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the Qinghai-strain is a reassortant of two Jiangxi-mallards
...
Investigators formerly believed that in-fluenza viruses are transmitted unidirec-tionally from wild migratory birds to do-mestic species. However, the A/BHGoose/Qinghai/65/05 (H5N1) virus is a reassortant that obtain edits M,NS,PA,PB1, and PB2 gene segments from A/Mallardduck/Jiangxi/1653/05 (H5N1) and it’s HA, NA,and NP segments from A/Mallard duck/Jiangxi/2136/05 (H5N1). In both cases, domestic ducks infected mallards that were over-wintering in southern China.Thus, the A/BH Goose/Qinghai/65/05 (H5N1)virus apparently contains gene segments from influenza viruses in domestic birds, along with gene segments that were spread in part by mi-gratory birds. The A/BH Goose/Qinghai/65/05(H5N1) virus contains lysine at residue 627 ofPB2, which is associated with pathogenicity in mammals. Did the selection of the PB2 lysine 627 variant occur in mammals in China. Investigators formerly believed that in-fluenza viruses are transmitted unidirec-tionally from wild migratory birds to do-mestic species. However, the A/BHGoose/Qinghai/65/05 (H5N1) virus is a reassortant that obtain edits M,NS,PA,PB1, and PB2 gene segments from A/Mallardduck/Jiangxi/1653/05 (H5N1) and it’s HA, NA,and NP segments from A/Mallard duck/Jiangxi/2136/05 (H5N1). In both cases, domestic ducks infected mallards that were over-wintering in southern China. Thus, the A/BH Goose/Qinghai/65/05 (H5N1)virus apparently contains gene segments from influenza viruses in domestic birds, along with gene segments that were spread in part by mi-gratory birds. The A/BH Goose/Qinghai/65/05(H5N1) virus contains lysine at residue 627 ofPB2, which is associated with pathogenicity in mammals. Did the selection of the PB2 lysine 627 variant occur in mammals in China ?
...
comparing the 3 viruses :
8 segments,
- : not both defined
.:match
o:no match 1st or 2nd position
x:no match 3rd position
I checked my 398 full genome H5N1 sequences for similarities
in segments with the Qinghai strain :
here again a table of selected Qinghai viruses to demonstrate the evolution since
2005 and to show the 4 subgroups with their markers:
(for 2 horizontal printer-sheets with small font)
...
Investigators formerly believed that in-fluenza viruses are transmitted unidirec-tionally from wild migratory birds to do-mestic species. However, the A/BHGoose/Qinghai/65/05 (H5N1) virus is a reassortant that obtain edits M,NS,PA,PB1, and PB2 gene segments from A/Mallardduck/Jiangxi/1653/05 (H5N1) and it’s HA, NA,and NP segments from A/Mallard duck/Jiangxi/2136/05 (H5N1). In both cases, domestic ducks infected mallards that were over-wintering in southern China.Thus, the A/BH Goose/Qinghai/65/05 (H5N1)virus apparently contains gene segments from influenza viruses in domestic birds, along with gene segments that were spread in part by mi-gratory birds. The A/BH Goose/Qinghai/65/05(H5N1) virus contains lysine at residue 627 ofPB2, which is associated with pathogenicity in mammals. Did the selection of the PB2 lysine 627 variant occur in mammals in China. Investigators formerly believed that in-fluenza viruses are transmitted unidirec-tionally from wild migratory birds to do-mestic species. However, the A/BHGoose/Qinghai/65/05 (H5N1) virus is a reassortant that obtain edits M,NS,PA,PB1, and PB2 gene segments from A/Mallardduck/Jiangxi/1653/05 (H5N1) and it’s HA, NA,and NP segments from A/Mallard duck/Jiangxi/2136/05 (H5N1). In both cases, domestic ducks infected mallards that were over-wintering in southern China. Thus, the A/BH Goose/Qinghai/65/05 (H5N1)virus apparently contains gene segments from influenza viruses in domestic birds, along with gene segments that were spread in part by mi-gratory birds. The A/BH Goose/Qinghai/65/05(H5N1) virus contains lysine at residue 627 ofPB2, which is associated with pathogenicity in mammals. Did the selection of the PB2 lysine 627 variant occur in mammals in China ?
...
comparing the 3 viruses :
8 segments,
- : not both defined
.:match
o:no match 1st or 2nd position
x:no match 3rd position
Code:
>A/Bar-headed Goose/Qinghai/65/05(H5N1) - >A/migratory duck/Jiangxi/1653/2005(H5N1) --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------............ .................................................. .................................................. ........... ......................................x........... .................................................. ........... ..............x................................... .................................................. ........... .................................................. .................................................. ....x...... .................................................. .................................................. ........... ...........x...................................... .................................................. ........... .......................x.......................... .................................................. ........... .................................................. 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...............------------------------------------------------------------------------------------------------ --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- 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.........................................x........ .........---------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- -------------------------------------------- .................................................. .................................................. ........... ...................o...........................x.. ..............................................o... ........... ..x..x.....x...o.............x.................x.o ........................x...........x............. ........... .................................................. ...x........................o..................... ........... .................................................. ....................................x............. ........... .....x.......................x.................... .................................................. .....o..... ...................................x.............. .................................................. ........... .........................................x........ .................................................. .......x... .................................................. ...................o.............................. ......o.... ...........x......................o............x.. .................................................. ..........x .................................................. .................................................. ........... ...........x....................x................. .......................o...xo..................... ........... ...---------------------------- .................................................. .................................................. 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--------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------............ .................................................. .................................................. 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.................................................. .................................................. ........... .................................................. .................................................. ........... .................................................. .................................................. ........... .........o.x......................o............... .................................................. ........... .................................................. .................................................. ........... .....x............................................ .................................................. ........... ...............---------------- .................................................. .............................................x.... ........... .................................................. ...............x.................................. ........... .................................................. .................................................. ........... ......................................x........... ..................x.....x..x...................... ..o........ .................................................. .................................................. ........... .................................................. .............................................x.... ........... .................................................. .................................................. ........... .................................................. .................................................. .......x... o..........................o................x..... ...........................................---- .....xo........................................... .................o................................ ........... .................................................. ...........................x..........ox.......... ........... 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--------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------............ .................................................. .................................................. ...o....... ......................................x........... .......o.......................................... 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.................................................. ..............o...x.....x..x...................... .......x... ..............x................................... .oo............................................... ........... ...................o.......................o..o... ............................o..................... ........... ...o.x...............................o............ ..................................o............... .....o..... .....................-----------------------------------
I checked my 398 full genome H5N1 sequences for similarities
in segments with the Qinghai strain :
Code:
compared with A/Dk/Novosibirsk/02/05: total #of differences differences in the 8 segments -------------------------------------------------------------------- + 198 >274 swan/Slovenia/760/06 22 14 15 10 15 8 4 5 - 191 >087 Dk/Fujian/897/05 14 14 20 64 37 46 4 2 - 201 >129 Gs/Shantou/2216/05 20 15 18 64 39 40 3 3 - 202 >135 migratory Dk/Jiangxi/2300/05 56 55 90 4 7 8 13 26 - 219 >090 Dk/Guangxi/2775/05 37 40 34 66 36 36 2 8 - 228 >204 peregrine falcon/HK/D0028/04 34 40 23 56 29 34 6 9 - 231 >107 Dk/Guangzhou/20/05 32 37 32 62 37 36 3 7 - 246 >105 Dk/Guangxi/793/05 29 41 32 36 35 37 3 6 - 259 >074 Ck/Guangxi/604/05 30 47 32 36 35 37 6 5 - 259 >067 Ck/Fujian/1042/05 16 12 16 63 37 37 6 4 *:segment from Qinghai virus . : segment not from Qinghai virus - 191 >087 Dk/Fujian/897/05 ***...** - 201 >129 Gs/Shantou/2216/05 ***...** - 202 >135 migratory Dk/Jiangxi/2300/05 ...***.. - 219 >090 Dk/Guangxi/2775/05 ......** - 228 >204 peregrine falcon/HK/D0028/04 *.*...** - 231 >107 Dk/Guangzhou/20/05 *.....** - 246 >105 Dk/Guangxi/793/05 *.....** - 259 >074 Ck/Guangxi/604/05 *.....** - 259 >067 Ck/Fujian/1042/05 ***...**
here again a table of selected Qinghai viruses to demonstrate the evolution since
2005 and to show the 4 subgroups with their markers:
(for 2 horizontal printer-sheets with small font)
Code:
000000000000000000000000000001111111111111111111111111112 0000000000000000000111111111111111111111112 0000000000000000011111111111111111
001122223334444566667777899990000111233444456666667888990 1122333344555568999001123333445677788899990 1222345555788888811355666777888889
135848890143889412393579702884488025118134490124686499672 1712116668445923157156974589287014514966788 3015095569101256757949356009145682
260962906575395927673949831262469188208713935707807903870 1036186933052471875464751032259861885901768 5765980977765091692323909144282011
-------------------------CACATGAGACATAAACAGCAGCACCCGGCGGTCAAGCATAATATGCCCAGAAGACAG ACAGAGGCCAGCTGGGTGCCAATCCCATATGCAGGCGCAGCTC TCGGTGACTGCGACGCCGGATGGCGCCCGAAGAC
12 2 11 12 121 221 1 1 2 12 1 2 1 1 12 11 2211 121 1 1 1 1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------
Qinghai-strain/index/05 ......................G.................................. ........................................... ..................................
BaHGs/Qinghai/62/05 ..A...GA.....G........G.................................. .........G................................. ..................................
Dk/Novosibirsk/02/05 ......................G.....T......................G..... ........................................... ..................................
Dk/Novosibirsk/56/05 ....A.................G.................................. .............A.............C.C............. ..........................T....A..
Grebe/Novosibirsk/29/05 .....A................G.................................. ........................................... ................T.............G...
GFowl/Shantou/1341/06 ......................G...T.............................. .........................T................. ....................C.............
+ + : + + + + + : + +
MSw/Astrakhan/2-4/05 ...G.....T............G................G.A.........GAG... ............C..A....G.................G...T ......G..............A...T...T....
MSw/Astrakhan/2-3/05 ...G.....T.C..........G................G................. ............C..A......................G...T .T..................CA.......T....
MSw/Croatia/1/05 ...G.....T.C..........G................G......TA......... ............C..A......................G...T .T...................A.......T....
Sw/Germany/R65/06 ...G.....T.C.....A....G................G......TA......... ............C..A..............A.......G...T .T...A...............A.......T....
Dk/Niger/914/06 ...G.....T.C.......T..G................G......TA......... G.G....T....C..AC.......T.....A.......GC..T .T..A................A.......T....
Ck/NGA/957-20/06 ...G.....T.C.......T..G................G......TA......... G.G.........C..AC.......T.....A.......GC..T .T..A.......G........A.......T....
Ck/NGA/1047-62/06 ...G.....T.C.......T..G...A............G......TA......... .....A..T........................AA.A...TC. .T..A.......G........A.......T....
+ + + + + + + + + + +
Azerbaijan/008-208/06 .G........G......A....G....A..A...G.....G....T..G........ ..........A...A..A.T..C...C........T....... C.A....T........T.......A..T..GA..
WSw/Iran/754/06 .G........G......A....G....A..A...G.....G....T..G........ ..........A...A..A.T..C...C........T....... C.A....T........T.................
MSw/Italy/742/06 .G........G......A....G....A..A...G.A...G....T..G........ ..........A...A..A.T..C...C........T....... .....................A.......T....
Ck/Afghanistan/1207/06 .G...T...........A....G...............C.G....T..G........ ...........T..A....................T....... C.A....T........T...........A.....
Grebe/Tyva/Tyv06-1/06 .G...............A....G...............C.G....T..G...A.... ...........T..A....................T.T..... C.A....T........T...........A.....
+ + + +
BaHGs/Mongolia/1/05 .............................A...T..................T...A ........................................T.. ...................G..............
WSw/Mongolia/3/05 .............................A...T.A................T.... .....A............................A.....T.. ................T.................
Ck/Sudan/1784-7/06 ....................AT..G..A....TT...............A..T...A ........T........................A......TC. ........C..........G..............
Dk/CIV/1787-18/06 ....................AT..G..A....TT...............A..T...A ........T........................A......TC. ........C..........G..............
Ck/NGA/641/06 ....................AT..G..A....TT...............A..T...A ........T........................AA.A...TC. ........C..........G..............
Ck/Kurgan/3/05 ........G...........A...........TT..................T...A ........T...............................T.. ...................G..............
Ck/Crimea/08/05 ............G.......A..T.......CTT.....GG...........AG.G. .............A.............C.C............. ......G...T..........A...T...T....
Ck/Kurgan/05/05 ........GT..........A..T.......CTT.....G.A..........AG.GA ........T...............................T.. ..........T........G.....T........
Dk/Kurgan/08/05 .........T.......................T.....G.A.........GAG... ...............A....T.................G.... ......G...T..............T...T....
Mallard/Italy/835/06 .........................T.......T.................GT.... .A...................G..................T.. ...........A......A...............
Turkey/Turkey/1/05 ....G....................T.......T..................T.... .A......................................T.. .....A.....A......A...A...........
Sw/Slovenia/760/06 .........................T.......T..................T.T.. .A.A....................T...............T.. ...........A......A...A...........
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