Announcement

Collapse
No announcement yet.

the birdflu index virus

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • the birdflu index virus

    calculated universal,central ancester of bird protein-sequences
    well, probably not exactly. Add 1-2 possible changes per segment
    HA and NA are not certain
    M1,M2 and NS1,NS2 consecutive in segments 7,8

    Code:
    >A/Index/birds/2000(H3N8a)
    MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN}
    MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLANIDLKYFNESTRKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK}
    MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNMKKTSQLKWALGENMAPEKVDFEDCKDVSDLKQYDSDEPESRSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALK}
    MKTIIVLSYLFCLALSQDYSGSNNSTATLCLGHHAVPNGTIVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGRDCTLIDALLGDPHCDVFQDETWDLYVERSSAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPASGFFSRLNWLTKSGSAYPVLNVTMPNNDNFDKLYVWGVHHPSTNQEQTNLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGQSGRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQSTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDIYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQRGNIRCNICI}
    MASQGTKRSYEQMETGGERQNATEIRASVGRMVGGIGRFYIQMCTELKLSDYEGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRRDGKWVRELILYDKEEIRRIWRQANNGEDATAGLTHLMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGYDFEREGYSLVGIDPFRLLQNSQVFSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTRVVPRGQLSTRGVQIASNENMETMDSSTLELRSRYWAIRTRSGGNTNQQRASAGQISVQPTFSVQRNLPFERATIMAAFTGNTEGRTSDMRTEIIRMMESARPEDVSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAEEYDN}
    MNPNQKIITIGSISLGLVVLNILLHIVSITVTVLVLPGNGNNGSCNETVIREYNETVRVEKVTQWHNTNVIEYIERPESGHFMNNTEALCDAKGFAPFSKDNGIRIGSRGHVFVIREPFVSCSPTECRTFFLTQGSLLNDKHSNGTVKDRSPYRTLMSVEIGQSPNVYQARFEAVAWSATACHDGKKWMTIGVTGPDAKAVAVVHYGGIPTDVINSWAGDILRTQESSCTCIQGECFWVMTDGPANRQAQYRAFKAKQGKIIGQAEISFNGGHIEECSCYPNEGKVECVCRDNWTGTNRPVLVISPDLSYRVGYLCAGLPSDTPRGEDSQFTGSCTSPMGNQGYGVKGFGFRQGNDVWMGRTISRTSRSGFEVLKVRNGWVQNSKEQIKRQVVVDNLNWSGYSGSFTLPVELTKRNCLVPCFWVEMIRGKPEEKTIWTSSSSIVMCGVDHEIADWSWHDGAILPFDIDKM}FTKKLLVSTR
    MSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEALMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYRKLKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQHRSHRQMVTTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVASQARQMVQAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQRFK}MSLLTEVETPTRNGWECKCSDSSDPLVIAASIIGILHLILWILDRLFFKCIYRRLKYGLKRGPSTEGVPESMREEYRQEQQSAVDVDDGHFVNIELE}
    MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILEEESDEALKMTIASVPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAIGVLIGGLEWNDNTVRVSETLQRFAWRSSNEDGRPPLPPKQKRKMARTIESEV}MDSNTVSSFQDILMRMSKMQLGSSSEDLNGMITQFESLKLYRDSLGEAVMRMGDLHSLQSRNGKWREQLSQKFEEIRWLIEEVRHRLKITENSFEQITFMQALQLLLEVEQEIRTFSFQLI}
    NS1, 2nd type (16HAs, 9 NAs , 2 NSs)

    Code:
    MDSNTITSFQVDCYLWHIRKLLSMRDMCDAPFDDRLRRDQKALKGRGSTLGLDLRVATMEGKKIVEDILKSETDENLKIAIASSPAPRYITDMSIEEISREWYMLMPRQKITGGLMVKMDQAIMDKRIILKANFSVLFDQLETLVSLRAFTDDGAIVAEISPIPSMPGHSTEDVKNAIGILIGGLEWNDNSIRASENIQRFAWGVRDENGGPPLPPKQKRYMARRVESEV}MDSNTITSFQDILQRMSKMQLESSSVDLNGMITQFERLKIYRDSLGESVMRMGDLHSLQSRNATWREELSQKFEEIRWLIAECRNILTKTENSFEQITFLQALQLLLEVESEIRTFSFQLI}

    closest to the index are:
    1, 0, 1,--, 2,--, 0, 0, =004 >A/Dk/Hokkaido/9/99(H9N2)
    1, 1, 2,--, 1,--, 0, 0, =005 >A/Mallard/Sweden/65/05(H4N3)


    full list of amino-acid differences of 1551 avian genomes in the 6 inner segments here:
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    Re: the birdflu index virus

    amino-acid differences to the bird-index in segments 1,2,3,5,7,8


    Code:
    Zhe:01,07,13,03,06,10*
    Akt:01,02,05,01,02,04*
    Zam:03,05,02,02,02,67
    Sti:15,06,19,30,07,08
    NL3:02,01,04,03,02,03
    H26:19,18,29,15,06,23
    Bol:12,23,13,11,03,06
    Ros:13,05,14,03,06,11
    779:03,04,03,06,02,01*
    17G:06,17,11,25,03,12
    GsG:11,14,17,04,03,11*
    QiH:12,08,11,07,08,14
    H16:03,08,08,04,07,07
    Brv:08,07,10,10,04,05
    546:05,04,03,04,02,04*
    Alt:01,01,00,03,02,02*
    _49:03,07,14,03,03,08*
    _59:04,07,06,04,01,02
    _73:01,04,03,03,03,01
    _27:10,05,13,07,03,09
    HK7:01,03,03,03,02,06*
    Miy:50,35,50,28,09,45
    Lex:51,48,42,36,15,55
    _07:34,29,31,34,10,29
    Mex:17,23,17,28,07,35
    _18:08,07,10,09,04,05
    ehu:13,08,16,17,05,11
    esw:18,1,16,07,04,15
    bat:242,156,206,139,99,168*
    sf1:6,5,13,6,2,9,1,3*
    sf2:3,2,5,-,2,-,2,2

    A/red-necked stint/Australia/02/2004(H4N8)
    A/Ck/Netherlands/1/2003(H7N7)
    A/Ck/Henan/26/2000(H9N2)
    A/cinnamon teal/Bolivia/4537/2001(H7N3)
    A/fowl/Rostock/1934(H7N1)
    A/pintail/Alaska/779/2005(H3N8)
    A/Dk/LA/17G/1987(H3N8)
    A/Gs/Guangdong/1/1996(H5N1)
    A/Gs/Qinghai/62/2005(H5N1)
    A/Ck/Henan/16/2004(H5N1)
    A/Brevig Mission/1/1918(H1N1)
    A/Dk/Memphis/546/1974(H11N9)
    A/Dk/Altai/1285(1991(H5N3)
    Aktau
    Zhejiang/11/2000(H5N1)
    Zam:Pelikan/Zambia
    Mex:******/2009
    Miy:Swine/Miyazaki/2007(H1N2)
    ehu:early human/Index/~1935
    esw:early swine/Index/~1935
    bat:A/little yellow-shouldered bat/Guatemala/153/2009/05/(H17N10)
    sf1:A/surface water/Minnesota/W07-2241/2007//(H3N8)
    sf2:A/surface water/Minnesota/NW1-T/2006//(H4N6)

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

    Code:
     0, 0, 0,--, 0,--, 0, 0, =000   >A/Index/birds/2000(H3N8a)
     0, 0, 0,--, 0,--, 0, 0,*=000   >A/Index/birds/2000(H3N8b)
     1, 0, 1,--, 2,--, 0, 0, =004   >A/Dk/Hokkaido/9/99(H9N2)
     1, 1, 2,--, 1,--, 0, 0, =005   >A/Mallard/Sweden/65/05(H4N3)
     1, 4, 2,--, 0,--, 0, 0, =007   >A/black-h gull/Netherlands/1/05(H6N8)
     1, 1, 0,--, 2,--, 0, 3,*=007   >A/Dk/Altai/1285/1991(H5N3)08/15
     1, 2, 2,--, 2,--, 0, 0, =007   >A/garganey/Altai/1213/07(H5N2)09
     1, 2, 2,--, 2,--, 0, 0, =007   >A/Mallard/Altai/1208/07(H3N6)09
     2, 1, 2,--, 3,--, 0, 0, =008   >A/blue-winged teal/ALB/580/1979(H4N2)08/11
     2, 0, 3,--, 2,--, 0, 1, =008   >A/Mallard Dk/ALB/294/1977(H11N9)08/31
     2, 1, 2,--, 2,--, 0, 1, =008   >A/Mallard Dk/NY/180/1986(H4N9)10/04
     1, 0, 5,--, 1,--, 0, 1, =008   >A/Mallard/Alberta/77/1977(H2N3)08/08
     2, 0, 3,--, 2,--, 0, 1, =008   >A/Mallard/Ohio/83/1986(H4N6)10/24
     2, 1, 2,--, 3,--, 0, 0, =008   >A/pintail Dk/ALB/599/1979(H4N2)08/11
     0, 2, 3,--, 1,--, 1, 2, =009   >A/common teal/Netherlands/1/05(H8N4)
     1, 2, 2,--, 4,--, 0, 0, =009   >A/Dk/MNG/47/01(H7N1)
    
    21,18,24,--,19,--,18,26, =126   >A/Ck/Beijing/8/98(H9N2)
    21,19,25,--,19,--,14,36, =134   >A/Ck/Henan/5/98(H9N2)
    39,33,47,--,22,--,10,41, =192   >A/Tk/IA/21089-3/1992(H1N1)
    
     5, 1, 5,21, 3,--, 0, 1, = 15   >A/seal/Massachusetts/3911/1992(H3N3)
     5, 1, 2,--, 4,--, 0, 3, = 15   >A/seal/Massachussetts/133/1982(H4N5)
    
    20,18,21,--,28,--,23,23, =133   >A/Alaska/1935(H1N1)
    20,19,27,--,28,--,20,19, =133   >A/Henry/1936(H1N1)
    19,18,24,--,25,--,17,17, =120   >A/Phila/1935(H1N1)
    20,14,19,--,24,--,14,19, =110   >A/Melbourne/35(H1N1)
    21,17,21,--,24,--,15,17, =115   >A/Wilson-Smith/33(H1N1)
    13, 8,16,--,17,--, 9,13, = 76   >A/Human/Index-early/1935(H1N1)
     8, 7,10,--, 9,--, 7, 5, = 46   >A/Brevig Mission/1/1918(H1N1)
    18,13,16,--, 7,--, 8,19, = 81   >A/Sw/Index-early/1935(H1N1)
    24,18,23,--,11,--,12,30, =118   >A/swine/1976/1931(H1N1)
    22,18,20,--,10,--, 9,28, =107   >A/swine/Jamesburg/1942(H1N1)
    24,18,22,--,11,--,10,28, =113   >A/swine/1931(H1N1)
    24,18,24,--,11,--,10,29, =116   >A/swine/Iowa/15/1930(H1N1)
    20,22,22,--,13,--, 9,27, =113   >A/swine/Ohio/23/1935(H1N1)
    
     6, 7, 5,--, 2,--, 1, 2, = 23   >A/turkey/Ontario/6118/1968(H8N4)
     5, 4,--,--, 6,--, 4, 5, = 24   >A/turkey/Ontario/7732/1966(H5N9)
     9, 7, 4,--, 3,--, 9, 0, = 32   >A/pintail duck/ALB/628/1979(H6N8)08/13
     3, 7, 5,--, 2,--, 0,--, =      >A/blue goose/WI/711/1975///
     2, 3,--,--,--,--, 1,--, =      >A/blue-winged teal/ALB/286/1977/08/10/
     6, 5, 3,--, 3,--, 1,--, =      >A/duck/Memphis/546/1974(///
     3, 3,--,--,--,--, 0, 0, =      >A/mallard duck/ALB/663/1979/08/13/ 
     6, 7, 8,--, 5,--,12,15, = 53   >A/Dk/Hunan/5106/2005(H5N1)  Z{3,3,15,14,0,8,0,4}
    
     9, 6,12,--, 3,--,10,12,*= 52   >A/Gs/Guangdong/3/1997(H5N1)
    11,14,17,--, 3,--, 6,14,*= 65   >A/Gs/Guangdong/1/1996(H5N1)
    20,13,23,--, 9,--,13,24, =102   >A/avian/Index-HK/1997(H5N1)
    21,14,24,--,10,--,14,22, =105   >A/Ck/HK/786/1997(H5N1)
     6, 6,10,--, 6,--,13,17, = 58   >A/avian/Indonesia-Index/2003(H5N1) {3,2,3,6,1,5,1,4}
     9, 6,15,--, 6,--,22,22, = 80   >A/IDN/CDC1047/2007(H5N1)   {6,4,13,20,2,8,10,9}
     3, 6, 7,--, 5,--,12,11, = 44   Index H5N1,Z  (henan/16:22180312) {0,0,0,0,0,0,0,0}  index se9agbi.26, i_genotz
     9, 8,10,--, 7,--,14,18, = 66   >A/avian/Index-Qinghai/2005(H5N1)  {6,2,3,8,2,3,2,11}
     5, 6, 7,--, 5,--,17,16, = 56   >A/avian/Index-Vietnam/2004(H5N1) {4,0,0,11,0,8,5,5}
     5, 6, 8,--, 5,--,13,15, = 52   >A/avian/Index-China/2003(H5N1) {2,0,13,5,0,3,1,2}
     9, 6,10,--, 5,--,13,19, = 62   >A/Fujian/1734/2005(H5N1) 
     9, 7, 7,--, 5,--,12,19, = 59   >i_fujc , index Fujian  Z{7,1,12,12,2,8,0,8}
     1, 7,13,--, 3,--, 6,10,*= 40   >A/Ck/Zhejiang/2000(H5N1)
     4, 7, 6,--, 4,--, 5, 1, = 27   >A/Ck/Scotland/1959(H5N1)
     3, 8, 8,--, 5,--,13,11, = 48   >A/Ck/Henan/16/04(H5N1)  {2,2,1,8,0,3,1,2}
    10, 6, 5,--, 2,--, 2, 3, = 28   >A/Ck/Henan/210/04(H5N1)     
    11, 2, 7,--, 4,--, 4, 5r,= 33   >A/tree sparrow/Henan/1/2004(H5N1)
     5, 2, 2,--, 4,--, 3, 7r,= 23   >A/tree sparrow/Henan/2/2004(H5N1)
     4, 2, 3,--, 5,--, 3, 1r,= 18   >A/tree sparrow/Henan/3/2004(H5N1)
     4, 6, 2,--, 3,--, 6, 5r,= 24   >A/tree sparrow/Henan/4/2004(H5N1)
     4, 6, 2,--, 5,--,11, 8, = 36   >A/Dk/Guangxi/35/2001(H5N1)
     4, 8,11,--, 7,--,11*1.27,14*1.15, = 55   >A/Dk/Guangxi/50/2001(H5N1)
     3, 8, 8,--, 5,--,13,11, = 48   >A/Ck/Henan/16/04(H5N1)
     7,10*1.46,15*1.15,--, 5,--, 9*1.07,18, =  71    >A/Ck/Hubei/wm/97(H5N1)      ancestor of henan/16 in 7
    
      19 >A/Index/birds/2000(H3N8)
    
    11,14,17,--, 3,--, 6,14*  Gs/Guangdong/1/1996,GsGd
    18,17,22,--, 9,--,13,29   Ck/HK/220/1997,GsGd
    20,19,24,--,12,--,13,22   HK/156/1997,GsGd
     5, 4,15,--, 7,--, 8, 7   Silky Ck/HK/SF189/2001,A
     3, 7, 9,--,10,--,14, 9   Ck/HK/YU562/2001,B
    10, 8, 6,--, 5,--,11,11   Dk/HK/2986.1/2000,C
     5, 7, 7,--,14,--,13, 7   Ck/HK/FY150/2001,D
     3, 7, 5,--, 5,--,13, 9   Ck/HK/715.5/2001,E
    11, 8,13,--, 7,--,14,18   Gs/Guangxi/345/2005,G
    12, 9, 8,--, 6,--,14,18   Ck/ST/4231/2003,V
     4, 7, 9,--, 4,--,13, 9   teal/China/2978.1/2002,W
    11, 6, 8,--, 6,--,13, 9   Gf/HK/38/2002,X0
     2, 6, 6,--, 6,--,11, 9   Ck/HK/31.2/2002,X1
    10, 6,12,--, 9,--,12, 8   Ck/HK/37.4/2002,X2
     4, 8, 4,--, 7,--,11,15   SCk/HK/YU100/2002,X3
    12, 7,11,--, 5,--,14,12   Ck/HK/96.1/2002,Y
     3, 8, 9,--, 5,--,12,12   Ck/HK/YU22/2002,Z
     6, 7, 8,--, 6,--,16,13   HK/212/2003,Z+
    
    
    
     8, 7,10,--, 9,--, 7, 5, = 46   >A/Brevig Mission/1/1918(H1N1)
     
     3, 6, 7,--, 5,--,12,11, = 44   Index H5N1,Z  (henan/16:22180312)
     9, 8,10,--, 7,--,14,18, = 66   >A/avian/Index-Qinghai/2005(H5N1)  Z{6,2,3,8,2,3,2,11}=37
     5, 6, 7,--, 5,--,17,16, = 56   >A/avian/Index-Vietnam/2004(H5N1) Z{4,0,0,11,0,8,5,5}=33
     6, 6,10,--, 6,--,13,17, = 58   >A/avian/Indonesia-Index/2003(H5N1) Z{3,2,3,6,1,5,1,4}=25
     8, 5,12,--, 6,--,20,20, = 71   >A/human/IDN-Index/2005(H5N1)  Z(5,3,8,13,2,7,10,6)=54  I(4,1,7,8,1,2,9,2)=34
     8, 8,13,--, 7,--,15,23, = 74   >A/IDN/CDC625/06(H5N1),Karo  Z(7,4,6,12,2,10,3,10)=54  I(5,2,3,8,1,5,2,6)=32  IH(9,3,10,16,2,7,9,8)
     8, 9,11,--, 7,--,15,23, = 73   >A/Ck/Dairi/BPPVI/2005(H5N1)  Z(5,5,4,9,2,8,3,10)=46 Karo(3,1,2,4,0,4,0,6)  I(2,3,1,3,1,3,2,6)=21  IH(6,4,8,11,2,5,9,8)
     9, 6,15,--, 6,--,22,22, = 80   >A/IDN/CDC1047/2007(H5N1)  Z(6,4,13,20,2,8,10,9)=72  I(6,2,12,15,1,3,9,5)=53  IH(4,1,6,6,0,1,2,3)
     
    2009
    10, 7, 6,--, 7,--,12,22, =064   >A/whooper swan/MNG/6/2009(H5N1)
    10, 7, 6,--, 7,--,13,23, =066   >A/rubby shelDk/MNG/X42/2009(H5N1)
    11, 7, 6,--, 7,--,13,23, =067   >A/bar-h Gs/MNG/X53/2009(H5N1)
    11, 7, 6,--, 7,--,13,23, =067   >A/common goldeneye/MNG/X60/2009(H5N1)
    12, 8, 6,--, 8,--,12,22, =068   >A/bean Gs/Tyva/10/2009(H5N1)06/22
    11, 9, 6,--, 7,--,12,24, =069   >A/grebe/Tyva/3/2009(H5N1)06/22
    10, 7, 5,--, 7,--,12,23, = 64   >A/avian/Mongolia/Index/2009(H5N1)  Z(7,3,10,33,2,15,0,12}
     4, 4, 3,--, 1,--, 2, 4,*= 18   >A/mallard/Hokkaido/24/2009(H5N1) [LP] Z(5,10,8,37,6,22,12,90) Q{11,12,11,40,8,24,14,91}
    
    2008
     4, 6, 7,--, 5,--,17,15, =054   >A/Ck/THA/ST-351/08(H5N1)  Z(3,0,0,12,0,14,5,3) VNM(1,0,0,3,0,7,0,4)
     4, 7, 7,--, 5,--,17,15, = 55   >A/little grebe/Phichit/2004  Z(3,1,0,11,0,13,5,3) VNM(1,1,0,2,0,6,0,4)  351(01030400)
     5,12, 8,--, 7,--,17,17, =066   >A/Kalij pheasant/THA/vsmu-1/08(H5N1)
     9, 9,12,--, 5,--,12,20, =067   >A/grey heron/HK/1046/08(H5N1)
    11, 9,10,--, 5,--,14,18, =067   >A/whooper swan/Hokkaido/1/08(H5N1) Z(8,5,17,24,0,14,4,5) Q{8,7,20,28,2,17,6,16}
    12, 7,10,--, 6,--,14,19, =068   >A/Ck/Primorje/1/08(H5N1)04/10
     9, 9,13,--, 5,--,12,20, =068   >A/great egret/HK/807/08(H5N1)
    11, 9,11,--, 5,--,14,18, =068   >A/whooper swan/Aomori/2/08(H5N1)
    10, 8,12,--, 6,--,12,21, =069   >A/magpie robin/HK/1897/08(H5N1)
    11, 9,11,--, 5,--,14,19, =069   >A/whooper swan/Aomori/1/08(H5N1)
    11, 9,12,--, 5,--,14,19, =070   >A/whooper swan/Akita/1/08(H5N1)
    10,10,12,--, 6,--,13,20, =071   >A/magpie robin/HK/1097/08(H5N1)
    12, 8,14,--, 5,--,13,21, =073   >A/black-crowned night heron/HK/659/08(H5N1)
     9, 9,12,--, 7,--,24,17, =078   >A/peregrine falcon/HK/2142/08(H5N1)
    10,12,11,--,11,--,14,21, =079   >A/Ck/Egypt/0836/08(H5N1)01/15
    10,12,11,--,11,--,15,21, =080   >A/Ck/Egypt/083/08(H5N1)01/02
    14,10,13,--, 5,--,18,20, =080   >A/Ck/Sukhothai/NIAH114843/08(H5N1)
    13,11,18,--, 8,--,14,20, =084   >A/Dk/Egypt/0871/08(H5N1)02/20
    16,12,13,--, 6,--,19,19, =085   >A/Ck/THA/ICRC-V586/08(H5N1)
    15,13,15,--,11,--,15,20, =089   >A/Ck/Egypt/0891/08(H5N1)09/26
    17,10,14,--, 5,--,20,23, =089   >A/Ck/Uthaithani/NIAH115067/08(H5N1)
    
    
    
    genotypes
    
    A,B,C,D,E,X,Y,Z,Z+,V
    
    A:aqa1,aqa1,gsgd,----,aqa1,----,gsgd,aqa1
    B:aqa1,aqa1,aqa1,----,aqa1,----,aqa1,aqa1
    C:aqa1,gsgd,aqa1,----,gsgd,----,aqa1,aqa1
    D:aqa1,gsgd,aqa1,----,y280,----,aqa1,aqa1
    E:aqa1,gsgd,aqa1,----,aqa2,----,aqa1,aqa1
    
    
    1999
    aaaaaaaa Gs/Gd
    2000
    aaaaaaaa Gs/Gd
    babaaabc C
    2001
    bbaabdac A
    bbbababc B
    babaaabc C
    babaeabc D
    babafabc E
    gggafdhi X0
    2002
    bbbafdjc Z
    bbbafajc Z+
    bbbafdbc Y
    bbbababc B
    abbafajc W
    kglafdmi X0-X3
    2003
    bbbafdjc Z
    bbbafajc Z+
    bboabdjc V
    2004
    bbbafdjc Z
    
    a-GsGd,W  b-C..  g-X0  k-X0-3
    a-GsGd,c,d,e  b-A..  g-X0
    a-GsGd,A  b-c,b,...   g-X0  l-X0.3   o-V
    a-GsGd
    a-GsGd,C  b-A,B,V   e-D  f-E,...
    a-GsGd   d-A,Y,Z,X,V
    a-GsGd   b-B,C...    h-X0   j-V,W,Z   m-X0.3
    a-GsGd   c-A,B,C..   i-X

    Code:
    new introductions into mammals had these distances from the bird- 
    index in the inner segments: 
    
    1918: 8+ 7+10+ 9+ 7+ 5   human H1N1
    1957:--+ 5+--+--+--+--   human H2N2
    1968:--+ 4+--(20)++--+--+--   human H3N2
    1979: 8+ 5+14+ 5+ 3+ 9   European swine H1N1
    1998:12+(15)+10+--+(26)+--+(10)+(35) US triple reassortant swine H3N2
    1963: 8+12+14+55+15+63+ 1+10  equine H3N8 (--canine/2003)
    1956:54+45+42+30+36+69  equine H7N7 (still exists ?)
    
    2011:06,09,06,24,06,25,02,01  harbor-seal,Mass./2011(H3N8)
    1980:(3,1,3,-),6,-,4,8  seal H7N7
    1982:5,1,2,-,4,-,0,3  seal 1982 (H4N5)
    1992:5,1,5,-,3,-,0,1  seal 1992 (H3N3)
    NL3:02,01,04,03,02,03
     8, 7,10,--, 9,--, 7, 5, = 46   >A/Brevig Mission/1/1918(H1N1)
    18,13,16,--, 7,--, 8,19, = 81   >A/Sw/Index-early/1935(H1N1)
    13, 8,16,--,17,--, 9,13, = 76   >A/Human/Index-early/1935(H1N1)
    bat:242,156,206,139,99,168*
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #3
      Re: the birdflu index virus

      for a high AT-score the sequences are supposed to have evolved for decades
      in mammals. This would also mean that they are not bound by the
      bird-index and evolve slowly away from it

      here is a graph of the AT-score vs. the distance from the bird-index
      in segments 1,2,3,5,7
      Attached Files
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • #4
        Re: the birdflu index virus

        counts of sequences at genbank with distance=0,1,... from the bird-index


        Code:
        Nov.2009
        seg
        ment  0     1     2     3     4     5     6     7    8    >8
        --------------------------------------------------------------
         1,   8 , 100 , 228 , 332 , 367 , 282 , 247 , 207 , 170 , 1054
         2,  62 , 225 , 276 , 286 , 308 , 261 , 296 , 307 , 246 ,  812
         3,   2 ,   8 ,  74 , 190 , 211 , 235 , 184 , 228 , 251 , 1525
         5,  16 , 138 , 342 , 350 , 238 , 412 , 319 , 246 , 182 ,  630
         7, 377 , 441 , 330 , 139 ,  74 ,  38 ,  58 ,  45 ,  41 , 1185
        41,   0 ,   7 ,   7 ,   7 ,  20 ,  14 ,  12 ,   7 ,   3 ,   34
        45,   0 ,   0 ,   0 ,   0 ,   1 ,   1 ,   2 ,   9 ,  11 ,  244
        61,   1 ,   4 ,   5 ,  20 ,  23 ,  52 ,  26 ,  20 ,  24 , 1576
        68,   1 ,   0 ,   5 ,   3 ,  12 ,  38 ,  18 ,  18 ,  23 ,  575
        81, 146 , 225 , 206 , 123 , 108 ,  88 ,  47 ,  27 ,  44 , 1619
        82,  36 ,  58 ,  73 ,  58 ,  58 ,  33 ,  26 ,  33 ,  27 ,  235
        
        
        Jan.2012
        seg
        ment  0     1     2     3     4     5     6     7    8    >8
        --------------------------------------------------------------
         1,  23 , 279 , 586 , 712 , 778 , 545 , 499 , 344 , 272 , 1615
         2, 111 , 479 , 687 , 769 , 723 , 554 , 489 , 457 , 364 , 1264
         3,   2 ,  23 , 150 , 479 , 561 , 580 , 432 , 448 , 506 , 2797
         5,  58 , 417 ,1051 , 915 , 578 , 610 , 442 , 384 , 281 , 1071
         7,1096 ,1096 , 802 , 370 , 171 ,  91 , 149 , 101 ,  88 , 2717
        41,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,  260
        43,  31 ,  32 ,  25 ,  24 ,  49 ,  41 ,  19 ,  23 ,  26 ,  608
        45,   0 ,   0 ,   0 ,   0 ,   1 ,   1 ,   2 ,   9 ,  11 ,  244
        61,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 ,   0 , 2422
        68,   1 ,   0 ,   5 ,   3 ,  12 ,  38 ,  18 ,  18 ,  23 ,  575
        81, 320 , 540 , 522 , 398 , 265 , 182 ,  78 ,  45 ,  74 , 2963
        82, 103 , 226 , 260 , 145 , 109 ,  64 ,  50 ,  78 ,  44 ,  330
        all avian flu , all hosts,mallards,chicken and turkeys

        -----segment1-------------
        22,271,555,681,747,520,474,323,260,205,250,212,163 ,139,99,82,61,43,35,28,22,33,29,18,15,20,11,5,0,2, 3
        12,144,228,281,227,130,86,34,12,7,8,5,3,0,0,1,0,0, 0,1,0,0,0,0,0,0,0,0,0,0,0
        0,4,21,46,53,71,92,66,82,82,104,104,69,82,60,42,38 ,29,24,17,18,30,20,11,7,10,4,4,0,1,2
        -----segment2-------------
        111,479,687,774,724,557,490,458,366,298,240,221,10 8,66,60,60,35,33,32,26,22,21,7,12,9,8,2,0,2,2,2
        54,214,279,270,233,123,61,27,4,4,3,1,2,0,0,3,0,0,0 ,0,0,0,0,0,0,0,0,0,0,0,0
        6,14,26,43,49,73,142,136,123,123,123,132,70,40,43, 37,22,26,24,18,12,10,5,6,4,4,2,0,1,2,1
        -----segment3-------------
        2,23,150,478,561,579,431,447,505,495,429,477,367,2 70,169,119,69,54,64,47,32,44,31,18,22,14,5,6,5,2,1
        0,12,45,164,183,193,105,112,119,94,91,82,45,19,6,3 ,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
        1,0,11,25,25,43,56,75,93,94,124,111,130,97,87,60,4 6,36,44,32,24,26,27,9,14,8,3,6,3,2,0
        -----segment5-------------
        53,391,1016,878,535,560,417,363,254,274,155,108,82 ,37,26,42,43,50,39,43,9,3,8,5,3,5,10,5,3,15,7
        12,139,457,285,160,56,36,10,3,5,3,2,0,0,0,0,1,0,4, 0,0,0,0,0,0,0,2,2,0,0,0
        2,9,38,61,57,146,163,126,133,152,85,58,42,25,16,23 ,17,28,15,19,6,2,5,3,2,0,1,0,1,5,6
        -----segment7-------------
        1070,1084,788,363,167,89,149,101,87,76,79,141,310, 397,450,311,158,262,164,108,59,33,22,36,12,12,6,4, 2,1,1
        425,398,243,102,21,9,8,4,1,1,5,7,7,5,3,1,3,14,8,4, 1,0,0,0,0,0,0,0,0,0,0
        52,74,61,43,36,31,47,41,48,27,32,48,85,173,238,165 ,84,110,62,48,35,22,21,32,10,11,5,4,1,1,1
        -----segment81-------------
        318,539,517,392,259,181,76,58,63,62,61,45,36,72,10 8,178,222,175,183,234,219,116,109,98,72,87,87,59,7 1,91,53
        148,199,204,129,62,30,11,5,3,2,2,0,0,1,2,3,2,0,2,2 ,2,2,1,3,0,0,0,0,0,0,0
        7,11,27,42,31,21,9,19,24,17,24,16,18,30,37,60,105, 77,99,127,119,66,52,45,27,54,47,33,38,32,17
        -----segment82-------------
        102,226,259,143,108,64,49,77,44,31,45,27,23,11,15, 11,6,5,7,12,16,20,10,29,18,9,12,13,3,0,2
        70,120,141,51,39,17,12,11,4,3,0,2,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0,0,0,0,0
        0,0,7,4,13,4,8,26,20,13,27,20,18,11,10,10,5,5,6,10 ,13,17,5,22,11,6,6,9,0,0,0
        -----segment43-------------
        30,32,25,24,49,41,19,23,26,8,2,33,27,21,23,44,66,8 0,86,34,21,18,12,4,5,6,9,8,9,6,13
        11,16,13,16,26,27,7,13,20,5,2,3,4,13,12,15,21,37,1 5,5,9,3,0,0,0,0,0,0,1,0,1
        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,2,0,0,0,0,0, 1,0,0,0,0,4
        -----segment68-------------
        4,4,16,42,9,9,7,13,25,22,70,55,49,41,34,30,55,14,1 3,5,6,2,6,10,6,3,0,0,0,3,0
        2,1,5,19,4,1,1,3,16,11,33,22,24,11,11,5,9,1,3,0,1, 0,0,0,2,1,0,0,0,0,0
        0,0,0,0,0,1,0,0,1,0,1,1,1,2,0,0,1,0,0,0,2,0,3,0,0, 0,0,0,0,0,0




        H5N1 avian flu , all hosts,mallards,chicken and turkeys

        -----segment1-------------
        2,3,9,23,56,82,127,120,101,100,132,140,121,60,32,3 2,22,10,9,9,1,4,4,1,2,0,2,0,0,0,0
        2,0,2,2,4,3,2,1,0,2,0,1,3,0,0,1,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,4,14,14,36,39,31,31,43,54,61,47,34,21,22,19,8, 6,5,0,3,1,1,1,0,1,0,0,0,0
        -----segment2-------------
        2,5,12,8,17,20,135,199,252,187,171,152,65,26,25,18 ,11,11,4,2,3,1,0,1,0,3,0,0,1,0,0
        2,1,1,1,4,1,6,0,0,1,3,1,2,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,3,5,7,5,59,59,74,67,83,89,40,17,21,13,7,10,3,0 ,0,1,0,0,0,1,0,0,0,0,0
        -----segment3-------------
        0,0,5,13,7,16,35,85,114,159,176,213,183,146,90,51, 29,9,10,3,3,5,9,5,8,3,0,1,0,0,1
        0,0,0,7,1,1,0,4,0,1,3,2,0,1,1,1,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,1,2,3,5,7,33,33,48,61,82,91,68,49,33,16,5,6,3, 2,2,8,3,5,1,0,1,0,0,0
        -----segment5-------------
        0,6,19,22,51,292,235,244,150,156,76,34,19,9,8,3,1, 0,0,0,0,0,0,0,0,1,1,0,0,0,1
        0,2,5,3,3,2,1,1,0,3,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,2,5,4,20,102,91,74,70,81,45,23,11,8,5,2,0,0,0,0, 0,0,0,0,0,0,1,0,0,0,1
        -----segment7-------------
        9,7,16,10,7,2,7,2,22,6,8,32,159,252,354,198,98,229 ,97,44,18,8,3,0,1,1,0,0,0,0,0
        3,3,1,4,1,1,1,0,0,0,0,0,1,2,3,1,0,6,1,0,0,0,0,0,0, 0,0,0,0,0,0
        2,2,9,0,0,1,2,0,12,2,3,7,31,104,187,102,55,98,47,2 7,7,3,3,0,0,0,0,0,0,0,0
        -----segment81-------------
        7,7,8,5,4,5,7,24,24,16,9,13,11,27,38,119,156,135,1 45,208,195,91,86,71,40,41,42,23,14,9,2
        5,0,2,1,2,0,0,0,0,0,1,0,0,1,0,2,1,0,2,2,1,0,0,2,0, 0,0,0,0,0,0
        0,3,3,3,1,0,3,14,14,11,0,4,7,8,12,50,76,56,77,115, 103,51,41,28,7,22,13,5,12,7,1
        -----segment82-------------
        0,1,1,2,1,1,1,0,4,3,7,4,1,0,2,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,0,0,0,0,4,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0


        H5N1 2009-2011 avian flu , all hosts,mallards,chicken and turkeys

        -----segment1-------------
        0,0,0,0,5,0,1,0,0,2,8,15,21,5,4,6,7,2,1,1,0,0,0,1, 0,0,0,0,0,0,0
        0,0,0,0,2,0,0,0,0,0,0,1,2,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,2,0,0,0,0,0,5,3,5,3,3,1,5,2,1,1,0,0,0,1,0, 0,0,0,0,0,0
        -----segment2-------------
        0,1,0,1,1,0,0,5,14,14,10,12,6,4,6,2,2,0,2,0,0,0,0, 0,0,0,0,0,0,0,0
        0,0,0,1,1,0,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,0,0,0,0,2,3,5,7,4,1,6,2,2,0,2,0,0,0,0,0,0, 0,0,0,0,0,0
        -----segment3-------------
        0,0,0,1,1,0,12,13,2,0,2,1,10,9,17,6,3,2,4,0,0,0,3, 0,1,1,0,0,0,0,0
        0,0,0,1,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,0,0,0,1,0,0,0,0,7,4,8,6,2,1,3,0,0,0,3,0,1, 1,0,0,0,0,0
        -----segment5-------------
        0,1,1,1,1,0,4,28,10,9,6,6,8,5,0,1,0,0,0,0,0,0,0,0, 0,0,0,0,0,0,0
        0,1,0,1,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,0,0,2,0,6,2,5,5,7,4,0,1,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        -----segment7-------------
        0,0,2,1,0,0,0,0,0,0,0,0,16,12,28,14,6,7,1,8,1,0,1, 0,0,0,0,0,0,0,0
        0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0, 0,0,0,0,0,0
        0,0,0,0,0,0,0,0,0,0,0,0,1,1,8,12,6,6,1,7,0,0,1,0,0 ,0,0,0,0,0,0
        -----segment81-------------
        0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,2,3,4,3,5,8,24,8 ,13,6,3,11,1,0
        0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0, 0,0,0,0,0,0
        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,2,4,3,4,3,3,0, 5,1,2,10,1,0



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

        Comment


        • #5
          Re: the birdflu index virus

          (only talking about amino-acid mutations below)

          this shows that flu rarely goes back to mallards once it had evolved away from the index.

          The current H5N1-viruses in Egypt,Indonesia,Bangladesh are already pretty far away
          from the index and less capable to enter the mallard population without reassortment of "fresh",
          index-close inner segments.

          Like human or swine or equine or bat viruses won't go back into mallards
          after long periods of mutation away from the index.

          We should examine that in the lab, why these chicken viruses distant from the index
          won't establish in mallards. Don't they enter or replicate so well in mallard intestinal cells ?
          Or don't they transmit so well between mallards ? (water-borne, by dabbling ?)

          For the longterm evolution of influenza, the successfull establishment of new strains,
          we made the experience that it's just the mallard - index-close strains that form
          new lineages and create pandemics.
          Except influenza-B, that successfully established in humans since many centuries.
          But flu-A is just waiting for the emergence of the next mallard-strain to evade existing immunity.

          OK, it could just pick a new HA - most HAs are not index-close in mallards.
          But new HAs often need to be "adapted" through different inner segments.
          And the chance of compatibility presumably goes down with distance from the index.

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

          mallards snippets:
          On December 7, 2010, H5N1 highly pathogenic avian influenza virus was isolated
          from a healthy mallard captured at the Mankyung River in South Korea.
          Phylogenetic analysis showed that this virus was classified into clade 2.3.2 and
          closely related to H5N1 viruses isolated from wild birds in Mongolia, Russia and
          China in 2009 and 2010.

          A number of H5N1 influenza outbreaks have occurred in aquatic birds in Asia. As aquatic birds are the natural reservoir of influenza A viruses and do not usually show clinical disease upon infection, the repeated H5N1 outbreaks have highlighted the importance of continuous surveillance on H5N1 virus …

          However, in mallard ducks, two isolates had low pathogenicity, while the other two were highly
          pathogenic and caused lethal infection.

          A/mallard/Huadong/Y/2003 (Y) and A/mallard/Huadong/hn/2005 (hn),from healthy domestic mallards
          A/mallard/Huadong/S/2005 (S) and A/mallard/Huadong/lk/2005 (lk), from dead domestic mallards.

          We conclude that the epidemiology of HPAIV H5N1 in mallards and probably
          other aquatic wild bird species is massively influenced by interfering immunity

          Molecular Changes in the Polymerase Genes (PA and PB1 ...
          6 Jun 2007 ... However, the currently circulating HP H5N1 viruses acquired a different
          phenotype and are able to cause mortality in mallards.

          was isolated from a healthy mallard in South Korea.

          The short virus shedding time suggests that individual mallards are less likely to
          spread the virus at continental or intercontinental scales

          The Korean LPAI H5N1 virus has the highest similarity with the Japanese LPAI
          H5N1 virus, A/mallard/Hokkaido/24/09 (H5N1),

          A/chicken/Korea/IS/06 (H5N1)
          mute swans, 100% mortality
          ruddy shelducks 100% mortality
          mandarin ducks only a single mortality
          greylag geese sick but lacked mortality
          mallards had asymptomatic infection

          : Molecular changes in the polymerase genes (PA and PB1) associated with high
          pathogenicity of H5N1 influenza virus in mallard ducks.

          A/Vietnam/1203/04 (H5N1) wild- type virus was more lethal to mallard ducks

          Table 1. H5N1 viruses characterized in mallard ducks
          Isolation site Virus Inoculated dead/total Contact dead/total Pathogenicity Days virus shed No. amino acid differences in HA
          Hong Kong A/Hong Kong/156/97 0/2 0/2 Low 7 0
          A/chicken/Hong Kong/YU562/01 0/2 0/2 Low 7 0
          A/chicken/Hong Kong/SSP94/03 0/2 1/2 High 11 0
          A/chicken/Hong Kong/AP111/03 0/2 0/2 Low 11 0
          Vietnam A/mallard/Vietnam/16D/03 1/2 2/2 High 17 11
          A/duck/Vietnam/40D/04 1/2 0/2 High 13 4
          A/Vietnam/1203/04 2/2 1/2 High 13 2
          A/Vietnam/3046/04 0/2 0/2 Low 13 10
          A/chicken/Vietnam/48C/04 1/2 0/2 High 17 6
          A/chicken/Vietnam/133/04 1/2 1/2 High 11 2
          Thailand A/Thailand/1 (Kan-1)/04 0/2 0/2 Low 11 0
          China A/chicken/Anhui-Chaohu/85/04 0/2 0/2 Low 17 2
          Indonesia A/chicken/Pangkal Pinang/BPPV3/04 0/2 0/2 Low 13 0
          Singapore A/duck/Singapore/3/97 (H5N3) 0/2 0/2 Low 7 0

          Two 4- to 6-week-old mallard ducks were inoculated with 106 EID50 of virus and placed after 4 hours with two contact ducks. The small number

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

          so, it could be that it's just the geographical spread. Mallards are most sampled
          in USA,Canada where we have little H5N1.
          However, there must be a reason why amino-acids in the inner segments in mallards
          do not move away from the index over centuries.
          The high mutants maybe don't spread so well by dabbling
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • #6
            Re: the birdflu index virus

            correlation coefficients of pairs of distance from the index("D")
            vs. AT-score (% of nucleotides that are A or T) ("S") in several segments
            full avian genomes from genbank
            (a:all) (correlation coefficient * 100)
            cordis5.bas


            Code:
            uploaded until 2011 , 2696 genomes
              |s1 s2 s3 s4 s5 s6 s7 s8 sa
            --|--------------------------
            Da|31 18 19 42 07 06 47 -2 52
            D1|31 04 18 26 12 09 23 03 39
            D2|24 15 15 30 04 05 32 02 39
            D3|23 22 01 29 07 02 26 -5 34
            D5|05 -4 05 11 31 05 10 14 19
            D7|18 22 16 43-12 03 60-17 42
            D8|33 14 21 37 04 04 41 04 48

            Code:
            uploaded since 2011 , 720 genomes
              |s1 s2 s3 s4 s5 s6 s7 s8 sa
            --|--------------------------
            Da|77 21 15 50 53-14 -9 40 77
            D1|54 02 14 23 37 -8 07 19 47
            D2|51 17 01 32 32 -5-16 16 47
            D3|65 32 04 33 29-23 07 22 55
            D5|21 06 15 22 50 10 04 17 40
            D7|64 07 09 46 32-11 -7 36 62
            D8|74 21 16 53 50-15-17 50 77
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • #7
              Re: the birdflu index virus

              automatic cloud analysis

              it should be possible and quite fast.
              but a bit tedious to implement. Has it been done already ?

              reads from a file of genbank records, filtered by keywords
              from the list of all genbank virus files
              picks those with at least k nucleotides and k/3 amino acids
              --------------------------------
              computes pairwise distances without alignment, by counting
              matching 13-subsequences (nucleotides , 4^13=67M) or matching
              6-subsequences (amino acids , 20^6=64M)
              process ~100 sequences at once, ~1M nucleotides=subsequences
              mark them in an 1-byte array , the array-entry pointing to an address
              where the matching sequence-numbers are stored.
              Then walk through all files, check the matches and increase the counters.
              Then the next ~100 sequences, etc.
              --------------------------------------------
              from that data print the corresponding cloud, adjust image size.
              With an option to pre-filter if there are too many sequences
              in the file. With an oprion to not consider all subsequences but only
              ~100 random ones to estimate the distances. Watch the cloud forming
              by randomly selecting subsequences with an option to interrupt
              if it takes long. Option to delete singletons, connected components
              of size <s. Option to filter large genbank files by keywords




              I tried Rabies and PRRS , complete genomes, Dengue needs prefiltering

              Rabies showed some "mallard-Index behaviour" , nucleotide differences
              increasing much with amin-acid differences only increasing little
              in some cloud-region
              PRRS was more uniform
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment


              • #8
                Re: the birdflu index virus

                swine with some segment close to the index:

                Code:
                  1 >A/Index/birds/2000,2000//,H3N8a,           ---,---,---,---,---,---
                 10 >>A/Sw/KU/10/2001,2001//,H11N6,             ---,---,---,---,---,  7
                 12 >>A/Sw/KU/4/2001,2001//,H11N6,              ---,---,---,---,---,  6
                 13 >>A/Sw/KU/2/2001,2001//,H11N6,                6,  4,  9,  4,  5,  7
                 14 >>A/Sw/KU/3/2001,2001//,H11N6,              ---,---,---,---,---,  6
                 11 >>A/Sw/Hong Kong/127/1982,1982//,H3N2,      ---,---,---, 24,  3,---
                 15 >>A/Sw/Ontario/01911-1/99,1999//,H4N6,        4,  4, 13,  2,  5,  3
                 16 >>A/Sw/Guangdong/K4/2011,2011/10/21,H4N8,     3,  5,  3,  1,  4, 12
                 17 >>A/Sw/Guangdong/L21/2011,2011/02/27,H3N2,    6,  9,  4,  4,  7, 11
                 18 >>A/Sw/Hong Kong/126/1982,1982//,H3N2,       11,  4,  5,  4, 15, 40
                 19 >>A/Sw/Hong Kong/81/1978,1978//,H3N2,         8,  3,  9, 16, 10, 36
                
                 20 >>A/Sw/Fujian/F2/2007,2007/10/05,H3N2,       35,  7, 37, 37, 15, 36
                 21 >>A/Sw/Colorado/1/1977,1977//,H3N2,          35,  7, 35, 37, 21, 37
                 22 >>A/Sw/Jilin/37/2008,2008/10/30,H3N2,        21, 14,  9, 41,  5,  1
                 23 >>A/Sw/Texas/4199-2/1998,1998//,H3N2,        11, 15,  9, 26, 11, 40
                 24 >>A/Sw/Korea/C13/2008,2008/02/,H5N2,         23,  4, 25, 29, 16,*10
                
                 25 >>A/Sw/Korea/C12/2008,2008/01/,H5N2,          4,  4,  4,  1,  2,*10
                 26 >>A/Sw/KU/16/2001,2001//,H7N2,                6,  3,  2,  2,  3,*10
                 28 >>A/Sw/Hubei/10/2008,2008/04/30,H10N5,        9,  3,  2,  3,---,  2
                 29 >>A/Sw/China/8/1978,1978//,H3N2,            ---,---,---,---,---,  1
                 30 >>A/Sw/Guangdong/K6/2010,2010/01/17,H6N6,     8, 10, 12,  7, 12, 17
                 32 >>A/Sw/Ontario/42729A/01,2001//,H3N3,         4,  2, 11,  2,  1,  1
                 33 >>A/Sw/Ontario/K01477/01,2001//,H3N3,         7,  2, 11,  2,  1,  1
                 34 >>A/Sw/Missouri/2124514/2006,2006//,H2N3,    18, 23,  9, 31, 14, 52
                
                 35 >>A/Sw/Minnesota/07002083/2007,2007//,H1N1,  18, 19,  9, 27, 13, 47
                 36 >>A/Sw/NC/00573/2005,2005//,H1N1,            18, 19,  9, 26, 14, 43
                 37 >>A/Sw/Saskatchewan/18789/02,2002//,H1N1,    10,  1, 12,  2,  1,* 6
                 38 >>A/Sw/Hong Kong/168/1993,1993//,H1N1,        2,---,---,  5,---, 10
                 39 >>A/Sw/Hong Kong/681/1993,1993/09/27,H1N1,    3, 12,  4,  4,---, 10
                 40 >>A/Sw/Hong Kong/644/1993,1993/09/20,H1N1,    4, 17,  4,  2,---, 10
                                                                            
                 51 >>A/Sw/Guangxi/wz/2004,2004//,H5N1,           6, 13,  8,  3,  8, 11
                 52 >>A/Sw/Anhui/cb/2004,2004//,H5N1,             8, 10,  8,  6, 13, 15
                 53 >>A/Sw/Henan/wy/2004,2004//,H5N1,             3,  7,  8,  5, 13, 13
                 54 >>A/Sw/Banten/UT3063/2005,2005//,H5N1,        7, 10, 12,  6, 15, 17
                 55 >>A/Sw/Banten/UT2071/2005,2005//,H5N1,        7, 10, 12,  6, 15, 17
                 56 >>A/Sw/Banten/UT3081/2005,2005//,H5N1,        7, 10, 12,  6, 15, 17
                 57 >>A/Sw/Banten/UT3062/2005,2005//,H5N1,        7, 10, 12,  6, 15, 17
                 58 >>A/Sw/Anhui/ca/2004,2004//,H5N1,             6,  8, 10,  5, 14, 10
                 59 >>A/Sw/Fujian/2003,2003//,H5N1,               6,  5, 10,  5, 12,  9
                 60 >>A/Sw/Fujian/1/2003,2003//,H5N1,             4,  4,  9,  3, 14,  8
                 61 >>A/Sw/Fujian/F1/2001,2001//,H5N1,            3,  7, 12,  3, 12,  9
                 62 >>A/Sw/Fujian/2001,2001//,H5N1,               5,  9, 13,  4, 12,  9
                 63 >>A/Sw/Shandong/2/03,2003//,H5N1,            12,  8, 10,  5, 13, 26
                
                 64 >>A/Sw/Shandong/fNY/2003,2003//,H9N2,        11,  7,  8,  6, 16, 26
                 65 >>A/Sw/Shandong/8/2003,2003//,H9N2,          10,  6,  8,  6, 16, 26
                 66 >>A/Sw/Shandong/fJN/2003,2003//,H9N2,        12, 11,  9,  5, 14, 26
                 67 >>A/Sw/Shandong/fHZ/2003,2003//,H9N2,        13, 11,  9,  5, 16, 26
                 68 >>A/Sw/Shandong/3/2003,2003//,H9N2,          11, 11, 11,  5, 13, 28
                 69 >>A/Sw/Shandong/w4/2003,2003//,H9N2,         15, 16, 16,  5, 13, 26
                 70 >>A/Sw/Shandong/na/2003,2003//,H9N2,         10,  8, 10,  5, 13, 26
                 71 >>A/Sw/Shandong/nb/2003,2003//,H9N2,          7,  9, 12,  5, 14, 25
                 72 >>A/Sw/Shandong/nc/2005,2005//,H9N2,          1,  7,  9,  6, 14, 26
                 73 >>A/Sw/Korea/S452/2004,2004//,H9N2,          12, 10, 13, 16,  2, 18
                
                
                 72 >>A/Sw/Shandong/nc/2005,2005//,H9N2,          1,  7,  9,  6, 14, 26
                 37 >>A/Sw/Saskatchewan/18789/02,2002//,H1N1,    10,  1, 12,  2,  1,* 6
                 26 >>A/Sw/KU/16/2001,2001//,H7N2,                6,  3,  2,  2,  3,*10
                 25 >>A/Sw/Korea/C12/2008,2008/01/,H5N2,          4,  4,  4,  1,  2,*10
                 32 >>A/Sw/Ontario/42729A/01,2001//,H3N3,         4,  2, 11,  2,  1,  1
                Attached Files
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment


                • #9
                  Re: the birdflu index virus

                  we have a North American index and an Eurasian index.
                  The North American index has 6 changes:

                  V478I(1),N375S(2),V323I(3),S400P(3),V105M(5),S450N (5)

                  closest viruses : (segments 4,6 omitted)

                  Code:
                  total protein-differences from the index-virus  in the 6 segments
                  total proteins available
                  protein differences in the 6 segments
                  number in my file
                  name,date,serotype,country,continent,host,segment,flugenome.org-substrain-code,my_code,submission date,lab,
                  
                  0004,03438, 001,000,001,002,000,000, 06737,>A/Dk/Hokkaido/9/99,1999//,H9N2,Japan,:ES,Avian,8,.81E.,.81bi51.,09-JUN-2006,Yukiko Tanakaœ Hokkaido Universityœ,
                  0005,03438, 001,002,001,001,000,000, 13173,>A/Sv/Italy/2698-27/2006,2006/01/18,H7N7,Italy,5EU,Avian,8,.81D.,.81bi51.,21-JUL-2011,on behalf of JCVI/Istituto Zooprofilattico,
                  0005,03438, 001,001,002,001,000,000, 10972,>A/Md/Sweden/65/2005,2005//,H4N3,Sweden,5EU,Avian,8,.81E.,.81E.,03-JUN-2009,on behalf of JCVI/Erasmus Medical,
                  0006,03438, 001,000,003,000,000,002, 10624,>A/Md/Netherlands/13/1999,1999//,mixed,Netherlands,5EU,Avian,8,.81E.,.81E.,25-JUN-2012,on behalf of JCVI/St Jude Childrens,
                  0006,03438, 001,000,003,000,000,002, 10620,>A/Md/Netherlands/12/1999,1999//,H2N9,Netherlands,5EU,Avian,8,.81E.,.81E.,25-JUN-2012,on behalf of JCVI/St Jude Childrens,
                  0006,03438, 001,000,003,000,000,002, 10618,>A/Md/Netherlands/11/1999,1999//,H2N9,Netherlands,5EU,Avian,8,.81E.,.81E.,25-JUN-2012,on behalf of JCVI/St Jude Childrens,
                  0006,03438, 000,001,001,004,000,000, 00264,>A/avian/Egypt/920431/2006,2006//,H9N2,Egypt,6NF,Avian,8,.81D.,.81bi51.,25-SEP-2009,Southeast Poultry Research Laboratoryœ USDA,
                  0006,03437, 000,002,002,002,000,000, 13329,>A/swan/Czech Republic/5416/2011,2011/04/06,H7N7,Czech Republic,5EU,Avian,8,.81D.,.81bi51.,27-OCT-2011,National Reference Laboratory for Avian,
                  
                  0004,03438, 001,002,000,000,000,001, 09444,>A/Md/NY/180/1986,1986/10/04,H4N9,USA,2NA,Avian,8,.81D.,.81D.,13-SEP-2006,Hartwell Center for Bioinformatics &,
                  0005,03085, 004,001,000,000,000,---, 08965,>A/gwTl/LA/213GW/1987,1987//,H1N1,USA,2NA,Avian,7,..7E.,.7.pNA_75.,01-OCT-2009,Southeast Poultry Research Laboratoryœ USDA,
                  0005,02721, 001,004,---,000,000,000,*09549,>A/Md/ALB/130/2003,2003/08/01,H1N1,Canada,2NA,Avian,8,.82B.,.82B.,24-NOV-2005,Hartwell Center for Bioinformatics &,
                  0006,03438, 001,001,002,002,000,000, 00004,>A/Index/birds/2000(H3N8a)
                  0006,03438, 001,001,002,002,000,000,*00005,>A/Index/birds/2000(H3N8b)
                  0006,03438, 000,001,004,000,000,001,*09706,>A/Md/ALB/76/2006,2006/07/26,H1N3,Canada,2NA,Avian,8,.82B.,.82B.,24-NOV-2010,on behalf of JCVI/St. Jude Children's,
                  0006,03438, 000,002,003,001,000,000, 09767,>A/Md/CA/11100/2008,2008/12/06,H11N2,USA,2NA,Avian,8,.81D.,.81D.,19-JUL-2011,on behalf of JCVI/UC Davis/NCBIœ National,
                  0006,03438, 001,000,003,001,001,000, 10032,>A/Md/iAK/8MP0547/2008,2008/08/11,H8N4,USA,2NA,Avian,8,.81D.,.81D.,23-DEC-2010,on behalf of JCVI/University of Alaska,
                  0006,03438, 001,001,003,000,000,001,*09578,>A/Md/ALB/20/1989,1989/08/02,H3N8,Canada,2NA,Avian,8,.82B.,.82B.,16-NOV-2011,on behalf of JCVI/St. Jude Children's,
                  0006,03438, 001,001,004,000,000,000,*09619,>A/Md/ALB/243/2006,2006/08/09,H7N3,Canada,2NA,Avian,8,.82B.,.82B.,16-NOV-2011,on behalf of JCVI/St. Jude Children's,
                  0006,03438, 002,000,002,000,000,002, 00564,>A/bwTl/ALB/295/1977,1977/09/01,H7N3,Canada,2NA,Avian,8,.81D.,.81D.,24-NOV-2005,Hartwell Center for Bioinformatics &,
                  0006,03438, 002,000,002,000,000,002, 14074,>A/Wd/ALB/284/1977,1977/09/01,H7N3,Canada,2NA,Avian,8,.81D.,.81D.,24-NOV-2005,Hartwell Center for Bioinformatics &,
                  0006,03438, 002,001,002,000,001,000, 12173,>A/Pt/ALB/293/1977,1977/09/03,H2N9,Canada,2NA,Avian,8,.81D.,.81D.,24-NOV-2005,Hartwell Center for Bioinformatics &,
                  0006,03438, 003,001,000,000,000,002,*00810,>A/bufflehead/OH/246/1986,1986//,H11N2,USA,2NA,Avian,8,.82B.,.82B.,12-OCT-2006,on behalf of TIGR/Ohio State,
                  0006,03438, 003,001,001,000,000,001, 10804,>A/Md/OH/83/1986,1986/10/24,H4N6,USA,2NA,Avian,8,.81D.,.81D.,21-SEP-2006,on behalf of TIGR/Ohio State,
                  0006,03435, 001,000,003,001,001,000, 10011,>A/Md/iAK/8BM1966R1/2008,2008/08/08,H8N4,USA,2NA,Avian,8,.81D.,.81D.,29-DEC-2010,on behalf of JCVI/University of Alaska,
                  Md=mallard,Sv=shoveler,Dk=duck,Tk=turkey,Ck=chicke n,Gs=goose,Qa=quail,Pt=pintail duck,Tl=teal
                  iAK = interior Alaska , etc,
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                  Comment


                  • #10
                    Re: the birdflu index virus



                    > segments 1,2,3,5,6,7,8, from A/Green Wing Teal/Ohio/175/1986 (H2N1)
                    > segment 4 from A/mallard/Ohio/265/1987 (H1N9)
                    > similar to the avian influenza virus consensus (see below),


                    3,0,7,-,3,-,0,1 A/Green Wing Teal/Ohio/175/1986 (H2N1) [9004]
                    4,3,5,-,2,-,0,1 A/mallard/Ohio/265/1987 (H1N9) [10751]
                    8,7,10,-,9,-,7,5 A/Brevig Mission/1/1918(H1N1) [3]
                    0,0,0,0,0,0,0,0 A/bird-index-a/2000(H3N8) {1]


                    [x} is the index in gb192av.p11

                    Code:
                                                      00000000000000 0000000000 000000000000000000 00000000000000000000000000000000000000000 00000000000 000000000000000000000000000000000000000 0000000 000000 
                                                      11111244445567 0113334566 000012233333444567 00000000000000011111122222222223333344444 00111233444 000000000000000001122222222333333333344 1222223 011222 
                                                      01899905773620 5177897745 125604612288027531 00011111256679913567800035577990112337799 13003815157 112456777788888898823566788011445558936 2366773 717029 
                                                      84759526589772 4325383654 485201922328036206 46913456230241717683323492369133255851717 63056337703 673237457901234638924647057713462475006 1479131 098971 
                                                      -------------- ---------- ------------------ ----------------------------------------- ----------- --------------------------------------- ------- ------ 
                                                      TVKDAVMNLVIDEK KVENEDVLVS VPDIVCRKIVESSIATEK KFFTTVLKVNSNVNIEASINTASEGDQKDNDLVIKVVRLEK GVRVLLFQNSN VVINIVVVGDATSVITPMGNVLTINTKDDQNIRDVSRQS TLGEKSQ EMIDES 
                    >A/Index/birds/2000(H1N1a)*       .............. .......... .................. ......................................... ........... ....................................... ....... ...... 
                    >A/Brevig Mission/1/1918(H1N1)    AI..S...M.VNKR R..SD.LIMN .LN.AY.RV.D.L..S.R RLLAAATNISKKISVDTALSVGTDDEPRGDNIIVRIIKIAR DIIMMPYK..S ....................................... AIEGRNK K.VNKN 
                    >A/mallard/Ohio/265/1987*         ...N.A.S.I.... .ID..E.... I.....K..I..PM.... ......................................... ...M.....N. ....................................... ....... ------ 
                    >A/GWTeal/Ohio/175/1986*          ..R...L..I.... .......... ...L.....I.GPMV.V. RLLAAATNISKKISVDTALSVGTDDEPRGDNIIVRIIKIAR ...M....SN. AIVSVILIEAIAPMTASISDIFVVSAENERYVKGANKRT ....... .I....



                    here we have afaik the first mentioning of the birdflu index in a public paper from a journal.
                    They call it the "avian influenza consensus"
                    You get their "avian influenza consensus" virus by adding mutations
                    V478I(1),S400P(3),V105M(5),S450N(5)
                    to my "birdflu-index" (ignoring HA,NA - I used H3N8 since it seemed the
                    most widespread serotype in wild birds)



                    J Virol. 2012 September; 86(17): 9211–9220. doi: 10.1128/JVI.00887-12 PMCID: PMC3416129
                    Analysis by Single-Gene Reassortment Demonstrates that the 1918 Influenza Virus Is
                    Functionally Compatible with a Low-Pathogenicity Avian Influenza Virus in Mice
                    Li Qi, A. Sally Davis, Brett W. Jagger, Louis M. Schwartzman, Eleca J. Dunham,
                    John C. Kash, and Jeffery K. Taubenberger
                    Received April 9, 2012; Accepted June 6, 2012.

                    ---------------------------------------------------------------------------------------------------------
                    Sequence analysis.The 1918 and AI gene sequences were compared to
                    consensus wild-bird- derived influenza virus sequences downloaded from
                    the Influenza Virus Resource database (4).
                    North American and Eurasian avian sequences were downloaded
                    from the Influenza Virus Resource database

                    The data set excluded gallinaceous avian sequences. Consensus sequences were
                    obtained after manually aligning the coding regions of each genesegment using
                    Se-Al(48).Sequence alignments consisted of the following coding regions for each segment:
                    1,116 PB2 (2,277-nucleotide [nt]) sequences,
                    1,116 PB1 (2,271-nt) sequences,
                    1,119 PA (2,148-nt) sequences,
                    212 HA (1,218-nt) sequences,
                    1,119 NP (1,494-nt)sequences,
                    865 neuraminidase (NA)
                    (1,410-nt)sequences,
                    514 M1/2 (1,002-nt) sequences, and
                    550 NS1/2 (831-nt) sequences.
                    These sequence alignments are available upon request. Sequence comparisons
                    were performed by aligning the 1918, AI H1N1, and avian influenza virus
                    consensus protein sequences in MegAlign (DNAStar Inc., Madison, WI),
                    and these sequence alignments are available upon request.
                    ---------------------------------------------------------------------------------------------------------------------


                    the result of that study is also interesting:
                    -----------------------------
                    In summary,of the eight 1918-AI chimeras produced, only the 1918 AI-PB2 virus was
                    attenuated in mice compared to the parental 1918 virus. This attenuation was corrected
                    by the single E627K amino acid change,

                    627K change may be critical in the mouse model
                    ... Both the 1918 and AI viruses used in this study encode a serine at position 66 in PB1-F2.
                    ... Surprisingly, in this study, the AI-derived HA gene did not attenuate the 1918 virus,
                    suggesting that the as yet unknown virulence properties of the 1918 HA might not reflect
                    unique 1918 virus-specific mutations. Instead, this virulence property may be shared
                    with LPAI-derived H1 genes, at least in the context of the 1918 genome in mice.
                    ...While isogenic chimeric seasonal human influenza viruses expressing the HA of the
                    1918, 1957, 1968, and 2009 pandemics are all more pathogenic in mice than seasonal
                    HA-expressing control viruses (45),
                    ------------------------------
                    I'm interested in expert panflu damage estimates
                    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                    Comment


                    • #11
                      Re: the birdflu index virus

                      googling "avian influenza consensus" gave 12 hits


                      2000: http://www.ars.usda.gov/research/pub..._no_115=106562
                      were compared to an avian influenza consensus sequence, which at the amino acid level
                      is highly conserved for all the internal viral proteins. The consensus sequence also provides
                      a common point of origin to compare all influenza viruses.
                      ----------------------------------------------------------------------
                      The 1918 PB1 protein differs from the conserved avian influenza consensus sequence
                      by only seven amino acid residues (99).

                      Resurrected Pandemic Influenza Viruses*
                      Annual Review of Microbiology
                      Vol. 63: 79-98 (Volume publication date October 2009)
                      First published online as a Review in Advance on April 22, 2009
                      DOI: 10.1146/annurev.micro.091208.073359
                      Terrence M. Tumpey and Jessica A. Belser
                      99. Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, Fanning TG. 2005.
                      Characterization of the 1918 influenza virus polymerase genes. Nature 437:889–93

                      In October 2005, the sequencing of the
                      1918 polymerase virus genes (PB1, PB2, and
                      PA) completed the entire genetic sequence
                      of the pandemic virus. Analysis of the 1918
                      polymerase protein sequences revealed strik-
                      ing similarities to the polymerase protein se-
                      quences found in the avian influenza consen-
                      sus sequences. The 1918 PB1 protein differs
                      from the conserved avian influenza consensus
                      sequence by only seven amino acid residues
                      (99).

                      109. Van Hoeven N, Pappas C, Belser JA, Maines TR, Zeng H, et al. 2009.
                      Human hemagglutinin and polymerase subunit PB2 proteins confer transmission
                      of an avian influenza virus through the air. Proc.Natl. Acad. Sci. USA 106:3366–7

                      ---------------------
                      see also the tables where they reassorted
                      1918 with Tx/91 and A/Duck/New York/15024/96

                      --------------------------------------------------------------
                      Taubenberger,Tumpey, ... usually just considered amino-acid mutations.
                      While others usually just considered only nucleotide mutations.
                      So they didn't notice that (mallard) viruses from America and Eurasia can be very similar
                      on the amino-acid level while being very different on the nucleotide level (?)
                      ---------------------------------------------------------------
                      Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific si …

                      > the signatures found in the internal proteins of H13 and H16 viruses are possibly
                      > related to host restriction.
                      gull viruses are mostly H13 and H16, and they are usually distant from the index
                      i.e. in segment 8, also to lesser degree in segment 5
                      see mutation picture below.
                      ------------------------------------------------------------
                      ================================================
                      ------------------------------------

                      Wild birds, including wild waterfowls, gulls, and shorebirds,
                      are the natural reservoirs for influenza A viruses, in which they
                      are thought to be in evolutionary stasis (2, 33)

                      2. Alexander, D. J. 2000. A review of avian influenza in different bird species.
                      Vet. Microbiol. 74:3–13.


                      33. Webster, R. G., W. J. Bean, O. T. Gorman, T. M. Chambers, and Y.
                      Kawaoka. 1992. Evolution and ecology of influenza A viruses. Microbiol.
                      Rev. 56:152–179.

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

                      > Avian protein root sequence, 1912-3
                      ### their "AVIAN 1" amino acid sequence in figure 2 is identical with the bird index in segment 5=NP
                      > 1918flu was avianlike, 5 amino acid differences from the avian root NP
                      ### so this was all known since at least 1991, at least for NP,segment 5,
                      ### but rarely mentioned since then, almost forgotten.
                      ### And I was really surprised, when I first noticed it in 2009
                      ### A/Brevig Mission/1918(H1N1) was not known in 1991, it has
                      ### 9 amino-acid differences to the bird-index=avian consensus=avian root in segment 5=NP
                      Attached Files
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment


                      • #12
                        Re: the birdflu index virus

                        dear search engines, can you please grasp :

                        MERIKELRDLMSQSRTREILTKTTVDH
                        MDVNPTLLFLKVPAQNAISTTFPYTGD
                        MEDFVRQCFNPMIVELAEKAMKEYG
                        ---
                        MASQGTKRSYEQMETGGERQNATE
                        ---
                        MSLLTEVETYVLSIVPSGPLKAEIAQR
                        MDSNTVSSFQVDCFLWHVRKRFADQ
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment


                        • #13
                          Re: the birdflu index virus

                          here an updated file "b5.gz" with the differences of the
                          19758 avian influenza genbank viruses (2014/05/17) from the bird index in the 6 inner segments

                          1,2,3,5,7,8,sum,total amino-acids available,access,name,date,country,serotype,avian


                          unzip it with gzip : gzip -d b5.gz
                          Attached Files
                          I'm interested in expert panflu damage estimates
                          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                          Comment


                          • #14
                            update Dec.2016, 8410 complete genbank genomes
                            data : http://magictour.free.fr/GENOMS16.DIS
                            chart : http://magictour.free.fr/GEDI16G.GIF

                            column 7 is the sum, "*" indicates 2nd type segment 8
                            (instead of HxNy we should say HxNyNSz with z in {1,2} )
                            ignore the last 50 or such, probably incorrectly aligned


                            ------------------------------------------
                            this list is currently incomplete due to incorrect sorting of the downloaded
                            genbank entries. I'm making a new list in the next days, and also a list with
                            all, including incomplete, 30570 avian genoms

                            165000 avian sequences =5.4MB compressed
                            list of bird-index-differences for 30566 avian viruses = 3MB bitsis.dis

                            sorted list of bird-index-differences for 14207 complete avian genomes = 1MB bitsisc.dis



                            Last edited by gsgs; December 17, 2016, 04:01 AM.
                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                            Comment

                            Working...
                            X