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  • gsgs
    replied
    Re: A list of relevant mutation position

    >Re: A list of relevant mutation position
    >
    >
    >My simple question
    >to gsgs is "Do you agree with the facts stated below?" This is
    >a yes or no answer, with an explanation as to which points you
    >differ and wish to add commentary here.

    I'll read this later, going top to bottom

    >As a follow on question,
    > "Do you expect there to be more polymorphism changes in the near
    >term based on the fact that both the cleavage and receptor sites
    >now, this year, are showing previously unrecognized changes? If
    >yes, do you have a formula for the rate or the direction of those
    >changes? If no, why not?

    I see no reason to assume that evolution at the RBD or cleavage site
    is much different here than normal evolution of other areas in other
    flu-viruses. Well, except that it's in HA and in the antigenic sites
    maybe but that's probably not so important in birds.
    I could do some statistics and compare the rate of mutation
    (number of differences) in the RBD of H5 with other areas
    and other viruses.
    Maybe later ... Is it important/wanted ? ...

    >To help you gsgs in your response,
    > as I do wish for you to get an answer based on facts, not skewed
    >so heavily towards inquisitive thinking alone, here's what Niman
    >just posted elsewhere on the internet,
    >
    >> The Shanxi sequence,
    > with the multiple changes in or near the receptor binding domain
    >and the acquisition of mammalian polymorphisms in PB1 and MP was
    >isolated in 2006, as were the two related sequences from Hunan
    >and the five Shantou sequences.
    >
    >> The large number of changes
    >in an around the receptor binding domain of an H5N1 isolate is
    >without precedent, so a year ago there were ZERO such sequences
    >reported.

    well, when you look at my posted lists, you will find many changes in the
    RBD. How important/relevant they are is another question.
    That Nature paper seems to give some importance which is larger
    than any other changes.


    >> The story is in the sequence, and it is becoming
    >increasingly easy to read. <
    >
    >Yet, I will agree with you that
    >it's possible that one year ago, the virologists sequencing weren'
    >t looking that closesly at receptor binding domains as they are
    >now, and thus the changes being seen are no different than the
    >changes that occur each year. That's to be further explained,
    >maybe by you?

    I first noticed the importance of the RBD earlier this year.
    I remember the Scipps paper in March which examined them.
    The number of available human H5N1-sequences has greatly increased
    this year, so it's no surprise that the changes in the RBD also
    increase. Earlier we concentrated in the risistance-mutations,
    the virulence-mutations, the cleavage site.
    We should make a list of all important mutations to watch
    and _then_ see, which of them do happen for a better overview.

    We have lots of sequences from Indonesia meanwhile,
    most with the new cleavage site but no changes in the RBD.
    We have some changes in the RBD in China,Egypt, but most sequences
    still have them not.
    There is no indication yet that these changes did produce
    strains which can go pandemic.
    We could just have been lucky that they didn't.
    It should be tested how dangerous these changes are and how
    much they increase the contagiousness.

    Can't we infect larger populations of -say- ferrets with
    these viruses in a natural surrounding, maybe on an island
    or a closed,quarantined area and see, how it evolves ?

    Leave a comment:


  • Mingus
    replied
    Re: A list of relevant mutation position

    Oh! I did'nt see that a debate was goin on here.

    I want to thank Dr.Niman for adding the recent non-synonimus changes that apear in china this year. Clearly, the appearance of a wider variety of polymorphism at the protein level is of great concern.

    I see this as a new major turning point in the H5N1 viral evolution & I aggree that it goes just like the prevailing recombination theory would predict.

    My only comment to gsgs would be to download a reliable sequence alignement editor and align many different H5 sequences including some H3 & checkspot the right AA position based on a previously existing mutation list before compiling too many quantitative data.

    The standard numerotation is like the H3 position & some article count them with H5 position & there is some gap when we align H5 seq with H3's. False data will just fool everyones

    Leave a comment:


  • Guest's Avatar
    Guest replied
    Re: A list of relevant mutation position

    My simple question to gsgs is "Do you agree with the facts stated below?" This is a yes or no answer, with an explanation as to which points you differ and wish to add commentary here.

    As a follow on question, "Do you expect there to be more polymorphism changes in the near term based on the fact that both the cleavage and receptor sites now, this year, are showing previously unrecognized changes? If yes, do you have a formula for the rate or the direction of those changes? If no, why not?

    To help you gsgs in your response, as I do wish for you to get an answer based on facts, not skewed so heavily towards inquisitive thinking alone, here's what Niman just posted elsewhere on the internet,

    > The Shanxi sequence, with the multiple changes in or near the receptor binding domain and the acquisition of mammalian polymorphisms in PB1 and MP was isolated in 2006, as were the two related sequences from Hunan and the five Shantou sequences.

    > The large number of changes in an around the receptor binding domain of an H5N1 isolate is without precedent, so a year ago there were ZERO such sequences reported.

    > The story is in the sequence, and it is becoming increasingly easy to read. <

    Yet, I will agree with you that it's possible that one year ago, the virologists sequencing weren't looking that closesly at receptor binding domains as they are now, and thus the changes being seen are no different than the changes that occur each year. That's to be further explained, maybe by you?

    Originally posted by niman
    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.
    Last edited by GaudiaRay; November 12, 2006, 05:27 PM.

    Leave a comment:


  • gsgs
    replied
    Re: A list of relevant mutation position

    "count" is the number of sequences at genbank with that
    particular pattern of amino-acids at those 35 positions near to the RBD.

    Leave a comment:


  • HenryN
    replied
    Re: A list of relevant mutation position

    The two isolates from Hunan, A/chicken/Hunan/2246/2006(H5N1) and A/chicken/Hunan/2292/2006(H5N1). which had two of the same changes in Shanxi, T192I and L194I, also had two additional changes, D187N and A189E.

    These are partial sequences, but have all of the receptor binding domain. The sequence goes through the HA cleavage site.
    Last edited by AlaskaDenise; November 12, 2006, 05:09 AM.

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • gsgs
    replied
    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.

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • gsgs
    replied
    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.

    Leave a comment:


  • gsgs
    replied
    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.

    Leave a comment:


  • G?nseerpel
    replied
    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

    Leave a comment:


  • AlaskaDenise
    replied
    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?

    .

    Leave a comment:


  • gsgs
    replied
    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]

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