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
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)
Comment