origin of Qinghai H5N1

gsgs · Mar 5, 2007

the Qinghai-strain is a reassortant of two Jiangxi-mallards

http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000002704/znw01206000559.pdf

...
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..........................  ..................................................  ...........
..................................................  ..................................................  ..o........
..................................................  ..................................................  ....x......
..................................................  ..............................x...................  ...........
..................................................  .................................x................  ...........
............--------------------------------------------------------------
 
.................x................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
.o................................................  ..................................................  ...........
......................................x...........  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ......................o...........................  ...........
...................................x..............  ..................................................  ...........
..................................................  ..................................................  ...........
...............------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------
 
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------....................................
..................................................  .........x........................................  ...........
.....x............................................  ...x....ox.............................x..........  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
.............................x....................  ..................................................  ...........
..............................................o...  ..................................................  ...........
..................................................  ..................................................  ...........
.................................o................  ..................................................  ...........
..................................................  ........................x.........................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  .o................................................  ...........
.................................---------------------------------------------
 
..................................................  ..................................................  ...........
........x...........x.............................  x..............x........x.................x.......  ...........
....................................o.......x.....  ......................oo..o.......................  ....xo.....
.....x............................................  .................................xo...............  ...........
................o.....o.o..........x..............  .................o.....................x..x.......  ...........
...................................x..............  ........o....................................x....  ...........
..........................x........x.....x........  ...............x..x........................o....x.  ....x......
........................o.........................  .......o.............x............................  ...........
.....x...................................x........  ..................................................  ...........
...............o................x...........x.....  ..................................................  .......x...
...........x..............x.......................  ..................................................  ...........
..................................................  x......................................x..........  ...........
..................................................  ................................................x.  ....x......
......................o.......o.......x...........  .............................................xo...  ...........
..x....................x..........................  ...............x..x........x..............x.......  ...........
..............x.................---
 
..................................................  ..............................................o...  .......x...
..................................................  ......x...................................x.......  .......xo..
..................................................  ...................o......o.......................  ...........
......................................x...........  ...............x..x...............................  ...........
.................x..x.............................  ..................................................  ....x.....x
..................................................  ..............................x..x................  .x.........
..................................................  ......x...o....x..................................  ...........
.............................x..x.................  ........................x.........................  ....x......
....................x.......................x.....  ..................................................  ...........
.........................................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.....................  ...........
...----------------------------
 
..................................................  ..................................................  ...........
..................................................  ......x...........................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
....o.............................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................-----------------------------
 
---------..................................................  ........o.........................................  ..
..................................................  ..................................................  ...........
..................................................  ..............................................o...  ...........
..................................................  ..................................................  ...........
.....x............................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
.....................-----------------------------------
 
>A/Bar-headed Goose/Qinghai/65/05(H5N1)  -  >A/migratory duck/Jiangxi/2136/2005(H5N1)
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------............
..................................................  ..................................................  ...o.......
..................................................  .......o..........................................  ...........
..............x...................................  ..................................................  ...........
...................o..............................  ..................................................  ...........
...........x...................................x..  ......x...o.............x.........................  ...........
.....x.....x...........x..........................  .............................................x....  ...........
...........x.....x.....x.................x...o....  ..................x...............................  ...........
..................................................  ...............x.............................x....  ..o........
..................................................  .......o................x.........................  ....x......
..............x.................................o.  ..............................x...................  ...........
.........................................x........  ...............x..........................x.......  ...........
..................................................  .......-----------------
 
..................................................  ................................................x.  ...........
...........................................o......  ..................................................  ...........
....................x.............................  ..............................x..............x....  ...........
............................................x.....  .......................................x..........  ...........
......................................x...........  ..................................................  ...........
....................x.................x...........  .....................x............................  ...........
........x.........................................  .......................................x..........  .....o.....
.........................................x........  ..................................................  ...........
................................x.................  ...x..........................x...................  ...........
...................................x...........x..  ........o.................................x.......  ...........
..................................................  .........x........................................  ...........
................................x..x............o.  ...x..............................................  ...........
..................................................  ............x..................o.............x....  ...........
...............................--------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------
 
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
------------------------------------------------------...................................x..x...........  ....oo.
.....x..x................................x........  .........x...o.........................x........x.  ....x......
........x.....x.....x.............................  ...x....o..........o...ox..............x..x.......  ...........
...o..........x...................................  ..................x....................x....o.....  ....x......
..............x...................................  ...........................x..x........x..........  ....x..x...
.................x................................  x........x..x..x.......................x..........  .x........x
....................x..x..x........x..x.....x.o...  ....o........................................x....  .x.........
..............x.................x........x..x..x..  x.............................x.....x.....x.......  .......x...
.....x..............x.....x......o................  ...............x.......................x.........o  ....x.....x
................................x..x..x..x........  x.................x.....x.........................  .......x...
........x.....x...................................  ...........................x..x........x........x.  ...........
.....x..x..............x..x..x..x.................  xo...........o.........................x..........  ...........
.o.............................................x..  .o................................................  ...........
..................o..............---------------------------------------------
 
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..........o.......................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..............................o...................  ..................................................  ...........
..................................................  ..................................................  ...........
................................---
 
..................................................  ..................x...........................o...  ...........
..................................................  ..................................................  ...........
..................................................  ..........................o.......................  ...........
......................................x...........  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..............................x...................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  .............................................x---------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
--------------------------------------------
 
------------------------------------------------------------------..........................x..................
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ....................................x.............  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  ...........
.........o.x......................o...............  ..................................................  ...........
..................................................  ..................................................  ...........
.....x............................................  ..................................................  ...........
...............----------------
 
..................................................  .............................................x....  ...........
..................................................  ...............x..................................  ...........
..................................................  ..................................................  ...........
......................................x...........  ..................x.....x..x......................  ..o........
..................................................  ..................................................  ...........
..................................................  .............................................x....  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  .......x...
o..........................o................x.....  ...........................................----
 
.....xo...........................................  .................o................................  ...........
..................................................  ...........................x..........ox..........  ...........
.................x....................x...........  x.............................................o...  ...........
..................................................  ..............o...x.....x..x......................  .......x...
.....x........x...................................  .oo...............................................  ...........
...................o.......................o..o...  ............................o.....................  ...........
...o.x...............................o............  ..................................o...............  .....o.....
......................o...........................  ....--
 
>A/migratory duck/Jiangxi/1653/2005(H5N1)  -  >A/migratory duck/Jiangxi/2136/2005(H5N1)
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------............
..................................................  ..................................................  ...o.......
......................................x...........  .......o..........................................  ...........
..................................................  ..................................................  ...........
...................o..............................  ..................................................  ....x......
...........x...................................x..  ......x...o.............x.........................  ...........
.....x.................x..........................  .............................................x....  ...........
...........x.....x.......................x...o....  ..................x...............................  ...........
..................................................  ...............x.............................x....  ...........
..................................................  .......o................x.........................  ...........
..............x.................................o.  ..................................................  ...........
.........................................x........  ...............x.................x........x.......  ...........
............--------------------------------------------------------------
 
.................x................................  ................................................x.  ...........
...........................................o......  ..................................................  ...........
....................x.............................  ..............................x..............x....  ...........
.o..........................................x.....  .......................................x..........  ...........
..................................................  ..................................................  ...........
....................x.................x...........  .....................x............................  ...........
........x.........................................  .......................................x..........  .....o.....
.........................................x........  ..................................................  ...........
................................x.................  ...x..........................x...................  ...........
...................................x...........x..  ........o.................................x.......  ...........
..................................................  .........x............o...........................  ...........
................................x...............o.  ...x..............................................  ...........
..................................................  ............x..................o.............x....  ...........
...............------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------
 
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------..............x..x...............oo.
.....x..x................................x........  .............o.........................x........x.  ....x......
.....x..x.....x.....x.............................  .........x.........o...ox.................x.......  ...........
...o..........x...................................  ..................x....................x....o.....  ....x......
..............x...................................  ...........................x..x........x..........  ....x..x...
.................x...........x....................  x........x..x..x.......................x..........  .x........x
....................x..x..x........x..x.....x.....  ....o........................................x....  .x.........
..............x.................x........x..x..x..  x.............................x.....x.....x.......  .......x...
.....x..............x.....x.......................  ...............x.......................x.........o  ....x.....x
................................x..x..x..x........  x.................x...............................  .......x...
........x.....x...................................  ...........................x..x........x........x.  ...........
.....x..x..............x..x..x..x.................  xo...........o.........................x..........  ...........
.o.............................................x..  ..................................................  ...........
..................o..............---------------------------------------------
 
..................................................  ..................................................  ...........
........x...........x.............................  x..............x........x.................x.......  ...........
....................................o.......x.....  ......................oo..o.......................  ....xo.....
.....x............................................  .................................xo...............  ...........
................o.....o.o..........x..............  .................o.....................x..x.......  ...........
...................................x..............  ........o....................................x....  ...........
..........................x........x.....x........  ...............x..x........................o....x.  ....x......
........................o.........................  .......o.............x............................  ...........
.....x...................................x........  ..................................................  ...........
...............o................x...........x.....  ..................................................  .......x...
...........x..............x.......................  ..........o.......................................  ...........
..................................................  x......................................x..........  ...........
..................................................  ................................................x.  ....x......
......................o...............x...........  .............................................xo...  ...........
..x....................x..........................  ...............x..x........x..............x.......  ...........
..............x..................--
 
..................................................  ..................x...............................  .......x...
..................................................  ......x...................................x.......  .......xo..
..................................................  ...................o..............................  ...........
..................................................  ...............x..x...............................  ...........
.................x..x.............................  ..................................................  ....x.....x
..................................................  .................................x................  .x.........
..................................................  ......x...o....x..................................  ...........
.............................x..x.................  ........................x.........................  ....x......
....................x.......................x.....  .............................................x---------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------
--------------------------------------------
 
------------------------------------------------------------------..........................x..................
...................o...........................x..  ..............................................o...  ...........
..x..x.....x...o.............x.................x.o  ........................x...........x.............  ...........
..................................................  ...x........................o.....................  ...........
..................................................  ..................................................  ...........
.....x.......................x....................  ..................................................  .....o.....
...................................x..............  ..................................................  ...........
.........................................x........  ..................................................  .......x...
..................................................  ...................o..............................  ......o....
.........o.....................................x..  ..................................................  ..........x
..................................................  ..................................................  ...........
.....x.....x....................x.................  .......................o...xo.....................  ...........
...----------------------------
 
..................................................  .............................................x....  ...........
..................................................  ......x........x..................................  ...........
..................................................  ..................................................  ...........
......................................x...........  ..................x.....x..x......................  ..o........
....o.............................................  ..................................................  ...........
..................................................  .............................................x....  ...........
..................................................  ..................................................  ...........
..................................................  ..................................................  .......x...
o..........................o................x.....  ..................-----------------------------
 
---------..................................................  ..................................................  ..
..................................................  ...........................x..........ox..........  ...........
.................x....................x...........  x.................................................  ...........
..................................................  ..............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...........
Dk/Egypt/2253-3/06       T...........G.G..........T..T....T..T......CA.......T.T.. .A.AG.AT..........A......T.....T........T.. .........A.A..T...A...............
Egypt/902782/06          T...........G.G..........T.......T.........CA.......T.T.. .A..G.A...........A............T...T....T.. .........A.A..T...A...............
Turkey/651242/06         ...............GG................T.A......G.......G.T.... .......................T....G...G....T..T.. ...A.........T.T.A.....T........GT
Turkey/15/06             ...............GG.G..............T.A.T....G.......G.T.... .......................T....G...G....T..T.. ...A.........T.T.A.....T........GT
Turkey/65596/06          ...............GG.G..............T.A.T....G.......G.T.... .......................T....G...G....T..T.. ...A.........T.T.A.....T........GT
Iraq/1/06                ................G................T........G.......G.T.... ............................G........T..T.. ...A.........T...A.....T........GT
Gs/Hungary/3413/07       .....T...........................T..................T.... .....................G..................T.. ...A......................T.....G.
                                                                                                                                                                 
                                                                                                                                                                 
                                                                                                                                                                 
                                                                                                                                                                 
















112 0000000000000000000000000000000011111111111111111 000000000000000000000000111111111 000000000000000000111111111 0000000000000000 00000000000000000000000   0 
990 0011111112223444555556666678899900011122333445556 000222223333444466788899001111122 012344444566677799000111122 1123344455666788 00112223344455666677778   0 
395 2324455683469036014581366954504956712323088330895 256236992336044835405978040158959 131800145114822709116036746 3691312345036701 06145890000756013628990   0 
526 2101734837076588813255316910295032132743239143708 816517498139647667489457877222079 806523449688309165178441410 2315976268030083 68133540658785596747692   0 
GAC CGCCGGAGTGCGCAGGGATCCGCCCCCTATCGTTGCCGGTCCCGGATCC TATGAGGGCTCGCTGGATTGAGGGAGGTAAACT GCCGTCACGATCAAGGCATCTGTCCGG GCTAGTGTCTGGGGGT TCCACGCCCGATAGACTTTGAAC   0 
  1 11    1         11     1  1                     2 1      211  1      11      2  2    1 1 1      2    2      12   1           21   2 21        121 111111   0 
-------------------------------------------------------------------------------------------------------------------------------------------------------------  0 
... ................A................................ ................................. ..................C........ ................ .......................   3 
..T ................A......................C......... .......A........G................ .................GC........ ................ .T.....................   14
... ................A................................ ............................G.... A.......................... ................ .......................   25
... ............A...A.C.....T................T....... ................................. ........A...............T.. ................ .......................   23
... ................A...T..................C......... ........................G........ ..................C........ ...G............ .......................   37
... ................A................................ ...............................T. ..........................A ................ ............G..........   38
    +               +                             +                                                                            +  +               +              
... T.................................AT...C....ATC.. .........C.....................A. ..................C........ ..............A. .............A...C....T   51
... T......................................C......C.. ................................. ..................C........ ...........A..A. .......................   36
... T......................................C......C.. ...................A............. ..................C........ ...........A..A. .........A...A.........   36
... T......................................C......C.. ...................A............. ..................C........ ...........A..A. ..........G..A.........   47
.G. T........A............................AC...A..C.. .............C.....A.A.A......... ..................C..T..... ...........A..A. C...T........A.....A...   58
.G. T........A.............................C...A..C.. .............C.....A.A........... ..................C..T..... ...........A..A. C...T........A.....A...   48
.G. .......A.....G.A.....A...........G............... ...A....T......A.......A.A....... .......T...T......C..T..... ...........A..A. ...G.AT....CG.....C....   65
            +       ++         +           +          +                ++           +             +        +         +                   +   +     + +           
... --.T..G.C.......AG.........C....C....A.C......... --C...........A..CC...........G.C ...A.....CCA..A....TC..T... .TC.......A.A... ....T...T.....G.C......   79
... ...T..G.C.......AG.........C...........C..T.....- C................CC...........G.C .........CC........T....... .TC.......A..... ....T...T...------.....   62
... ...T..G.C...A...AG.........C...........C......... C................CC...........G.C .........CC........T.....A. .TC.......A..... ....T...T.....G.C......   58
... .A..A...C.T.....AG.........C...........CT......T. C................CC......A....G.. ..T.......C.....T..T....T.. .T......A....... ....T...T.....G.C......   53
... .A......C.T.....AG.........C...........CT......T. C................CC...........G.. ..........C..G.....T....T.. .T......A....... ....T...T.....G.C......   60
           +                                             +                                          +                                      +     +               
... .......A..............................A.....A.... ...A............................. ............G...T.......... ................ ......T.....G.......TT.   53
... .......A......................................... ...A.......A..................... ............G.............. ................ ......T.....G.......TT.   50
... .......A.....G......TA..T........G.......T....... ...A....T......A............G.... A.......A...G.........CT... A.....TA........ ...G..T..A.CG.....C....   68
... .......A.....G.......A........................... ...A....T......A................. ........A...G.........CT... A.....TA........ ...G..T....CG.....C....   51
... .......A.....G.......A........................... ...A....T......A.......A......... ........A...G.........CT... A.....TA........ ...G.AT....CG.....C....   46
... .......A.....G.......A........A...........T...... ...A.........................G... ........A...G.............. ......T......... ...G..T.....G..........   39
... ................A................G............... ...........A..........A.......... .....TG.A.................. .TC.A........... ....T...T..............   52
... ..T....A.....G..............................A.... ...A..................A.......... .....TG.A...G.............. ......T......... .............A...C....T   39
... T.................................AT...C....ATC.. ...A.......................C..... .....TG.....G.....C.......A ................ ......T.....G..........   43
... .......A..............TT.T.....T................- ...AG.....T................C.G... .T..........G.......C....A. ................ ..T...T.....------.....   65
... --.....A..............T..T..G..T................. --.AG......................C..... .T..........G.......C...... ................ ..T...T.....G..........   52
... .......A..............T..T..G.TT................. ...AG....C..........G......C..... .T..........G.......C...... ................ ..T...T...G.G..........   58
T.. .......A......AA......T..TT.GC.T................T ...AG...............G...C.AC..... .TT.........G.......C.....A .....C.......A.. ..T...T.....G..........   66
T.. --.....A......AA......T..TT.GC.T................T -G.AG.....T...A.....G.....AC..... .TT.........GG......C.....A .....C.......A.. ..T...T.....G..........   74
... --A....A...........T..........A.....T............ --.A.AA.......................... ....C.......G..A........... ...G.....G.....C -.....TT....G..........   49
... --A..A.A...A.......T..........A.....T............ --.A.AA.....T.................... ....C.......G..A........... ...G.....G.....C -.....TT....G..T.......   55
... --A..A.A...A.......T..........A.....T..........T. --.A.AA.....T.................... ....C.......G..A........... ...G.....G.....C -.....TT....G..T.......   57
... --A....A...........T..........A.....T............ -G.A..A.......................... ....C.......G..A........... ...GA....G.....C -.....TT....G..........   55
... .......A..........C.............................. ...A............................. ....C..T....G..A........... ...G............ ......T.....G..........   40

gsgs · Apr 6, 2007

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

In 2004 we had sequences

A/peregrine falcon/Hong Kong/D0028/2004 ("falcon")
A/Ck/ST/4231/2003 ("2003")

they were 16,18,60,28,19,20,15,23 0/00 different in the 8 segments.
So apparantly the PA-segment had been reassorted before.

Now, until 2005 they had evolved to viruses similar to :

A/Gs/Shantou/2216/2005 ("Shantou")
A/migratory Dk/Jiangxi/2295/2005 ("Jiangxi")

these steps involved
11,11,09,11,08,13,07,12 0/00 differences for falcon-->Shantou
14,06,02,14,07,10,02,08 0/00 differences for 2003 --> Jinagxi

Shantou and Jiangxi were 18,21,68,35,25,26,14,33 0/00 apart.

Then some bird was infected with 2 strains similar to
Shantou and Jiangxi and reassorted to a virus similar to

A/Bar-headed Gs/Qinghai/65/2005 ("Qinghai")

which is
09,05,09,36,25,28,02,06 0/00 apart from Shantou
24,21,69,02,03,03,12,34 0/00 apart from Jiangxi

and this virus proved very fit for intercontinental travel
it spread to Qinghai-lake and probably independently
to Novosibirsk and then through Russia and Turkey to Europe and Africa

Code:

 /        falcon----------16,18,60,28,19,20,15,23----------2003           \
|  11,11,09,11,08,13,07,12                        14,06,02,14,07,10,02,08  |
 \        Shantou---------18,21,68,35,25,26,14,33--------Jiangxi          /
  \            09,05,09,36,25,28,02,06     24,21,69,02,03,03,12,34       /
   16,10,12,32,18,22,05,13-----------Qinghai------22,22,65,14,13,12,14,28

I just discovered 12 other full-genome sequences from Qinghai from lanl ,
which are much different to the Qinghai genomes from genbank.
31 genomes in total, checking now...
A/bar-headed Gs/Qinghai/2/2005 is similar to the Jiangxi/2300 virus, but even more
distant to the other Qinghai-viruses .
Also many differences Shantou/2216 - Qinghai/65 also are differences Shantou-Qinghai/2
I don't understand this yet...

----------edit 2009-----------------------
distances from bird-index:

Code:

falcon :09,07,12,--,06,--,--,10
2003   :12,09,08,--,06,--,--,10
shantou:08,09,09,--,05,--,--,12
jiangxi:07,07,11,--,06,--,13,09
qinghai:11,08,13,--,08,--,14,13

gsgs · Apr 7, 2007

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

ahh, this was all known since Febr. 2006 , I just found this:

http://www.pnas.org/cgi/content/abstract/0511120103v1

the paper at the start of this thread was just a later summary !

gsgs · Apr 9, 2007

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

where/how were those Qinghai sequences collected
which are so similar to the Qinghai virus outside China
A/barheaded goose/Qinghai/65/2005 and similars ?

This series of viruses /59../75 is rather uniform
and different from the series /1,.../10
from the Chen et.al paper.

These latter viruses -public since a few months only by niman's intervention-
are strange and different from what we see elsewhere.
So different, that I wonder whether this is this some different
kind of flu-evolution, whether there are frequent errors in the
sequences or what is going on.

I'm still trying to make sense of the Qinghai-lake sequences.
This isn't normal, isn't what we usually see with related influenza sequences.

Well, except these Qinghai-lake sequences at genbank, they behave well,
and they are similar to the Qinghai sequences outside China.

These are:
A/bar-headed goose/Qinghai/0510/2005
A/bar-headed goose/Qinghai/12/2005
A/bar-headed goose/Qinghai/59/2005
A/bar-headed goose/Qinghai/60/2005
A/bar-headed goose/Qinghai/61/2005
A/bar-headed goose/Qinghai/62/2005
A/bar-headed goose/Qinghai/65/2005
A/bar-headed goose/Qinghai/67/2005
A/bar-headed goose/Qinghai/68/2005
A/bar-headed goose/Qinghai/75/2005
A/environment/Qinghai/31/2005
A/brown-headed gull/Qinghai/3/2005
A/black-headed gull/Qinghai/1/2005
A/black-headed goose/Qinghai/1/2005
A/black-headed goose/Qinghai/2/2005

Let's exclude A/bar-headed goose/Qinghai/1A/2005 , where only HA and NA
are available and which seem to behave well.

Then we have A/great black-headed gull/Qinghai/1/2005
which behaves well in segments 1,2,7,8 but shows some signs of
rebellion in segments 4,5,6 and in a small part of segment 3.
Still not as naughty as the other sequences below.

Now, A/bar-headed goose/Qinghai/5/2005 behaves well in segments 2,4,5,6,7,8
but entirely naughty in 1,3.

A/ruddy shelduck/Qinghai/1/2005 behaves well in the first half of segment 1,
and in the other segments, except possibly 3 polymorphisms in HA which are
from the naughty sequences, and entirely
naughty in the second half of segment 1, indicating recombination in segment 1.

A/Qinghai/bar-headed goose/2/2005 is much different from everything else
in segments 1,2,3,7,8 and just "only" naughty in segments 4,5,6.
It's similar to A/migratory duck/Jiangxi/2300/2005 but still a bit more
distant to the well behaving Qinghai-lake sequences than the Jingxi
virus, which is assumed to have reassorted with A/migratory duck/Jiangxi/1653
at Poyang lake in 2004 or early 2005 1700km west of Qinghai lake
so to form the well behaving Qinghai sequences.

2 is equal to 4 in segment 7 - another reassortment

Now it remains this list of 11 naughty Qinghai-lake viruses:

Code:

                                                0000000000000000000000000000000011111111111111111111111111111111111111111111111111111122222222222222 00000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111112222222 00000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111222 0000000000000000000000000111111111111111111111111111 0000000000000000000000000000000000000000000000000000000111111111111111111111 00000000000001111111111 00000000000000000000000000000000 000000000000000000000000000000000000 
                                                0022333344444455666678888889999901111222222222233334555556667777777888888888899999999900000000011122 01122222334445566666677888888999999990000011111222222222333333333344444444444555556677778888888888889990000033 22222223334444555555666677788888888999900011111111111111122222223334444445555555556666677777788888888899999999011 1122223333444555677778889001111333444555556667777777 1112223333333333333444444455556666666666666677788999999000001111222222234455 11223334478880111122234 11123344445555556677777777888889 222223333333444444444455555555666667 
                                                4667566667888938035582588881116900124012336667805565235891281223459011135668922346899903445667804602 84413467782584833667838045679333668892346806799013589999011222559902234556777012244413480333455667793452377800 00567780173389034489479989911235778457929901122334455668903335992570447781223456776666604589901234579901346689947 4845990445778138735591258372249224599125690670456678 7882692444555555669134467901570112233466678988937114668134894589368888941145 45193451384483036903891 77844401141477880744588999245591 023461688899134555688900244457223481 
                                                8178717987256218362438815675890459788134363491186956107767039281624013551347389417202817699786302384 20635078862255125890622758134039034899242306639924416789579369092540870269015611757841084235867031898165136526 57870680522592110672406932846578690512007848967166756245910137366041016750483696892456770810295718186984892513280 3571067782342869081818786815796281139422861793414584 7178102568124579683491764973393581468235917769243581064387009203631457343485 79241646472793533547332 69496832924117095228449348000820 124998945659358069239812845670357928 
-codon-position--------------------------------- 1 2 11   22      1    2 12  1 1 21 211    1 2     1                21 2  1  2 2 221      1 1 1    1 122 1  2 222222222 12 2 2          1      22 22  1   12   2        1    12 12 2    11   12 2 2   2          12 1                 2121     1      1     2  2 12 2 1 11  21 1         1 1 1 1 12  1 2 12   221   1        2  111 1 22122212 12 22211 12222 2   2 222 2222112 222212 122  11  21 1  1 1 2 2  1  1 1  1       2  2 2 1       2   2   1  12    1    1 1   2 11 2212111122111212 221 1 11211111112 1111 12 1 1 11     2   122 2 1        1 12 2 211111 
---Index----------------------------------------GTGGGGGTCTCATTCAGGGTACACGCTTGAACTGGAAGGAAGGGTGAATTAAGTCTGAGTGCATCGGTGATGAACAAAGGGGGAGCTATTGATGGAGAAG TAGAAAGCAAGAAAAAGGCAATACACCACTACTTTAGGAGCAAAGCGCAGCCTCTGTCTAGATCCAACAACTTACACGGATTAACAAAGATTAATTGGATCCAAACTAAG ATAATAGTTAGAGGAACCGCAAGCAGTTGGCTACCACGGGTCAAAAGGGCGCACACGGAGACCAATCCCCTCCAGATAGCTATCTCGGCAGCCAAAGAACACCAAGTATCTGA GCCCGTAGATAAAGCGAAGATCTACAGGGGCAAACGCCGGCTAACGAAATAG TAATAGGAATTAGAGAGACGGGACAAGGTGGGAGGGTTCACGCAGAGTATGGTATGGAGGGTAAAGACAGCATGAA AACCTAGATAGCCTTTCTGATTG CCCGGTCGCTCCACAGCTGTATAGGGAATGGG AGAGTCACAAAACCGCAACCAACGTAATACTAGAGG 
  1 >A/bar-headed Gs/Qinghai/4/2005             .........G........AG................G...............A...AGAA.T..T........T.............G.C...A...C.. ...CCC..........A....C...ATG.........A.A.G.G....G.T.CTGA.T...G........T.C.T.G.T.......G........CT.......GA.GG. ..T........GA.C..T...C....CCT.T............G....A......TC.CAGT..GC.TTT.................................G.C..C.... ..G........G..TAG..G.....G........T.T.AS.........G.. .CCGT...TCCCAGA.A.......C.T.....C..A..T.................A.........C....G..G. .........C............. ....T..A..ATGAG.T....C....G..AA. .T.....T.G....A.T.T.C...............      127    127 ,    127    127      1:>A/bar-headed Gs/Qinghai/4/2005             
  2 >A/brown-headed gull/Qinghai/1/2005         .C....................G.......GT.A.G..............G...T....................G........A...C....A.G...A C...C.....A.G..GA.......C.....G.C..CA....C..............C.............T.C...G.TG....A.G........CT............. ..T........GA.C..T...C....CCT.T............G....A......TC.CAGT..GC.TTT.................................G.C..C.... .....A.....GTT........C..GA.....G..T......CT......C. ...G............A....ACAC..AA...C......CT.....................G......T....G. G..........T.CC........ ...A...............G.C.......... .................G...G...........T..       98     98 ,     98     98      2:>A/brown-headed gull/Qinghai/1/2005         
  3 >A/great cormorant/Qinghai/3/2005           .................A.G..........GT.A..G...........CC...G........G..........T...C..A..G.TC.C..........A ...............GA....C.......AGTCC........G.............C.............T.....G.T.....A.G........CT.......GG..G. ................A...G.................A....G....A......T.......G........T.......C..........T.....GG.G.....GG..... ...A.A.....G..T.G.AG.A....A......................... C.................T.AA..CC.AA...C.............................G......TT.CTGG GG...G.....T..C...A.... ...................G.C.......... ..G..............G....A..G...GCC...A       94     94 ,     94     94      3:>A/great cormorant/Qinghai/3/2005           
  4 >A/bar-headed Gs/Qinghai/3/2005             .........G...GT.A..GC.G.......GT...............G.C......................G..G.C...............A..ACGA .G......GGAG.................CG.CCCCA.T.........G...............................CC..AGG...C.....C......G...... GC..C....G.G...GATA.............GTT............................G..T.....T..............T...T.....GG.G.....GG.T... ...A.A....C..T............A.A...G..T.T..TC.......... C..........................A.....A.A..T.TC..A...G..ACTG.A...AC.....TC..G.... ..............C.....AG. ....TGA..........C.CG........... .................G.................A      105    105 ,    105    105      4:>A/bar-headed Gs/Qinghai/3/2005             
  5 >A/whooper swan/Qinghai/1/2005              A.A........C.....................A.G.....A.......C.....C.............G.....G........A............... CG............G.....G..T.ATG..............G.ATA.GA......CTC.AG.A.........CT......C..A...A.......T.GC......C... ...........G.A.GAT...........................................T.GG.T.....T.........CTCGAT...T.....GGAG.....GG.T..G A..A.......G..T.G...AA......A......T.T...C...A..T..A .........C...........A........A......AT.T.................A...........T..... GG.A..A...AT.....C.G... ...A...............G.C.......... ..................................A.       99     99 ,     99     99      5:>A/whooper swan/Qinghai/1/2005              
  6 >A/bar-headed Gs/Qinghai/1/2005             A.A........C.....................A.G.....A.......C.....C.............G.....G........A............... CG............G.....G..T.ATG..............G.ATA.GA......CTC.AG.A.........CT......C..A...A.......T.GC......C... ...........G.A.GAT...........................................T.GG.T.....T.........CTCGAT...T.....GGAG.....GG.T..G .....ACATC.G..T......A....A...................CC..C. .........C...........A........A......AT.T.................A...........T..... ...............GG...... ........T............C.........A ..................................A.       91     91 ,     91     91      6:>A/bar-headed Gs/Qinghai/1/2005             
  7 >A/bar-headed Gs/Qinghai/8/2005             .....A.C..........................................G..G................G..TA.......A.A............C.. ..A.............A......T.AT............A...G......T...........C.AG.GGG.CCCT..A.................C.C.ATTG....... .....G.AC.....C....T..T...CC...C.....AAA...G................G.......TT..T....................GGGA...G.......C..A. .................G...A...G.....GG..TT..A............ C.....CC.........C.A.........TA...A....................A......G......T....G. ..T.CG...C..T.......... ..............................A. TT.A...T......A................CA...       92     92 ,     92     92      7:>A/bar-headed Gs/Qinghai/8/2005             
  8 >A/bar-headed Gs/Qinghai/9/2005             .....AAC.G.............GCT........AG..AC..CCACG....G.G...........A.A..GA.TA.CC.A.AAG...GCC...A..A... ..A.........G........C...ATG...........ATG...TAT........C.............TC..........GG...G..CC............GG...A .....GAA..A........T...T.A.........G.A....G..G.............AG.T......T......CC..............TG.G.....TAG....C.... ...A.............G......AG......G......A.CC......... C..G.A.............A..........A...AAA.....TC.GAA....CT..A.AAA..GG.C.G....... ..T......C............. .........C....GA..A.G..A.....AA. .................G.................A      125    125 ,    125    125      8:>A/bar-headed Gs/Qinghai/9/2005             
  9 >A/great black-headed gull/Qinghai/2/2005   .........G..............CTG.....CA..GA............G.........A........G.A......A..AA.............A..A .G...C.....G....A....C.............................T.......G.G....G.....A..C.A..CCGG..CG..CCGC.C.......G...... ...T...A....A.C.......T.GA.........GA...ATGGG..AAT.T.T.....A........T.C..CAC..ATCC.........T..G............GCT.A. ...AA........TT........T...A.A.G.C....A.....T....... C.............................A...A...........................G......T....-- G....G...C............. TT.A.......................GCA.. ....A............G...G.............A      107    107 ,    105    105      9:>A/great black-headed gull/Qinghai/2/2005   
 10 >A/great black-headed gull/Qinghai/3/2005   ....A.........T.......G.......G.C..G..A.GA........G...T.....A..A....AG.A...G...A.AA.A.....CCA.A..... ..A.C........GG.......C.....TAGTCCCCAA....G............................C.....A...CGG..CG..CCG.C........G...... .......AC.A.A......T...............G..A...G..GA.ATCTC.C..C.A........T...................TGA..G.......T.GG....T... .T...........T...G..C..T..A...T.......AA.CC......... ...G.A...CGCAGAGA.......C..A...AC..A..........AA.....T..A.........C.G..G.... GG.......C.T........... ..G........................GCA.. ..G..TG.C.CC.T..G......C.GG.........      132    132 ,    132    132     10:>A/great black-headed gull/Qinghai/3/2005   
 11 >A/bar-headed Gs/Qinghai/10/2005            ...T....AGT.CG.G.....TC....GATG...................G..............AA.RG.A....CCAA.AA..T.GCC.......C.A ..A.G.CG......G..AGCG................AT.TG......G..TCT.A...G.G..AT.GGG.C...........G...G.TCC.......C...G...... ..G.....C.A...C....T.......C.A.CGT...........................T.G..T...CA..........C....T....T..........G......CA. ....A...............CA...G............AA.C.......G.. ...G.A...C.CAGAGA....A..C..A...AC..A..T.......AA.CA.CT..AGA......AC.G....... .....G.CC.............C .........C....GA....G.G.CA..C..A .......T....A.AT...T..A.CG.ATG.....A      146    146 ,    146    146     11:>A/bar-headed Gs/Qinghai/10/2005            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
---Index----------------------------------------GTGGGGGTCTCATTCAGGGTACACGCTTGAACTGGAAGGAAGGGTGAATTAAGTCTGAGTGCATCGGTGATGAACAAAGGGGGAGCTATTGATGGAGAAG TAGAAAGCAAGAAAAAGGCAATACACCACTACTTTAGGAGCAAAGCGCAGCCTCTGTCTAGATCCAACAACTTACACGGATTAACAAAGATTAATTGGATCCAAACTAAG ATAATAGTTAGAGGAACCGCAAGCAGTTGGCTACCACGGGTCAAAAGGGCGCACACGGAGACCAATCCCCTCCAGATAGCTATCTCGGCAGCCAAAGAACACCAAGTATCTGA GCCCGTAGATAAAGCGAAGATCTACAGGGGCAAACGCCGGCTAACGAAATAG TAATAGGAATTAGAGAGACGGGACAAGGTGGGAGGGTTCACGCAGAGTATGGTATGGAGGGTAAAGACAGCATGAA AACCTAGATAGCCTTTCTGATTG CCCGGTCGCTCCACAGCTGTATAGGGAATGGG AGAGTCACAAAACCGCAACCAACGTAATACTAGAGG 
-codon-position--------------------------------- 1 2 11   22      1    2 12  1 1 21 211    1 2     1                21 2  1  2 2 221      1 1 1    1 122 1  2 222222222 12 2 2          1      22 22  1   12   2        1    12 12 2    11   12 2 2   2          12 1                 2121     1      1     2  2 12 2 1 11  21 1         1 1 1 1 12  1 2 12   221   1        2  111 1 22122212 12 22211 12222 2   2 222 2222112 222212 122  11  21 1  1 1 2 2  1  1 1  1       2  2 2 1       2   2   1  12    1    1 1   2 11 2212111122111212 221 1 11211111112 1111 12 1 1 11     2   122 2 1        1 12 2 211111 
                                                0000000000000000000000000000000011111111111111111111111111111111111111111111111111111122222222222222 00000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111112222222 00000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111222 0000000000000000000000000111111111111111111111111111 0000000000000000000000000000000000000000000000000000000111111111111111111111 00000000000001111111111 00000000000000000000000000000000 000000000000000000000000000000000000 
                                                0022333344444455666678888889999901111222222222233334555556667777777888888888899999999900000000011122 01122222334445566666677888888999999990000011111222222222333333333344444444444555556677778888888888889990000033 22222223334444555555666677788888888999900011111111111111122222223334444445555555556666677777788888888899999999011 1122223333444555677778889001111333444555556667777777 1112223333333333333444444455556666666666666677788999999000001111222222234455 11223334478880111122234 11123344445555556677777777888889 222223333333444444444455555555666667 
                                                4667566667888938035582588881116900124012336667805565235891281223459011135668922346899903445667804602 84413467782584833667838045679333668892346806799013589999011222559902234556777012244413480333455667793452377800 00567780173389034489479989911235778457929901122334455668903335992570447781223456776666604589901234579901346689947 4845990445778138735591258372249224599125690670456678 7882692444555555669134467901570112233466678988937114668134894589368888941145 45193451384483036903891 77844401141477880744588999245591 023461688899134555688900244457223481 
                                                8178717987256218362438815675890459788134363491186956107767039281624013551347389417202817699786302384 20635078862255125890622758134039034899242306639924416789579369092540870269015611757841084235867031898165136526 57870680522592110672406932846578690512007848967166756245910137366041016750483696892456770810295718186984892513280 3571067782342869081818786815796281139422861793414584 7178102568124579683491764973393581468235917769243581064387009203631457343485 79241646472793533547332 69496832924117095228449348000820 124998945659358069239812845670357928

A/bar-headed goose/Qinghai/4/2005 is equal to
A/brown-headed gull/Qinghai/1/2005 in segment 3, but not the other segments,
so that's another likely reassortment.

A/whooper swan/Qinghai/1/2005 is equal to A/bar-headed goose/Qinghai/1/2005
in segments 1,2,3,5,8 but different in 4,6,7 - another reassortment.

A/bar-headed goose/Qinghai/8/2005 and A/great black-headed gull/Qinghai/2/2005
are well behaved in segment 5 but naughty elsewhere for another reassortment.

A/whooper swan/Qinghai/1/2005 in segments 3 and 7
A/bar-headed goose/Qinghai/3/2005 in segment 8
A/great cormorant/Qinghai/3/2005 in segment 7
A/brown-headed gull/Qinghai/1/2005 in segments 6,7
A/bar-headed goose/Qinghai/8/2005 in segment 5
A/great black-headed gull/Qinghai/2/2005 in segments 5,8
A/bar-headed goose/Qinghai/8/2005 in segment 8

many common polymorphisms, but these are shared by varying
groups of viruses, not constant fixed groups.
not what we usually see
frequent recombination ?
frequent infections with different viruses, mixed samples ?
due to the sandstorm ?
many errors ?

gsgs · Apr 9, 2007

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

seems that all those viruses isolated at Qinghai lake have subsequently
died without successors and what we see in Liaoning and outside
China is from another ancestor.
So it didn't fly from Qinghai to Mongolia and Siberia.
It came from elsewhere. Qinghai-lake was just a sidestep of the virus,
not important for and unrelated to its global spread.

mixin · Sep 1, 2009

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

Thanks for linking to this. It was before my flubie days and I had never seen it.

Now, 2 years later, how have your thoughts changed on all this (if they have)?

gsgs · Sep 1, 2009

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

I should look again at the Qinghai-lake sequences including upates...
maybe later

I remember we had one other recombination (/1a or /f ?)
one year later, then some completely different sequences,
not ancestors of 2005 and now some genes from the pikas
while others are from earlier Chinese birds, not found in 2005
at Qinghai-lake (?)

the 4 Qinghai-lake markers in PB2 of well-behaving 59-75
are still not seen elsewhere.

We saw quite some strange mutations which turned out to be
likely lab-errors in the meantime, I didn't know this in 2007.

I'm a bit wondering whether these naughty sequences
and also the pika sequences contain contaminations=errors.
Maybe from the same Chinese lab in Qinghai

there must be one thread with a list of later
recombinations, reassortments in the Qinghai virus
(e.g. Kurgan , Nigeria , Crimea )
but these were few as compared to Qinghai-lake 2005

the virus evolved rather constant (except Hungary/Sussex)
with a mutation rate of
45 mutations per genome per year.
This is not necessarily seen in other Chinese H5N1 where we
have periods of lower mutation rates.

Few recent Qinghai genomes (2008,2009), so I'm not sure
how it continued the last 2 years

mixin · Sep 1, 2009

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

So it didn't fly from Qinghai to Mongolia and Siberia.
It came from elsewhere. Qinghai-lake was just a sidestep of the virus,

I've seen the explanation that the virus just suddenly changed and went virulent, which never quite makes sense to me. Do you still think what you said in the quote or has there been evidence to the contrary?

gsgs · Sep 5, 2009

Re: origin of the Qinghai virus

Re: origin of the Qinghai virus

well, almost all of the (~20) viruses which had been sampled from
Qinghai-lake in 2005 had the 4 markers in PB2 which were never seen elsewhere.

There could have been H5N1 in/near Qinghai lake in 2005
which qualifies as ancestor of the African,European viruses
but which was not sampled.
But then, that ancestor could have been elsewhere as well.

We know that Qinghai had many viruses and reassortment,
(recombination ?) in 2005 and that there was early H5N1,
although the one from Siberia,Europe,Africa. was not found.
But if one H5N1 can go to Qinghai-lake then another one
might have too ?!

The pikas near Qinghai-lake had not the virus from 2005,
but a new one from Korea,Nigeria with mutations that
were aquired elsewhere, not in Qinghai lake.
They got imported virus-parts

origin of Qinghai H5N1

gsgs

Registered User

gsgs

Registered User

gsgs

Registered User

gsgs

Registered User

gsgs

Registered User

mixin

Well-known member

gsgs

Registered User

mixin

Well-known member

gsgs

Registered User