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  • recombinations in influenza A

    Code:
    recombination in PB2 , 07.March 2007
    ----------------------------------------------------
    p=0.0000000000000000000   6 Sw/MI/PU243/04                 547 Sw/Ontario/53518/03
    p=0.0000000000000000000 123 SCk/Hong Kong/YU100/02          69 Hong Kong/213/03
    p=0.0000000000000000000 127 Ck/Henan/210/04                191 Ck/Hubei/wj/97
    p=0.0000000000000000000 165 Ck/Guiyang/1655/06             262 Dk/Guiyang/2231/05
    p=0.0000000000000000000 169 Gr.black h.gull/Qinghai/3/05   166 ruddy shelDk/Qinghai/1/05
    p=0.0000000000000000000 188 Dk/Guangxi/668/04              192 Ck/Viet Nam/10/05
    p=0.0000000000000000000 204 tree sparrow/Henan/4/04        521 tree sparrow/Henan/2/04
    p=0.0000000000000000000 377 Ck/Jilin/53/01                 520 Ck/Yokohama/aq120/01
    p=0.0000000000000000000 415 laughing gull/DE/5/03          379 laughing gull/DE/94/00
    p=0.0000000000000000006 108 wild Dk/Guangdong/314/04       172 Ck/China/Guangxi1/00
    p=0.0000000000000000013 446 turkey/California/189/66       481 turkey/Wisconsin/1/66
    p=0.0000000000000000040 533 pintail/Alaska/211/05          429 mallard/Alaska/256/05
    p=0.0000000000000094571 247 black Dk/AUS/4045/80           318 tree sparrow/Henan/1/04
    p=0.0000000000001170048 140 Ck/Jiangsu/ng/01               142 Environment/Hong Kong/437-4/99
    p=0.0000000000001170680 167 Dk/Guiyang/1558/06             163 Dk/Fujian/10934/05
    p=0.0000000000003644895  31 Hong Kong/498/97                34 Udorn/307/72
    
    p=0.0000000000115195666 588 Sw/Tennessee/25/77             591 Sw/Ontario/55383/04
    p=0.0000000001218197565 560 Sw/Hong Kong/10/98             452 Ck/Beijing/1/94
    p=0.0000000003025031488 466 shorebird/DE/236/03            420 mallard/Ohio/170/99
    p=0.0000000003339268865  80 Ck/Jilin/hf/02                  86 Ck/Jilin/hg/02
    p=0.0000000009258338256 524 mallard/Alberta/52/97          369 mallard/Alberta/130/03
    p=0.0000000010058414511 456 mallard/Alberta/125/99         511 semi-palmated sandpiper/Brazil/43/90
    p=0.0000000013226932138 599 Sw/Ontario/11112/04            598 Sw/Ontario/23866/04
    p=0.0000000018431043192 572 Ck/Heilongjiang/35/00          220 Dk/Taiwan/0526/72
    p=0.0000000028147483086 297 mallard Dk/Alberta/57/76       155 Gs/Guangdong/3/97
    p=0.0000000034960826604  10 Ck/Dubai/338/01                205 Ck/Taiwan/ns2/99
    p=0.0000000040252024017 568 green wing teal/Ohio/59/89     335 mallard/Ohio/64/89
    p=0.0000000041060483445  61 Sw/Ontario/00130/97             32 Memphis/8/88
    p=0.0000000046298830119 557 Dk/NZL/41/84                   532 turkey/England/50-92/91
    p=0.0000000066587704020  91 Ck/Hubei/wf/02                 112 Ck/Thailand/Kanchanaburi/CK-160/05
    
    
    recombination in PB1 , 07.March 2007
    -----------------------------------------------------
    p=0.0000000000000000000 533 Ck/Jilin/hl/04                   1 Memphis/1/90
    p=0.0000000000000000000 553 Ck/Jilin/hf/02                   2 N2
    p=0.0000000000000000000  67 Memphis/104/76                  29 Hong Kong/14/74
    p=0.0000000000000000000 440 Dk/Jiangsu/nf/02                85 Ck/Jilin/ha/03
    p=0.0000000000000000000 376 Ck/Hubei/wl/97                 140 tree sparrow/Henan/1/04
    p=0.0000000000000000085 108 Gs/Guangdong/xb/01             331 Dk/Anyang/AVL-1/01
    p=0.0000000000000001985 211 Sw/Guangxi/wz/04               128 Ck/Guangdong/178/04
    p=0.0000000000000007407 385 Dk/Yangzhou/02/05              242 Gs/Guangdong/1/96
    p=0.0000000000007144218 281 Dk/Hubei/wq/03                 101 Ck/Jilin/he/02
    p=0.0000000000555332544 445 Ck/Beijing/ne/99               280 Ck/Jilin/hg/02
    p=0.0000000001651553174  91 Sw/Anhui/ca/04                 160 Ck/Hubei/wf/02
    p=0.0000000004074277674 397 Dk/Taiwan/0526/72              442 Ck/Taiwan/G2/87
    p=0.0000000011573136423  68 w.-t.shearw./W.Austr./2576/79   93 gray teal/Australia/1/79
    p=0.0000000066288770919 138 Ck/Jilin/9/04                   74 Dk/Zhejiang/52/00
    p=0.0000000068976694433 217 Sw/Saskatchewan/18789/02       407 snow Gs/Maryland/364/05
    
    
    
    
    recombination in PA , 07.March,2007
    ---------------------------------------------------------
    p=0.0000000000000000000 230 Sw/Ontario/57561/03             20 Murakami/4/64
    p=0.0000000000000000000 378 Ck/China/Guangxi1/00            27 Pheasant/HongKong/FY155/0MB
    p=0.0000000000000000000 459 Dk/Hubei/wp/03                 104 Ck/Jiangxi/25/04
    p=0.0000000000000000155 293 Ck/Jilin/ha/03                 106 Ck/Thailand/Kanchanaburi/CK-160/05
    p=0.0000000000000004614  48 SCk/Hong Kong/YU100/02         136 Dk/Anyang/AVL-1/01
    p=0.0000000000000154270 457 Ck/Jilin/hg/02                 285 Gs/Jilin/hb/03
    
    p=0.0000000000012829736 569 Sw/Tennessee/25/77             572 Sw/Ontario/53518/03
    p=0.0000000000057179136 239 Sw/Ontario/55383/04            237 Sw/Ontario/48235/04
    p=0.0000000000330950383 321 Ck/Hubei/wl/97                 268 Ck/Jilin/9/04
    p=0.0000000000365346028 395 Ck/Jilin/hj/03                  61 Ck/Thailand/Nontaburi/CK-162/05
    p=0.0000000000421404465 148 Ck/Hebei/326/05                 85 Ck/Hebei/108/02
    p=0.0000000006579815191 341 Dk/Zhejiang/bj/02              270 Dk/Hong Kong/2986.1/00
    
    p=0.0000000012465634840 421 Ck/Taiwan/PF1/02               455 Ck/Taiwan/PF2/02
    p=0.0000000012658157712 499 mallard Dk/Alberta/210/77      157 mallard/Maryland/789/02
    p=0.0000000017966303416 562 Ck/Pennsylvania/1/83            74 mallard/Alberta/743/83
    p=0.0000000030654763896 539 blue-winged teal/Alberta/685/82469 Ck/Victoria/85
    p=0.0000000032652359962 149 Sw/Korea/S81/04                438 Ck/Taiwan/0222/02
    p=0.0000000032708173691 520 Gull/MD/19/77                  478 Ck/New York/14677-13/98
    p=0.0000000047405495057 534 Gull/Maryland/704/77           453 Ck/Pakistan/34669/95
    p=0.0000000053040670369 334 Sw/Korea/S10/04                335 mallard/Netherlands/12/00
    p=0.0000000058937276655 164 Ck/Korea/S5/03                 545 ruddy turnstone/Delaware/34/93
    
    
    
    
    
    
    recombination in NP , 07.March 2007
    ----------------------------------------------
    p=0.0000000000000000000 155 Sw/Hangzhou/1/06               284 Ck/Guangdong/56/01
    p=0.0000000000000000000 618 Ck/Jilin/hq/03                 274 Ck/Jilin/hn/03
    p=0.0000000000000000003 158 Ck/Italy/1067/99                30 mallard/Bavaria/1/05
    p=0.0000000000000000006  71 Ck/Hong Kong/37.4/02           389 Ck/Hong Kong/31.4/02
    p=0.0000000000000000254 604 Dk/Guangxi/13/04               109 Indonesia/298H/06
    
    p=0.0000000000000219706 161 Qa/Shantou/243/00              156 guinea fowl/HongKong/NT184/03
    p=0.0000000000003268515 165 Sw/Ohio/891/01                 162 Sw/Iowa/930/01
    p=0.0000000000007141299  32 Ck/Guangxi/3791/05             301 Ck/Viet Nam/10/05
    p=0.0000000000012868025  92 Dk/NJ/5832-13/96               110 mallard/MN/107/98
    p=0.0000000000014628822 382 Ck/Jilin/hl/04                 585 Ck/Beijing/8/98
    p=0.0000000000032968355 689 Sw/Korea/S452/04               229 Ck/Jilin/xv/02
    p=0.0000000000049764357 251 Dk/Zhejiang/bj/02               28 Dk/Zhejiang/03/01
    p=0.0000000000378777633  98 Ck/NY/13237-6/98               135 mallard/MN/346233/00
    
    p=0.0000000003424356796 113 mallard/MN/347/99              124 mallard/MN/192/99
    p=0.0000000003823746628 305 31                             342 Ck/Taiwan/7-5/99
    p=0.0000000004395791161 288 Ck/Henan/210/04                 25 Ck/Yamaguchi/7/04
    p=0.0000000009669313859 517 Sw/May/54                      316 bar-headed Gs/Mongolia/1/05
    p=0.0000000015527886617 575 Dk/NZL/76/84                    52 Dk/Hong Kong/366/78
    p=0.0000000017052553159 690 Sw/Nebraska/209/98             657 Wisconsin/10/98
    p=0.0000000027677587193 399 Sw/29/37                       516 Ck/Taiwan/0114/04

    pictures are here:


    .:match
    o:difference
    -:not both defined
    Last edited by gsgs; March 25, 2007, 02:07 PM. Reason: many deletions due to obvious sequencing or alignment errors
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    Re: recombinations in influenza A

    I took the 3930 full genomes from genbank, 11.April 2008,
    aligned them with MAFFT, completed the few missing nucleotides
    at the start and end by the common average, encoded 3 nucleotides into
    64 codon-characters and concentrated on the 3 big polymerase
    segments only. That gave 3930 sequences of lengths 760,760,725.
    I also included artificial hybrid-sequences consisting of the first
    half of segment 1 and the second half of segment 2 to demonstrate
    the effect of reassortment.
    I also included random sequences, obtained by applying all sequences
    in the database to one random permutation of the 760 positions
    (same permutation for all sequences).

    Then I checked all pairs of these for recombinations with one
    breakpoint at positions 21,41,..,741.
    The p-value was calculated and pairs counted with p-values
    between 10^(-k) and 10^(-k-1) , k=0,..,26

    The same was redone for human sequences only (2433)
    and the rest (1497), consisting mainly of avian and swine sequences.

    The used program is here:

    C-source code attached to the executable or here:

    (in progress, could be updated later)

    command line (DOS/Windows) was:
    recfa file 1 741 i20 b1 l27
    or for randomized files:
    recfa file 1 741 i20 b1 l27
    result is printed in file "kkzpf"
    If someone can run it with the b2 switch instead of b1,
    and report the result here, that's appreciated
    (takes an estimated 10 hours per segment/file)


    Code:
    
    total (3930 genomes)
    
     segment 1 segment 2 segment 3 1-2 hybrid  randomized
    -----------------------------------------------------
     221587275 186251275 191975341 134660277    196582200
      32809984  43827039  50034521  68308690     48565220
       4020090  12420201  13901891  26976994      6882059
        896777   4702124   4483275  11515220       764062
        283532   1061848   1334793   7510835        49479
         77957     97535    272604   5357678         3706
         26018     23237     45056   4396940          334
         13316     16100     15646   3003213           33
          8907     11811     10534   1549345           10
          6335      8718      6914    903419            4
    
          4261      6901      5289    617967            0
          2828      5294      4486    470475            0
          2221      4255      3901    330685            0
          1827      2880      3208    198329            0
          1342      2102      2300    123261            0
           914      1366      1780     80408            0
           618       855      1533     55008            0
           500       573      1043     43070            0
           373       394       977     32757            0
           327       254       599     23423            0
           268       142       378     18062            0
           227        93       267     14807            0
           218        66       177     11363            0
           194        37       159      8628            0
           171        35       127      7228            0
           109        28        72      5403            0
            74        20        41      4678            0
    ------------------------------------------------------------------------
     259746663 248445183 262106912 266228163    252000000  sum,all
         16472     25295     26337   2045552            0  sum,lower part
                                               
    
    
    
    human, 2433 genomes
       segm.1   segm.2   segm.3 1-2 hybrid  randomized
    ---------------------------------------------------
     92473176 78882282 86998613 55513028    78375750
      9307854 10904550 11603294  6674723    18352230
       672551  1330464  1655911  4885742     3381651
        37223   703117   222684  4977229      437504
         2757   232688    55196  4223455       23562
         1353    15073     7476  3824136         844
          147      341      195  2686547          22
           24       42        3  1338050           4
            0        7        0   739147           0
            0        0        0   484633           0
    
            0        0        0   364688           0
            0        0        0   250808           0
            0        0        0   135674           0
            0        0        0    67865           0
            0        0        0    33618           0
            0        0        0    18455           0
            0        0        0    13837           0
            0        0        0     9868           0
            0        0        0     6035           0
            0        0        0     3778           0
            0        0        0     2592           0
            0        0        0     1956           0
            0        0        0     1435           0
            0        0        0      793           0
            0        0        0      595           0
            0        0        0      498           0
    -------------------------------------------------
    102495085 92068564 00543372 03262519        101M
    
    
    
    rest, 1497 genomes
       segm.1   segm.2   segm.3 1-2 hybrid  randomized
    -----------------------------------------------
     26666228 24823505 24393284 19015885   26750210
      8777014 10243337  9422600 10618627    9720524 
      1891339  2275489  2812280  4600622    2054897 
       684071   435843   867064  2273511     381318 
       236030    94173   274589  1099555      64666 
        61117    31857    76336   523124       6451 
        20862    18540    22207   272305        576 
        10930    13142     9364   146311         58 
         7739     9821     5506    84970         19 
         5524     7345     4266    57163          6
    
         3766     5773     3697    39586          4
         2435     4515     3395    27459          1
         1995     3636     3082    19310          0
         1653     2429     2582    13206          0
         1183     1840     1839     9434          0
          767     1158     1449     7423          0
          516      720     1315     6126          0
          400      519      853     4946          0
          301      364      885     4023          0
          282      244      537     3531          0
          231      142      322     2863          0
          192       93      247     2327          0
          176       66      156     1913          0
          160       37      146     1593          0
          132       35      112     1469          0
           90       28       68     1148          0
           60       20       39      957          0
    ------------------------------------------------
     38375193 37974671 37908220 38839387   38978730   sum,total
        14339    21619    20724   147314          5   sum,lower part


    there could be some effect of the (short,~100codons) extra-frame of PB1-F2
    in segment 2 and the packaging region in PA.
    These could suggest smaller p-values to be confused with recombinations.

    The high counts in the hybrid are off course due to reassortments.

    There is almost no recombination effect detectable in human
    sequences (the rest could be explained by "forces" of nearby
    mutations to the neighbor-codons).

    But there is quite some effect in avian+swine sequences,
    which however is clearly smaller than the effect from
    reassortment in the hybrid.

    The data-files are here:

    (self expanding executable, creates 12 files)

    -----------edit1--------------
    see [http://www.setbb.com/fluwiki2/viewtopic.php?p=861]here[/url] about the randomized runs
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #3
      Re: recombinations in influenza A

      Originally posted by gsgs View Post
      I took the 3930 full genomes from genbank, 11.April 2008,
      aligned them with MAFFT, completed the few missing nucleotides
      at the start and end by the common average, encoded 3 nucleotides into
      64 codon-characters and concentrated on the 3 big polymerase
      segments only. That gave 3930 sequences of lengths 760,760,725.
      I also included artificial hybrid-sequences consisting of the first
      half of segment 1 and the second half of segment 2 to demonstrate
      the effect of reassortment.
      I also included random sequences, obtained by applying all sequences
      in the database to one random permutation of the 760 positions
      (same permutation for all sequences).

      Then I checked all pairs of these for recombinations with one
      breakpoint at positions 21,41,..,741.
      The p-value was calculated and pairs counted with p-values
      between 10^(-k) and 10^(-k-1) , k=0,..,26

      The same was redone for human sequences only (2433)
      and the rest (1497), consisting mainly of avian and swine sequences.

      The used program is here:

      C-source code attached to the executable or here:

      (in progress, could be updated later)

      command line (DOS/Windows) was:
      recfa file 1 741 i20 b1 l27
      or for randomized files:
      recfa file 1 741 i20 b1 l27
      result is printed in file "kkzpf"
      If someone can run it with the b2 switch instead of b1,
      and report the result here, that's appreciated
      (takes an estimated 10 hours per segment/file)


      Code:
       
       
      total (3930 genomes)
       
       segment 1 segment 2 segment 3 1-2 hybrid  randomized
      -----------------------------------------------------
       221587275 186251275 191975341 134660277    196582200
        32809984  43827039  50034521  68308690     48565220
         4020090  12420201  13901891  26976994      6882059
          896777   4702124   4483275  11515220       764062
          283532   1061848   1334793   7510835        49479
           77957     97535    272604   5357678         3706
           26018     23237     45056   4396940          334
           13316     16100     15646   3003213           33
            8907     11811     10534   1549345           10
            6335      8718      6914    903419            4
       
            4261      6901      5289    617967            0
            2828      5294      4486    470475            0
            2221      4255      3901    330685            0
            1827      2880      3208    198329            0
            1342      2102      2300    123261            0
             914      1366      1780     80408            0
             618       855      1533     55008            0
             500       573      1043     43070            0
             373       394       977     32757            0
             327       254       599     23423            0
             268       142       378     18062            0
             227        93       267     14807            0
             218        66       177     11363            0
             194        37       159      8628            0
             171        35       127      7228            0
             109        28        72      5403            0
              74        20        41      4678            0
      ------------------------------------------------------------------------
       259746663 248445183 262106912 266228163    252000000  sum,all
           16472     25295     26337   2045552            0  sum,lower part
       
       
       
       
      human, 2433 genomes
         segm.1   segm.2   segm.3 1-2 hybrid  randomized
      ---------------------------------------------------
       92473176 78882282 86998613 55513028    78375750
        9307854 10904550 11603294  6674723    18352230
         672551  1330464  1655911  4885742     3381651
          37223   703117   222684  4977229      437504
           2757   232688    55196  4223455       23562
           1353    15073     7476  3824136         844
            147      341      195  2686547          22
             24       42        3  1338050           4
              0        7        0   739147           0
              0        0        0   484633           0
       
              0        0        0   364688           0
              0        0        0   250808           0
              0        0        0   135674           0
              0        0        0    67865           0
              0        0        0    33618           0
              0        0        0    18455           0
              0        0        0    13837           0
              0        0        0     9868           0
              0        0        0     6035           0
              0        0        0     3778           0
              0        0        0     2592           0
              0        0        0     1956           0
              0        0        0     1435           0
              0        0        0      793           0
              0        0        0      595           0
              0        0        0      498           0
      -------------------------------------------------
      102495085 92068564 00543372 03262519        101M
       
       
       
      rest, 1497 genomes
         segm.1   segm.2   segm.3 1-2 hybrid  randomized
      -----------------------------------------------
       26666228 24823505 24393284 19015885   26750210
        8777014 10243337  9422600 10618627    9720524 
        1891339  2275489  2812280  4600622    2054897 
         684071   435843   867064  2273511     381318 
         236030    94173   274589  1099555      64666 
          61117    31857    76336   523124       6451 
          20862    18540    22207   272305        576 
          10930    13142     9364   146311         58 
           7739     9821     5506    84970         19 
           5524     7345     4266    57163          6
       
           3766     5773     3697    39586          4
           2435     4515     3395    27459          1
           1995     3636     3082    19310          0
           1653     2429     2582    13206          0
           1183     1840     1839     9434          0
            767     1158     1449     7423          0
            516      720     1315     6126          0
            400      519      853     4946          0
            301      364      885     4023          0
            282      244      537     3531          0
            231      142      322     2863          0
            192       93      247     2327          0
            176       66      156     1913          0
            160       37      146     1593          0
            132       35      112     1469          0
             90       28       68     1148          0
             60       20       39      957          0
      ------------------------------------------------
       38375193 37974671 37908220 38839387   38978730   sum,total
          14339    21619    20724   147314          5   sum,lower part


      there could be some effect of the (short,~100codons) extra-frame of PB1-F2
      in segment 2 and the packaging region in PA.
      These could suggest smaller p-values to be confused with recombinations.

      The high counts in the hybrid are off course due to reassortments.

      There is almost no recombination effect detectable in human
      sequences (the rest could be explained by "forces" of nearby
      mutations to the neighbor-codons).

      But there is quite some effect in avian+swine sequences,
      which however is clearly smaller than the effect from
      reassortment in the hybrid.

      The data-files are here:

      (self expanding executable, creates 12 files)
      Your approach is c`onceptually flawed. It targets the "obvious" recombination that involves sequences that are diverse and happen rarely, producing long stretches of recombination. Most recombination, however, is between closely related sequences, and acquired polymorphsims are scattered because of subsequent recombination.

      Recombination accounts for almost ALL newly acquired polymorphisms (which look like single nucleotide polymorphisms and would be missed by your approach).

      Comment


      • #4
        Re: recombinations in influenza A

        why should recombination "scatter" more than reassortment ?
        compare with the hybrid-sequences.

        Recombination of related strains should still increase the
        counts of the larger p-values : e.g. between 10^-4 and 10^-5
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • #5
          Re: recombinations in influenza A

          Originally posted by gsgs View Post
          why should recombination "scatter" more than reassortment ?
          compare with the hybrid-sequences.

          Recombination of related strains should still increase the
          counts of the larger p-values : e.g. between 10^-4 and 10^-5
          As I said, your approach is conceptually flawed. Reassortment involves WHOLE genes, so a FULL SET of changes moves as a group, making such movement OBVIOUS.

          Recombination however, involves pieces of genes, which integrated WITHIN a gene, so each integratuion makes the recombination SMALLER and LESS obvious. Programs such as yours therefore miss the recombination as the recombined region gets smaller, or breaks up into multiple pieces. The most common recombination happens between CLOSELY related sequences, because closely related sequences are found in teh same area, leading to co-infections by such closely related sequences.

          Thus, your conceptually flawed approach creates false negatives (and uses a VERY biased database. Many sequences are partial sequences because the obvious recombination has been withheld.

          The example of the HA Shanghai tiger sequences in the multiple recent sequences from southern Egypt are a good example of recombination that is missed by your approach.

          Comment


          • #6
            Re: recombinations in influenza A

            does the most common reassortment also happen between closely related sequences ?
            Your argument applies to reassortment too.

            > closely related sequences are found in teh same area, leading to co-infections by such
            > closely related sequences.


            the database can hardly be biased on the small recombinations
            which can't be detected individually but only statistically. Recombinations who survive and
            spread should sooner or later enter the database. Those who don't are statistically
            irrelevant.

            Do you claim, there are long obvious recombinations of 500-1000 nucleotides
            and many 1-nucleotide recombinations, but nothing inbetween ? Why ?

            No HA examined yet. HA is not so good, because of many nonsynonymous mutations
            and possible difference in HA1 and HA2 and sometimes conserved regions
            in HA2.
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • #7
              Re: recombinations in influenza A

              Originally posted by gsgs View Post
              does the most common reassortment also happen between closely related sequences ?
              Your argument applies to reassortment too.

              > closely related sequences are found in teh same area, leading to co-infections by such
              > closely related sequences.


              the database can hardly be biased on the small recombinations
              which can't be detected individually but only statistically. Recombinations who survive and
              spread should sooner or later enter the database. Those who don't are statistically
              irrelevant.

              Do you claim, there are long obvious recombinations of 500-1000 nucleotides
              and many 1-nucleotide recombinations, but nothing inbetween ? Why ?

              No HA examined yet. HA is not so good, because of many nonsynonymous mutations
              and possible difference in HA1 and HA2 and sometimes conserved regions
              in HA2.
              Please. I have posted examples of 2 or 3 polymorphisms, although 1 is most common. I have also explained why the acquistions scatter. These small numbers of acqusitions are missed by your approach. The changes are spread throughout the gene(s). The J Virol paper cited 240 examples of small regions in (HUMAN) NA and stated the odds were a BILLION to one against chance causing the clustering.

              Comment


              • #8
                Re: recombinations in influenza A

                your explanation, why the acquisitions scatter should apply to
                reassortment as well. Yet we see different statistical behaviour.
                We do see largely increased numbers of those less obvious (scattered)
                recombination-signs in avian viruses. But not in human viruses. See above. Why ?

                that paper says:

                > Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

                it's the subject line and we had a long thread here with the same subject line.
                It's confirmed by my numbers above.
                So you must be misinterpreting something.
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment


                • #9
                  Re: recombinations in influenza A

                  Originally posted by gsgs View Post
                  your explanation, why the acquisitions scatter should apply to
                  reassortment as well. Yet we see different statistical behaviour.
                  We do see largely increased numbers of those less obvious (scattered)
                  recombination-signs in avian viruses. But not in human viruses. Why ?

                  that paper says:

                  > Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

                  it's the subject line and we had a long thread here with the same subject line.
                  It's confirmed by my numbers above.
                  So you must be misinterpreting something.
                  Please. Finding reassortment (involving whole genes) is a far cry from finding recombination (which invoves pieces of genes which are frequently VERY short).

                  The J Virol paper had data that were STATISTICALLY SIGNIFICANT, as stated in the abstract (and were a BILLION to one for NA).

                  You continue to post nonsense. This is NOT your field, which is VERY clear from your comments and logic. Internet based education has its drawbacks.

                  Comment


                  • #10
                    Re: recombinations in influenza A

                    Originally posted by gsgs View Post
                    your explanation, why the acquisitions scatter should apply to
                    reassortment as well. Yet we see different statistical behaviour.
                    We do see largely increased numbers of those less obvious (scattered)
                    recombination-signs in avian viruses. But not in human viruses. See above. Why ?

                    that paper says:

                    > Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

                    it's the subject line and we had a long thread here with the same subject line.
                    It's confirmed by my numbers above.
                    So you must be misinterpreting something.
                    Abstact says (emphasis added):

                    Using an exhaustive search and a nonparametric<SUP> </SUP>test for mosaic structure, we identified 315 sequences (2&#37<SUP> </SUP>in five different RNA segments that, after a multiple comparisons<SUP> </SUP>correction, had statistically significant mosaic signals compatible<SUP> </SUP>with homologous recombination.

                    Comment


                    • #11
                      Re: recombinations in influenza A

                      I wish you would toddle over to Fluwiki and post the same argument over there, Niman. Just quote the abstract and explain the use of boundary constraints in evolutionary relationship models (phylogenetic trees). They worship the ground that any 'bird flu expert' trods, yet - and despite repeatedly quoting your near-daily commentary - they are in firmly in denial of any evidence of HR (and are quick to mention this Taubenberger paper as gospel). They apparently do not read your posts here that explicitly document many homologous recombination events in H5N1 strains.

                      Comment


                      • #12
                        Re: recombinations in influenza A

                        Originally posted by Oracle View Post
                        I wish you would toddle over to Fluwiki and post the same argument over there, Niman. Just quote the abstract and explain the use of boundary constraints in evolutionary relationship models (phylogenetic trees). They worship the ground that any 'bird flu expert' trods, yet - and despite repeatedly quoting your near-daily commentary - they are in firmly in denial of any evidence of HR (and are quick to mention this Taubenberger paper as gospel). They apparently do not read your posts here that explicitly document many homologous recombination events in H5N1 strains.
                        Yes, they are in denial and have banned any posts from me (which is how they defend the indefensible).

                        Comment


                        • #13
                          Re: recombinations in influenza A

                          I'm updating my files ...
                          and rerunning the recombination-searcher
                          here is what I have so far: (together with the data from Jan.2008)
                          (to be completed later)


                          se7a1.nam, 14143 sequences

                          0000000000000 648 SCk/HK/YU100/02(H5N1) 10 HK/213/03(H5N1)
                          0000000000000 2832 Dk/VNM/N-TB/05(H5N1) 643 Ck/VNM/C57/04(H5N1)
                          0000000000000 758 Ck/Henan/210/04(H5N1) 3112 Ck/Hubei/wj/1997(H5N1)
                          0000000000000 3137 Ck/Jilin/ho/03(H5N1) 762 WildDk/Guangdong/314/2004(H5N1)
                          0000000000000 2640 Dk/Guangxi/668/04(H5N1) 1521 Ck/VNM/10/05(H5N1)
                          0000000000000 2546 Tree sparrow/Henan/4/04(H5N1) 2544 Tree sparrow/Henan/2/04(H5N1)
                          0000000000000 3142 Ck/Hunan/fg/04(H5N1) 2545 Tree sparrow/Henan/3/04(H5N1)
                          0000000000000 3092 Ck/Guiyang/1655/06(H5N1) 2971 Dk/Guiyang/2231/05(H5N1)
                          0000000000000 3083 Dk/Guiyang/1558/06(H5N1) 3085 Dk/Guiyang/1722/06(H5N1)
                          0000000000001 3122 mallard/Guangxi/wt/04(H5N1) 3130 Ck/Jilin/hg/02(H5N1)
                          0000000000006 3131 Ck/Jilin/hh/02(H5N1) 632 Gs/Thailand/79/04(H5N1)
                          0000000000499 3123 Ck/Henan/wu/04(H5N1) 654 Ck/HK/2133.1/03(H5N1)
                          0000000094571 2543 Tree sparrow/Henan/1/04(H5N1) 1070 black Dk/AUS/4045/1980(H6N5)
                          0000000198497 2833 Dk/VNM/317/05(H5N1) 96 Dk/HK/Y439/97(H9N2)
                          0000000435027 3126 Ck/Jilin/ha/03(H5N1) 3129 Ck/Jilin/he/02(H5N1)
                          0000001685924 3134 Ck/Jilin/hl/04(H5N1) 3136 Ck/Jilin/hn/03(H5N1)
                          0000707733215 3139 Ck/Jilin/hq/03(H5N1) 755 tiger/Thailand/CU-T7/04(H5N1)
                          0001626612604 3110 Ck/Hubei/wh/1997(H5N1) 684 Ck/HongKong/SSP101/03(H9N2)
                          0003671337389 3132 Ck/Jilin/hj/03(H5N1) 721 Ck/Ayutthaya/Thailand/CU-23/04(H5N1)
                          0000000000000 3497 Ck/Guangxi/6/00(H9N2) 1 parakeet/Chiba/1/97(H9N2)
                          0000000000000 3508 Sw/Guangxi/S15/05(H9N2) 2 parakeet/Narita/92A/98(H9N2)
                          0000000000000 3498 Dk/Guangxi/51/05(H9N2) 19 Ck/Yokohama/aq55/01(H9N2)
                          0000000000000 2532 Ck/Jilin/53/01(H9N2) 26 Ck/Yokohama/aq120/01(H9N2)
                          0000000000000 2783 Ck/China/Guangxi1/00(H9N2) 208 Ck/Guangdong/10/00(H9N2)
                          0000000000000 262 Dk/Shantou/1881/00(H9N2) 1951 partridge/Shantou/3720/01(H9N2)
                          0000000000000 3506 bird/Guangxi/H1/06(H9N2) 2015 Ck/Guangxi/1857/04(H9N2)
                          0000000000000 3353 Sw/Guangxi/58/05(H9N2) 2964 robin/HK/75/06(H5N1)
                          0000000000013 2542 turkey/Wisconsin/66(H9N2) 105 Turkey/California/189/66(H9N2)
                          0000000000069 3150 Ck/Jiangsu/ng/01(H9N2) 370 Gs/HK/ww26/00(H5N1)
                          0000000000075 3156 Ck/Beijing/ne/1999(H9N2) 493 Ck/Shanghai/F/98(H9N2)
                          0000000033340 3499 Ck/Guangxi/55/05(H9N2) 2654 Ck/Guangxi/2439/04(H5N1)
                          0000000369230 3153 Ck/Hebei/nj/02(H9N2) 3148 Ck/Henan/nd/1998(H9N2)
                          0000006347328 249 Dk/Shantou/1042/00(H9N2) 248 Dk/Shantou/1043/00(H9N2)
                          0000519777496 740 Ck/Korea/S4/03(H9N2) 729 Sw/Korea/S452/04(H9N2)
                          0000000000000 2626 Sw/Ontario/53518/03(H1N1) 89 Sw/Texas/4199-2/98 (H3N2)
                          0000000000000 1028 laughing gull/DE/94/00(H12N4) 894 laughing gull/DE/5/03(H9N1)
                          0000000000001 1024 shorebird/DE/236/03(H11N9) 1002 shorebird/DE/231/03(H9N4)
                          0000000000014 1482 pintail/Alaska/211/05(H3N8) 1469 mallard/Alaska/256/05(H3N8)
                          0000000008766 3679 HK/498/97(H3N2) 5140 Albany/1/1976(H3N2)
                          0000000733766 3552 Dk/Jiangxi/1786/03(H7N7) 3551 Dk/Jiangxi/1760/03(H7N7)
                          0000003273490 2625 Sw/Ontario/55383/04(H1N2) 3643 Sw/Tennessee/24/1977(H1N1)
                          0000214655866 2628 Sw/Ontario/48235/04(H1N2) 1168 Sw/Tennessee/25/1977(H1N1)
                          0013226932138 2630 Sw/Ontario/11112/04(H1N1) 2629 Sw/Ontario/23866/04(H1N1)

                          se9a1.10 , 03.Feb.2009 , recombination candidates in PB2
                          ---------------------------------------------------------
                          p=0.0000000000000000000 3449/mallard/MD/185/2003(H5N2) 3440/blue-winged teal/Ohio/907/2002(H1N6)
                          p=0.0000000000000000000 6878/Sw/Korea/CY08/2007(H1N2) 3674/mallard/MN/192/1999(H4N6)
                          p=0.0000000000000000000 5774/mallard/ZhaLong/88/2004(H4N6) 4439/Ck/Suphanburi/NIAH108192/2005(H5N1)
                          p=0.0000000000000000000 6404/Ck/China/Guangxi14/2000(H9N2) 4440/golden pheasant/Thailand/VSMU-21-SPB/2005(H5N1)
                          p=0.0000000000000000000 6860/mallard/Yan chen/2005(H4N6) 4477/egret/Hong Kong/757.2/03(H5N1)
                          p=0.0000000000000000000 5075/Dk/Vietnam/205/2005(H5N1) 4968/Ck/Vietnam/202/2005(H5N1)
                          p=0.0000000000000000000 6707/Ck/Shandong/B2/2007(H9N2) 5464/Ck/Jiangsu/L1/2004(H9N2)
                          p=0.0000000000000000000 6507/Ck/Shandong/B3/2007(H9N2) 6647/Ck/Shandong/B1/2000(H9N2)
                          p=0.0000000000000000000 6508/Ck/Shandong/B4/2007(H9N2) 6663/Ck/Hebei/31/00(H9N2)
                          p=0.0000000000000000000 6708/Ck/Hebei/B1/2001(H9N2) 6664/Ck/Beijing/L1/2005(H9N2)
                          p=0.0000000000000013495 6702/Sw/Jiangxi/1/2004(H9N2) 6699/Sw/Guangdong/wxl/2004(H9N2)
                          p=0.0000000000000366438 6722/Ck/Henan/L1/2008(H9N2) 6723/Ck/Henan/L3/2008(H9N2)
                          p=0.0000000000000446895 5744/Ck/Jilin/ha/2003(H5N1) 5268/Ck/Jilin/he/2002(H5N1)
                          p=0.0000000000000828964 5763/Ck/Nigeria/OG5/2007(H5N1) 4804/Ck/Nigeria/OG2/2007(H5N1)
                          p=0.0000000000003068018 6725/Ck/Guangxi/55/2005(H9N2) 5671/Gs/Guangxi/1198/2004(H5N1)
                          p=0.0000000000014821944 5082/pheasant/ST/3535/2003(H5N1) 5560/partridge/Shantou/2886/2003(H5N1)
                          p=0.0000000000033515783 5456/bird/Guangxi/H1/2006(H9N2) 5454/Qa/Guangxi/B1/2006(H9N2)
                          p=0.0000000000977910096 5741/Ck/Jilin/hm/2003(H5N1) 5742/Ck/Jilin/xw/2003(H5N1)
                          p=0.0000000001270778317 3753/Sw/Korea/CN22/2006(H3N1) 3754/Sw/Korea/PZ72-1/2006(H3N1)

                          ================================================== ==========================
                          se7a2,m=5284
                          00000000000 2717 Ck/Hebei/718/01(H5N1) 5 Ck/Yamaguchi/7/04(H5N1)
                          00000000002 2985 Sw/Guangxi/wz/04(H5N1) 2999 Ck/Jilin/hq/03(H5N1)
                          00000000004 3018 Gs/Guangdong/xb/01(H5N1) 570 Dk/Shanghai/38/01(H5N1)
                          00000000005 2974 Ck/Hubei/wl/97(H5N1) 754 Ck/Henan/210/04 (H5N1)
                          00000000024 2907 BarHGs/Qinghai/F/06(H5N1)2908 BlackHGull/Qinghai/3/06(H5N1)
                          00000000235 652 Ck/HK/37.4/02(H5N1) 650 Gf/HK/38/02(H5N1)
                          00000000398 2975 Ck/Hubei/wm/97(H5N1) 2997 Ck/Jilin/ho/03(H5N1)
                          00000001000 2989 Ck/Jilin/he/02(H5N1) 2708 Mallard Dk/VNM/133/05(H5N1)
                          00000001069 3021 Ck/Jilin/xw/03(H5N1) 699 Dk/HK/821/02(H5N1)
                          00000004703 2990 Ck/Jilin/hg/02(H5N1) 2979 Dk/Hubei/wq/03(H5N1)
                          00000020475 3020 Ck/Jilin/xv/02(H5N1) 2872 VNM/CL01/04(H5N1)
                          00000027446 2969 Dk/Hubei/wg/02(H5N1) 555 Dk/Fujian/19/00(H5N1)
                          00000432602 3000 Ck/Jilin/hf/02(H5N1) 654 Ck/HK/YU22/02(H5N1)
                          00010042551 2983 Ck/Henan/wu/04(H5N1) 2544 Tree Sparrow/Henan/1/04(H5N1)
                          00483848523 2968 Ck/Hubei/wf/02(H5N1) 2891 Dk/Hubei/3/05(H5N1)
                          00762344806 2986 Ck/Jilin/ha/03(H5N1) 2697 Ck/Salatiga/BBVet-I/05(H5N1)
                          00867829828 2736 Ck/Taiwan/G2/87(H6N1) 2735 Dk/Taiwan/0526/72(H6N1)
                          01867972859 2994 Ck/Jilin/hl/04(H5N1) 2537 Ck/Ningxia/4/99(H9N2)
                          03518670153 2998 Ck/Jilin/hp/03(H5N1) 1515 CgCg/Iran/754/06(H5N1)
                          41093085434 680 Ck/Jilin/9/04(H5N1) 237 Dk/HK/646.3/01 (H5N1)
                          66288770919 2988 Ck/Jilin/hd/02(H5N1) 572 Dk/Zhejiang/52/00(H5N1)
                          00000000000 100 Ck/Beijing/1/94(H9N2) 99 Ck/HK/739/94(H9N2)
                          00000000000 3495 Ck/Guangxi/4/99(H9N2) 130 Teal/HK/W312/97(H6N1)
                          00000000000 3510 Dk/Guangxi/51/05(H9N2) 545 Dk/HK/821/02 (H5N1)
                          00000000000 3511 Ck/Guangxi/55/05(H9N2) 668 PerFalcon/HK/D0028/04(H5N1)
                          00000000000 3516 Bird/Guangxi/A1/06(H9N2) 2794 Ck/China/Guangxi14/00(H9N2)
                          00000000000 3009 Dk/Jiangsu/nf/02(H9N2) 2901 Dk/Zhejiang/03/01(H9N2)
                          00000000008 3010 Ck/Jiangsu/ng/01(H9N2) 2981 Ck/Jiangsu/wa/02(H9N2)
                          00000000023 3512 Bird/Guangxi/62/05(H9N2) 3514 Bird/Guangxi/83/05(H9N2)
                          00000003972 3262 Qa/Shantou/2615/03(H9N2) 3423 Qa/Shantou/1052/03(H6N1)
                          00000009587 3269 Qa/Shantou/4038/03(H9N2) 3268 Qa/Shantou/3856/03(H9N2)
                          00000041365 3013 Ck/Hebei/nj/02(H9N2) 3011 Ck/Yunnan/nh/01(H9N2)
                          00000000169 3375 Garganey/SanJiang/160/06(H5N2) 3117 Ck/Guiyang/4059/05(H5N1)
                          00076804117 1066 Gray Teal/AUS/1/79(H6N1) 2505 Eurasian Coot/W-AUS/2727/1979(H6N2)
                          00000010605 3033 Dk/Yangzhou/02/05(H8N4) 88 Gs/Guangdong/1/96(H5N1)


                          se9a2.nam
                          p=0.0000000000000000000 2508/Ck/Guangxi/4/99(H9N2) 9/HK/1073/99(H9N2)
                          p=0.0000000000000000000 296/bird/Guangxi/A1/06(H9N2) 207/Ck/Guangxi/6/00(H9N2)
                          p=0.0000000000000000000 2507/Dk/Guangxi/51/05(H9N2) 208/Sw/Guangxi/FS2/05(H9N2)
                          p=0.0000000000000000000 5845/Ck/Guangxi/55/05(H9N2) 386/Ck/Kuwait/KISR2/07(H5N1)
                          p=0.0000000000000000000 1481/Ck/Hebei/718/01(H5N1) 566/Ck/HK/YU22/02(H5N1)
                          p=0.0000000000000000000 1856/Gs/Guangdong/xb/01(H5N1) 1834/Ck/HK/37.4/02(H5N1)
                          p=0.0000000000000000000 5819/Sw/Korea/CY09/07(H3N2) 4043/Shiga/20/95(H3N2)
                          p=0.0000000000000000018 2506/bird/Guangxi/62/05(H9N2) 1229/bird/Guangxi/83/05(H9N2)
                          p=0.0000000000000000203 5829/garganey/SanJiang/160/06(H5N2) 932/Ck/Guiyang/4059/05(H5N1)
                          p=0.0000000000000000811 1480/Ck/Jilin/xw/03(H5N1) 594/Dk/HK/821/02(H5N1)
                          p=0.0000000000000013345 1866/Dk/Yangzhou/02/05(H8N4) 1603/Gs/Guangdong/1/96(H5N1)
                          p=0.0000000000000397745 5827/Sw/Guangxi/wz/04(H5N1) 917/Ck/Guangdong/178/04(H5N1)
                          p=0.0000000000000409697 1479/Ck/Jilin/xv/02(H5N1) 1114/Ck/Kyoto/3/04(H5N1)
                          p=0.0000000000000654395 5826/Sw/Korea/CAS05/04(H3N2) 5675/Dk/NC/91347/01(H1N2)
                          p=0.0000000000004879564 2505/Ck/Jilin/he/02(H5N1) 1478/Dk/Hubei/wq/03(H5N1)
                          p=0.0000000000007761991 3119/Sw/Saskatchewan/18789/02(H1N1) 3116/blue winged teal/TX/27/02(H1N1)
                          p=0.0000000000063706480 5811/gray teal/AUS/1/1979(H6N1) 5808/Eurasian coot/W.AUS/2727/1979(H6N2)
                          p=0.0000000000411594023 2126/Ck/Hubei/wf/02(H5N1) 1191/Dk/Hubei/3/05(H5N1)
                          p=0.0000000000732366379 1601/Ck/Jilin/hk/04(H5N1) 1600/Dk/Guangdong/40/00(H5N1)
                          p=0.0000000000856207551 2001/Ck/Taiwan/G2/87(H6N1) 2000/Dk/Taiwan/0526/72(H6N1)
                          p=0.0000000000856320468 2011/Tree sparrow/Henan/4/04(H5N1) 2009/Tree sparrow/Henan/2/04(H5N1)
                          p=0.0000000005224282579 1468/Dk/VNM/208/05(H5N1) 1007/Dk/VNM/207/05(H5N1)
                          p=0.0000000007404154566 5585/TW/229/03(H3N2) 4891/Ohio/UR07-0043/08(H3N2)


                          ================================================== ============================
                          se7a5.nam, 7973 sequences
                          p=0.0000000000000000000 5480 Qa/Shantou/1218/03(H6N1) 5 Ck/Beijing/1/96(H9N2)
                          p=0.0000000000000000000 323 China/Tax119240/00(??) 785 Ck/Shanghai/F/98(H9N2)
                          p=0.0000000000000000002 5226 Qa/Shantou/243/00(H9N2) 5238 Qa/Shantou/1425/01(H9N2)
                          p=0.0000000000000000004 950 Ck/HK/37.4/02(H5N1) 948 Gf/HK/38/02(H5N1)
                          p=0.0000000000000000006 5020 Ck/Beijing/nl/02(H9N2) 5015 Ck/Jiangsu/ng/01(H9N2)
                          p=0.0000000000000000037 4944 swine/Hangzhou/1/06(H9N2) 4718 Dk/Guangxi/13/04(H5N1)
                          p=0.0000000000000000300 5168 Ck/Guangxi/3791/05(H5N1) 5169 Dk/Guangxi/3819/05(H5N1)
                          p=0.0000000000000004902 4623 swine/Ontario/53518/03(H1N1) 334 Swine/Nebraska/209/98(H3N2)
                          p=0.0000000000000115237 481 Dk/Shantou/2088/01(H9N2) 4975 Ck/Hubei/wh/97(H5N1)
                          p=0.0000000000000176048 4823 Dk/VNM/283/05(H5N1) 5025 Ck/Jilin/xv/02(H5N1)
                          p=0.0000000000000946692 4999 Ck/Jilin/hl/04(H5N1) 4482 Ck/Hebei/31/00(H9N2)
                          p=0.0000000000002992080 411 Swine/Iowa/930/01(H1N2) 407 Swine/Ohio/891/01(H1N2)
                          p=0.0000000000005029488 4433 Dk/NJ/5832-13/96(H6N8) 4419 mallard/MN/253/99(H6N5)
                          p=0.0000000000050825930 4435 Ck/NY/13237-6/98(H6N8) 4443 mallard/MN/355803/00(H6)
                          p=0.0000000000063726539 1065 Ck/Henan/210/04(H5N1) 3359 IDN/CDC1046/07(H5N1)
                          p=0.0000000000063726539 4988 Ck/Henan/wu/04(H5N1) 3360 IDN/CDC1046T/07(H5N1)
                          p=0.0000000000092805891 5367 Dk/Jiang Xi/2374/05(H3N6) 70 Dk/Hokkaido/84/02(H5N3)
                          p=0.0000000000142971832 345 HK/498/97(H3N2) 1248 NY/136/02(H3N2)
                          p=0.0000000000320478520 1052 Ck/Korea/S16/03(H9N2) 4600 HK/2108/03(H9N2)
                          p=0.0000000000587042040 4994 Ck/Jilin/he/02(H5N1) 5009 Dk/Zhejiang/bj/02(H5N1)
                          p=0.0000000001315421425 5021 Ck/Beijing/ne/99(H9N2) 5014 Dk/Jiangsu/nf/02(H9N2)
                          p=0.0000000002943460474 4979 Ck/Hubei/wl/97(H5N1) 5007 Ck/Hunan/fg/04(H5N1)
                          p=0.0000000006457697339 4468 mallard/MN/347/99(H4N8) 4414 mallard/MN/192/99(H4N6)
                          p=0.0000000018065135090 5003 Ck/Jilin/hp/03(H5N1) 483 Dk/Shantou/1881/00(H9N2)
                          p=0.0000000044466785510 5001 Ck/Jilin/hn/03(H5N1) 4816 Ck/Pangkalpinang/BPPV3/04(H5N1)
                          p=0.0000000074842833935 5004 Ck/Jilin/hq/03(H5N1) 127 Ck/HK/SF2/99(H9N2)
                          p=0.0000000088844332453 4422 mallard/MN/31/98(H6N8) 4457 mallard/OH/66/99(H6N1)


                          se9a5.nam
                          ----------------------------------------------------------------------------
                          p=0.0000000000000021842 7178/Dk/LA/17G/1987(H3N8) 6988/Sw/Guangxi/17/05(H1N2)
                          p=0.0000000000000302284 422/Ck/Guangxi/4/99(H9N2) 420/Ck/China/Guangxi14/00(H9N2)
                          p=0.0000000000085789044 2086/blackbird/Hunan/1/04(H5N1) 1328/Dk/Hubei/wp/03(H5N1)
                          p=0.0000000000101653523 3132/green-winged teal/OH/72/99(H6) 3067/mallard/Ohio/56/99(H1N1)
                          p=0.0000000008742013699 7171/s.palm.sandpiper/Brazil/43/1990(H2N1) 472/Dk/Nanchang/2-0486/00(H2N9)


                          ================================================== ============================0


                          se9a7.nam
                          --------------------------------------------------------------------------------
                          se7a7,m= 6122
                          p=0.0000000000000000000 5237/THA/M38/05(H5N1) 7/Ck/Yamaguchi/7/04(H5N1)
                          p=0.0000000000000000000 5304/Ck/Hunan/fg/04(H5N1) 8/Ck/Oita/8/04(H5N1)
                          p=0.0000000000000000251 838/Dk/Hokkaido/86/01(H2N3) 5658/Dk/Yunnan/435/02(H5N3)
                          p=0.0000000000003701964 224/Taiwan/3513/96(H3N2) 301/HK/497/97(H3N2)
                          p=0.0000000000039774883 4001/partridge/Shantou/6415/04(H9N2) 5645/human/Ohio/06(H3N2)
                          p=0.0000000000077004189 283/Dk/HK/P50/97(H11N9) 3511/Western Australia/18/01(H1N1)
                          p=0.0000000000139522452 4777/Dk/MN/1564/81(H5N2) 1145/dove/Korea/S11/03(H3N2)



                          se9a7.11, m=8481
                          p=0.0000000000000539219 6889/human/Ohio/06(H3N2) 6285/Darwin/20/07(H3N2)
                          p=0.0000000000230532654 7157/Hanoi/ISBM27/05(H1N1) 8278/Budgerigar/Hokkaido/1/77(H4N6)
                          p=0.0000000000235887807 2038/pheasant/Shantou/6607/04(H9N2) 5733/NY/236/04(H3N2)
                          p=0.0000000000244351701 8242/Dk/Shantou/7488/04(H9N2) 3655/Ck/SK/HR-00011/07(H7N3)
                          p=0.0000000000278333106 1640/Dk/Hokkaido/W268/05(H6N1) 7737/Canterbury/78/00(H1N1)
                          p=0.0000000000298447352 2066/pheasant/Shantou/3716/03(H9N2) 6921/Trinidad/697/70(H3N2)
                          p=0.0000000000317961959 2039/Guinea fowl/Shantou/6627/04(H9N2) 5734/NY/470/04(H3N2)
                          p=0.0000000000370268278 1760/Dk/HK/P54/97(H11N9) 6939/Fort Worth/50(H1N1)
                          p=0.0000000000404026628 2581/Ck/Shantou/2686/03(H9N2) 7806/Victoria/501/07(H1N1)
                          p=0.0000000000421833684 2715/Sw/Schwerin/103/89(H1N1) 7561/Tennessee/UR06-0473/07(H1N1)
                          p=0.0000000000428225783 2036/pheasant/Shantou/5588/04(H9N2) 6307/NY/55/04(H3N2)
                          p=0.0000000000576230916 2041/chukkar/Shantou/5866/04(H9N2) 5730/NY/380/04(H3N2)
                          p=0.0000000000576230916 2042/Qa/Shantou/6046/04(H9N2) 5731/Christchurch/13/04(H3N2)
                          p=0.0000000000769330806 2670/equine/Jilin/1/1989(H3N8) 5732/NY/395/05(H3N2)
                          p=0.0000000000774719435 2048/silky Ck/Shantou/1169/05(H9N2) 6239/Kansas/UR07-0135/08(H3N2)
                          p=0.0000000000971779444 2065/silky Ck/Shantou/3581/05(H9N2) 6341/Hawaii/13/07(H3N2)
                          I'm interested in expert panflu damage estimates
                          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                          Comment


                          • #14
                            Re: recombinations in influenza A

                            recombination candidates in segment 1 per 05.Jan.2009:
                            -------------------------------------------------------

                            Code:
                            p=0.0000000000000000000  2808/Sw/Alberta/56626/03(H1N1)              2807/Sw/Ontario/57561/03(H1N1)
                            p=0.0000000000000000000  3779/Sw/Ontario/53518/03(H1N1)              2894/Wisconsin/10/98(H1N1)
                            p=0.0000000000000000000  6878/Sw/Korea/CY08/07(H1N2)                 2907/blue-winged teal/ALB/103/1990(H4N5)
                            p=0.0000000000000000000  4148/pintail/Alaska/211/05(H3N8)            3297/mallard/Alaska/256/05(H3N8)
                            p=0.0000000000000000000  3449/mallard/MD/185/03(H5N2)                3440/blue-winged teal/Ohio/907/02(H1N6)
                            p=0.0000000000000000000  3669/laughing gull/DE/94/00(H12N4)          3668/ruddy turnstone/DE/1444/00(H12N5)
                            p=0.0000000000000000000  4158/shorebird/DE/236/03(H11N9)             3671/shorebird/DE/231/03(H9N4)
                            p=0.0000000000000000000  5763/Ck/Nigeria/OG5/07(H5N1)                4439/Ck/Suphanburi/NIAH108192/05(H5N1)
                            p=0.0000000000000000000  5774/mallard/ZhaLong/88/04(H4N6)            4440/golden pheasant/THA/VSMU-21-SPB/05(H5N1)
                            p=0.0000000000000000000  6404/Ck/China/Guangxi14/00(H9N2)            4441/Qa/THA/Nakhon Pathom/QA-161/05(H5N1)
                            p=0.0000000000000000000  6860/mallard/Yan chen/05(H4N6)              4643/Dk/HK/2986.1/00(H5N1)
                            p=0.0000000000000000000  6721/Sw/Guangxi/58/05(H9N2)                 4946/Dk/Guangxi/288/06(H5N1)
                            p=0.0000000000000000000  5075/Dk/VNM/205/05(H5N1)                    4968/Ck/VNM/202/05(H5N1)
                            p=0.0000000000000000000  6411/Ck/HK/37.4/02(H5N1)                    5341/Ck/HK/96.1/02(H5N1)
                            p=0.0000000000000000000  6402/Sw/Guangxi/S15/05(H9N2)                5444/Ck/Guangdong/56/01(H9N2)
                            p=0.0000000000000000000  5456/bird/Guangxi/H1/06(H9N2)               5449/bird/Guangxi/62/05(H9N2)
                            p=0.0000000000000000000  6403/Dk/Guangxi/51/05(H9N2)                 5450/Sw/Guangxi/FS2/05(H9N2)
                            p=0.0000000000000000000  6401/Ck/Guangxi/6/00(H9N2)                  5475/Qa/Nanchang/2-0460/00(H9N2)
                            p=0.0000000000000000000  5735/Dk/Guangxi/668/04(H5N1)                5647/teal/China/2978.1/02(H5N1)
                            p=0.0000000000000000000  5736/Ck/Guiyang/1655/06(H5N1)               5649/Dk/Guangxi/13/04(H5N1)
                            p=0.0000000000000000000  6407/Tree sparrow/Henan/4/04(H5N1)          6070/Tree sparrow/Henan/2/04(H5N1)
                            p=0.0000000000000000000  6507/Ck/Shandong/B3/07(H9N2)                6647/Ck/Shandong/B1/00(H9N2)
                            p=0.0000000000000000000  6508/Ck/Shandong/B4/07(H9N2)                6663/Ck/Hebei/31/00(H9N2)
                            p=0.0000000000000000000  6620/Ck/Henan/wu/04(H5N1)                   6618/Ck/Hubei/wj/97(H5N1)
                            p=0.0000000000000000000  6622/Ck/China/Guangxi1/00(H9N2)             6686/Ck/Guangdong/10/00(H9N2)
                            p=0.0000000000000000000  6708/Ck/Hebei/B1/01(H9N2)                   6664/Ck/Beijing/L1/05(H9N2)
                            p=0.0000000000000000000  6709/Ck/Jilin/53/01(H9N2)                   6692/Ck/Yokohama/aq120/01(H9N2)
                            p=0.0000000000000000004  5766/WildDk/Guangdong/314/04(H5N1)          5559/Ck/Jilin/hg/02(H5N1)
                            p=0.0000000000000000008  5767/mallard/Guangxi/wt/04(H5N1)            5744/Ck/Jilin/ha/03(H5N1)
                            p=0.0000000000000000030  6707/Ck/Shandong/B2/07(H9N2)                6651/Ck/Shandong/6/96(H9N2)
                            p=0.0000000000000000034  5737/Dk/Guiyang/1558/06(H5N1)               5654/Ck/Guiyang/237/06(H5N1)
                            p=0.0000000000000000127  2767/Sw/Tennessee/24/1977(H1N1)             2802/Sw/Ontario/55383/04(H1N2)
                            p=0.0000000000000001326  6699/Sw/Guangdong/wxl/04(H9N2)              6702/Sw/Jiangxi/1/04(H9N2)
                            p=0.0000000000000002751  6621/Ck/Henan/210/04(H5N1)                  4680/Dk/Korea/ESD1/03(H5N1)
                            p=0.0000000000000005888  6619/Tree sparrow/Henan/1/04(H5N1)          6610/black Dk/AUS/4045/1980(H6N5)
                            p=0.0000000000000014257  2804/Sw/Ontario/23866/04(H1N1)              2805/Sw/Ontario/11112/04(H1N1)
                            p=0.0000000000000052336  6722/Ck/Henan/L1/08(H9N2)                   6723/Ck/Henan/L3/08(H9N2)
                            p=0.0000000000000067723  4083/turkey/Wisconsin/66(H9N2)              4081/turkey/Wisconsin/1/1966(H9N2)
                            p=0.0000000000000186696  6725/Ck/Guangxi/55/05(H9N2)                 6724/Ck/Henan/L2/08(H9N2)
                            p=0.0000000000000202403   618/HK/498/97(H3N2)                         504/Albany/1/1976(H3N2)
                            p=0.0000000000000256201  6511/Ck/Hebei/nj/02(H9N2)                   5408/Ck/Henan/nd/98(H9N2)
                            p=0.0000000000000274417  5770/Ck/Jilin/hj/03(H5N1)                   5738/Ck/Jilin/xv/02(H5N1)
                            p=0.0000000000000938837  2803/Sw/Ontario/48235/04(H1N2)              2766/Sw/Tennessee/25/1977(H1N1)
                            p=0.0000000000011231230  5741/Ck/Jilin/hm/03(H5N1)                   4688/Gs/Jilin/hb/03(H5N1)
                            p=0.0000000000028841339  3753/Sw/Korea/CN22/06(H3N1)                 3754/Sw/Korea/PZ72-1/06(H3N1)
                            p=0.0000000000123926987  5082/pheasant/Shantou/3535/03(H5N1)         5560/partridge/Shantou/2886/03(H5N1)
                            p=0.0000000001133603060  5984/Dk/Yangzhou/02/05(H8N4)                5636/Gs/Guangdong/1/96(H5N1)
                            p=0.0000000001308504134  4646/Ck/HK/NT873.3/01-MB(H5N1)              6726/Ck/Hubei/wh/97(H5N1)
                            p=0.0000000002761164157  4640/Dk/Guangxi/xa/01(H5N1)                 4667/Ck/Hebei/718/01(H5N1)
                            p=0.0000000002904210082  3743/Sw/Korea/CAN01/04(H1N1)                3744/Sw/Korea/CAS08/05(H1N1)
                            p=0.0000000005882223284  5320/Dk/VNM/37/07(H5N1)                     5289/Dk/VNM/NCVD-19/07(H5N1)
                            p=0.0000000006424289595  6069/Tree sparrow/Henan/3/04(H5N1)          6072/Ck/Hubei/wi/97(H5N1)
                            p=0.0000000008364510204  6792/Dk/Korea/S8/03(H3N2)                   6788/Dk/Korea/S9/03(H3N2)
                            p=0.0000000008539049353  4666/Ck/HK/YU562/01(H5N1)                   5625/Gs/HK/ww26/00(H5N1)
                            p=0.0000000011054149657  3927/environment/NY/19019-6/98(H3N8)        5156/Ck/Kulon Progo/BBVW/05(H5N1)
                            p=0.0000000014927294734  1774/TW/872/02(H3N2)                        1750/NY/198/03(H3N2)
                            p=0.0000000020647852040  5271/Ck/Hubei/wf/02(H5N1)                   4443/Ck/THA/Nontaburi/CK-162/05(H5N1)
                            p=0.0000000021401485607  5743/Ck/Jilin/hf/02(H5N1)                   5338/Ck/Shanxi/2/06(H5N1)
                            p=0.0000000024978737119  1775/TW/875/04(H3N2)                        1762/Morioka/35/05(H3N2)
                            p=0.0000000027652400240  4687/blackbird/Hunan/1/04(H5N1)             4685/Dk/Hubei/wp/03(H5N1)
                            p=0.0000000032500843031  3915/pintail/Ohio/339/1987(H3N8)            5141/Ck/Guangdong/178/04(H5N1)
                            p=0.0000000037019297991  5273/Dk/Shantou/4610/03(H5N1)               2851/Ck/Aguascalientes/124-3705/98(H5N2)
                            p=0.0000000046496986966  3906/green-winged teal/Ohio/59/1989(H6N8)   3904/mallard/Ohio/64/1989(H6N8)
                            p=0.0000000079138232850  4698/Beijing/01/03(H5N1)                    6433/Ck/Hubei/wm/97(H5N1)
                            p=0.0000000094578748926  3712/Sw/Illinois/100085A/01(H1N2)           3711/Sw/Indiana/9K035/99(H1N2)
                            p=0.0000000103829630847  4904/Ck/Krasnodar/300/07(H5N1)              5384/grey teal/AUS/2/1979(H4N4)
                            p=0.0000000107549102397  6743/Ck/Pakistan/34669/1995(H7N3)           6746/Ck/Rawalpindi/NARC72/02(H7N3)
                            p=0.0000000111391734905  5150/Ck/Purwakarta/BBVet-IV/04(H5N1)        3933/mallard Dk/ALB/253/1990(H6N3)
                            p=0.0000000124239188678  5151/Ck/Malang/BBVet-IV/04(H5N1)            3931/mallard Dk/ALB/155/1990(H6N3)
                            p=0.0000000170138319974  6118/HK/482/97(H5N1)                        6126/HK/482/97(H5N1)
                            p=0.0000000181481673261  4766/Ck/Nigeria/1071-3/07(H5N1)             3025/Ck/Jalisco/28159-600/1995(H5N2)
                            p=0.0000000208358682714  5154/Ck/Kulon Progo/BBVet-XII-1/04(H5N1)    3919/guinea fowl/NJ/14190-23/96(H4N8)
                            p=0.0000000259468759447  6373/Gs/VNM/3/05(H5N1)                      6361/Pigeon/HK/Y233/97(H9N2)
                            p=0.0000000285075718262  5575/Dk/Nanchang/1904/1992(H7N1)            3921/mallard/Alberta/125/99(H11N6)
                            p=0.0000000314640443878  5153/Dk/IDN/MS/04(H5N1)                     3932/mallard Dk/ALB/191/1990(H6N3)
                            p=0.0000000321344146673  5633/Dk/Shanghai/08/01(H5N1)                3022/Ck/Michoacan/28159-530/1995(H5N2)
                            p=0.0000000368331907307  4650/Pheasant/HK/FY155/01-MB(H5N1)          6522/starling/Victoria/5156/1985(H7N7)
                            p=0.0000000370879678239  6510/Ck/Beijing/ne/99(H9N2)                 5407/Ck/Henan/ni/01(H9N2)
                            p=0.0000000409975259466  5564/migratory Dk/HK/MPS180/03(H4N6)        3918/pheasant/MD/4457/1993(H5N2)
                            p=0.0000000462484256521  5586/Dk/Hokkaido/49/98(H9N2)                2850/Ck/Puebla/28159-474/95(H5N2)
                            p=0.0000000462484256521  4929/CO/Astrakhan/Ast05-2-2/05(H5N1)        2852/Ck/Puebla/231-5284/98(H5N2)
                            ----------------------------------------------------

                            graphics of these pairs at http://magictour.free.fr/panflu/re9a1.txt
                            o:difference
                            .:same nucleotid
                            -:not available

                            when the "o" form clusters, that's indication for homologuous
                            recombination. The p-value shows how likely this clustering
                            were to appear with random mutations only

                            6900 sequences,42 breakpoints
                            24M sequence-pairs, 800 breakpoint pairs ,
                            ==>20B configurations examined

                            (rerunning with random sequences now...)


                            --------------
                            here the involved sequences again in normal notation so it can be found with keyword search:

                            A/swine/Ontario/55383/2004(H1N2)
                            A/chicken/Aguascalientes/124-3705/1998(H5N2)
                            A/blue-winged teal/ALB/103/1990(H4N5)
                            A/chicken/Mexico/31381-2/1994(H5N2)
                            A/chicken/Jalisco/28159-600/1995(H5N2)
                            A/chicken/Chis/15224/1997(H5N2)
                            A/shorebird/DE/231/2003(H9N4)
                            A/swine/Indiana/9K035/1999(H1N2)
                            A/swine/Korea/PZ72-1/2006(H3N1)
                            A/swine/Korea/CAS05/2004(H3N2)
                            A/green-winged teal/Ohio/466/1987(H3N8)
                            A/ruddy turnstone/NJ/47/1985(H4N6)
                            A/mallard/Ohio/64/1989(H6N8)
                            A/mallard Dk/ALB/191/1990(H6N3)
                            A/chicken/THA/Nontaburi/CK-162/2005(H5N1)
                            A/chicken/Hebei/718/2001(H5N1)
                            A/duck/Hubei/wp/2003(H5N1)
                            A/Gs/Jilin/hb/2003(H5N1)
                            A/duck/Guangxi/288/2006(H5N1)
                            504/Albany/1/1976(H3N2)
                            A/duck/VNM/NCVD-19/2007(H5N1)
                            A/chicken/Shanxi/2/2006(H5N1)
                            A/aquatic bird/Korea/CN-2/2004(H3N2)
                            A/chicken/Henan/ni/2001(H9N2)
                            A/chicken/Henan/nd/1998(H9N2)
                            A/bird/Guangxi/62/2005(H9N2)
                            A/swine/Guangxi/FS2/2005(H9N2)
                            A/partridge/Shantou/2886/2003(H5N1)
                            A/Gs/HK/ww26/2000(H5N1)
                            A/duck/Guangxi/13/2004(H5N1)
                            A/chicken/Guiyang/237/2006(H5N1)
                            A/chicken/Jilin/xv/2002(H5N1)
                            618/HK/498/1997(H3N2)
                            A/chicken/Hubei/wj/1997(H5N1)
                            A/chicken/HK/NT366/2003(H9N2)
                            A/chicken/Beijing/L1/2005(H9N2)
                            A/chicken/Guangdong/10/2000(H9N2)
                            A/chicken/Yokohama/aq120/2001(H9N2)
                            A/chicken/Henan/L3/2008(H9N2)
                            A/chicken/Henan/L2/2008(H9N2)
                            A/chicken/Rawalpindi/NARC72/2002(H7N3)
                            A/duck/Korea/S9/2003(H3N2)
                            A/NY/198/2003(H3N2)
                            A/Morioka/35/2005(H3N2)
                            A/TW/872/2002(H3N2)
                            A/TW/875/2004(H3N2)
                            A/swine/Tennessee/25/1977(H1N1)
                            A/swine/Tennessee/24/1977(H1N1)
                            A/swine/Ontario/48235/2004(H1N2)
                            A/swine/Ontario/23866/2004(H1N1)
                            A/swine/Ontario/11112/2004(H1N1)
                            A/swine/Ontario/57561/2003(H1N1)
                            A/swine/Alberta/56626/2003(H1N1)
                            A/chicken/Puebla/8623-607/1994(H5N2)
                            A/chicken/Puebla/28159-474/1995(H5N2)
                            A/chicken/Puebla/231-5284/1998(H5N2)
                            A/Wisconsin/10/1998(H1N1)
                            A/ruddy turnstone/Delaware/34/1993(H2N1)
                            A/chicken/Michoacan/28159-530/1995(H5N2)
                            A/chicken/Jalisco/14589-660/1994(H5N2)
                            A/chicken/Hidalgo/28159-460/1995(H5N2)
                            A/chicken/Guanajuato/28159-331/1995(H5N2)
                            A/chicken/Puebla/14587-644/1994(H5N2)
                            A/environment/Maryland/1172/2005(H3N6)
                            A/mallard/Alaska/256/2005(H3N8)
                            A/blue-winged teal/Ohio/907/2002(H1N6)
                            A/mallard/MD/185/2003(H5N2)
                            A/ruddy turnstone/DE/1444/2000(H12N5)
                            A/laughing gull/DE/94/2000(H12N4)
                            A/swine/Illinois/100085A/2001(H1N2)
                            A/turkey/Ohio/313053/2004(H3N2)
                            A/swine/Korea/CAN01/2004(H1N1)
                            A/swine/Korea/CAS08/2005(H1N1)
                            A/swine/Korea/CN22/2006(H3N1)
                            A/swine/Ohio/891/2001(H1N2)
                            A/swine/Iowa/930/2001(H1N2)
                            A/swine/Ontario/53518/2003(H1N1)
                            A/green-winged teal/Ohio/59/1989(H6N8)
                            A/turkey/Minnesota/1/1988(H7N9)
                            A/mallard/ALB/394/1988(H3N3)
                            A/pintail/Ohio/339/1987(H3N8)
                            A/Qa/IN/38685/1993(H1N1)
                            A/pheasant/MD/4457/1993(H5N2)
                            A/guinea fowl/NJ/14190-23/1996(H4N8)
                            A/mallard/Alberta/125/1999(H11N6)
                            A/N.shoveler/TX/56/2000(H10N7)
                            A/gadwall/Ohio/37/1999(H6N2)
                            A/duck/NJ/117228-7/2001(H5N2)
                            A/environment/NY/19019-6/1998(H3N8)
                            A/mallard Dk/ALB/155/1990(H6N3)
                            A/mallard Dk/ALB/253/1990(H6N3)
                            A/turkey/Wisconsin/1/1966(H9N2)
                            A/turkey/Wisconsin/1966(H9N2)
                            A/pintail/Alaska/211/2005(H3N8)
                            A/shorebird/DE/236/2003(H11N9)
                            A/chicken/Suphanburi/NIAH108192/2005(H5N1)
                            A/golden pheasant/THA/VSMU-21-SPB/2005(H5N1)
                            A/Qa/THA/Nakhon Pathom/QA-161/2005(H5N1)
                            A/duck/Guangxi/xa/2001(H5N1)
                            A/duck/HK/2986.1/2000(H5N1)
                            A/chicken/HK/NT873.3/01-MB(H5N1)
                            A/Pheasant/HK/FY155/01-MB(H5N1)
                            A/chicken/HK/YU822.2/01-MB(H5N1)
                            A/chicken/HK/YU562/2001(H5N1)
                            A/duck/Korea/ESD1/2003(H5N1)
                            A/blackbird/Hunan/1/2004(H5N1)
                            A/Beijing/01/2003(H5N1)
                            A/chicken/Nigeria/1071-3/2007(H5N1)
                            A/chicken/Krasnodar/300/2007(H5N1)
                            A/CO/Astrakhan/Ast05-2-2/2005(H5N1)
                            A/CO/Astrakhan/Ast05-2-6/2005(H5N1)
                            A/CO/Astrakhan/Ast05-2-5/2005(H5N1)
                            A/CO/Astrakhan/Ast05-2-10/2005(H5N1)
                            A/CO/Astrakhan/Ast05-2-4/2005(H5N1)
                            A/CO/Astrakhan/Ast05-2-7/2005(H5N1)
                            A/chicken/VNM/202/2005(H5N1)
                            A/duck/VNM/205/2005(H5N1)
                            A/pheasant/Shantou/3535/2003(H5N1)
                            A/chicken/Guangdong/178/2004(H5N1)
                            A/chicken/Purwakarta/BBVet-IV/2004(H5N1)
                            A/chicken/Malang/BBVet-IV/2004(H5N1)
                            A/duck/IDN/MS/2004(H5N1)
                            A/chicken/Kulon Progo/BBVet-XII-1/2004(H5N1)
                            A/chicken/Kulon Progo/BBVet-XII-2/2004(H5N1)
                            A/chicken/Kulon Progo/BBVW/2005(H5N1)
                            A/IDN/CDC644/2006(H5N1)
                            A/IDN/CDC938E/2006(H5N1)
                            A/chicken/Tebing Tinggi/BPPVI/2005(H5N1)
                            A/chicken/Hubei/wf/2002(H5N1)
                            A/duck/Shantou/4610/2003(H5N1)
                            A/duck/VNM/37/2007(H5N1)
                            A/chicken/HK/96.1/2002(H5N1)
                            A/Gs/HK/10/1976(H3N2)
                            A/dk/HK/293/1978(H7N2)
                            A/grey teal/AUS/2/1979(H4N4)
                            A/chicken/Guangdong/56/2001(H9N2)
                            A/bird/Guangxi/H1/2006(H9N2)
                            A/Qa/Nanchang/2-0460/2000(H9N2)
                            A/chicken/Jilin/hg/2002(H5N1)
                            A/migratory Dk/HK/MPS180/2003(H4N6)
                            A/duck/Nanchang/1904/1992(H7N1)
                            A/swan/Hokkaido/51/1996(H5N3)
                            A/duck/Hokkaido/49/1998(H9N2)
                            A/chicken/Taiwan/A37/2002(H6N1)
                            A/gull/Moscow/3100/2006(H6N2)
                            A/Environment/HK/437-4/1999(H5N1)
                            A/Gs/HK/ww28/2000(H5N1)
                            A/duck/Shanghai/08/2001(H5N1)
                            A/Gs/Guangdong/1/1996(H5N1)
                            A/duck/Guangxi/07/1999(H5N1)
                            A/teal/China/2978.1/2002(H5N1)
                            A/duck/Guangxi/668/2004(H5N1)
                            A/chicken/Guiyang/1655/2006(H5N1)
                            A/duck/Guiyang/1558/2006(H5N1)
                            A/chicken/Jilin/hm/2003(H5N1)
                            A/chicken/Jilin/hf/2002(H5N1)
                            A/chicken/Jilin/ha/2003(H5N1)
                            A/chicken/Nigeria/OG5/2007(H5N1)
                            A/WildDk/Guangdong/314/2004(H5N1)
                            A/mallard/Guangxi/wt/2004(H5N1)
                            A/chicken/Jilin/hj/2003(H5N1)
                            A/mallard/ZhaLong/88/2004(H4N6)
                            A/duck/Yangzhou/02/2005(H8N4)
                            A/Tree sparrow/Henan/3/2004(H5N1)
                            A/Tree sparrow/Henan/2/2004(H5N1)
                            A/chicken/Hubei/wi/1997(H5N1)
                            A/HK/482/1997(H5N1)
                            A/HK/482/1997(H5N1)
                            A/Pigeon/HK/Y233/1997(H9N2)
                            A/Gs/VNM/3/2005(H5N1)
                            A/chicken/Guangxi/6/2000(H9N2)
                            A/swine/Guangxi/S15/2005(H9N2)
                            A/duck/Guangxi/51/2005(H9N2)
                            A/chicken/China/Guangxi14/2000(H9N2)
                            A/Tree sparrow/Henan/4/2004(H5N1)
                            A/chicken/HK/37.4/2002(H5N1)
                            A/chicken/Hubei/wm/1997(H5N1)
                            A/chicken/Shandong/B3/2007(H9N2)
                            A/chicken/Shandong/B4/2007(H9N2)
                            A/chicken/Beijing/ne/1999(H9N2)
                            A/chicken/Hebei/nj/2002(H9N2)
                            A/chicken/Victoria/224/1992(H7N3)
                            A/starling/Victoria/5156/1985(H7N7)
                            A/black Dk/AUS/4045/1980(H6N5)
                            A/Tree sparrow/Henan/1/2004(H5N1)
                            A/chicken/Henan/wu/2004(H5N1)
                            A/chicken/Henan/210/2004(H5N1)
                            A/chicken/China/Guangxi1/2000(H9N2)
                            A/chicken/Shandong/B1/2000(H9N2)
                            A/chicken/Shandong/6/1996(H9N2)
                            A/chicken/Hebei/31/2000(H9N2)
                            A/swine/Guangdong/wxl/2004(H9N2)
                            A/swine/Jiangxi/1/2004(H9N2)
                            A/chicken/Shandong/B2/2007(H9N2)
                            A/chicken/Hebei/B1/2001(H9N2)
                            A/chicken/Jilin/53/2001(H9N2)
                            A/swine/Guangxi/58/2005(H9N2)
                            A/chicken/Henan/L1/2008(H9N2)
                            A/chicken/Guangxi/55/2005(H9N2)
                            A/chicken/Hubei/wh/1997(H5N1)
                            A/chicken/Pakistan/34669/1995(H7N3)
                            A/duck/Korea/S8/2003(H3N2)
                            A/mallard/Yan chen/2005(H4N6)
                            A/swine/Korea/CY08/2007(H1N2)
                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                            Comment


                            • #15
                              Re: recombinations in influenza A

                              xx..+..yy-->xxyy in Qinghai H5N1

                              in PB2233 sequences from genbank)
                              1240 231 >A/turkey/Saudi Arabia/6732-6/07(H5N1)
                              934 180 >A/Ck/Jalgaon/12419/06(H5N1)
                              720 226 >A/Ck/Crimea/08/05(H5N1)
                              200 89 >A/Dk/Kurgan/08/05(H5N1)
                              88 212 >A/bar-h Gs/Qinghai/F/06(H5N1)
                              38 45 >A/Ck/Nigeria/AB13/06(H5N1)
                              18 29 >A/Ck/Tula/Russia/Oct-5/05(H5N1)
                              16 72 >A/peregrine/Denmark/6632/06(H5N1)
                              8 166 >A/Ck/Moscow/2/07(H5N1)

                              in PB1 (225 sequences):
                              520 222 >A/turkey/Saudi Arabia/6732-6/07(H5N1)
                              72 183 >A/Ck/Nigeria/228-5/06(H5N1)
                              48 184 >A/Ck/Nigeria/228-6/06(H5N1)
                              60 204 >A/turkey/Ivory Coast/4372-2/06(H5N1)
                              76 205 >A/turkey/Ivory Coast/4372-3/06(H5N1)
                              92 206 >A/turkey/Ivory Coast/4372-4/06(H5N1)
                              72 217 >A/Dk/Guangxi/2775/05(H5N1)
                              34 155 >A/Ck/Nigeria/LAG6/07(H5N1)
                              24 170 >A/turkey/Israel/345/06(H5N1)
                              36 171 >A/Ck/Gaza/450/06(H5N1)
                              48 172 >A/turkey/Israel/364/06(H5N1)
                              60 173 >A/Ck/Gaza/714/06(H5N1)
                              60 215 >A/Dk/Guangzhou/20/05(H5N1)
                              70 216 >A/Dk/Guangxi/793/05(H5N1)
                              8 145 >A/Ck/Nigeria/1071-15/07(H5N1)
                              4 153 >A/Ck/Nigeria/1071-10/07(H5N1)

                              in NP(261 sequences):
                              18 210 >A/domestic Gs/Germany/R1400/07(H5N1)
                              18 217 >A/domestic Gs/Pavlodar/1/05(H5N1)
                              (A/Ck/Kuwait/KISR9/2007)
                              (A/Ck/Kuwait/KISR3/2007)

                              in HA (852 sequences):
                              ...running... (takes some days)
                              I'm interested in expert panflu damage estimates
                              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                              Comment

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