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  • #16
    Re: A list of relevant mutation position

    I based my list on the relevant H5 position ddetermined in that study
    Computational studies of H5N1 hemagglutinin binding with SA-α-2, 3-Gal and SA-α-2, 6-

    Brevig mission is a H1 sequence so...

    My questions are:
    - Wich numbering system did you use?
    - How did you determine the equivalent relevant position? (source, article, link)

    Comment


    • #17
      Re: A list of relevant mutation position

      Brevig mission is a H1 sequence so...

      My questions are:
      - Wich numbering system did you use?
      - How did you determine the equivalent relevant position? (source, article, link)
      First I start un alignment using a H5N1 sequence with known positions with ClustalW (on pr level) and I check the plausibility (insertions deletions presumably correctly displayed etc). If the alignment is correct, the relevant positions can be identified.
      If one compares with H2 or H3 HA by counting it starts to be really difficult, but ligning up the sequences you can try to get something out of it.

      The correct numbering of Brevig mission can be found in Tautenbergers description of the 1918 HA Gene

      YSVSWIHERLQ DQ095618.2| A/Bar-headed Goose/Qinghai/61/05 H5N1
      YSVSWIHERLQ DQ419819.1| A/swine/Guangdong/2/2003 H5N1
      YKVTWTHDSLQ AF116575.1| A/Brevig_Mission/1/18(HA) H1N1
      YGGSWTHESLL AF348176 | A/Hong Kong/1/68 H3N2
      YGGSWTHETLL CY014976.1| A/Japan/305/1957 H2N2

      Comment


      • #18
        Re: A list of relevant mutation position

        So, thank you Mr.G?nseerpel.

        Y
        KVTWTHDSLQ AF116575.1| A/Brevig_Mission/1/18(HA) H1N1

        YGGSWTHESLL AF348176 | A/Hong Kong/1/68 H3N2
        YGGSWTHETLL CY014976.1| A/Japan/305/1957 H2N2
        <!-- / message --><!-- controls -->
        YSVSWIHERLQ DQ095618.2| A/Bar-headed Goose/Qinghai/61/05 H5N1
        YSVSWIHERLQ DQ419819.1| A/swine/Guangdong/2/2003 H5N1

        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

        Red is a pandemic strain
        Bold is a position that have the same in one of the pandemic strain.

        Note :This is just for comparison, there is no proof the amino acid must be the same than the previous pandemic.

        Comment


        • #19
          Re: A list of relevant mutation position

          Note :This is just for comparison, there is no proof the amino acid must be the same than the previous pandemic.
          When the strains are very different, one has to have a very critical look on the alignment. It is just for comparison.

          Comment


          • #20
            Re: A list of relevant mutation position

            Check this article from Taubenberger
            Structure and Receptor Specificity of the Hemagglutinin from an H5N1 Influenza Virus

            from that article


            __________________________________________________ __________________________________________________ _______________________________

            <table cellpadding="0" cellspacing="10" width="100%"><tbody><tr><td rowspan="2" align="left" valign="top"> Viral strain </td> <td colspan="14" align="center" valign="top"> Amino acid position
            <hr noshade="noshade" size="1"></td> <td colspan="2" align="center" valign="top"> Specificity
            <hr noshade="noshade" size="1"></td> </tr> <tr> <td align="center" valign="top"> 98 </td> <td align="center" valign="top"> 136 </td> <td align="center" valign="top"> 153 </td> <td align="center" valign="top"> 183 </td> <td align="center" valign="top"> 190 </td> <td align="center" valign="top"> 193 </td> <td align="center" valign="top"> 194 </td> <td align="center" valign="top"> 216 </td> <td align="center" valign="top"> 221 </td> <td align="center" valign="top"> 222 </td> <td align="center" valign="top"> 225 </td> <td align="center" valign="top"> 226 </td> <td align="center" valign="top"> 227 </td> <td align="center" valign="top"> 228 </td> <td align="center" valign="top"> 2-3 </td> <td align="center" valign="top"> 2-6 </td> </tr> <tr><td colspan="17"><hr></td></tr><tr> <td align="left" valign="top"> H1 serotype </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> </tr> <tr> <td align="left" valign="top"> A/Duck/Alberta/35/1976 </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> T </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> A </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Duck/Alberta/35/1976 (E190D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> T </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> A </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Duck/Alberta/35/1976 (G225D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> T </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> A </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> O </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Duck/Alberta/35/1976 (E190D,G225D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> T </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> A </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> O </td> <td align="center" valign="top"> </td> </tr> <tr> <td align="left" valign="top"> H5 serotype </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> <td align="center" valign="top">
            </td> </tr> <tr> <td align="left" valign="top"> A/Duck/Singapore/Q-F119-3/1997 </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (E190D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (G225D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (E190D,G225D) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> D </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> O </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (Q226L) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> O </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (S227N) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> N </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (G228S) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> <sup>*</sup> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (Q226L,G228S) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> <sup>*</sup> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (R216E) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> ND </td> <td align="center" valign="top"> ND </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (S221P) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> R </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> </td> </tr> <tr> <td align="left" valign="top"> A/Vietnam/1203/2004 (R216E,S221P) </td> <td align="center" valign="top"> Y </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> W </td> <td align="center" valign="top"> H </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> L </td> <td align="center" valign="top"> E </td> <td align="center" valign="top"> P </td> <td align="center" valign="top"> K </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> Q </td> <td align="center" valign="top"> S </td> <td align="center" valign="top"> G </td> <td align="center" valign="top"> </td> <td align="center" valign="top"> </td></tr></tbody></table>

            Comment


            • #21
              Re: A list of relevant mutation position

              counts of occurances
              A:avian,H:human,S:swine

              Code:
               
               
              [FONT=Fixedsys]A-H1N1: YKVTWTHESLQ,25
              H-H1N1: YKVTWTHDAIQ,142
              H-H1N1: Y-VSWTHDALQ,363
              S-H1N1: YRVTWVHDSLQ,35
               
              A-H2N2: Y-GSWTHETLQ,18
              A-H2N3: Y-GSWTHETLQ,21
              H-H2N2: Y-GSWTHEALL,26
              H-H2N2: Y-GSWTHETLL,29
               
              A-H3N8: Y-GSWTHENLQ,28
              S-H3N2: Y-GSWYHENLL,38
              H-H3N2: Y-TSWTHDFLI,61
              H-H3N2: Y-GSWHHENLL,74
              H-H3N2: Y-ESWHHESLL,85
              H-H3N2: Y-KSWHHDSLI,120
              H-H3N2: Y-GSWYHENLL,124
              H-H3N2: Y-KSWHHDSLL,207
              H-H3N2: Y-TSWTHDSLI,361
              H-H3N2: Y-TSWTHDSLV,458
              H-H3N2: Y-TSWHHDSLV,1048
               
              A-H4N6: Y-KSWTHENLQ,30
               
              A-H5N1: YSVSWIHEKLQ,169
              A-H5N1: YSVSWIHERLQ,189
              A-H5N1: YLVSWIHEKLQ,220
              A-H5N2: YSVSWIHEKLQ,125
              H-H5N1: YLVSWIHERLQ,13
              H-H5N1: YLVSWIHEKLQ,20
              H-H5N1: YSVSWIHEKLQ,22
              H-H5N1: YSVSWIHERLQ,41
               
              A-H6N2: YSVTWIHENLQ,28
               
              A-H7N1: Y-TTWSHEKLQ,28
              A-H7N3: Y-ATWSHEKLQ,39
              A-H7N2: Y-ATWSHEKL-,47
              A-H7N1: Y-ATWSHEKLQ,51
               
              A-H8N4: Y-TSWTHETLQ,7
               
              A-H9N2: Y-TSWTHANLL,29
              A-H9N2: Y-TSWTNANLL,58
              A-H9N2: Y-TSWTHENLQ,66
               
              A-H10N: YATTWSHEDLQ,18
               
              A-H11N: YAVTWIHEDLQ,12
               
              A-H12N: Y-TSWTHEKLQ,9
               
              A-H15N: Y-ATWSHEKLQ,7
               
              [/FONT]
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment


              • #22
                Re: A list of relevant mutation position

                Mingus:

                I often wondered if our H5 was developing any of the 190 changes as in NY/1918/H1N1 - thanks for satisfying my curiosity. Yet, it isn't as lethal as the NY strain - why? Re the different HA cleavage schemes impacting pathogenicity?

                .
                "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


                • #23
                  Re: A list of relevant mutation position

                  counts of occurances
                  A:avian,H:human,S:swine
                  @ gsgs
                  Could you put a reference strain of each group?

                  A-H9N2: Y-TSWTNANLL,58 seems to be one the few without 179/182 H

                  Comment


                  • #24
                    Re: A list of relevant mutation position

                    Originally posted by G&#228;nseerpel
                    @ gsgs
                    Could you put a reference strain of each group?

                    A-H9N2: Y-TSWTNANLL,58 seems to be one the few without 179/182 H
                    sorry, I had missed that.

                    here they are sorted by count with representative
                    positions 98,129,131,132,149,151,179,186,189,190,222

                    Code:
                     
                    985 H-H3N2:    YNTSWHHDSLV     A/zhejiang/8/2002(H3N2)
                    443 A-H5N1:    YSVSWIHEKLQ     A/white-backed munia/Hong Kong/2469/2006(H5N1)
                    387 H-H3N2:    YNTSWTHDSLI     A/Zhejiang/550/04(H3N2)
                    379 H-H3N2:    YNTSWTHDSLV     A/Zhejiang/95/03(H3N2)
                    370 H-H1N1:    YTVSWTHDALQ     A/Wyoming/4/2003(H1N1)
                    308 A-H5N1:    YLVSWIHEKLQ     A/wild bird/Vietnam/434/2005(H5N1)
                    209 H-H3N2:    YDKSWHHDSLL     A/Wyoming/1/93(H3N2)
                    203 A-H5N1:    YSVSWIHERLQ     A/wild duck/Shanghai/59/04(H5N1)
                    147 H-H1N1:    YKVTWTHDAIQ     A/Yokohama/24/2000(H1N1)
                    126 A-H5N2:    YSVSWIHEKLQ     A/wigeon/Ohio/379/1988(H5N2)
                    121 H-H3N2:    YDKSWHHDSLI     A/West_Virginia/1/95(H3N2)
                      91 H-H3N2:    HNTSWTHDSLV     A/Western Australia/46/2003(H3N2)
                      91 A-H5N1:    YLVSWIHERLQ     A/tree sparrow/HK/864/2002(H5N1)
                      89 H-H3N2:    YSGSWYHENLL     A/Yokohama/C5/85(H3N2)
                      85 H-H3N2:    YSESWHHESLL     A/Washington/15/91(H3N2)
                      83 H-H3N2:    YDTSWHHDSLV     A/Yokohama/68/96(H3N2)
                      72 H-H3N2:    YSGSWHHENLL     A/Yamaneshi/497(H3N2)
                      66 H-H3N2:    YNTSWTHDFLI     A/Zhejiang/209/05(H3N2)
                      58 A-H9N2:    LSTSWTNANLL     A/Silky Chicken/Hong Kong/SF44/99(H9N2)
                      54 E-H3N8:    YNRSWTHEKLQ     A/Equine/Yvelines/2136/89(H3N8)
                      51 H-H1N1:    YTVSWTHNALQ     A/Yokohama/62/2002(H1N1)
                      50 H-H5N1:    YSVSWIHERLQ     A/Indonesia/CDC742/2006(H5N1)
                      48 H-H3N2:    YDGSWHHDSLQ     A/Yokohama/73/92(H3N2)
                      45 A-H7N2:    ENATWNHEKL-     A/turkey/VA/67/02(H7N2)
                      43 A-H7N1:    ENATWNHEKLQ     A/turkey/Italy/977/99 (H7N1)
                      42 H-H1N2:    YTVSWTHDTLQ     A/Yokohama/47/2002(H1N2)
                      40 H-H3N2:    -NTSWHHDSLV     A/Zaragoza/RR658/00(H3N2)
                      40 A-H7N7:    ENATWNHEKLQ     A/turkey/Northern Ireland/VF-1545 C5/98(H7N7)
                      40 A-H7N3:    ENATWNHEKLQ     A/widgeon/ALB/284/1977(H7N3)
                      39 H-H3N2:    YNTSWHHDSLI     A/Wellington/34/2001(H3N2)
                      38 H-H3N2:    YDGSWHHDSLL     A/Wuzhou/4/93(H3N2)
                      36 S-H1N1:    YKATWVHDSLQ     A/swine/St. Anthonis/16F/96(H1N1)
                      36 A-H9N2:    LSTSWTHENLQ     A/Turkey/Pavia/40/83(H9N2)
                      36 A-H4N6:    YNKSWKHENLQ     A/ruddy turnstone/NJ/47/1985(H4N6)
                      35 S-H1N1:    YRVTWVHDSLQ     A/Swine/Wisconsin/458/98(H1N1)
                      33 A-H7N1:    ENTTWNHEKLQ     A/turkey/Italy/984/99 (H7N1)
                      32 H-H3N2:    YNGSWYHENLL     A/Yamagata/96/85(H3N2)
                      31 H-H1N1:    YKVTWTHDTIQ     A/Ohio/101/1983(H1N1)
                      30 H-H3N2:    YDKSWHHDSLQ     A/Wuzhou/1/94(H3N2)
                      29 A-H9N2:    LTTSWTHANLL     A/turkey/Tzur Moshe/1565/04(H9N2)
                      29 A-H5N3:    YSVSWIHEKLQ     A/tern/South Africa/1961(H5N3)
                      29 A-H3N8:    YNGSWTHENLQ     A/pintail/Ohio/454/1987(H3N8)
                      28 S-H3N2:    YNGSWYHENLL     A/Swine/Wisconsin/194/80(H3N2)
                      28 H-H2N2:    YTGSWTHETLL     A/Yokosuka/3/62(H2N2)
                      28 A-H9N2:    LTTSWTHENLQ     A/turkey/Yedidia/911/02(H9N2)
                      26 A-H1N1:    YKVTWTHESLQ     A/turkey/Minnesota/1661/81(H1N1)
                      25 H-H1N1:    YRVTWTHDTIQ     A/USSR/92/77(H1N1)
                      24 H-H3N2:    YNGSWTHESLL     A/Northern Territory/1960(H3N2)
                      24 H-H1N1:    YTVSWTHDAIQ     A/Yokohama/50/1998(H1N1)
                      23 S-H1N2:    YRVTWVHDSLQ     A/Swine/Ohio/891/01(H1N2)
                      23 H-H5N1:    YLVSWIHEKLQ     A/Viet Nam/DN-33/2004(H5N1)
                      23 H-H2N2:    YTGSWTHEALL     A/Taiwan/1964(H2N2)
                      23 A-H9N2:    LSTSWTNVNLL     A/wild duck/Nanchang/2-0480/2000(H9N2)
                      22 H-H5N1:    YSVSWIHEKLQ     A/Indonesia/CDC759/2006(H5N1)
                      22 H-H3N2:    YNGSWYHESLL     A/Udorn/72(H3N2)
                      22 A-H9N2:    LSTSWTNVNLQ     A/Wild Duck/Shantou/4808/01(H9N2)
                      22 A-H9N2:    LSTSWTNANLQ     A/Chicken/Yunnan/1/99(H9N2)
                      21 H-H1N2:    YTVSWTHNTLQ     A/Wisconsin/12/2001(H1N2)
                      21 A-H2N3:    YTGSWTHETLQ     A/Silky chicken/PA/9600897/96 (H2N3)
                      20 A-H10N:    EATTWKHEDLQ     A/Shorebird/Taiwan/31-4/99)]
                      19 H-H3N2:    YSDSWHHESLL     A/Umea/2000/92(H3N2)
                      19 H-H3N2:    YNTSWTHDNLV     A/Zhejiang/80/03(H3N2)
                      19 A-H2N2:    YTGSWTHETLQ     A/Pintail/Praimoric/625/76 (H2N2)
                      17 H-H3N2:    YNGSWYHEDLL     A/Rotterdam/8179/77(H3N2)
                      17 H-H3N2:    YDTSWHHDSLI     A/Washington/5/96(H3N2)
                      17 A-H6N2:    TSVTWKHENLQ     A/shoveler/ALB/114/1985(H6N2)
                      16 H-H3N2:    YNTSWTHDSLX     A/New York/473/2003(H3N2)
                      16 H-H1N1:    YTVSWTHDAL-     A/Taiwan/3896/2001 (H1N1)
                      16 A-H6N8:    TSVTWKHENLQ     A/Redhead/Alberta/291/94(H6N8)
                      15 H-H5N1:    YLVSWIHERLQ     A/Thailand/NKNPHA/2005(H5N1)
                      15 H-H3N2:    YNTSWHHDSIV     A/Zhangzhou/51/1999(H3N2)
                      15 A-H6N2:    VSVTWKHETLQ     A/turkey/Germany/R26/99(H6N2)
                      14 A-H11N:    EAVTWIHEDLQ     A/swan/Shimane/48/1997(H11N2)
                      13 S-H3N2:    YNTSWHHDSLV     A/swine/Hong Kong/q066/99(H3N2)
                      13 S-H1N1:    YKVTWVHDSLQ     A/swine/Taichung/200-8/2002(H1N1)
                      13 A-H9N2:    LSTSWTNTNLQ     A/duck/Zhejiang/03/2001(H9N2)
                      13 A-H7N2:    ENATWNHEKLQ     A/Turkey/New York/4450-5/94 (H7N2)
                      13 A-H6N1:    VSVTWKHETLQ     A/turkey/Germany/R30/99(H6N1)
                      13 A-H4N2:    YNKSWKHENLQ     A/turkey/Minnesota/833/1980(H4N2)
                      12 H-H3N2:    YNDSWHHESLL     A/Wellington/66/92(H3N2)
                      12 H-H1N1:    YTVSWTHVAIQ     A/Nanchang/9/1996(H1N1)
                      12 H-H1N1:    YKVTWTHDAI-     A/human/Taiwan/2200/95(H1N1)
                      12 A-H6N5:    VSVTWKHETLQ     A/turkey/Germany/R43/98(H6N5)
                      12 A-H4N8:    YNKSWKHENLQ     A/red-necked stint/Australia/4189/1980(H4N8)
                      11 A-H5N1:    YSVSWIHERIQ     A/Duck/Hunan/191/05(H5N1)
                      11 A-H3N2:    YNGSWTHENLQ     A/pintail duck/ALB/86/1976(H3N2)
                      10 S-H1N2:    YKVTWTHDAIQ     A/swine/IDT/Bakum1832/2000(H1N2)
                      10 H-H2N2:    YTGSWTHETLQ     A/RI/5-/57 (H2N2)
                      10 H-H1N1:    YRVTWTHDTLQ     A/Marton/43(H1N1)
                      10 A-H9N2:    LTTSWTHENLL     A/turkey/Yedidia/625/02 (H9N2)
                      10 A-H6N8:    VSVTWKHETLQ     A/turkey/France/01062/2001(H6N8)
                      10 A-H6N2:    VSVSWKHETLQ     A/duck/Hong Kong/3600/99 (H6N2)
                      10 A-H5N9:    YSVSWIHEKLQ     A/mallard/Sweden/80/02(H5N9)
                      10 A-H2N9:    YTGSWTHETLQ     A/teal/Alberta/16/97(H2N9)
                    Code:
                     
                    [FONT=Fixedsys]
                    [/FONT]

                    Last edited by gsgs; November 11, 2006, 10:15 AM.
                    I'm interested in expert panflu damage estimates
                    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                    Comment


                    • #25
                      Re: A list of relevant mutation position

                      here is a table with a largerly interpreted receptor binding domain (RBD).

                      RBD in HA in flu-A-viruses
                      amino-positions 98(?),132-136,151-153,183-195,216-228 in HA
                      (sequences with less than 5 counts are deleted, unless they are
                      unique in the group)



                      Code:
                       
                        species serotype
                        count | |   98 132-6 151-3   183-195       216-228     representative
                      --------------------------------------------------------------------------------------
                          9 A-H01:   Y GVTAA WIT HHPPTTSEQQSLY EIAARPKVRGQAG  A/turkey/Minnesota/1661/81(H1N1)
                       
                                     ....S.S..L......NIGD.RA......K.....D.E.
                        326 H-H01:   Y GVSAS WLT HHPPNIGDQRALY EIAKRPKVRDQEG  A/Wyoming/4/2003(H1N1)
                         65 H-H01:   . ..T.. ... ...S.......I. .............  A/Switzerland/5389/95 (H1N1)
                         44 H-H01:   . ..... ... .......N..... .............  A/Yokohama/62/2002(H1N1)
                         35 H-H01:   . ..... ... ..........T.. ..T..........  A/Scotland/15/02(H1N2)
                         26 H-H01:   . ..T.. ... ...S..E..KTI. .........N...  A/Ohio/201/1983(H1N1)
                         22 H-H01:   . ..... ... .........K... .............  A/New York/4/2006(H1N1)
                         17 H-H01:   . ..T.. ... ...S..E..KTI. ...E.....G.A.  A/USSR/92/77(H1N1)
                         16 H-H01:   . ..T.. ... ...S.......I. .........G...  A/Taiwan/01/1986(H1N1)
                         14 H-H01:   . ..T.. ... ...S.M.....I. .............  A/Yokohama/24/2000(H1N1)
                         13 H-H01:   . ..... ... .......N..T.. ..T..........  A/Switzerland/3100/2002(H1N2)
                          8 H-H01:   . ..... ... .......N..T.. .............  A/Wisconsin/12/2001(H1N2)
                          8 H-H01:   . ..T.. ... ...S.......I. ..T..........  A/New York/694/1995(H1N1)
                          7 H-H01:   . ..... ... ..........T.. .............  A/Yokohama/47/2002(H1N2)
                          7 H-H01:   . ..... ... ...S...V...I. .........G...  A/Nanchang/9/1996(H1N1)
                          7 H-H01:   . ..T.. ... ...S..R....I. .............  A/Suita/1/89/(R)(H1N1)
                          7 H-H01:   . ..T.. ... ...S.M.....I. ...R.........  A/South Australia/64/2000(H1N1)
                          5 H-H01:   . ..... ... .......B..... .............  A/Wellington/18/2000(H1N1)
                          5 H-H01:   . ..... ... ...S.......I. .............  A/Singapore/15/96(H1N1)
                          5 H-H01:   . ..... ... ...S...V...I. .............  A/Nanchang/17/1996(H1N1)
                          5 H-H01:   . ..T.A ... ...S..E..KT.. ...E.....G.A.  A/Rhodes/47(H1N1)
                          5 H-H01:   . ..T.. ... ...S..E..KTI. .............  A/Memphis/7/1980(H1N1)
                       
                                     ...AT.A..IV.....TSN..QS......A.....G.A.
                         11 S-H01:   Y GATAA WIV HHPPTSNDQQSLY EIAARPKVRGQAG  A/swine/Nederweert/13O/96(H1N1)
                         11 S-H01:   . .V... .L. ......T...... .............  A/swine/Wisconsin/1/61(H1N1)
                         10 S-H01:   . ..... ... .....N....... .............  A/Swine/Netherlands/477/93(H1N1)
                          6 S-H01:   . .V... .L. ......T...... ...T.........  A/Swine/Indiana/1726/1988(H1N1)
                          6 S-H01:   . .V... .L. ...S..A...... ...T.....D...  A/Swine/Ohio/891/01(H1N2)
                          5 S-H01:   . ..... ... ......S...... ...........T.  A/swine/Best/5R/96(H1N1)
                          5 S-H01:   . .V... .L. ......T...... ...S.........  A/Swine/Wisconsin/457/98(H1N1)
                       
                                     ...GSR...LT....NDDTE.RT......T....N..G.
                         12 A-H02:   Y GGSRA WLT HHPNDDTEQRTLY EIATRPKVNGQGG  A/Pintail duck/Alberta/293/77 (H2N3)
                          6 A-H02:   . ..... ... .....E....... .............  A/mallard/Potsdam/178-4/83 (H2N2)
                          5 A-H02:   . ..... ... ......A...... .............  A/Silky chicken/PA/9600897/96 (H2N3)
                       
                                     .....K...........EA...A......A......L.S
                          5 H-H02:   Y GGSKA WLT HHPNDEAEQRALY EIAARPKVNGLGS  A/Taiwan/1/67(H2N2)
                       
                                     .....N.........STNQ..TN...N.GS..W.R.QSG
                         15 A-H03:   Y GGSNA WLT HHPSTNQEQTNLY NIGSRPWVRGQSG  A/pintail duck/ALB/169/1980(H3N8)
                          6 A-H03:   . ..... ... ............. .............  A/pintail duck/ALB/86/1976(H3N2)
                          5 A-H03:   . ...G. ... ..........T.. ......L......  A/duck/Korea/S9/03(H3N2)
                       
                                     ...R.G..........S.....K.........L......
                          3 C-H03:   Y GRSGA WLT HHPSSNQEQTKLY NIGSRPLVRGQSG  A/canine/Texas/1/2004(H3N8)
                       
                                     ................................W......
                         16 E-H03:   Y GRSGA WLT HHPSSNQEQTKLY NIGSRPWVRGQSG  A/equine/Wisconsin/1/03(H3N8)
                         15 E-H03:   . ..... ... ......K...... .............  A/equine/Suffolk/89(H3N8)
                          8 E-H03:   . ..... ... ......N...... .............  A/Equine/LaPlata/1/93(H3N8)
                          8 E-H03:   . ..... ... .......Q..E.. .............  A/equine/Oklahoma/2000(H3N8)
                       
                                     ...T.S....H.....TDSD.IS.............V.S
                        323 H-H03:   Y GTSSA WLH HHPSTDSDQISLY NIGSRPWVRGVSS  A/Western Australia/9/2000(H3N2)
                        262 H-H03:   . ..... ..T ...G......... ......R..D...  A/Western Australia/50/2003(H3N2)
                        262 H-H03:   . ...Y. ... .........T... .............  A/Yokohama/68/96(H3N2)
                        222 H-H03:   . ..... ..T ...G..N...... ......R..DIP.  A/Zhejiang/546/04(H3N2)
                        209 H-H03:   . ..... ... ...G......... .............  A/Western Australia/36/2002(H3N2)
                        109 H-H03:   . .K.Y. ... .........T... ..........I..  A/West_Virginia/1/95(H3N2)
                         89 H-H03:   H ..... ..T ...G......... ......R..D...  A/Western Australia/46/2003(H3N2)
                         89 H-H03:   . ..... ... .........T... .............  A/zhejiang/06/99(H3N2)
                         72 H-H03:   . .E.Y. ... ......RE.T... ..........L..  A/Victoria/2/90(H3N2)
                         67 H-H03:   . .K.Y. ... .........T... ..........L..  A/Wellington/59/93(H3N2)
                         65 H-H03:   . ..... ..T ...G.YN...... ......R..DIP.  A/Western Australia/78/2005(H3N2)
                         58 H-H03:   . .K.Y. ... .........T... ...F......L..  A/Pennsylvania/9/93(H3N2)
                         57 H-H03:   . ..... ..T ...G..N...F.. ......R..NIP.  A/Zhejiang/209/05(H3N2)
                         57 H-H03:   . ..... ..T ...G..N...... ......R..D.P.  A/Zhejiang/95/03(H3N2)
                         45 H-H03:   . .K.Y. ... .........T... D..Y......L..  A/Texas/5/94(H3N2)
                         44 H-H03:   . .G.Y. ..Y ......KE.TN.. ..........L..  A/Wellington/4/85(H3N2)
                         44 H-H03:   . ..... ..T ...G.NN...... ......R..DIP.  A/Whanganui/69/2004(H3N2)
                         38 H-H03:   . .G.Y. ... .........T... ..........Q..  A/Yokohama/73/92(H3N2)
                         36 H-H03:   . .G.Y. ... ......RE.TN.. ..........L..  A/Wellington/5/89(H3N2)
                         35 H-H03:   . ..... ... ...G......... ......R..D...  A/zhejiang/8/2002(H3N2)
                         32 H-H03:   . .G.Y. ... .........T... ..........L..  A/Wuzhou/4/93(H3N2)
                         29 H-H03:   . ..... ... ...G......... ....G........  A/New York/97/2002(H3N2)
                         27 H-H03:   . ...Y. ... .........T... ..........I..  A/Washington/5/96(H3N2)
                         25 H-H03:   . ...F. ... .........T... .............  A/Zhejiang/18/98(H3N2)
                         24 H-H03:   . .D.Y. ... ......RE.T... ..........L..  A/Wellington/66/92(H3N2)
                         22 H-H03:   . .G.N. ..T .....NQE.T... ..........L..  A/Northern Territory/1960(H3N2)
                         21 H-H03:   . .G.N. ..Y ......QE.T... ..........L..  A/Udorn/72(H3N2)
                         18 H-H03:   . .G.Y. ... ...I..RE.TN.. ..........L..  A/Tokyo/1276/(H3N2)
                         15 H-H03:   . ..... ..T ...G......... ......R..DI..  A/Western Australia/58/2004(H3N2)
                         14 H-H03:   . .G.Y. ... ......R..T... ..........Q..  A/Shanghai/24/90(H3N2)
                         13 H-H03:   . .G.Y. ..Y ......KE.TN.. ...P......L..  A/Stockholm/4/(H3N2)
                         13 H-H03:   . ..... ..T ...G......N.. ......R..D.P.  A/Zhejiang/80/03(H3N2)
                         12 H-H03:   . .G... ..Y ......KE.TD.. .V........L..  A/Rotterdam/5828/77(H3N2)
                         12 H-H03:   . ..... ..T ...G......... ......R..D.P.  A/Zhejiang/92/03(H3N2)
                         11 H-H03:   . .G.Y. ..Y ......KE.TN.. .V........L..  A/Texas/1/77(H3N2)
                         11 H-H03:   . .K.Y. ... .........T... ..........Q..  A/Wuzhou/1/94(H3N2)
                         11 H-H03:   . ..... ... ...G......... ......R..DI..  A/StaCatarina/327/02(H3N2)
                         10 H-H03:   . ..... ..T ...G..N...... ......R..D...  A/Singapore/C5-14/2003(H3N2)
                         10 H-H03:   . ...Y. ... .........T.I. ..........I..  A/zhejiang/10/98(H3N2)
                          9 H-H03:   . .E.Y. ... ...I..RE.T... ..........L..  A/Washington/15/91(H3N2)
                          9 H-H03:   . .G.N. ..Y ......QE.TN.. ..........L..  A/Port Chalmers/73(H3N2)
                          9 H-H03:   . ..... ..T ...G..N..T... ......R..DIP.  A/Waikato/2/2005(H3N2)
                          9 H-H03:   . ..... ..T ...G......... ......R..DX..  A/New York/473/2003(H3N2)
                          8 H-H03:   . ..... ... .........T... ..........I..  A/Shenzhen/157/96(H3N2)
                          7 H-H03:   . .K.Y. ... .........T... ...F......Q..  A/Vermont/3/94(H3N2)
                          7 H-H03:   . .K.YS ... .........T... D..Y......L..  A/Spain/378/95(H3N2)
                          7 H-H03:   . ...F. ... ...G.....T... .............  A/Virginia/21817/99(H3N2)
                          7 H-H03:   . ..... ..T ...G..N...... S.....RI.D.P.  A/Turkey/2108/2005(H3N2)
                          7 H-H03:   . ...Y. ... .........T.I. .............  A/Wuzhou/19/96(H3N2)
                          6 H-H03:   . .G.Y. ..Y .....EKE.TN.. ..........L..  A/Yokohama/C5/85(H3N2)
                          6 H-H03:   . .G.YT ..Y ......KE.TN.. ..........L..  A/Memphis/7/85(H3N2)
                          6 H-H03:   . ..... ... ............. ....G........  A/South Australia/71/2000(H3N2)
                          6 H-H03:   . ..... ..T ...G..N...F.. S.....R..NIP.  A/Sri Lanka/146/2005(H3N2)
                          6 H-H03:   . ..... ..T ...G..N...... ......R..DI..  A/Zhejiang/550/04(H3N2)
                          5 H-H03:   . .K.Y. ... .........T... D..Y......Q..  A/Paris/363/95(H3N2)
                          5 H-H03:   . .K.YS ... .........T... ...F......L..  A/Washington/41/93(H3N2)
                          5 H-H03:   . .K.YS ... .........T... ..........L..  A/Stockholm/1/93(H3N2)
                          5 H-H03:   . .K.YT ... .........T... ..........L..  A/Wyoming/1/93(H3N2)
                       
                                     H..G.N....Y.......RE..N....V........L..
                          6 S-H03:   H GGSNA WLY HHPSTDREQINLY NVGSRPWVRGLSS  A/swine/Hong Kong/9745/01(H3N2)
                          6 S-H03:   Y ...S. ... ............. .............  A/Swine/Spain/39139/2002(H3N2)
                          6 S-H03:   Y ...YS ..H ......S..TS.. .I........I..  A/Swine/Texas/4199-2/98(H3N2)
                          6 S-H03:   Y .S.Y. ..H ...G...D.T... .I........V..  A/swine/Quebec/Biovet1/05(H3N2)
                          6 S-H03:   Y .T.Y. ..H ......SD.TS.. .I........V..  A/Swine/Wisconsin/14094/99(H3N2)
                       
                                     Y..K.G....K.......T..T.....I........Q.G
                         28 A-H04:   Y GKSGA WLK HHPSTDTEQTNLY NIGSRPWVRGQSG  A/pintail/Alberta/269/2001(H4N6)
                         12 A-H04:   . ..... ... ............. .............  A/turkey/Minnesota/833/1980(H4N2)
                         10 A-H04:   . ..... ... ............. .............  A/pintail duck/ALB/220/1977(H4N8)
                       
                                     ....................................L.S
                          2 S-H04:   Y GKSGA WLK HHPSTDTEQTNLY NIGSRPWVRGLSS  A/Swine/Ontario/01911-2/99 (H4N6)
                       
                                     ...V.S....I...SNDAA...K...K.AT.SK.N.Q.G
                        250 A-H05:   Y GVSSA WLI HHSNDAAEQTKLY KIATRSKVNGQSG  A/white-backed munia/Hong Kong/2469/2006(H5N1)
                        204 A-H05:   . ..... ... ..P.......... R............  A/white peafowl/Bangkok/Thailand/CU-29/04(H5N1)
                        202 A-H05:   . ..... ... ..P.......R.. .............  A/wild duck/Shanghai/59/04(H5N1)
                        119 A-H05:   . ..... ... ..P.......... .............  A/tree sparrow/Henan/4/2004(H5N1)
                         40 A-H05:   . ..... ... ..P.NE....R.. .............  A/grey heron/Hong Kong/837/2004(H5N1)
                         38 A-H05:   . ..... ... ..P.......... E....P.......  A/Silky Chicken/Hong Kong/p17/97 (H5N1)
                         33 A-H05:   . ..... ... ..P......I... E....P.......  A/chicken/Taiwan/1209/03(H5N2)
                         32 A-H05:   . ..... ... ..P.......... E....P.......  A/wigeon/Ohio/379/1988(H5N2)
                         30 A-H05:   . ..... ... ..P......I... .............  A/tree sparrow/Henan/3/2004(H5N1)
                         28 A-H05:   . ..... ... ..P.......... E....P.......  A/tern/South Africa/1961(H5N3)
                         28 A-H05:   . ..... ... ..P..E....R.. .............  A/quail/Viet Nam/15/2005(H5N1)
                         13 A-H05:   . ..... ... ..P......I... T............  A/goose/Guiyang/337/2006(H5N1)
                         11 A-H05:   . ..... ... ..P.......RI. .............  A/Duck/Hunan/191/05(H5N1)
                         10 A-H05:   . ..... ... ..P.......... E....P.......  A/mallard/Sweden/80/02(H5N9)
                         10 A-H05:   . ..... ... ..P.NE....... .............  A/goose/Guangxi/3714/2005(H5N1)
                          7 A-H05:   . ...A. ... ..P.......... R............  A/wild bird/Vietnam/434/2005(H5N1)
                          7 A-H05:   . ..... ... ..P.......... E....PR......  A/duck/NY/44018-2/00(H5N2)
                          6 A-H05:   . ...A. ... ..P.......... .............  A/slaty-backed gull/Shandong/59/04(H5N1)
                          6 A-H05:   . ..... ... ..P......A... I....P.......  A/Chicken/Pennsylvania/10210/86(H5N2)
                          6 A-H05:   . ..... ... ..P......A... .....P.......  A/Turkey/Virginia/6962/83(H5N2)
                          6 A-H05:   . ..... ... .........I... .............  A/goose/Shantou/11989/2006(H5N1)
                          6 A-H05:   . ..... ... ............. .....PQ....R.  A/chicken/Guatemala/45511-5/00 (H5N2)
                          5 A-H05:   . ..... ... ..P...T...... .............  A/goose/Guiyang/3610/2005(H5N1)
                          5 A-H05:   . ..... ... ..P.N.E...... ......R......  A/Goose/Hong Kong/ww491/2000(H5N1)
                       
                                     ..............P...........R............
                          2 C-H05:   Y GVSSA WLI HHPNDAAEQTKLY RIATRSKVNGQSG  A/dog/Thailand-Suphanburi/KU-08/04(H5N1)
                       
                                     ..........................E....P.......
                          3 E-H05:   Y GVSSA WLI HHPNDAAEQTKLY EIATRPKVNGQSG  A/environment/NY/5626-2/98(H5N2)
                       
                                     ......................R...K....S.......
                          1 F-H05:   Y GVSSA WLI HHPNDAAEQTRLY KIATRSKVNGQSG  A/feline/Indonesia/CDC1/2006(H5N1)
                       
                                     .......................................
                         46 H-H05:   Y GVSSA WLI HHPNDAAEQTRLY KIATRSKVNGQSG  A/Indonesia/CDC742/2006(H5N1)
                         18 H-H05:   . ..... ... ..........K.. R............  A/Viet Nam/DN-33/2004(H5N1)
                         17 H-H05:   . ..... ... ..........K.. E....P.......  A/Hong Kong/486/97(H5N1)
                       
                                     ......................K...R............
                          1 L-H05:   Y GVSSA WLI HHPNDAAEQTKLY RIATRSKVNGQSG  A/leopard/Suphanburi/Thailand/Leo-1/04(H5N1)
                       
                                     ..........................K............
                          2 S-H05:   Y GVSSA WLI HHPNDAAEQTKLY KIATRSKVNGQSG  A/swine/Fujian/F1/2001(H5N1)
                       
                                     ..........................R............
                          8 T-H05:   Y GVSSA WLI HHPNDAAEQTKLY RIATRSKVNGQSG  A/tiger/Thailand/SPB-1(H5N1)
                       
                                     ..........................E....P.......
                          2 U-H05:   Y GVSSA WLI HHPNDAAEQTKLY EIATRPKVNGQSG  A/unknown/NY/118547-11/01(H5N2)
                       
                                     T...T....IK....P.EV..AN......D..PA...R.
                         13 A-H06:   T GVTSA WIK HHPPDEVEQANLY EIADRPPANGQRG  A/Redhead/Alberta/291/94(H6N8)
                         10 A-H06:   V ..S.. ... .....TN..NT.. ...A..AV.....  A/duck/Hong Kong/3600/99 (H6N2)
                          9 A-H06:   . ..... ... ............. .............  A/pintail/Ohio/351/1987(H6N2)
                          9 A-H06:   V ...K. ... .....TN..NT.. ...A..AV.....  A/turkey/Germany/R30/99(H6N1)
                          9 A-H06:   V ...N. ... .....TTV.D... ...A..AV....S  A/duck/Taiwan/WB239/03(H6N1)
                          8 A-H06:   V ...K. ... .....TN..NT.. ...A..AV.....  A/Pekin Duck/France/M-92/00(H6N2)
                          7 A-H06:   V .T.RS ... ....NTD..DT.. ...A..AV.....  A/Teal/Hong Kong/W312/97(H6N1)
                          7 A-H06:   V ...K. ... .....TN..NT.. ...A..AV.....  A/turkey/France/01062/2001(H6N8)
                          7 A-H06:   V ...K. ... .....TN..NT.. ...A..AV.....  A/turkey/Germany/R43/98(H6N5)
                          6 A-H06:   I ...R. ... .....TDA.N... ...A..VV.....  A/chicken/California/905/01(H6N2)
                          6 A-H06:   V ...N. ... .....TTV.DT.. ...A..AV....S  A/chicken/Taiwan/1215/01(H6N1)
                          5 A-H06:   I ...R. ... .....TNA.N... ..SA..VV.....  A/Chicken/California/6643/2001(H6N2)
                          5 A-H06:   M ..... ... .....DN...... ...S...V.....  A/pintail duck/ALB/133/1978(H6N2)
                          5 A-H06:   . ..... ... ............. .............  A/mallard duck/ALB/76/1985(H6N3)
                          5 A-H06:   . ..... ... ............. .......V.....  A/widgeon/ALB/256/1982(H6N6)
                       
                                     E..T..T..LN...SGSTT..TK...SPGE..QV...S.
                         22 A-H07:   E GTTST WLN HHSGSTTEQTKLY SPGERPQVNGQSG  A/turkey/Italy/5074/99 (H7N1)
                         20 A-H07:   . .A..A ... ............. ...A.........  A/turkey/Germany/R11/01(H7N7)
                         20 A-H07:   . .A..A ... ............. ...A.........  A/turkey/Italy/977/99 (H7N1)
                         15 A-H07:   . .A..A ... ............. ...A.........  A/turkey/Oregon/1971(H7N3)
                         14 A-H07:   . .A..A ... .....A....... ...A.........  A/Turkey/Colorado/13356/91 (H7N3)
                          8 A-H07:   . .A.NA ... ............. ...A.........  A/Mallard/Sweden/93/02(H7N7)
                          7 A-H07:   . .A..A ... .....VS...... ...A.........  A/Chicken/Rhode Island/4328/95 (H7N2)
                          6 A-H07:   . .V..A ... .....AN...... ...A.........  A/turkey/Chile/4418/02(H7N3)
                          5 A-H07:   . ....A ... ............. ...A.........  A/turkey/Italy/4857/99 (H7N1)
                          5 A-H07:   G .A..A ... ......A...... ...A.........  A/parrot/England/1174/94(H7N1)
                       
                                     ...E..A...........A...R...N..P...I.....
                          6 E-H07:   E GETSA WLN HHSGSTAEQTRLY NPGPRPQINGQSG  A/equine/Sao Paulo/1/76(H7N7)
                       
                                     ...A.............AT...K...S..A...V.....
                          1 H-H07:   E GATSA WLN HHSGSATEQTKLY SPGARPQVNGQSG  A/Canada/rv504/2004(H7N3)
                       
                                     ...T.............T....R................
                          1 S-H07:   E GTTSA WLN HHSGSTTEQTRLY SPGARPQVNGQSG  A/seal/Mass/1/80(H7N7)
                       
                                     L...SK....K...PPD.K...T...NI.P..L.R..Q.
                          7 A-H08:   L GTSKA WLK HHPPDTKEQTTLY NIGPRPLVRGQQG  A/Turkey/Ontario/6118/68(H8N4)
                       
                                     ..........T.N...TDTA..N...L.......N.L..
                         40 A-H09:   L GTSKA WLT NHPPTDTAQTNLY LIGPRPLVNGLQG  A/Silky Chicken/Hong Kong/SF44/99(H9N2)
                         22 A-H09:   . ..... ... H......E..... V.........Q..  A/turkey/Yedidia/911/02(H9N2)
                         17 A-H09:   . ..... ... .......V..... .............  A/wild duck/Nanchang/2-0480/2000(H9N2)
                         16 A-H09:   . ..... ... H............ V......A.....  A/turkey/Tzur Moshe/1565/04(H9N2)
                         14 A-H09:   . ..... ... H......E.M... V.........Q..  A/silky chicken/Korea/S3/03(H9N2)
                         11 A-H09:   . ..... ... .......V..... ..........Q..  A/duck/Hubei/W1/2004(H9N2)
                         10 A-H09:   . ..... ... H............ V............  A/turkey/Kfar Vitkin/616/02 (H9N2)
                          9 A-H09:   . ..... ... ............. V.........Q..  A/chicken/Shandong/7/96(H9N2)
                          8 A-H09:   . ..... ... ............. M.........Q..  A/Chicken/Shanghai/F/98(H9N2)
                          6 A-H09:   . ..... ... ............. V............  A/quail/Nanchang/2-0460/2000(H9N2)
                          6 A-H09:   . ..... ... .......T..... .............  A/Quail/Shanghai/8/96(H9N2)
                          6 A-H09:   . ..... ... .......V..... V.........Q..  A/Chicken/Sichuan/5/97(H9N2)
                          6 A-H09:   . ...R. ... H......E..... V.........Q..  A/turkey/Germany/R33/96(H9N2)
                          6 A-H09:   . ...R. ... H....Y.E..... V............  A/Quail/Hong Kong/SSP10/99(H9N2)
                          5 A-H09:   . ..... ... H.....AE..... V.........Q..  A/mallard/Alberta/743/83(H9N1)
                          5 A-H09:   . ..... ... H............ V.........Q..  A/chicken/United Arab Emirates/AG537/99(H9N2)
                          5 A-H09:   . ..... ... H......E.I... V.....P...Q..  A/chicken/SNU0146/2000(H9N2)
                          5 A-H09:   . ..... ... .......T..... ..........Q..  A/chicken/Yunnan/Xie-1/1999(H9N2)
                          5 A-H09:   . ..... ... .......T..... V.........Q..  A/duck/Nanjing/2/97(H9N2)
                          5 A-H09:   . ...R. ... .......V..E.. M.........Q..  A/Chicken/Shijiazhuang/2/99(H9N2)
                       
                                     .....R......H....Y.E......V............
                          3 H-H09:   L GTSRA WLT HHPPTYTEQTNLY VIGPRPLVNGLQG  A/Hong Kong/1074/99(H9N2)
                       
                                     .....K...........D...M..............Q..
                          4 S-H09:   L GTSKA WLT HHPPTDTEQMNLY VIGPRPLVNGQQG  A/swine/Korea/S83/2004(H9N2)
                       
                                     E...T.....K....SSTQ.KND....V.A..Q....S.
                         17 A-H10:   E GTTKA WLK HHPSSTQEKNDLY VVGARPQVNGQSG  A/Shorebird/Taiwan/31-4/99)]
                       
                                     ............................R..........
                          1 M-H10:   E GTTKA WLK HHPSSTQEKNDLY VVRARPQVNGQSG  /Mink/4(HA)/H10N4/Sweden/1984
                       
                                     ...V.A....I....ATLK.HQ....EIST..K....A.
                         12 A-H11:   E GVTAA WLI HHPATLKEHQDLY EISTRPKVNGQAG  A/swan/Shimane/48/1997(H11N2)
                       
                                     Q..TSK....T....P.SD.QVK...N.GP..L.R..Q.
                          6 A-H12:   Q GTSKA WLT HHPPTSDEQVKLY NIGPRPLVRGQQG  A/ruddy turnstone/DE/97/2000(H12N5)
                       
                                     N...TS...FI....VSV..TKT...ET.V..GYN..RS
                          3 A-H13:   N GTTSA WFI HHPVSVDETKTLY ETGVRPGYNGQRS  A/Gull/Maryland/704/77(H13N6)
                       
                                     Y..SS....LK....S.DN.QTD...NI.S..RVRN.SG
                          1 A-H14:   Y GSSSA WLK HHPSSDNEQTDLY NIGSRPRVRNQSG  A/mallard duck/Astrakhan/263/1982(H14N5)
                       
                                     E..AT.....S...S..LD..NK...SP.A..K.NG.A.
                          5 A-H15:   E GATSA WLS HHSSSLDEQNKLY SPGARPKVNGQAG  A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)


                      RBD in human H5N1 is still almost the same as avian.
                      Same for canine,swine,feline H5N1.

                      This is clearly different from H1 or H3 and maybe also H2,H4
                      but less clearly since fewer sequences are available here.

                      For H1 and H3 you can see, how the human RBD differs from the
                      avian and the swine RBD is inbetween human and avian wrt.this aspect.

                      The reason could be, that H5 had not yet had enough
                      opportunity to evolve in mammals over several generations.
                      Or, that H5 is just not capable to well adapt to humans in the RBD,
                      just as H1 and H3 is apparantly not capable to adapt so well
                      to birds as H4,H5,H6,H7,H9 are.
                      Last edited by gsgs; November 12, 2006, 04:05 AM.
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment


                      • #26
                        Re: A list of relevant mutation position

                        The table would be more useful if all of the recent changes were added, since they change H5N1 quite significantly. These changes include D187N, A188E, A189T, T192I, L194I, R220K, K222E, K222R, V223Y, S227N, S227R. I think more are interested in where H5N1 is going, and how dramatic the 2006 changes are, than an analysis of old isolates, many of which are low path.

                        Changes in the receptor binding domain, coupled with changes in the HA cleavage site, are a dangerous combination, and not really addreesed in the table, since none of the 2006 sequences are included.

                        Looking at where H5N1 is going, might be more useful than where it has been. Earlier H5N1 isolates from Japan and northern China are also absent from the table. H5N1 is the name of the game, and it is currently (2006) undergoing dramatic change.

                        The table doesn't even have S227N!
                        Last edited by AlaskaDenise; November 12, 2006, 03:51 AM.

                        Comment


                        • #27
                          Re: A list of relevant mutation position

                          Here are a few comments to put the above table in perspective. Most attention is focused on H5N1 because it has a polybasic HA cleavage site and has caused virtually all reported human fatalities from avian influenza. The common cleavage site, first described in 1996 is undergoing rapid change, especially in 2005 and 2006. In fact each major strain of H5N1 causing human fatalities has a different cleavage site. Clade 1 in southeast Asia has the original site, QRERRRKKR. The Qinghai stain, killing people in Turkey, Iraq, Azerbaijan, and Egypt has QGERRRKKR. In Indonesia it is QRESRRRKKR. In China it is the Fujian strain with LRERRRKR.
                          In the past two years, there have been dramatic changes in the receptor binding domain, which are regionally present and not yet in humans. That list may grow in the upcoming season.
                          In addition to the rapid evolution of the HA cleavage site, there is now rapid change in the receptor binding domain. Most of those changes are not in the above table. The most widely discussed is S227N (The above table should be labeled 214-228 (not 214-218) for the last domain listed.
                          WHO is focused on positions 226 and 228 (with some interest in 190. New isolates in 2006 have a number of changes near the above three positions.
                          S227N has been detected in 2 of the 4 human isolates from Turkey as well as one of the human isolates from Egypt at the beginning of this year.
                          In birds however, the changes have been more dramatic this year.
                          In the sequences released last week, 5 isolates from Shantou had three changes in this area (one was partial and had 2/3 - the third was not reported). These changes are K222R, V223I, and S227R (they also have V214M, which is not in the table).
                          Isolates from Hunan have SIX changes (D187N, A189E, T192I, L184I, R220K, K222E).
                          The isolate from Shanxi has FOUR changes (A188E, A189T, T192I, L194I).
                          Since all of these isolates are from 2006, they are co-circulating, which offers the opportunity of more recombination to create more diversity, as is happening in the HA cleavage site.
                          The affect of these various combinations has not been reported and many recent sequences have been withheld, especial HA sequences from northern China (as well as 6 of the 8 gene segments from southern China).
                          It is these combinations of changes in a rapidly evolving H5N1 that is causing the concern.

                          Comment


                          • #28
                            Re: A list of relevant mutation position

                            Originally posted by niman
                            The table would be more useful if all of the recent changes were added, since they change H5N1 quite significantly. These changes include D187N, A188E, A189T, T192I, L194I, R220K, K222E, K222R, V223Y, S227N, S227R. I think more are interested in where H5N1 is going, and how dramatic the 2006 changes are, than an analysis of old isolates, many of which are low path.

                            Changes in the receptor binding domain, coupled with changes in the HA cleavage site, are a dangerous combination, and not really addreesed in the table, since none of the 2006 sequences are included.

                            Looking at where H5N1 is going, might be more useful than where it has been. Earlier H5N1 isolates from Japan and northern China are also absent from the table. H5N1 is the name of the game, and it is currently (2006) undergoing dramatic change.

                            The table doesn't even have S227N!

                            all of the recent sequences are included (7630 HA's from genbank,
                            but only those where all of the amino acids in question are available).
                            That your mentioned changes don't show up is because their
                            counts are less than 5.
                            The complete table is too long to post here, I will upload
                            it to http://magictour.free.fr/rbd7.txt

                            I didn't know about the connection with the cleavage site,
                            do you have a reference ?


                            edit: the same table but ignoring all sequences before 2004 is here:
                            http://magictour.free.fr/rbd7k.txt
                            Last edited by gsgs; November 12, 2006, 05:11 AM.
                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                            Comment


                            • #29
                              Re: A list of relevant mutation position

                              Originally posted by gsgs
                              all of the recent sequences are included (7630 HA's from genbank,
                              but only those where all of the amino acids in question are available).
                              That your mentioned changes don't show up is because their
                              counts are less than 5.
                              The complete table is too long to post here, I will upload
                              it to http://magictour.free.fr/rbd7.txt

                              I didn't know about the connection with the cleavage site,
                              do you have a reference ?
                              I am not sure what your "count" is based on, but these are full HA sequences, so I think your programming has some counting issues.

                              There are five Shantou sequences and 4 go through the receptor binding domain. Two are full HA sequences and have K222R, V223I, S227R
                              A/goose/Shantou/239/2006(H5N1)
                              A/goose/Shantou/2086/2006(H5N1)

                              K222R alone is in

                              A/cat/Dagestan/87/06(H5N1)
                              A/goose/Jilin/hb/2003(H5N1)
                              A/duck/Guangdong/07/2000(H5N1)
                              A/Duck/Hong Kong/ww381/2000(H5N1)
                              A/Duck/Hong Kong/ww487/2000(H5N1)
                              A/Duck/Hong Kong/ww461/2000(H5N1)

                              V223I alone is in

                              A/bar-headed goose/Mongolia/1/05(H5N1)
                              A/chicken/Vietnam/398/2005(H5N1)
                              A/duck/Vietnam/376/2005(H5N1)
                              A/chicken/Yamaguchi/7/2004(H5N1)

                              Thus, your table leaves out some of he most dramatic changes. The Shanxi sequence is a full sequence and I believe the two Hunan sequences are also full sequences.

                              I am not sure how you can miss the most dramatic changes, but these differences have been described many times now, and posting the table on almost everything except the critical sequences is curious.

                              Comment


                              • #30
                                Re: A list of relevant mutation position

                                Originally posted by gsgs
                                all of the recent sequences are included (7630 HA's from genbank,
                                but only those where all of the amino acids in question are available).
                                That your mentioned changes don't show up is because their
                                counts are less than 5.
                                The complete table is too long to post here, I will upload
                                it to http://magictour.free.fr/rbd7.txt

                                I didn't know about the connection with the cleavage site,
                                do you have a reference ?
                                The HA cleavage site and receptor binding domain are both on H5. The sequences are at GenBank and Los Alamos.

                                Comment

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