the birdflu index virus

gsgs · Nov 30, 2009

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:
http://magictour.free.fr/panflu/SE9AGBI.DIS

gsgs · Jan 30, 2010

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

elikan/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*

gsgs · Jan 23, 2012

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

gsgs · Apr 29, 2012

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-------------
111,479,687,774,724,557,490,458,366,298,240,221,108,66,60,60,35,33,32,26,22,21,7,12,9,8,2,0,2,2,2
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-------------
2,23,150,478,561,579,431,447,505,495,429,477,367,270,169,119,69,54,64,47,32,44,31,18,22,14,5,6,5,2,1
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
1,0,11,25,25,43,56,75,93,94,124,111,130,97,87,60,46,36,44,32,24,26,27,9,14,8,3,6,3,2,0
-----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-------------
318,539,517,392,259,181,76,58,63,62,61,45,36,72,108,178,222,175,183,234,219,116,109,98,72,87,87,59,71,91,53
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-------------
30,32,25,24,49,41,19,23,26,8,2,33,27,21,23,44,66,80,86,34,21,18,12,4,5,6,9,8,9,6,13
11,16,13,16,26,27,7,13,20,5,2,3,4,13,12,15,21,37,15,5,9,3,0,0,0,0,0,0,1,0,1
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-------------
4,4,16,42,9,9,7,13,25,22,70,55,49,41,34,30,55,14,13,5,6,2,6,10,6,3,0,0,0,3,0
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-------------
2,3,9,23,56,82,127,120,101,100,132,140,121,60,32,32,22,10,9,9,1,4,4,1,2,0,2,0,0,0,0
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
2,2,9,0,0,1,2,0,12,2,3,7,31,104,187,102,55,98,47,27,7,3,3,0,0,0,0,0,0,0,0
-----segment81-------------
7,7,8,5,4,5,7,24,24,16,9,13,11,27,38,119,156,135,145,208,195,91,86,71,40,41,42,23,14,9,2
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]

gsgs · May 5, 2012

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.

http://www.ncbi.nlm.nih.gov/pubmed/19937535
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

gsgs · May 11, 2012

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

gsgs · May 20, 2012

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

gsgs · Nov 1, 2012

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

gsgs · Nov 4, 2012

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=chicken,Gs=goose,Qa=quail,Pt=pintail duck,Tl=teal
iAK = interior Alaska , etc,

gsgs · Mar 26, 2013

Re: the birdflu index virus

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416129/

> 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)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416129/

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
http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
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),
------------------------------

gsgs · Mar 26, 2013

Re: the birdflu index virus

googling "avian influenza consensus" gave 12 hits

2000: http://www.ars.usda.gov/research/publications/publications.htm?seq_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).
http://www.annualreviews.org/doi/full/10.1146/annurev.micro.091208.073359
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 (?)
---------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pubmed/23646204
> 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.
------------------------------------------------------------
================================================
------------------------------------
http://jvi.asm.org/content/83/17/8428.full.pdf
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.
http://birdflubook.com/resources/Alexande3.pdf

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.

-------------------------------------------
http://jvi.asm.org/content/65/7/3704.full.pdf
> 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

gsgs · Jun 6, 2013

Re: the birdflu index virus

dear search engines, can you please grasp :

MERIKELRDLMSQSRTREILTKTTVDH
MDVNPTLLFLKVPAQNAISTTFPYTGD
MEDFVRQCFNPMIVELAEKAMKEYG
---
MASQGTKRSYEQMETGGERQNATE
---
MSLLTEVETYVLSIVPSGPLKAEIAQR
MDSNTVSSFQVDCFLWHVRKRFADQ

gsgs · Sep 7, 2014

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

gsgs · Dec 16, 2016

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
http://magictour.free.fr/bitsis.dis
sorted list of bird-index-differences for 14207 complete avian genomes = 1MB bitsisc.dis
http://magictour.free.fr/bitsisc.dis

http://magictour.free.fr/BITSISCC.GIF

the birdflu index virus

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