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  • Sequences at Genbank!

    http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html
    I'm interested in expert panflu damage estimates
    my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

  • #2
    Re: sequences at genbank !

    data in this thread:
    http://www.flutrackers.com/forum/sho...d.php?t=101181
    I'm interested in expert panflu damage estimates
    my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

    Comment


    • #3
      Re: sequences at genbank !

      Is there anything we should be worried about in those sequences gsgs.....?

      Comment


      • #4
        Re: sequences at genbank !

        differences to other selected genomes in promille for each of the 8 segments:
        (some segments may be missing, where "0" is listed)

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

        Comment


        • #5
          Re: sequences at genbank !

          Code:
          13: 30, 36, 45, 49, 31,499,113, 41   A/Turkey/MO/24093/99(H1N2)
          153:158,136,132,255,156, 82, 43,179   A/swine/Virginia/670/1987(H1N1)
          154:158,128,125,246,158, 80, 50,171   A/swine/Germany/2/1981(H1N1)=1578
          155:161,145,144,259,159, 80, 60,185   A/swine/Spain/53207/2004(H1N1)
          I'm interested in expert panflu damage estimates
          my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

          Comment


          • #6
            Re: sequences at genbank !

            So it's clearly a human-swine-avian recombinant. Just like they said. And large sections of the genome have been copied faithfully for years and years. The swine part, in particular, is especially stable.

            And it has happened pretty recently, as such things go.

            Comment


            • #7
              Re: sequences at genbank !

              here the best matches in the 8 segments

              this is from my last update, early 2009 (maybe only 2007 in PB1, as I just see)


              columns are:

              difference in promille
              different nucleotides
              length of matching part
              enumeration
              strain


              0 0 2280 6904 California/04/2009-04-01/(H1N1)

              Code:
              --------------------------------------------------------------
               304   24  787 2897 Turkey/MO/24093/99(H1N2)
               306   69 2249 3703 mallard Dk/South Dakota/Sg-00127/07(H3N2)
               306   69 2249 3704 mallard Dk/South Dakota/Sg-00128/07
               307   69 2246 3702 pintail Dk/South Dakota/Sg-00126/07(H3N2)
               307   69 2247 3701 mallard Dk/South Dakota/Sg-00125/07(H3N2)
               321   50 1557 2887 Sw/Texas/4199-2/98(H3N2)
               333   52 1557 2888 Sw/Minnesota/9088-2/98(H3N2)
               333   52 1557 2895 Sw/Iowa/8548-1/98
               342   78 2280 3760 Sw/Korea/JNS06/04(H3N2)
               343   54 1573 2894 Wisconsin/10/98(H1N1)
               346   79 2280 3705 Sw/Minnesota/55551/00(H1N2)
              -------------------------------------------------------------
               312   71 2271 5644 Wisconsin/10/98(H1N1)
               340   77 2259 5652 mallard Dk/South Dakota/Sg-00125/07(H3N2)
               351   80 2274 5656 Sw/Indiana/9K035/99(H1N2)
               365   83 2271 5638 Sw/Nebraska/209/98(H3N2)
               365   83 2271 5639 Sw/Iowa/533/99(H3N2)
               365   83 2271 5640 Sw/Iowa/569/99(H3N2)
               365   83 2271 5641 Sw/Minnesota/593/99(H3N2)
               369   84 2271 5657 Sw/Korea/CAN04/05(H3N2)
               369   84 2274 5675 Dk/NC/91347/01(H1N2)
               374   43 1149 4066 Sw/Minnesota/9088-2/98(H3N2)
               374   43 1149 4068 Sw/Iowa/8548-1/98
               374   85 2271 5668 Sw/Illinois/100085A/01(H1N2)
               374   85 2271 5670 Sw/Ohio/891/01(H1N2)
               378   86 2271 5654 Sw/Iowa/930/01(H1N2)
               378   86 2271 5682 Sw/Korea/CY04/07(H3N2)
               378   86 2271 5683 Sw/Korea/CY05/07(H3N2)
               382   44 1149 4067 Sw/Texas/4199-2/98(H3N2)
               383   87 2271 5658 Sw/Korea/CAS07/05(H3N2)
               383   87 2271 5659 Sw/Korea/CAS09/06(H3N2)
               383   87 2271 5690 Sw/Indiana/P12439/00(H1N2)
              ------------------------------------------------------------------
               370   79 2130 4925 mallard duck/South Dakota/Sg-00128/2007
               370   79 2131 4923 pintail duck/South Dakota/Sg-00126/2007(H3N2)
               373   79 2117 4922 mallard duck/South Dakota/Sg-00125/2007(H3N2)
               381   79 2073 4924 mallard duck/South Dakota/Sg-00127/2007(H3N2)
               390   84 2151 2977 Swine/Nebraska/209/98 (H3N2)
               390   84 2151 2978 Swine/Iowa/533/99 (H3N2)
               390   84 2151 2979 Swine/Iowa/569/99 (H3N2)
               390   84 2151 2980 Swine/Minnesota/593/99 (H3N2)
               390   84 2151 3015 Swine/Illinois/100084/01 (H1N2)
               399   86 2151 3011 Swine/Minnesota/55551/00 (H1N2)
              ----------------------------------------------------------------
               470   80 1700  344 Swine/Indiana/P12439/00 (H1N2)
               482   82 1700  280 Swine/Indiana/9K035/99 (H1N2)
               500   85 1700  504 Turkey/MO/24093/99(H1N2)
               505   86 1700 2468 swine/Minnesota/1192/2001(H1N2)
               511   87 1700  339 Swine/Ohio/891/01(H1N2)
               517   88 1700  549 SW/MN/23124-T/01(H1N2)
               517   88 1700 2115 swine/Guangxi/17/2005(H1N2)
               529   90 1700  550 SW/MN/23124-S/01(H1N2)
               529   90 1700  552 SW/MN/16419/01(H1N2)
               535   91 1700  345 Swine/Illinois/100085A/01 (H1N2)
               542   56 1032  296 Wisconsin/10/98 (H1N1)
              ------------------------------------------------------------------
               250   13  520 6925 Sw/Oklahoma/18717/99(H3N2)
               251   13  516 6921 Sw/Colorado/23619/99(H3N2)
               262   14  533 6922 Sw/Wisconsin/14094/99(H3N2)
               262   14  533 6924 Sw/Illinois/21587/99(H3N2)
               263   14  531 6923 Sw/Oklahoma/18089/99(H3N2)
               312   16  512 6926 Sw/NorthCarolina/16497/99(H3N2)
               316   31  980 6927 Turkey/MO/24093/99(H1N2)
               329   48 1457 6963 Sw/Iowa/533/99(H3N2)
               336   49 1457 6961 Sw/Indiana/P12439/00(H1N2)
               336   49 1457 6969 Sw/Korea/CY04/07(H3N2)
               336   49 1457 6970 Sw/Korea/CY05/07(H3N2)
               337   33  979 6928 Sw/Texas/4199-2/98(H3N2)
               337   33  979 6929 Sw/Iowa/8548-1/98
               339   19  560 6972 SW/NC/45319/99(H1N2)
               339   19  560 6973 SW/NC/17366/01(H1N2)
               339   19  560 6974 SW/CO/17871/01(H1N2)
               343   50 1457 6971 Sw/Korea/CY09/07(H3N2)
              ------------------------------------------------------------------
               589   83 1409 1741 Sw/England/195852/92(H1N1)
               652   92 1409 1742 Sw/Germany/Vi5698/95(H1N1)
               712   98 1376 1746 Sw/Belgium/74/85(H1N1)
               751  101 1344 1773 Sw/Ille et Vilaine/1455/99(H1N1)
               753  105 1394 1772 Sw/Cotes d'Armor/1488/99(H1N1)
               754  106 1404 1749 Italy/1424-4/95(H1N1)
               765  108 1410 1737 Sw/Belgium/1/83(H1N1)
               777  104 1338 1777 Sw/Italy/1492/97(H1N1)
               786  103 1310 1778 Sw/Italy/1513-8/98(H1N1)
               787  111 1410 1739 turkey/France/87075/87(H1N1)
               787  111 1410 1788 Sw/Italy/53949/04(H1N1)
               787  111 1410 1789 Sw/Italy/65296/04(H1N1)
               794  112 1410 1738 Sw/Finistere/3616/84(H1N1)
               795  102 1282 1750 Sw/Italy/1424-3/95(H1N1)
               801  113 1410 1736 Sw/Lot/2979/82(H1N1)
               801  113 1410 1790 Sw/Spain/53207/04(H1N1)
               801  113 1410 1791 Sw/Italy/247578/04(H1N1)
               801  113 1410 1793 Sw/Spain/51915/03(H1N1)
               812  106 1305 1774 Cotes d'Armor/1121/00(H1N1)
               815  115 1410 1794 Sw/Virginia/671/1987(H1N1)
              --------------------------------------------------------------------
               230   22  955 2735 Sw/HK/5190/99(H3N2)
               230   22  955 2736 Sw/HK/5200/99(H3N2)
               230   22  955 2737 Sw/HK/5212/99(H3N2)
               261   25  955 2739 Sw/HK/1197/02(H3N2)
               261   25  955 2740 Sw/HK/1144/02(H3N2)
               272   26  955 2738 Sw/HK/9745/01(H3N2)
               272   26  955 2743 HK/1774/99(H3N2)
               293   28  955 2741 Sw/HK/7982/00(H3N2)
               314   30  955 2742 Sw/HK/9296/01(H3N2)
               345   33  955 2721 Sw/Leipzig/145/92(H3N2)
               366   35  955 2726 Sw/Cotes d'Armor/1482/99(H1N1)
               397   38  955 2722 wild boar/Germany/WS169/06(H3N2)
               397   38  955 2727 Sw/Italy/1521/98(H1N2)
              ------------------------------------------------------------
               346   29  838 6427 Sw/Texas/4199-2/98(H3N2)
               346   29  838 6428 Sw/Minnesota/9088-2/98(H3N2)
               357   30  838 6429 Sw/Iowa/8548-1/98
               381   32  838 6444 Sw/Indiana/9K035/99(H1N2)
               395   33  835 6436 Sw/North Carolina/98225/01(H1N2)
               395   33  835 6437 Sw/Minnesota/55551/00(H1N2)
               395   33  835 6445 SW/MN/3327/00(H1N2)
               395   33  835 6453 SW/IN/14810-T/01(H1N2)
               395   33  835 6454 SW/IN/14810-S/01(H1N2)
               395   33  835 6455 Sw/Korea/CAS09/06(H3N2)
               407   34  835 6456 Sw/Korea/CAN04/05(H3N2)
               407   34  835 6457 Sw/Korea/CAS07/05(H3N2)
               407   34  835 6467 Sw/Korea/CAS08/05(H1N1)
               407   34  835 6506 Sw/Iowa/930/01(H1N2)
               417   35  838 6430 Sw/Nebraska/209/98(H3N2)
               417   35  838 6438 Turkey/MO/24093/99(H1N2)
               417   35  838 6483 turkey/OH/313053/04(H3N2)
              I'm interested in expert panflu damage estimates
              my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

              Comment


              • #8
                Re: sequences at genbank !

                from post #4:

                (deleted data)


                Interesting history, eh?

                GS - what exactly are you comparing - the whole sequence?

                .
                Last edited by AlaskaDenise; April 27th, 2009, 06:41 PM. Reason: delete misleading data
                "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                Comment


                • #9
                  Re: sequences at genbank !

                  Originally posted by vinny View Post
                  Is there anything we should be worried about in those sequences gsgs.....?
                  On the contrary, the fact that all of the California sequences have a Lysine at position 627 of the PB2 segment is fantastic news. Years of research would suggest that the California virus does not replicate well in the cooler temperatures of the upper respiratory system. Perhaps that is why we are seeing patients complain of nausea, vommiting and diarrhea. This thing replicates better in the digestive tract?

                  Suggests perhaps that the virus is more transmittable through touch and contaminated surfaces than coughs and sneezes. Might also suggest that the best way to detect the virus in a suspect patient is through anal swabs rather than nasal swabs. Virus loads in the intestines probably greater than the respiratory tract.

                  Now, what about the other sequences, particullary Mexico, where we have a large number of deaths. Is the E627K mutation present?

                  Comment


                  • #10
                    Re: sequences at genbank !

                    well, this is similar to American swine e.g.
                    A/swine/OH/511445/2007(H1N1)
                    in segments 123458

                    67 are European swine , but also A/swine/Virginia/670/1987(H1N1)
                    I'm interested in expert panflu damage estimates
                    my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                    Comment


                    • #11
                      Re: sequences at genbank !

                      Mama - would that suggest that the Mexican strain has undergone more mutation?

                      .
                      "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                      Comment


                      • #12
                        Re: sequences at genbank !

                        Originally posted by AlaskaDenise View Post
                        from post #4:



                        Interesting history, eh?

                        GS - what exactly are you comparing - the whole sequence?

                        .
                        The H5N1 are not good matches. gsgs's numbers indicate the number of differences between A/california segments and the segments in the list of sequences he compared A/Calif with. The sequences only match in a segment if there are 0 differences. Hence my comment. If you look down column by column and spot the 0s and ignore the rest, you end up with with a 100% match to A/calif, and individual 100% matches to a mallard and to various swine sequences.

                        My comment about the recency of the recombination is based on the lack of tiny changes in the sequences gsgs chose to compare with. If the new strain was old, then there would likely be several near matches with just 1 or 2 differences. But for the most part, either the whole segment is the same, zero differences, or completely different. This suggests that the new strain is, errrm, new.

                        Oh, and pigs don't fly, but mallards do, and it's the intercontinental shorebird and anseriform traffic that could be moving the european swine sequences around.

                        Comment


                        • #13
                          Re: sequences at genbank !

                          Thanks WetDirt - now I wish I had taken the time to learn all this sequence stuff.

                          .
                          "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                          Comment


                          • #14
                            Re: sequences at genbank !

                            does this mean we can stop worrying so much........?

                            Comment


                            • #15
                              Re: sequences at genbank !

                              Originally posted by AlaskaDenise View Post
                              Mama - would that suggest that the Mexican strain has undergone more mutation?

                              .

                              Perhaps. It may also mean that California is just one amino acid mutation away from having a serious pandemic threat. Not a good time to get complacent.

                              Comment

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