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  • A list of relevant mutation position

    Hello,

    I said often that it is hard to reduce the mutations necessary to produce a pandemic strain to a simple list of mutation.

    Especially when talking about the surface Hemagglutinin gene because there is no example of previous human H5 subtype.

    The fact is that 3D shape & positionnal mutation are in inter-relation.

    Others early list of relevant mutation where bases on comparison with others subtype like H3, H2, H1.

    A recent publication developped a model that seem to be of good predicting value.
    Computational studies of H5N1 hemagglutinin binding with SA-α-2, 3-Gal and SA-α-2, 6-

    This thread is intended to record them for a quick recall whe it is needed.

    Also, If others mutation on others genes are relevant for human adaptation we could list them here.

    There is the amino acid code for translation and for the single letter vs tree letter code.
    The Amino Acid Code - Reference

  • #2
    Re: A list of relevant mutation position

    Many here like that kind of list, it is also usefull when scaning new sequences for "something of concern".

    From the article listed up here.

    Standard H3 numbering

    Y98
    L133
    V135
    S136
    W153
    I155
    H183
    E190
    K193
    L194
    Q226

    The amino acid listed in thoses we now see mostly in asiatic H5.
    Assume that every change seen may impact the Avian-Human affinity. Q226 seem the most capital.
    Last edited by Mingus; October 4, 2006, 09:45 PM.

    Comment


    • #3
      Re: A list of relevant mutation position

      The standard numbering in the H3 numbering.

      If you alignement are cut with the

      DQICIG being the first amino acid, you will have to substract 4 to have the position.
      This standard for alignement is often seen and some sequence are already cut there.

      Here is the list for alignement starting with DQICIG
      The first one Y98 is at the same place and there is a 4 AA deletion when compared with H3 sequences between this position and the next relevant one.

      Theses amino acids are listed from that article and the computationnal analysys have been made from the Viet-Nam 2004 reference strain.

      H5 numbering


      <table x:str="" style="border-collapse: collapse; width: 60pt;" border="0" cellpadding="0" cellspacing="0" width="80"><col style="width: 60pt;" width="80"> <tbody><tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt; width: 60pt;" x:num="" align="right" height="17" width="80">Y98</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">L129</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">V131</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">S132</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">W149</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">I151</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">H179</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">E186</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">K189</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">L190</td> </tr> <tr style="height: 12.75pt;" height="17"> <td style="height: 12.75pt;" x:num="" align="right" height="17">Q222</td> </tr> </tbody></table>

      If we note this horizontally it give us:

      YLVSWIHEKLQ for A/Vietnam/1194/2004
      Last edited by Mingus; October 4, 2006, 09:45 PM.

      Comment


      • #4
        Re: A list of relevant mutation position

        YLVSWIHEKLQ for A/Vietnam/1194/2004 Group 1
        YSVSWIHERLQ for most Indonesians & Quigai strains Group 2
        YSVSWIHEKLQ for A/Zhejiang/16/2006 & chineses sequences Group 3

        YSVSWIHERLR the only so far A/Indonesia/CDC329/2006


        So theoretically the Indonesians & Quigai strains are different in their affinity for glycans...
        The chineses are something between.

        There is clearly tree majors group of strains looking for polymorphisms pattern regarding the RBS affinity position from the computational study.

        Wich is the most mammalian ? who knows the question still there...

        There is also that S227N that is know to change the affinity, is this a direct link with the glycan or a indirect impact on the Q226 link with the glycan ?

        Reference for that list:
        Computational studies of H5N1 hemagglutinin binding with SA-α-2, 3-Gal and SA-α-2, 6-
        Last edited by Mingus; October 4, 2006, 09:51 PM.

        Comment


        • #5
          Re: A list of relevant mutation position

          I must have some wrong enumeration with the first Y here:

          http://www.flutrackers.com/forum/showthread.php?t=3547

          I'll try to correct...


          sorry, but you have 98 in both lists.
          Unless you make the first one 102, the list at the link should
          be correct.
          Vietnam 1194 would be DLVSWIHEKLQ
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • #6
            Re: A list of relevant mutation position

            gsgs,

            I did not check sequences that have been release later than
            Indonesia/699 ...

            I let you with that ? It is late for me here

            Have fun! I know you'll like to do that.

            Comment


            • #7
              Re: A list of relevant mutation position

              Originally posted by gsgs
              I must have some wrong enumeration with the first Y here:

              http://www.flutrackers.com/forum/showthread.php?t=3547

              I'll try to correct...


              sorry, but you have 98 in both lists.
              Unless you make the first one 102, the list at the link should
              be correct.
              Vietnam 1194 would be DLVSWIHEKLQ
              I'm not sure to understand ?

              I've check my alignement and Vietnam 1194 do have a Y at 98.
              But there is a D at 88 ... did you confuse ?

              Your link also mention S at 98 in HA

              Did you cut the H5 to have DQICIG as the first amino acids ?

              Comment


              • #8
                Re: A list of relevant mutation position

                >gi|50296051|gb|AAT73273| /Human/4(HA)/H5N1/Viet Nam/2004/// hemagglutinin [Influenza A virus (A/Viet Nam/1194/2004(H5N1))]
                ---MEKIVLLFAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILE KTHNGKL
                CDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCY PGDFNDYEEL
                KHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLI KKNSTYPTIK
                RSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVP RIATRSKVNG
                QSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEY GNCNTKCQTP
                MGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKRG LFGAI-----
                ---------AGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSII D
                KMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERT LDFHDSNVKN
                LYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEAR LKREEISGVK
                LESIGIYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCR---


                and now 50 amino acids per row:

                ---MEKIVLLFAIVS
                LVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDG
                |................................................|
                1................................................5 0
                VKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFN
                ...............................................|
                ...............................................98

                DYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRN
                VVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                YISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGN
                .........................|
                .........................226
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment


                • #9
                  Re: A list of relevant mutation position

                  gi|54126496|gb|AY747609.1| Influenza A virus (A/swine/Fujian/1/2003(H5N1)) hemagglutinin (HA) gene, complete cds
                  gi|50261904|gb|AY646424.1| Influenza virus A (A/swine/Shandong/2/03(H5N1)) hemagglutinin (HA) gene, complete cds
                  gi|54126527|gb|AY747617.1| Influenza A virus (A/swine/Fujian/F1/2001(H5N1)) hemagglutinin (HA) gene, complee cds

                  From theses swine Chineese sequences,

                  The H5 RBS pattern:
                  YSVSWIHEKLQ
                  The typical chineese pattern

                  Comment


                  • #10
                    Re: A list of relevant mutation position

                    aren't these the monotreme's retracted sequences ?
                    I get a "D" at position 98 in all 3

                    (one line = 50 amino acids):

                    >gi|54126497|gb|AAV30828| /Swine/4(HA)/H5N1/China/2003/// hemagglutinin [Influenza A virus (A/swine/Fujian/1/2003(H5N1))]g
                    MEKIVLLLAIVS
                    LVKGDQICTGYYANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDG
                    VKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFN
                    DYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYQGRSSFFRN
                    VVWLIEKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                    YISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGN
                    FIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                    LTIGECPKYVKSNRLVLATGLRNSPQREIRRKKRGLFGAIAGFIEGGWQG
                    MVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                    GREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVK
                    NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA
                    RLNREEISGVKLESIGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                    QCRICI

                    >gi|54126528|gb|AAV30836| /Swine/4(HA)/H5N1/China/2001/// hemagglutinin [Influenza A virus (A/swine/Fujian/F1/2001(H5N1))]
                    MEKIVLLLAIVS
                    LVKGDQICTGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDG
                    VKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFN
                    DYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYQGRSSFFRN
                    VVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                    YISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGN
                    FIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                    LTIGECPKYVKSNRLVLATGLRNSPQREIRRKKRGLFGAIAGFIEGGWQG
                    MVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                    GREFNNLERRIENLNKKMEDGFLDVWTYNAEILVLMENERTLDFHDSNVK
                    NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA
                    RLNREEISGVKLESIGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                    QCRICI


                    >gi|50261905|gb|AAT72505| /Swine/4(HA)/H5N1/China/2003/// hemagglutinin [Influenza virus A (A/swine/Shandong/2/03(H5N1))]
                    MEKIVLLLAIVS
                    LVKSDQVCIGYHANNSTEQVDTIMEKNVTVTHAQDILERTHNGKLCDLNG
                    VKPLILRDCSVAGWLLGNPMCDEFTNVPEWSYIVEKASPANDLCYPGDFN
                    DYEELKHLLSRINHFEKIQIIPKSSWSNHDASSGVSSACPYHGRSSFFRN
                    VVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                    YISVGTSTLNQRLVPEIATRPKVNGQSGRIEFFWTILKPNDAINFESNGN
                    FIAPEYAYKIAKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                    LTIGECPKYVKSNRLVLATGLRNTPQRERRRKKRGLFGAIAGFIEGGWQG
                    MVDGWYGYHHSNKQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                    GREFNNLERRIESLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVK
                    NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYPQYSEEA
                    RLNREEISGVKLESMGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                    QCRICI
                    I'm interested in expert panflu damage estimates
                    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                    Comment


                    • #11
                      Re: A list of relevant mutation position

                      Originally posted by gsgs
                      aren't these the monotreme's retracted sequences ?
                      I get a "D" at position 98 in all 3

                      (one line = 50 amino acids):

                      >gi|54126497|gb|AAV30828| /Swine/4(HA)/H5N1/China/2003/// hemagglutinin [Influenza A virus (A/swine/Fujian/1/2003(H5N1))]g
                      MEKIVLLLAIVS
                      LVKGDQICTGYYANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDG
                      VKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFN
                      DYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYQGRSSFFRN
                      VVWLIEKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                      YISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGN
                      FIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                      LTIGECPKYVKSNRLVLATGLRNSPQREIRRKKRGLFGAIAGFIEGGWQG
                      MVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                      GREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVK
                      NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA
                      RLNREEISGVKLESIGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                      QCRICI

                      >gi|54126528|gb|AAV30836| /Swine/4(HA)/H5N1/China/2001/// hemagglutinin [Influenza A virus (A/swine/Fujian/F1/2001(H5N1))]
                      MEKIVLLLAIVS
                      LVKGDQICTGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDG
                      VKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPANDLCYPGDFN
                      DYEELKHLLSRINHFEKIQIIPKSSWSNHEASSGVSSACPYQGRSSFFRN
                      VVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                      YISVGTSTLNQRLVPKIATRSKVNGQSGRMEFFWTILKPNDAINFESNGN
                      FIAPEYAYKIVKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                      LTIGECPKYVKSNRLVLATGLRNSPQREIRRKKRGLFGAIAGFIEGGWQG
                      MVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                      GREFNNLERRIENLNKKMEDGFLDVWTYNAEILVLMENERTLDFHDSNVK
                      NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA
                      RLNREEISGVKLESIGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                      QCRICI


                      >gi|50261905|gb|AAT72505| /Swine/4(HA)/H5N1/China/2003/// hemagglutinin [Influenza virus A (A/swine/Shandong/2/03(H5N1))]
                      MEKIVLLLAIVS
                      LVKSDQVCIGYHANNSTEQVDTIMEKNVTVTHAQDILERTHNGKLCDLNG
                      VKPLILRDCSVAGWLLGNPMCDEFTNVPEWSYIVEKASPANDLCYPGDFN
                      DYEELKHLLSRINHFEKIQIIPKSSWSNHDASSGVSSACPYHGRSSFFRN
                      VVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTT
                      YISVGTSTLNQRLVPEIATRPKVNGQSGRIEFFWTILKPNDAINFESNGN
                      FIAPEYAYKIAKKGDSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
                      LTIGECPKYVKSNRLVLATGLRNTPQRERRRKKRGLFGAIAGFIEGGWQG
                      MVDGWYGYHHSNKQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAV
                      GREFNNLERRIESLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVK
                      NLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYPQYSEEA
                      RLNREEISGVKLESMGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSL
                      QCRICI
                      None of the above sequences have been retracted.

                      Comment


                      • #13
                        Re: A list of relevant mutation position

                        aren't these the monotreme's retracted sequences ?
                        I get a "D" at position 98 in all 3

                        (one line = 50 amino acids):

                        gsgs, I tell you twice, cut your sequence to make them begin with DQI !

                        Comment


                        • #14
                          Re: A list of relevant mutation position

                          Dr.Niman, I checked the H5 RBS pattern this morning and At that time of the swine sequence you linked in your thread, some where'nt available, only the taxonomic data was available.

                          Comment


                          • #15
                            Re: A list of relevant mutation position

                            YKVTWTHDSLQ Brevig mission
                            YLVSWIHEKLQ for A/Vietnam/1194/2004 Group 1
                            YSVSWIHERLQ for most Indonesians & Quigai strains Group 2
                            YSVSWIHEKLQ for A/Zhejiang/16/2006 & chineses sequences Group 3
                            YSVSWIHERLR the only so far A/Indonesia/CDC329/2006

                            Comment

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