Niedrigpathogene H5 strains seit 2000

[Sarcelle]

AAY57191 564 Avian 4 (HA) H5N3 Sweden 2002 Influenza A virus (A/mallard/Sweden/39/02(H5N3))
AAY57192 564 Avian 4 (HA) H5N6 Sweden 2002 Influenza A virus (A/mallard/Sweden/40/02(H5N6))
ABB83598 564 Avian 4 (HA) H5N2 Denmark 2004 Influenza A virus (A/duck/Denmark/65047/04(H5N2))
ABD46889 564 Avian 4 (HA) H5N2 Germany 2005 Influenza A virus (A/mallard/Bavaria/1/2005(H5N2))
ABG57087 544 Avian 4 (HA) H5N3 Italy 2005 Influenza A virus (A/teal/Italy/3812/2005(H5N3))
ABG75831 561 Avian 4 (HA) H5N2 Italy 2005 Influenza A virus (A/teal/Italy/3931/2005(H5N2))
ABQ84476 564 Avian 4 (HA) H5N3 Italy 2000 Influenza A virus (A/mallard/Italy/208/2000(H5N3))
ABQ84478 563 Avian 4 (HA) H5N3 Italy 2002 Influenza A virus (A/mallard/Italy/36/2002(H5N3))
ABQ84479 536 Avian 4 (HA) H5N3 Italy 2002 Influenza A virus (A/mallard/Italy/37/2002(H5N3))
CAF21870 559 Avian 4 (HA) H5N3 Russia 2001 Influenza A virus (A/duck/Primorie/2633/01(H5N3))
CAF21874 349 Avian 4 (HA) H5N2 Russia 2001 Influenza A virus (A/duck/Primorie/2621/01(H5N2))
CAG14996 564 Avian 4 (HA) H5N3 France 2002 Influenza A virus (A/duck/France/02166/2002(H5N3))
CAG14997 564 Avian 4 (HA) H5N2 France 2003 Influenza A virus (A/chicken/France/03426a/03(H5N2))
CAI96163 564 Avian 4 (HA) H5N3 France 2005 Influenza A virus (A/duck/France/05054a/2005(H5N3))
CAI99404 564 Avian 4 (HA) H5N2 France 2005 Influenza A virus (A/duck/France/05057b/2005(H5N2))
CAJ01911 564 Avian 4 (HA) H5N2 France 2005 Influenza A virus (A/duck/France/05056a/2005(H5N2))
CAJ32556 318 Avian 4 (HA) H5 Germany 2003 Influenza A virus (A/mallard/Germany/WV1349/03(H5))
AAT07996 564 Avian 4 (HA) H5N7 Denmark 2003 Influenza A virus (A/mallard/Denmark/64650/03(H5N7))
AAY57183 564 Avian 4 (HA) H5N2 Sweden 2002 Influenza A virus (A/mallard/Sweden/2/02(H5N2))
AAY57184 564 Avian 4 (HA) H5N2 Sweden 2002 Influenza A virus (A/mallard/Sweden/7/02(H5N2))
AAY57185 564 Avian 4 (HA) H5N2 Sweden 2002 Influenza A virus (A/mallard/Sweden/21/02(H5N2))
AAY57186 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/22/02(H5N9))
AAY57187 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/27/02(H5N9))
AAY57188 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/28/02(H5N9))
AAY57189 564 Avian 4 (HA) H5N2 Sweden 2002 Influenza A virus (A/mallard/Sweden/31/02(H5N2))
AAY57190 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/37/02(H5N9))
AAY57193 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/49/02(H5N9))
AAY57194 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/52/02(H5N9))
AAY57195 564 Avian 4 (HA) H5N3 Sweden 2002 Influenza A virus (A/mallard/Sweden/58/02(H5N3))
AAY57196 564 Avian 4 (HA) H5N2 Sweden 2002 Influenza A virus (A/mallard/Sweden/64/02(H5N2))
AAY57197 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/79/02(H5N9))
AAY57198 564 Avian 4 (HA) H5N9 Sweden 2002 Influenza A virus (A/mallard/Sweden/80/02(H5N9))
ABO77045 565 Avian 4 (HA) H5N2 Italy 2005 Influenza A virus (A/turkey/Italy/1258/2005(H5N2))
ABR37330 565 Avian 4 (HA) H5N2 Italy 2005 Influenza A virus (A/turkey/Italy/1325/2005(H5N2))
ABR37341 564 Avian 4 (HA) H5N2 Italy 2005 Influenza A virus (A/teal/Italy/3931-38/2005(H5N2))
ABR37352 564 Avian 4 (HA) H5N3 Italy 2005 Influenza A virus (A/teal/Italy/3812/2005(H5N3))
ABS89310 564 Avian 4 (HA) H5N3 Italy 2004 Influenza A virus (A/duck/Italy/775/2004(H5N3))
AAY25499 442 Avian 4 (HA) H5N3 Russia 2003 Influenza A virus (A/Anas platyrhynchos/Chany Lake/9/03(H5N3))

[gsgs]

davon H5N1:
RK----KR A/chicken/Scotland/1959(H5N1)
KE----TR A/teal/Germany/WV632/2005(H5N1)
RE----TR A/duck/France/05066b/2005(H5N1)
RE----TR A/mallard/Italy/3401/2005(H5N1)

(nur Europa)


mallard:Stockente
chicken:Huhn
turkey:Truthan/Pute
teal:Krickente
duck:Ente

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

vorangestellte Buchstaben sind die Aminosaeuren der "cleavage-site",
der Ausschnitt aus dem Virus-Genom von ca. 5000 Amino-saeuren
der das HA-Gen auftrennt und besonders wichtig ist zur
Funktion des Virus in verschiedenen Zell-Arten.
hoch pathogenes H5N1 Typ Qinghai hat hier normalerweise GERRRKKR,
das Fehlen der 4 Aminosaeuren in der Mitte bedeutet
niedrig-pathogen

[gsgs]

Vergleich der Eurasischen niedrig-pathogenen H5 Protein-Sequenzen
Gelistet sind nur die (von 568 ) Positionen, wo wenigstens
2 der Viren sich von den anderen unterscheiden.
. : Uebereinstimmung mit Index
X: abweichende Aminosaeure

{Influenza hat 8 Segmente:
PB2,PB1,PA,HA,NP,NA,M,NS
mit 2341,2341,2233,1778,1565,1413,1027,890 Nukleotiden
und 11 Proteinsequenzen (Gene):
PB2,PB1,PB1-F1,PA,HA,NP,NA,M2,M1,NS2,NS1
mit 759,757,91,716,568,498,252,97,225,121 Aminosaeuren,
wobei jeweils 3 Nucleotide eine Aminosaeure bilden.
Zahlen fuer H5N1-Qinghai, leichte Abweichung bei anderen Typen
http://www.microbiologybytes.com/vir...xoviruses.html
}

zum Vergleich ist die Katze aus Ruegen mit reingenommen,
obwohl hoch-pathogen. Man sieht, dass die hoch-pathogenen
H5s sich doch deutlich unterscheiden, und zwar nicht
nur in der Cleavage.

Po-                                        00000000000000000111111111111111111111222222222222222222222233333333333344444444444444455555555
si-                                        00000011111345579000011223344555777779001112223345557778889901223334469911112234566779901122444
tion                                       23478902456071239023408371502246017890141493683420243792461827053690544701341362626372943579049
Index :----------------------------------  EKILLAISVKSEDKTVDNVNGDKSFQRNDPNRNNKRSVATTVSQVEPKMKNAVDAKGENMNEKDLVRETVIKEAGKRIDAFKDRKNRDRNMTAAV
01 A/Ck/Scotland/1959(H5N1)                .R.........K.R....I.S.........I.D....I......I............ADV.......KK...K....V.V...KR......V..I
02 A/Dk/Hong Kong/819/1980(H5N3)           ....F........R.....Y.........S..D....I......T...I.............................G....KR.K.....T.I
03 A/Dk/Hong Kong/342/1978(H5N2)           ....F...A....R.......................I..........I.K.............................L..KR.KN......I
04 A/goose/Hong Kong/23/1978(H5N3)         ....F........R.........R..K..........I.............................................KR.KN......I
05 A/Dk/Hong Kong/205/1977(H5N3)           .............R...................S...I......................................K.....NKR.KN......I
06 A/Dk/Hong Kong/698/1979(H5N3)           .............R...................S...I.........R........EK....................N....KR.KN......I
07 A/Dk/Hong Kong/23/1976(H5N3)            .............R..............N.....N..I.......................K.....................KR.KN......I
08 A/Dk/Hong Kong/394/1978(H5N3)           .RT..........R.......................I.I...........................................KR.KN.K....I
09 A/turkey/England/N28/73(H5N2)           .R.F.VVG.....R....T..................I.........................NP..................KR.KN...V.TI
10 A/turkey/Italy/1980(H5N2)               ......V..R....................I......I.IS....K....DV.G..........P....I.............KRD.N......I
11 A/Dk/Potsdam/2216-4/1984(H5N6)          ......V..R...................S........................................VR...........KRD.NK.....I
12 A/Dk/Potsdam/1402-6/86(H5N2)            ........AE........I..................I...........................................R..R.KN......I
13 A/Dk/Singapore/3/1997(H5N3)             .........................R...........I...............G.........G......................K....I..I
14 A/Dk/Malaysia/F119-3/97(H5N3)           .........................R...........I...............G.........G......................K....I..I
15 A/Pekin Dk/Singapore/F59/04/98(H5N2)    .......N...........Y.....R......S....IT.N..........V..................................K....I..I
16 A/mallard/Italy/36/02(H5N3)             ........................L.....I....................V..................................K........
17 A/Ck/Italy/22A/1998(H5N9)               ...................D....L..........E...I....I...................P.K...............E...KN....V.I
18 A/Dk/France/05056a/05(H5N2)             ....F.......N...............................I.........T.A.D.......K..I...S............KNK....VI
19 A/mallard/Sweden/58/02(H5N3)            ....F..N............................N....I..............E....................T................I
20 A/mallard/Sweden/64/02(H5N2)            ....F.VN.................................I....L................................................
21 A/mallard/Sweden/31/02(H5N2)            ....F.V................R.......................................................................
22 A/mallard/Sweden/28/02(H5N9)            ....F.V................R.........................................I.............................
23 A/mallard/Sweden/49/02(H5N9)            ....F.V................N..............................T..........I.............................
24 A/mallard/Sweden/40/02(H5N6)            ....F.V...............................................T..........I......G......................
25 A/mallard/Sweden/37/02(H5N9)            ....F.V..............................................G...........I.............................
26 A/mallard/Sweden/22/02(H5N9)            ....F.V..........................................................I............V................
27 A/mallard/Sweden/27/02(H5N9)            ....F.V..........................................................I............N................
28 A/mallard/Sweden/79/02(H5N9)            ....F.V..........................................................I.......T.....................
29 A/mallard/Sweden/80/02(H5N9)            ....F.V..........................................................I.......T.....................
30 A/mallard/Sweden/52/02(H5N9)            ....F.V..........................................................I........E....................
31 A/Dk/Jiang Xi/1850/05(H5N2)             ....F............SI.......................................................R..........D....I....
32 A/garganey/SanJiang/160/06(H5N2)        ....F............SI..............D...................................................D....I....
33 A/Dk/Jiang Xi/6146/03(H5N3)             A...F.........K..SI.....................................E............................D....I....
34 A/Dk/Jiang Xi/1286/05(H5N2)             AGV.F............SI...........A......................................................D....I....
35 A/migr.Dk/Hong Kong/MP206/04(H5N2)      ....F............SI..N...............................................................D....I....
36 A/Dk/MNG/54/01(H5N2)                    ....F............SI........D........N.T.........I...A..E......R......................D....I....
37 A/Dk/Hokkaido/Vac-1/04(H5N1)            ....F............SI........D........N.T.........I...A..E......R......................D....I....
38 A/R(Dk/MNG/54/01-Dk/MNG/47/01)(H5N1)    ....F............SI........D........N.T.........I...A.........R......................D....I....
39 A/Dk/France/05066b/05(H5N1)             .....VT...G..R...S...............S......N...........I..................R................K......
40 A/Ck/France/03426a/03(H5N2)             .....V....G.N........N..................................E......NP.......................K......
41 A/mallard/Italy/208/00(H5N3)            ..........G....................................................................V...............
42 A/mallard/Sweden/21/02(H5N2)            ..................................T.....................E............I........G................
43 A/mallard/Netherlands/3/99(H5N2)        ...............A...............................................................................
44 A/mallard/Sweden/39/02(H5N3)            ..............A..............................................K.................................
45 A/mallard/Sweden/7/02(H5N2)             ..............A.......R.......S..................R..........................K..................
46 A/mallard/Sweden/2/02(H5N2)             ..............A.......R.......S..................R..........................K..................
47 A/teal/Germany/WV632/05(H5N1)           .......N......A..........R.....K...............R................P.K.........G..................
48 A/Dk/Denmark/65047/04(H5N2)             ..............A................................R..................K......T.N...................
49 A/mallard/Denmark/64650/03(H5N7)        ..............A........................M........I..............N..K.............L..............
50 A/turkey/Italy/1325/05(H5N2)            ...P.......K..A...............H...........P................IS...................L.......K......
51 A/turkey/Italy/1258/05(H5N2)            ...P.......K..A...............H...........P................IS..................V........K......
52 A/teal/Italy/3812/05(H5N3)              ..............A...........................L.I...........................X.....................I
53 A/mallard/Bavaria/1/05(H5N2)            ..............A...............................................................N...............I
54 A/Dk/France/05054a/05(H5N3)             ..............AIN..................KN......H..................................................I
55 A/Dk/France/05057b/05(H5N2)             ..............A..............L.K...........H.....R............................................I
56 A/teal/Italy/3931-38/05(H5N2)           ..............A.......................................V..........................R............I
57 A/mallard/Italy/3401/05(H5N1)           ......V.......A...I....N....E.................................................................I
58 A/Dk/Italy/775/04(H5N3)                 ..............A...A....R.R.D.......................................D....................K.....I
59 A/cat/Germany/R606/06(H5N1)             ....F...........I.A.D..R..KDE.Q.D........I...KS.......T.E..I...N.SG.K.V....R.............KI....
Index :----------------------------------  EKILLAISVKSEDKTVDNVNGDKSFQRNDPNRNNKRSVATTVSQVEPKMKNAVDAKGENMNEKDLVRETVIKEAGKRIDAFKDRKNRDRNMTAAV

[Sarcelle]

kannst du auf die schnelle einstellen, welche der stains full genome sequenziert sind?

Hatte vor einigen Monaten mal angefangen, mir Gedanken über die T zell immunity und der Identität von NP PBA etc mit den Clade 2.2 strains zu machen, habe aber feststellen müssen dass kaum einer der strains sequenziert ist.

[gsgs]

voll-Genom H5-low-path Viren bei Genbank:
---------------------------------------------------
Eurasische Viren:
KETR A/chicken/Italy/22A/1998(H5N9)
KETR A/duck/Denmark/65047/04(H5N2)
KETR A/mallard/Denmark/64650/03(H5N7)
RDTR A/duck/Italy/775/2004(H5N3)
RETR A/R(duck/Mongolia/54/01-duck/Mongolia/47/01) (H5N1)
RETR A/chicken/Ibaraki/1/2005(H5N2)
RETR A/duck/Hokkaido/Vac-1/04(H5N1)
RETR A/duck/Hong Kong/205/1977(H5N3)
RETR A/duck/Hong Kong/23/1976(H5N3)
RETR A/duck/Hong Kong/312/1978(H5N3)
RETR A/duck/Hong Kong/342/1978(H5N2)
RETR A/duck/Hong Kong/394/1978(H5N3)
RETR A/duck/Hong Kong/819/1980(H5N3)
RETR A/duck/Jiang Xi/1286/2005(H5N2)
RETR A/duck/Jiang Xi/6146/2003(H5N3)
RETR A/duck/Potsdam/1402-6/1986(H5N2)
RETR A/duck/Potsdam/2216-4/1984(H5N6)
RETR A/garganey/SanJiang/160/2006(H5N2)
RETR A/goose/Gui Yang/3799/2005(H5N2)
RETR A/goose/Hong Kong/23/1978(H5N3)
RETR A/mallard/Italy/1980/1993(H5N2)
RETR A/mallard/Italy/3401/2005(H5N1)
RETR A/mallard/Italy/36/2002(H5N3)
RETR A/mallard/Italy/37/2002(H5N3)
RETR A/migratory duck/Jiang Xi/13487/2005(H5N3)
RETR A/shorebird/DE/101/2004(H5N7)
RETR A/shorebird/DE/75/2004(H5N7)
RETR A/teal/Italy/3812/2005(H5N3)
RETR A/teal/Italy/3931-38/2005(H5N2)
RETR A/turkey/Italy/1258/2005(H5N2)
RETR A/turkey/Italy/1325/2005(H5N2)
RETR A/turkey/Italy/1980(H5N2)


die Amerikanischen Sequenzen unterscheiden sich
in einigen Markern:

KKKR A/chicken/Pennsylvania/1/1983(H5N2)
REKR A/chicken/TX/167280-4/02(H5N3)
RETR A/avian/NY/31588-3/00(H5N2)
RETR A/black duck/New York/184/1988(H5N2)
RETR A/chicken/Chis/15224/1997(H5N2)
RETR A/chicken/Hidalgo/28159-232/1994(H5N2)
RETR A/duck/Minnesota/1516/1981(H5N2)
RETR A/duck/NJ/117228-7/01(H5N2)
RETR A/duck/NY/185502/02(H5N2)
RETR A/duck/NY/44018-1/00(H5N2)
RETR A/herring gull/NJ/402/1989(H5N3)
RETR A/mallard duck/ALB/57/1976(H5N2)
RETR A/mallard duck/New York/189/1982(H5N2)
RETR A/mallard/Maryland/789/2002(H5N2)
RETR A/wigeon/Ohio/379/1988(H5N2)
RKKR A/chicken/TX/298313/04(H5N2)

[Sarcelle]

KKKR A/chicken/Pennsylvania/1/1983(H5N2)

Sieht aber nicht niedrigpathogen aus. Eher multibasisch

rnvpqkkkrglf

Influenza A virus (A/Chicken/Pennsylvania/10210/86(H5N2))
rnvpqkkkrglf

Influenza A virus (A/chicken/Massachusetts/11801/86(H5N2))
nvpqkkkrglf

Influenza A virus (A/chicken/Mexico/31381-7/1994(H5N2))
nvpqretrglf