolina/2003(H3N2)
    62 02Y s7 0315 0307 0306 0382 0053 0092 0010 0107       66  65 A/swine/Manitoba/12707/2005(H3N2)   A/swine/North Carolina/2003(H3N2)
    62 02Y s7 0298 0316 0325 0405 0053 0113 0010 0119       67  65 A/swine/Alberta/14722/2005(H3N2)   A/swine/North Carolina/2003(H3N2)
    61 02Y s7 0199 0178 0260 0407 0190 0231 0010 0224       39  30 A/swine/Minnesota/5892-7/1979(H1N1)   A/swine/Tennessee/64/1977(H1N1)
    61 02Y s7 0199 0178 0260 0407 0189 0231 0010 0222       39  31 A/swine/Minnesota/5892-7/1979(H1N1)   A/swine/Tennessee/65/1977(H1N1)
    30 02Y s8 0042 0021 0035 0045 0031 0034 0108 0000       94  93 A/swine/Fujian/1/2003(H5N1)   A/swine/Fujian/F1/2001(H5N1)
    
    30 01Y s3 0000 0000 0000 0011 0178 0021 0040 0011       64  63 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/Minnesota/593/99 (H3N2)
    30 01Y s3 0000 0000 0000 0011 0204 0049 0051 0059       64  62 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/Iowa/569/99 (H3N2)
    30 01Y s4 0000 0000 0000 0000 0204 0014 0020 0047       64  61 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/Iowa/533/99 (H3N2)
    30 01Y s7 0064 0030 0050 0103 0065 0070 0000 0035       20  19 A/swine/Minnesota/27/1976(H1N1)   A/swine/Iowa/1/1977(H1N1)
    
    30 00Y s8 0070 0026 0074 0041 0006 0092 0000 0000       68  66 A/swine/Ontario/33853/2005(H3N2)   A/swine/Manitoba/12707/2005(H3N2)
    30 00Y s8 0038 0043 0013 0028 0006 0000 0000 0000       11  10 A/swine/Tennessee/1/1975(H1N1)   A/swine/Illinois/1/1975(H1N1)
    30 00Y s8 0030 0017 0013 0028 0026 0245 0170 0000       14  13 A/swine/Tennessee/62/1977(H1N1)   A/swine/Tennessee/79/1977(H1N1)
    30 00Y s8 0026 0026 0004 0000 0026 0007 0040 0000       3  2 A/swine/Ontario/42729A/01(H3N3)   A/swine/Ontario/K01477/01(H3N3)
    30 00Y s8 0013 0008 0009 0022 0006 0014 0010 0000       43  41 A/swine/Ontario/4/1981(H1N1)   A/swine/Ontario/7/1981(H1N1)
    30 00Y s8 0004 0000 0004 0005 0000 0007 0000 0000       46  45 A/swine/Iowa/1/1985(H1N1)   A/swine/Iowa/3/1985(H1N1)
    30 00Y s8 0004 0000 0004 0000 0000 0000 0020 0000       25  24 A/swine/Tennessee/19/1977(H1N1)   A/swine/Tennessee/21/1977(H1N1)
    30 00Y s8 0000 0000 0009 0000 0000 0000 0000 0000       17  16 A/swine/Tennessee/3/1976(H1N1)   A/swine/Tennessee/7/1976(H1N1)
    30 00Y s8 0000 0000 0004 0000 0000 0000 0000 0000       33  32 A/swine/Tennessee/17/1976(H1N1)   A/swine/Tennessee/15/1976(H1N1)
    30 00Y s8 0000 0000 0000 0000 0000 0000 0000 0000       31  30 A/swine/Tennessee/65/1977(H1N1)   A/swine/Tennessee/64/1977(H1N1)
    30 00Y s7 0114 0043 0055 0129 0019 0099 0000 0023       69  67 A/swine/British Columbia/28103/2005(H3N2)   A/swine/Alberta/14722/2005(H3N2)
    30 00Y s7 0114 0004 0055 0041 0006 0113 0000 0011       68  67 A/swine/Ontario/33853/2005(H3N2)   A/swine/Alberta/14722/2005(H3N2)
    30 00Y s7 0092 0000 0000 0000 0000 0000 0000 0023       60  59 A/swine/Korea/CN22/2006(H3N1)   A/swine/Korea/PZ72-1/2006(H3N1)
    30 00Y s7 0070 0065 0074 0129 0019 0078 0000 0011       69  66 A/swine/British Columbia/28103/2005(H3N2)   A/swine/Manitoba/12707/2005(H3N2)
    30 00Y s7 0052 0021 0037 0035 0013 0021 0000 0011       67  66 A/swine/Alberta/14722/2005(H3N2)   A/swine/Manitoba/12707/2005(H3N2)
    30 00Y s7 0013 0004 0004 0005 0000 0014 0000 0023       43  40 A/swine/Ontario/4/1981(H1N1)   A/swine/Ontario/1/1981(H1N1)
    30 00Y s7 0012 0021 0013 0017 0019 0007 0000 0046       18  17 A/swine/Iowa/1/1976(H1N1)   A/swine/Tennessee/3/1976(H1N1)
    30 00Y s7 0012 0021 0013 0017 0019 0007 0000 0046       18  16 A/swine/Iowa/1/1976(H1N1)   A/swine/Tennessee/7/1976(H1N1)
    30 00Y s7 0004 0013 0004 0000 0006 0000 0000 0023       37  35 A/swine/Wisconsin/641/1980(H1N1)   A/swine/Wisconsin/629/1980(H1N1)
    30 00Y s7 0004 0000 0004 0005 0000 0000 0000 0011       36  35 A/swine/Wisconsin/661/1980(H1N1)   A/swine/Wisconsin/629/1980(H1N1)
    30 00Y s7 0000 0039 0046 0099 0013 0028 0000 0011       69  68 A/swine/British Columbia/28103/2005(H3N2)   A/swine/Ontario/33853/2005(H3N2)
    30 00Y s7 0000 0013 0000 0005 0006 0000 0000 0035       37  36 A/swine/Wisconsin/641/1980(H1N1)   A/swine/Wisconsin/661/1980(H1N1)
    30 00Y s5 0025 0004 0000 0034 0000 0021 0010 0035       24  23 A/swine/Tennessee/21/1977(H1N1)   A/swine/Tennessee/31/1977(H1N1)
    30 00Y s5 0021 0004 0004 0034 0000 0021 0010 0035       25  23 A/swine/Tennessee/19/1977(H1N1)   A/swine/Tennessee/31/1977(H1N1)
    30 00Y s3 0000 0000 0000 0011 0063 0049 0051 0047       63  62 A/Swine/Minnesota/593/99 (H3N2)   A/Swine/Iowa/569/99 (H3N2)
    30 00Y s3 0000 0000 0000 0011 0038 0014 0020 0023       63  61 A/Swine/Minnesota/593/99 (H3N2)   A/Swine/Iowa/533/99 (H3N2)
    30 00Y s3 0000 0000 0000 0011 0025 0035 0030 0023       62  61 A/Swine/Iowa/569/99 (H3N2)   A/Swine/Iowa/533/99 (H3N2)
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    Re: recombination and preserved regions in swine-flu

    Code:
    C: evidence for recombination
    A:evidence for reassortment
    
    C3,A7    :A/Sw/Alberta/56626/03(H1N1)     A/Sw/31(H1N1)
    C168,A7  :A/Sw/Kansas/3228/1987(H1N1)     A/Sw/31(H1N1)
    C3468,A7 :A/Sw/Tianjin/01/04(H1N1)        A/Sw/31(H1N1)
    C7,A468  :A/Sw/Ontario/019111/99 (H4N6)   A/Sw/31(H1N1)
    C13,A4678:A/Sw/Ontario/55383/04(H1N2)     A/Sw/Tennessee/25/77(H1N1)
    C27,A7   :A/Sw/Alberta/56626/03(H1N1)     A/Sw/Ontario/4/1981(H1N1)
    C13      :A/Sw/Ontario/48235/04(H1N2)     A/Sw/Tennessee/3/1976(H1N1)
             :A/Sw/Ontario/7/1981(H1N1)       A/Sw/Ontario/1/1981(H1N1)
    A278     :A/Sw/Tennessee/10/1977(H1N1)    A/Sw/Kentucky/1/1976(H1N1)
    C7,A3    :A/Sw/Tianjin/01/04(H1N1)        A/Sw/Henan/01/06(H1N1)
    A57      :A/Sw/North Carolina/2003(H3N2)  A/Sw/Ontario/33853/2005(H3N2)
    C12      :A/Sw/Fujian/F1/2001(H5N1)       A/Sw/Fujian/1/2003(H5N1)
    C567     :A/Sw/Minnesota/593/99 (H3N2)    A/Sw/Nebraska/209/98 (H3N2)
    C5       :A/Sw/Iowa/533/99 (H3N2)         A/Sw/Nebraska/209/98 (H3N2)
    A7       :A/Sw/Iowa/1/1977(H1N1)          A/Sw/Minnesota/27/1976(H1N1)
             :A/Sw/Illinois/1/1975(H1N1)      A/Sw/Tennessee/1/1975(H1N1)
             :A/Sw/Iowa/3/1985(H1N1)          A/Sw/Iowa/1/1985(H1N1)
    C4,A26   :A/Sw/Alberta/14722/2005(H3N2)   A/Sw/Ontario/33853/2005(H3N2)
             :A/Sw/Iowa/569/99 (H3N2)         A/Sw/Minnesota/593/99 (H3N2)

    evidence for preservation of genes (marked *)

    Code:
       72Y s3 1174 1038*0560 1369 1135 1271 0780 1239       52  7 A/swine/Alberta/56626/03(H1N1)   A/Swine/31(H1N1)
    72 27Y s1*0201 1901*0365 2166 0758 4630 0616 0781       75  12 A/swine/Ontario/55383/04(H1N2)   A/swine/Tennessee/25/77(H1N1)
    55 22Y s2 0622*0091 0731 0558 0507 0591 0417 0560       52  43 A/swine/Alberta/56626/03(H1N1)   A/swine/Ontario/4/1981(H1N1)
    76 28Y s3*0294 1872*0229 2169 0748 4604 0529 0736       74  17 A/swine/Ontario/48235/04(H1N2)   A/swine/Tennessee/3/1976(H1N1)
    65 02Y s8 0029*0012 0206 0016 0031 0028 0165*0011       6  5 A/swine/Henan/01/06(H1N1)   A/swine/Tianjin/01/04(H1N1)
    62 02Y s7 0315 0321 0334 0388 0046 0092*0010 0107       68  65 A/swine/Ontario/33853/2005(H3N2)   A/swine/North Carolina/2003(H3N2)
    30 02Y s8 0042 0021 0035 0045 0031 0034 0108*0000       94  93 A/swine/Fujian/1/2003(H5N1)   A/swine/Fujian/F1/2001(H5N1)
    30 01Y s3*0000*0000*0000 0011 0204 0049 0051 0059       64  62 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/Iowa/569/99 (H3N2)
    30 01Y s4*0000*0000*0000*0000 0204 0014 0020 0047       64  61 A/Swine/Nebraska/209/98 (H3N2)   A/Swine/Iowa/533/99 (H3N2)
    30 01Y s7 0064 0030 0050 0103 0065 0070*0000 0035       20  19 A/swine/Minnesota/27/1976(H1N1)   A/swine/Iowa/1/1977(H1N1)
    Last edited by gsgs; August 1, 2007, 06:06 AM.
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #3
      Re: recombination and preserved regions in swine-flu



      shows differences of pairs in PB2 before and after elimination
      of 30 sequences which are supposed to either be fallacious
      (e.g. wrong date) or lab-strains or frozen lab-strains
      escaped after years without evolution or PB2 from
      viruses surviving in the environment without evolution
      or just non-mutationg viruses for whatever reason.

      You see, when you remove those 30 PB2s, the rest
      evolves pretty predictable with constant minimum
      change-rate of 3.64 mutations per PB2 per year
      (the diagonal line in the pictures). This is 22 mutations
      for the whole genome. These are only the surviving
      (sequenced) mutations, the actual mutations are higher.
      Also higher in HA,NA. And maybe higher when new strains emerge.

      pairs of H1N1 before 1957 and after 1977 are excluded.
      This is the only clear example where conservation of a PB2 actually
      influenced evolution i.e. it appeared later after a period of conservation
      and then continued to evolve.
      It is speculated that this was a lab-escape.


      here are those 30 sequences which are either fallacious or show
      preserved PB2:

      Code:
      >DQ009923g,63054914,A/Canada/720/2005,Canada,2005,Human,1,H2N2,,,,,,,,
      
      >CY011151l,106908541,A/Memphis/2/1986,,1986,Human,1,H3N2,,,,,,,,
      >CY015515g,115289308,A/Victoria/1968,Australia,1968,Human,1,H3N2,,,A/Victoria/1968,Australia,1968,Human,1,H3N2
      >DQ376870g,87247380,A/Dk/Taiwan/0526/1972,Taiwan,1972,Avian,1,H6N1,,,A/Dk/Taiwan/0526/1972,Taiwan,1972,Avian,1,H6N1
      
      >CY014998g,115279113,A/fowl/Dobson/1927,USA,1927,Avian,1,H7N7,,,A/fowl/Dobson/1927,,1927,Avian,1,H7N7
      >X58691g,60700,A/fowl/Dobson/1927,United Kingdom,1927,Avian,1,H7N7,,,A/FPV/Dobson/1927,United Kingdom,1927,Avian,1,H7N7
      
      >CY014686g,115278300,A/Dk/England/1/1956,United Kingdom,1956,Avian,1,H11N6,,,A/Dk/England/1/1956,United Kingdom,1956,Avian,1,H11N6
      
      >M91713g,324903,A/Great Lakes/0389/1965,USA,1965,Human,1,H2N2,,,A/Great Lakes/389/1965,USA,1965,Human,1,H2N2
      
      >CY004412g,82623874,A/ruddy turnstone/NJ/65/1985,USA,1985,Avian,1,H7N3,,,A/ruddy turnstone/New Jersey/65/1985,USA,1985,Avian,1,H7N3
      >AB243417g,83305694,A/Dk/Hokkaido/Vac-2/2004,LAB,NON,Avian,1,H7N7,,,A/Dk/Mongolia/736/02-Dk/Hokkaido/49/1998,Mongolia,1998,Avian,1,1
      >AB259709g,101918559,A/Dk/Hokkaido/Vac-1/2004,Japan,2004,Avian,1,H5N1,,,A/Dk/Hokkaido/Vac-1/2004,Japan,2004,Avian,1,H5N1
      >AY724251g,51340270,A/Ck/Hebei/1/2002,China,2002,Avian,1,H7N2,,,A/Ck/Hebei/1/2002,China,2002,Avian,1,H7N2
      >CY005822g,82754949,A/Dk/Czechoslovakia/1956,Czech Republic,1956,Avian,1,H4N6,,,A/Dk/Czechoslovakia/1956,Czech Republic,1956,Avian,1,H4N6
      
      >AY585523g,47156264,A/Dk/Zhejiang/11/2000,China,2000,Avian,1,H5N1,,,A/Dk/Zhejiang/11/2000,,2000,Avian,1,H5N1
      >CY005559g,82654681,A/Dk/Hong Kong/7/1975,Hong Kong,1975,Avian,1,H3N2,,,A/Dk/Hong Kong/7/1975,Hong Kong,1975,Avian,1,H3N2
      
      >CY009923g,90592283,A/Sw/Tennessee/25/1977,USA,1977,Sw,1,H1N1,,,A/Sw/Tennessee/25/1977,USA,1977,Sw,1,H1N1
      >M73513g,324049,A/Sw/Tennessee/24/1977,USA,1977,Sw,1,H1N1,,,A/Sw/Tennessee/24/1977,USA,1977,Sw,1,H1N1
      
      >CY014678g,115278281,A/Ck/Germany/N/1949,Germany,1949,Avian,1,H10N7,,,A/Ck/Germany/N/1949,Germany,1949,Avian,1,H10N7
      >CY006770g,83026962,A/Nanjing/49/1977,China,1977,Human,1,H3N2,,,A/Nanjing/49/1977,China,1977,Human,1,H3N2
      
      >CY010867l,94959758,A/USA/L3/1947,,1947,Human,1,H1N1,,,,,,,,
      >CY014799g,115278638,A/turkey/Minnesota/3/1992,USA,1991,Avian,1,H5N2,,,A/turkey/Minnesota/3/1992,USA,1992,Avian,1,H5N2
      >AF258842g,13274643,A/Hong Kong/498/1997,Hong Kong,1997,Human,1,H3N2,,,A/Hong Kong/498/1997,Hong Kong,1997,Human,1,H3N2
      
      >CY005652g,78097676,A/Dk/Hong Kong/562/1979,Hong Kong,1979,Avian,1,H10N9,,,A/Dk/Hong Kong/562/1979,Hong Kong,1979,Avian,1,H10N9
      >AB253760g,109452569,A/R(Dk/Mongolia/54/01-Dk/Mongolia/47/2001,Mongolia,2001,Avian,1,H5N1,,,,,,,,
      >AB253760l,90567982,A/Dk/Mongolia/54/01-Dk/Mongolia/47/2001,Mongolia,2001,Avian,1,,,,,,,,,
      
      >CY005412g,82654263,A/wedge-tailed shearwater/Western Australia/2576/1979,Australia,1979,Avian,1,H15N9,,,A/wedge-tailed shearwater/Western Australia/2576/1979,Australia,1979,Avian,1,H15N9
      >CY015088g,115279330,A/Ck/Scotland/1959,United Kingdom,1959,Avian,1,H5N1,,,A/Ck/Scotland/1959,United Kingdom,1959,Avian,1,H5N1
      
      >CY000696l,61970807,A/New York/173/2000,USA,2000,Human,1,H3N2,,,,,,,,
      >CY005582g,78097555,A/Dk/Hong Kong/342/1978,Hong Kong,1978,Avian,1,H5N2,,,A/Dk/Hong Kong/342/1978,Hong Kong,1978,Avian,1,H5N2
      >M73524g,324055,A/Korea/426/1968,South Korea,1968,Human,1,H2N2,,,A/Korea/426/1968,South Korea,1968,Human,1,H2N2
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

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