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  • Re: Sequences at Genbank!

    South America:


    Code:
                                                   2 0011 1 00000000000111111 011 0000000000 000000 00  
                                                   1 8838 2 01345667789112445 212 1223577788 466888 34  
                                                   6 4569 6 04939571173048025 944 5231944559 906112 61  
                                                   3 4569 3 45026825610731887 838 0036127654 200563 74  
    -codon-position--------------------------------  1 1    11  21 121    1   1    121 1        2 1 1   
    ---Index---------------------------------------G CTCT C ACGCCTCGAGGCCACAG GGG TTAGCAAATC GGGACT AT  
       1 >A/******/index/2009/02/01                . .... . ................. ... .......... ...... ..  
      47 >A/Sao Paulo/53823/2009/08/01             - ---- - G.........T...T.. --- ---------- ------ --  
      79 >A/Rio de Janeiro/2459/2009/07/02         - ---- - G.........T...T.. --- ---------- ------ --  
      80 >A/Sao Paulo/2233/2009/05/27              - ---- - G.........T...T.. --- ---------- ------ --  
      81 >A/Sao Paulo/53838/2009/08/01             - ---- - G......A..T...T.. --- ---------- ------ --  
      82 >A/Sao Paulo/57831/2009/08/09             - ---- - G.........T...T.. --- ---------- ------ --  
      83 >A/Santa Catarina/423/2009 /06/01         - ---- - G.........T...T.. --- ---------- ------ --  
      84 >A/Rio de Janeiro/5090/2009/07/23         - ---- - G.........T...T.. --- ---------- ------ --  
      85 >A/Rio Grande do Sul/7019/2009/07/29      - ---- - G.........T...T.. --- ---------- ------ --  
      86 >A/Rio Grande do Sul/5395/2009/07/23      - ---- - G.........T...T.. --- ---------- ------ --  
      87 >A/Rio de Janeiro/9685/2009/08/10         - ---- - G.........T...T.. --- ---------- ------ --  
      89 >A/Parana/4597/2009/07/12                 - ---- - G.........T...T.. --- ---------- ------ --  
      49 >A/Sao Paulo/43812/2009/07/03             - ---- - ..........T..GT.. --- ---------- ------ --  
      52 >A/Minas Gerais/65/2009/04/27             - ---- - ---------........ --- ---------- ...CTC --  
      48 >A/Rio de Janeiro/290/2009/05/24          - ---- - ----------------- --- ---------- AA.CTC --  
      50 >A/Rio de Janeiro/125/2009/05/06          - ---- - ----------------- --- ---------- ...CT- --  
      76 >A/Rio de Janeiro/118/2009/05/05          - ---- - ----------------- --- ---------- ...CT- --  
      78 >A/Santa Catarina/296/2009/05/25          - ---- - ----------------- --- ---------- ...CTC --  
      90 >A/Rio de Janeiro/332/2009/05/30          - ---- - ----------------- --- ---------- AA.CTC --  
      92 >A/Rio de Janeiro/307/2009/05/27          - ---- - ----------------- --- ---------- AA.CT- --  
      91 >A/Chile/9113/2009/05/19                  - ---- - .A.........------ --- .......... ------ --  
      11 >A/Colombia/08/2009/04/25                 - ---- - -A..-......------ --- --------.. ------ --  
      16 >A/Sao Paulo/1454/2009/04/29              - ---- - ..............T.. --- ...A.G.... ...... --  
       6 >A/La Paz/WR0096T/2009/06/22              . TG.. . ..............T.. AA. ...A.G.... ...... ..  
       9 >A/Sao Paulo/2303/2009/06/01              - ---- - ..............T.. --- ...A.G.... ...... --  
      15 >A/Parana/2529/2009/06/30                 - ---- - ....A.........T.. --- ---------- ------ --  
      88 >A/Guayaquil/1/2009/05/                   - ---- - -.........T------ --- ---------- ------ --  
       5 >A/Guayaquil/2/2009/07/                   - ---- - -..........------ --- ---------- ------ --  
       7 >A/Guayaquil/3/2009/07/                   - ---- - ...........------ --- ---------- ------ --  
       8 >A/Bogota/224/2009/04/25                  - ---- - -----......------ --- ---------- ------ --  
      10 >A/Colombia/213/2009/04/30                - ---- - -----......------ --- ---------- ------ --  
      12 >A/Bogota/176/2009/04/27                  - ---- - -----......------ --- --------.. ------ --  
      13 >A/Guayaquil/4/2009/07/                   - ---- - -..........------ --- ---------- ------ --  
      14 >A/Colombia/450/2009/05/06                - ---- - -----......------ --- --------.. ------ --  
      46 >A/Argentina/Malbran017/2009//            - ---- - ----------------- --- ---------- ...--- --  
    
       2 >A/Argentina/HNRG42/2009/06/27            - ---- - .....A.....T..TG. --- ...A--GG.. AAA... --  
       4 >A/Argentina/HNRG36/2009/06/21            - ---- - .....A........TG. --- ...A--GG.. AA.... --  
      17 >A/Chile/8886/2009/05/18                  - ---- - .....A.....------ --- ...A.G.... ------ --  
       3 >A/Guayaquil/5/2009/07/                   - ---- - -....A.....------ --- ---------- ------ --  
      37 >A/Sao Paulo/55115/2009/08/05             - ---- - .....A........T.. --- ---------- ------ --  
      35 >A/Sao Paulo/2261/2009/05/29              - ---- - .....A........T.. --- ---------- ------ --  
      33 >A/Sao Paulo/2275/2009/05/29              - ---- - .....A........T.. --- ---------- ------ --  
      31 >A/Santa Catarina/460/2009/06/10          - ---- - .....A........T.. --- ---------- ------ --  
      18 >A/Sao Paulo/54392/2009/08/01             - ---- - .....A........T.A --- ---------- ------ --  
      19 >A/Rio Grande do Sul/4509/2009/07/18      - ---- - ....AA........T.A --- ---------- ------ --  
      20 >A/turkey/Chile/28317-6504-3/2009/08/17   A .... T .....A........T.- AAA ...A.G.... AA.... GC  
      21 >A/Argentina/HNRG3/2009/06/18             A ...C T .....A........T.. AAA ...A.G..A. AA.... GC  
      22 >A/Bogota/0466N/2009/06/25                A ..A. . ..A..AT..A..T.T.. AAA CC.A.G.... AA.... G.  
      23 >A/Bogota/WR0090N/2009/06/16              A TGA. . ..A..AT..A..T.T.. AAA CC.A.G.... AA.... G.  
      24 >A/Argentina/HNRG45/2009/06/16            - ---- - .....A........T.. --- ...A.G.... AA.... --  
      25 >A/Chile/8947/2009/05/17                  - ---- - .....A.....------ --- ...A.G.... ------ --  
      26 >A/Mato Grosso/2329/2009/05/28            - ---- - .....A........T.. --- ...A.G.... ------ --  
      27 >A/Chile/8949/2009/05/18                  - ---- - .....A.....------ --- ...A.G.... ------ --  
      28 >A/Argentina/HNRG44/2009/06/30            - ---- - .....A.....T..T.. --- ...A.G.... AA.... --  
      29 >A/Argentina/HNRG39/2009/06/23            - ---- - .....A.....T..T.. --- ...A..GG.. AA.... --  
      30 >A/Argentina/HNRG32/2009/06/22            - ---- - .....A........T.. --- ...A..GG.. AA.... --  
      32 >A/Argentina/HNRG5/2009/06/22             - ---- - .....A........T.. --- ...A-.GG.T AA.... --  
      34 >A/Argentina/HNRG48/2009/06/25            - ---- - .....A........T.. --- ...AT.GG.T AA.... --  
      36 >A/Argentina/HNRG13/2009/06/05            A ...C T .....A........T.. AAA ..GA.G.G.. AA.... GC  
      38 >A/Argentina/HNRG18/2009/07/01            - ---- - .....A........T.. --- -..A-.GG.. AA.... --  
      39 >A/Sao Paulo/53845/2009/08/02             - ---- - .....A.A......T.. --- ---------- ------ --  
      40 >A/Argentina/HNRG8/2009/06/11             - ---- - .....A.A......--- --- ...ATG..A. AA.... --  
      41 >A/Castro/JXP/2009/06/11                  - .... - .....A........T.. --- ---------- ------ --  
      42 >A/Argentina/HNRG20/2009/06/19            - ---- - .....A........T.- --- ..GA-.GG.. AA.... --  
      43 >A/Argentina/HNRG30/2009/06/17            - ---- - .....A........T.- --- -----.GG.. AA.... --  
      44 >A/Argentina/HNRG37/2009/06/22            - ---- - .....A........T.. --- -----.GG.. AA.... --  
      45 >A/Santiago/3221/2009/06/30               - ---- - -....A.....------ A-- ---------- ---... --  
      51 >A/Sao Paulo/55312/2009/08/05             - ---- - .....A........T.. --- ---------- ------ --  
      53 >A/Sao Paulo/53225/2009/08/01             - ---- - .....A..G.....T.. --- ---------- ------ --  
      54 >A/Argentina/HNRG16/2009/06/29            - ---- - .....A..G.....T.. --- ...A.G.... AA.... --  
      55 >A/Rio de Janeiro/5826/2009/07/28         - ---- - .....A..G....GT.. --- ---------- ------ --  
      56 >A/Sao Paulo/53206/2009/07/19             - ---- - .....A..G.....T.. --- ---------- ------ --  
      58 >A/Santa Catarina/459/2009/06/11          - ---- - .....A........T.. --- ---------- ------ --  
      60 >A/Rio Grande do Sul/4782/2009/07/20      - ---- - .....A........T.. --- ---------- ------ --  
      62 >A/Rio Grande do Sul/7108/2009/07/29      - ---- - .....A........T.. --- ---------- ------ --  
      64 >A/Sao Paulo/2193/2009/05/29              - ---- - .....A........T.. --- ---------- ------ --  
      57 >A/Argentina/HNRG31/2009/06/17            - ---- - .....A........T.. --- ...A--GG.. AA.... --  
      59 >A/Argentina/HNRG41/2009/06/26            - ---- - .....A........T.. --- ...A...... AAA... --  
      61 >A/Argentina/HNRG14/2009/05/27            - ---- - .....A........T.. --- ...A-.GG.. AA.... --  
      63 >A/Argentina/HNRG33/2009/06/24            - ---- - .....A........T.. --- ...A-.GG.. AA.... --  
      66 >A/Argentina/HNRG17/2009/06/01            - ---- - .....A........T.. --- -----.GG.. AA.... --  
      67 >A/Argentina/HNRG21/2009/07/01            - ---- - .....A........T.. --- ...A-.GG.. AA.... --  
      65 >A/Argentina/HNRG40/2009/06/24            - ---- - .....A........T.. --- ...AT.GG.. AA.... --  
      68 >A/Argentina/HNRG23/2009/07/27            - ---- - ...T.A........T.. --- ------GGA. AA.... --  
      69 >A/Argentina/HNRG15/2009/07/20            - ---- - ...T.A........T.. --- ...AT.GGA. AA.... --  
      70 >A/Rio de Janeiro/290/2009 /05/24         - ---- - ----.A........T.. --- ---------- ------ --  
      71 >A/Rio Grande do Sul/4772/2009/07/20      - ---- - .....A........T.. --- ---------- ------ --  
      72 >A/Santa Catarina/478/2009/06/11          - ---- - --...A........T.. --- ---------- ------ --  
      73 >A/Sao Paulo/2056/2009/05/20              - ---- - .....A........T.. --- ---------- ------ --  
      74 >A/Distrito Federal/2611/2009/06/05       - ---- - .....A........T.. --- ...A.G.... ------ --  
      75 >A/Puerto Montt/Bio87/2009/06/19          - ---- - .....A........T.. --- ---------- ------ --  
      77 >A/Santiago/2009/2009/06/18               - ---- - -....A.....------ --- ---------- ------ --  
      93 >A/Santiago/3827/2009/07/07               - ---- - --...A......----- --- ---------- ------ --  
      94 >A/Cancun--Y/Index/2009/04/15             A .... . .....A........T.. AAA ...A.G.... AA.... G.  
                                                                                                        
    ---Index---------------------------------------G CTCT C ACGCCTCGAGGCCACAG GGG TTAGCAAATC GGGACT AT  
    -codon-position--------------------------------  1 1    11  21 121    1   1    121 1        2 1 1   
                                                   2 0011 1 00000000000111111 011 0000000000 000000 00  
                                                   1 8838 2 01345667789112445 212 1223577788 466888 34  
                                                   6 4569 6 04939571173048025 944 5231944559 906112 61  
                                                   3 4569 3 45026825610731887 838 0036127654 200563 74


    -----experimenting-----------



    85 >A/Rio Grande do Sul/7019/2009/07/29 - ---- - G.........T...T.. --- ---------- ------ --
    86 >A/Rio Grande do Sul/5395/2009/07/23 - ---- - G.........T...T.. --- ---------- ------ --
    87 >A/Rio de Janeiro/9685/2009/08/10 - ---- - G.........T...T.. --- ---------- ------ --
    89 >A/Parana/4597/2009/07/12 - ---- - G.........T...T.. --- ---------- ------ --
    49 >A/Sao Paulo/43812/2009/07/03 - ---- - ..........T..GT.. --- ---------- ------ --
    52 >A/Minas Gerais/65/2009/04/27 - ---- - ---------........ --- ---------- ...CTC --
    qwertzuiop&#252;asdfghjkl&#246;&#228;yxcvbnm,.-<#+QWERTZUIOP&#220;&#196;*'&#214;LKJHGFSDAYXCVBNNM ;:_>

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

    Comment


    • Re: Sequences at Genbank!

      Gs, I don't understand (from your table) what positions those mutations are in?
      The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

      Comment


      • Re: Sequences at Genbank!

        the positions are marked vertically by 4 digits in the first 4 rows

        the segments are separated by blank columns


        so the first position is 2163 in segment 1, which is one of the 11 Cancun markers etc.



        use a ruler or paper to follow the vertical columns

        or maybe I should use another symbol instead of "." ? e.g. "|"
        and different colors ?
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • Re: Sequences at Genbank!

          Ok, I see now how the letters and the letters, "_", and "." all line up. Is there any way to tell if the mutation is at 225, etc?

          >so the first position is 2163 in segment 1,

          I didn't realize those were all the segments. So the bolded one is HA?
          G CTCT C ACGCCTCGAGGCCACAG GGG TTAGCAAATC GGGACT AT
          The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

          Comment


          • Re: Sequences at Genbank!

            yes, and the positions are numbered above.
            Usually I only consider positions where at least 2 viruses
            in the database differ from the index at that position,
            but this can easily be changed.
            ( "seqa 8-file t1" for at least one)

            so, find the 716 in the 4th segment, scroll down the column,
            write down all sequence names which have a letter in that row,
            and you get the travel-log.
            All travel-logs in one table, when read vertically.
            All mutations of a virus when the same is done horizontally.

            But the main purpose of the table is to find substrains=subgroups
            which share multiple mutations
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • Re: Sequences at Genbank!

              > so, find the 716 in the 4th segment
              Well, now.. that right there is the problem

              I don't understand how to find 716
              The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

              Comment


              • Re: Sequences at Genbank!

                you have ACGCCTCGAGGCCACAG
                as you correctly found was the index at the selected positions in segment 4.

                above the 2nd A , you find : 0,7,1,6,2
                ( in that column, read from top to bottom)

                0,7,1,6 is 716, the position in HA
                and 2 is the position in the codon (1,2 or 3 - blank is 3)
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment


                • Re: Sequences at Genbank!

                  Finally!! Thank you. I read where you said "vertical" but I just wasn't making the connection.
                  The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                  Comment


                  • Re: Sequences at Genbank!

                    lung samples vs. throat ?

                    Assuming that they usually won't take lung samples from living, conscious people

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

                    Comment


                    • Re: Sequences at Genbank!

                      Gs,
                      2 samples are from "lung wash" and I found this with a quick google search. I assumed the 2 patients were not dead:
                      During the bronchoscopy procedure, your doctor may perform a "lung wash" or bronchoalveolar lavage to obtain samples of suspicious cells. ...
                      The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                      Comment


                      • Re: Sequences at Genbank!

                        Originally posted by gsgs View Post
                        Cancun-marker.
                        The Cancun-strain is dominant now.
                        I guesstimate that 60% are meanwhile Cancun.

                        G2163A(1)


                        T658A(4),C1408T(4)
                        G298A(5),G1143A(5),G1248A(5)
                        G316A(6),A742G(6)
                        G492A(7),G600A(7)
                        A367G(8)
                        When we find Cancun markers in one segment, do we always find the other Cancun markers in the other segments?

                        If we find T658A(4),C1408T(4) but not G298A(5),G1143A(5),G1248A(5), then do we know it reassorted, recombined (or whatever)?
                        The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                        Comment


                        • Re: Sequences at Genbank!

                          > When we find Cancun markers in one segment, do we always find the other
                          > Cancun markers in the other segments?

                          not always, but usually. The pre-Cancun substrain has 5 of the 11 markers,
                          early Japan-viruses had 3. Some Cancun-mutation can occasionally be "undone", mutated
                          again so it is again original. But this is unlikely.
                          It happened however in one of the markers in the years since swine-triple-reassortant 1998.
                          I think it was G492A(7).
                          And then segments can shuffle=reassort. We had some examples with ******
                          Israel,Russia,

                          > If we find T658A(4),C1408T(4) but not G298A(5),G1143A(5),G1248A(5),
                          > then do we know it reassorted, recombined (or whatever)?

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

                          Comment


                          • Re: Sequences at Genbank!

                            Originally posted by mixin View Post
                            Are G610K and C870M of any significance? ...
                            Mutations at the 610-612 codon are rare.
                            870 was found mostly in Santo Domingo; except for the rare trip to other places.

                            C:\gs>travel1 mxha6 610
                            N >A/Colombia/08/2009/04/25
                            N >A/Singapore/ON313/2009/06/19
                            2 -:121 G:1783 N:2

                            C:\gs>travel1 mxha6 611
                            N >A/Colombia/08/2009/04/25
                            G >A/Singapore/ON1138/2009/07/13
                            2 -:121 A:1783 G:1 N:1

                            C:\gs>travel1 mxha6 612
                            N >A/Colombia/08/2009/04/25
                            T >A/NY/3744/2009/05/15
                            T >A/Wisconsin/629-D01779/2009/05/28
                            T >A/Wisconsin/629-D00119/2009/06/14
                            4 -:121 C:1781 N:1 T:3

                            -------------------------------------------------

                            C:\gs>travel1 mxha6 868
                            T >A/Texas/43122467/2009
                            1 -:147 C:1758 T:1

                            C:\gs>travel1 mxha6 869
                            0 -:147 A:1759

                            C:\gs>travel1 mxha6 870
                            T >A/Chile/9113/2009/05/19
                            T >A/Kaluga/01/2009/05/22
                            T >A/Santo Domingo/0574/2009/05/23
                            T >A/Santo Domingo/0574T/2009/05/23
                            T >A/Santo Domingo/0573N/2009/05/24
                            T >A/Santo Domingo/572N/2009/05/24
                            T >A/Santo Domingo/565T/2009/05/26
                            T >A/Santo Domingo/568T/2009/05/26
                            T >A/Catalonia/317/2009/05/28
                            T >A/Paris/2709/2009/06/02
                            T >A/Santo Domingo/1066N/2009/06/17
                            T >A/Santo Domingo/WR1056T/2009/06/25
                            T >A/Santo Domingo/WR1068N/2009/06/25
                            T >A/Santo Domingo/WR1059N/2009/06/30
                            T >A/Santo Domingo/WR1057N/2009/07/02
                            T >A/Santo Domingo/WR1058N/2009/07/02
                            T >A/Norway/3689/2009/10/02
                            T >A/Catalonia/S1637/2009/10/28
                            T >A/Catalonia/S2016/2009/12/01
                            19 -:147 C:1740 T:19
                            The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                            Comment


                            • Re: Sequences at Genbank!

                              (from mild cases? fatal ones?)
                              I haven't looked at every one of the newly updated sequences, but if they don't specifically state "fatal", then I assume he draws his conclusions from the method of sampling. For the first 21 releases, there were: lung wash, swab, original RTPCR, nose-pharyngeal wash, Oropharyngeal (fatal), lungs (fatal), MDCK2 and clinical sample.

                              I'd be surprised if these poor countries are testing any mild cases.
                              The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                              Comment


                              • Re: Sequences at Genbank!

                                Novosibirsk/02/2009/07/21{12}:
                                R6 + C

                                Tomsk/03/2009/07/19{16}:
                                G546A(1),C1412T(1),C1425T(2),T252C(4),A516G(4),A82 9G(4)
                                +R6 + C4a+C4b+C5a+C5b+C5c+C6a+C6b+C7a+C7b
                                reassorted:
                                1,3,4,5 from Tomsk/02 (or vice versa)
                                2 from Moscow IIV05
                                7,8 from Tomsk/01
                                6 from Moscow/IIV02
                                or similar

                                Russia/2009/09/01{9}: R1a,R1b,R1c,R4,R6,R7a,R7b,R7c,R8
                                G426A(1),Norway/3364-02/2009/09/08
                                A1020T(1),Norway/2924/2009/08/10
                                C2137T(1),Norway/2924/2009/08/10
                                A1281G(4),Italy/129/2009/06/16
                                T1221C(6),Moscow/03/2009/05/26
                                G333A(7),Norway/3364-02/2009/09/08
                                G414A(7),Norway/3364-02/2009/09/08
                                G555A(7),Catalonia/S1096/2009/07/14
                                A252G(8),Norway/2924/2009/08/10


                                Cancun/2009/04/10{11}: C1,C4a,C4b,C5a,C5,C5c,C6a,C6b,C7a,C7b,C8
                                G2163A(1),T658A(4),C1408T(4),G298A(5),G1143A(5),G1 248A(5)
                                G316A(6),A742G(6),G492A(7),G600A(7),A367G(8)
                                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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