reassortment in Indonesia

[gsgs]

I found several examples of probable reassortment in Indonesian H5N1.
I haven't seen anyone yet who had mentioned this, neither
Kandun nor WHO nor CDC.

(1) CDC1046 and CDC1047 have PB1,PA,HA,NS in common with CDC1032.
But PB2,NP,NA,M are different and closest to CDC292, although no exact match. This one is most obvious.
Also 3 differences in PB1 between CDC1046 and CDC1047 which I can't
make sense off unless there was another reassortment or a mixed
infection.

(2) CDC759,CDC836,CDC940 have all but PB1 in common
with CDC669,CDC739, while PB1 is similar to CDC326,CDC329,
maybe even recombination.

(3) CDC644 is different from CDC644T in PB1 (same patient !).
CDC644 has PB1 as in CDC669P, CDC644T has PB1 as in CDC582

(4) CDC742 has PB2 in common with CDC610,CDC835 and the other
segments with CDC357 and similar viruses.
This last one is not so clear, but still likely (>50&#37 IMO.
__________________



list of Indonesian mutations

full human genome-viruses from genbank 1.Feb.2007, except
CDC184/05,CDC7/05,370,390,623,624 which form an extra group

only polymorphisms which occur at least twice are included
I could print this list with wordpad courier new, size=8 and then
glue the 4 pieces with tape.

 
[FONT=Arial]0000000000000000000000000000000000001111111111111111111111111111222222222 000000000000[/FONT]
[FONT=Arial]1122233333444445556677777788888899990000012223334444455666678899000111122 111234444566[/FONT]
[FONT=Arial]3405544599037990793612233801367835574477901580254678905035535712166456722 069242489003[/FONT]
[FONT=Arial]7697968528773160263536817260015856943603134331255407983922596512126799125 828920197703[/FONT]
 
[FONT=Arial]222211 12222221222 22 22222 2 2 22222222222222222 22221 2222 211222 222 1 2 [/FONT]
[FONT=Arial]AAGGCCACGTACATGTAGTGGTGTTGTATCGATGTATCACACTGTACCAGGGCGGGTCTGGAGAAACACCGTG TACAGATAAAGA[/FONT]
[FONT=Arial]IDN/CDC610/06 .......................C.....................G..............A............ .........T..[/FONT]
[FONT=Arial]IDN/CDC835/06 ...A...................C....................................A............ ....T....T..[/FONT]
[FONT=Arial]IDN/CDC669/06 ............G..........CC..................A................A............ .........T..[/FONT]
[FONT=Arial]IDN/CDC669P/06 ............G..........CC..................A................A............ .........T..[/FONT]
[FONT=Arial]IDN/CDC739/06 .......................CC..................A.G..........C...A............ .........T..[/FONT]
[FONT=Arial]IDN/CDC759/06 .......................CC..................A..T.............A.A.......... A..GA...G...[/FONT]
[FONT=Arial]IDN/CDC940/06 .......................CC..................A................A............ A..GA...G...[/FONT]
[FONT=Arial]IDN/CDC836/06 ...............C.....C.CC......GC..........A.......A........A.........A.. A..GA...G.A.[/FONT]
[FONT=Arial]IDN/CDC836T/06 ...............C.....C.CC......GC..........A.......A........A.........A.. A..GA...G.A.[/FONT]
[FONT=Arial]IDN/CDC326/06 .........................T..........CT....C.............C................ .G..........[/FONT]
[FONT=Arial]IDN/CDC326N/06 .........................T..........CT....C.............................. .G..........[/FONT]
[FONT=Arial]IDN/CDC326T/06 .........................T..........CT....C.............C................ .G..........[/FONT]
[FONT=Arial]IDN/CDC329/06 .........................T..........CT....C.............................. ............[/FONT]
[FONT=Arial]feline/IDN/CDC1/06 .........................T..........C.....C.............................. ............[/FONT]
[FONT=Arial]IDN/CDC292T/05 ................G..A................C.....C......................C....... ............[/FONT]
[FONT=Arial]IDN/CDC357/06 ................G...................C.....C.............C................ ............[/FONT]
[FONT=Arial]IDN/CDC287E/05 ......................................................................... ............[/FONT]
[FONT=Arial]IDN/CDC742/06 .......................C....................................A............ ............[/FONT]
[FONT=Arial]IDN/CDC582/06 ......G.............A.....C..........................A........A.......... .........T..[/FONT]
[FONT=Arial]IDN/CDC634/06 G.....G....T........A.....C.............G............A................T.A .........T..[/FONT]
[FONT=Arial]IDN/CDC634P/06 G.....G....T........A.....C.............G............A................T.A .........T..[/FONT]
[FONT=Arial]IDN/CDC634T/06 G.....G....T........A.....C.............G............A................T.A .........T..[/FONT]
[FONT=Arial]IDN/CDC644/06 ......G....T..A.....A.....C.............G............AA.........G.T...T.. .........T..[/FONT]
[FONT=Arial]IDN/CDC644T/06 ......G....T..A.....A.....C.............G............AA.........G.T...T.. .........T..[/FONT]
[FONT=Arial]IDN/CDC699/06 ....T............A....................................................... ............[/FONT]
[FONT=Arial]IDN/CDC523/06 .................A.............................TT............G........... ............[/FONT]
[FONT=Arial]IDN/CDC523E/06 .................A.............................TT............G........... ............[/FONT]
[FONT=Arial]IDN/CDC523T/06 .................A.............................TT............G........... ............[/FONT]
[FONT=Arial]IDN/CDC1031/07 ..AA......G......A.........G.....T..............T.A......T....A..G...T... .....G.G...G[/FONT]
[FONT=Arial]IDN/CDC1031RE2/07 ..AA......G......A.........G.....T..............T.A......T.......G...T... .....G.G...G[/FONT]
[FONT=Arial]IDN/CDC1031T/07 ..AA......G......A.........G.....T..............T.A...R..T.......G...T... .....G.G...G[/FONT]
[FONT=Arial]IDN/CDC1031T2/07 ..AA......G......A.........G.....T..............T.A......T.......G...T... .....G.G...G[/FONT]
[FONT=Arial]IDN/CDC887/06 ..AA...........C.A......................G.......T.A..............G...T... .......G...G[/FONT]
[FONT=Arial]IDN/CDC938/06 ..AA.G..T........A...........T....CT........C...T.A.A......A.....G...T... .......G...G[/FONT]
[FONT=Arial]IDN/CDC938E/06 ..AA.G..T........A...........T....CT....G...C...T.A.A......A.....G...T... .......G...G[/FONT]
[FONT=Arial]IDN/CDC1032/07 ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G[/FONT]
[FONT=Arial]IDN/CDC1032N/07 ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G[/FONT]
[FONT=Arial]IDN/CDC1032T/07 ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G[/FONT]
[FONT=Arial]IDN/CDC1046/07 .G..T..T.A...C..G.CA..A.....C.T.....C.GT.TC...T........A.......G.C.GT..C. ..T...CG...G[/FONT]
[FONT=Arial]IDN/CDC1047/07 .G..T..T.A...C..G.CA..A.....C.T.....C.GT.TC...T........A.......G.C.GT..C. ......CG...G[/FONT]
 
 
[FONT=Arial]0000000001111111111111111111112222 000000000000000000000111111111111111111111111111111222 000000000000000000000[/FONT]
[FONT=Arial]6667889990001122334567788889990011 133334444566788899999011222344455566667777788999999000 000011222333445666777[/FONT]
[FONT=Arial]6672670773784537496852911991571215 322390357525902724689799556914905723790345638035689289 456847389258243223156[/FONT]
[FONT=Arial]0886499583509599444798278034346521 968446312925023821326609481607818976202571978567349395 557749624177310592702[/FONT]
 
[FONT=Arial]2 11 1 2 12 121111111111111212 1 222 111 1111111111112211 11111111 11 22 2122 [/FONT]
[FONT=Arial]GGACTCTGTTTGCTTCAAGCGCTTGCAGTGTTCT AACAGACGCCAATAATGTAGTAAAGACCACACCGGGGAGACAAAGAGAATGGTA GGCTGAGCTGGCATTGCCAAC[/FONT]
[FONT=Arial].........C..T..T.........A........ .G...........G.C............G.GAT..............GG..... ---........T.........[/FONT]
[FONT=Arial].........C..T..T.........A........ .G...........GTC............G.GAT...........A..GG..... ...........T.........[/FONT]
[FONT=Arial].........C.A...T.................. .GT.......G..G.C............G.GAT..............GG..... R..........T.........[/FONT]
[FONT=Arial].........C.A...T.......C.......... .GT.......G..G.C............G.GAT..............GG..... ...........T.........[/FONT]
[FONT=Arial].........C.A...T.................. .GT..........G.C............G.GAT..............GG..... .....G.....T.........[/FONT]
[FONT=Arial]..G...............A.A..CAT.A.....C .GT..........G.C............G.GAT..............GG..... ...........T.........[/FONT]
[FONT=Arial]..G...............A.A...AT.A.....C .GT..........G.C........A...G.GAT..............GG..... ...........T.........[/FONT]
[FONT=Arial]T.G........A......A.A...AT.A.....C .GTG.........GTC........AG..GTGAT..............GG..... ..T........T.C.......[/FONT]
[FONT=Arial]T.G........A......A.A...AT.A.....C .GTG.........GTC........AG..GTGAT..............GG..... ..T........T.C.......[/FONT]
[FONT=Arial]..G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G...............A.A...A..A...... .G...........G.C..............GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G........................AC..... .G...........G.C..............GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G............................... .G.....A.....G.C.C............GA..........G....GG..... ---..................[/FONT]
[FONT=Arial]..G............................... .G...........G.C..............GA..........G....GG..... ---.......A.........T[/FONT]
[FONT=Arial]..G............................... .G...........G.C..............GA..........G....GG..... ---.......A..........[/FONT]
[FONT=Arial]..G............................... .G.........G.G.C..............GA..........G.A..GG..... ---.......A..........[/FONT]
[FONT=Arial]..........C....................... .....................................................G ---..................[/FONT]
[FONT=Arial]......C...C........T.............. ............C.....G..C..................T............G ---...............G..[/FONT]
[FONT=Arial]......C...C........T.............. ............C.....G..C..................T............G ---...............G..[/FONT]
[FONT=Arial]......C...C........T.............. ............C.....G..C..................T............G ---...............G..[/FONT]
[FONT=Arial].........C.A...T.......C.......... ............C.....G.C...................T............G ---..................[/FONT]
[FONT=Arial]..........C.................G..... ............C.....G.C...................T............G ---..................[/FONT]
[FONT=Arial].................................. ...........G..............T...................A....... .....G...............[/FONT]
[FONT=Arial]....C...........G.............C... ..........................T...................A....... ...A...........A.....[/FONT]
[FONT=Arial]....C...........G.............C... .......A..................T...................A....... ---A...T.......A.....[/FONT]
[FONT=Arial]....C...........G.............C... ..........................T...................A....... ---A...T.......A.....[/FONT]
[FONT=Arial]...T.T.......C...T...TC......CC.T. C.....A..T.......C......A.T.......TA.G.T......A..KAA.. ---.....C...G..AA...T[/FONT]
[FONT=Arial]...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. .T......C...G..AA...T[/FONT]
[FONT=Arial]...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. ---.....C...G..AA...T[/FONT]
[FONT=Arial]...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. ---.....C...G..AA...T[/FONT]
[FONT=Arial]...T.............T...TC.......C.T. ........T........C.....GAG.......AT...........A...AA.. AT......C...G..AA....[/FONT]
[FONT=Arial]...T..........C..T...TC......CC.T. ........T........C.....G..TT.....AT.T.........A...AA.. .T......CA..G.CAA....[/FONT]
[FONT=Arial]...T..........C..T...TC......CC.T. ........T........C.....GA.TT.....AT.T.........A...AA.. .T......CA..G.CAA....[/FONT]
[FONT=Arial].A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G.[/FONT]
[FONT=Arial].A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G.[/FONT]
[FONT=Arial].A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G.[/FONT]
[FONT=Arial].A.T....C........T...TC......CCCT. ..A.AG..T.......AC.....G..T......AT...A....G.GA...AAC. .T..A.A.CA..G..AAA.G.[/FONT]
[FONT=Arial]...T....C........T...TC......CC.T. ..A.AG..T.......AC.....G..T......AT...A....G.GA...AAC. .T..A.A.CA..G..AAA.G.[/FONT]
 
 
[FONT=Arial]000000000011111111111111111111 0000000000000000000001111111 00000000000000000000000011111 00000000000000000000 [/FONT]
[FONT=Arial]777778888900111122334444555666 0000111224455666777790001223 11122223345677778888899912223 00123355566778888899 [/FONT]
[FONT=Arial]688890479907234836692366279347 5999199151418228037983690128 33300393402335570577927890892 06101801509360468803 [/FONT]
[FONT=Arial]903687462341879833855415729877 4369728984742451234272221810 37927902713550940405616363322 45826582947065006778 [/FONT]
 
[FONT=Arial]1 1 1 2 1 1 1 1 1211 2222212 22 22 122 222 12111112111111 21212 [/FONT]
[FONT=Arial]AATTCTAAGTAATGCCTCTCCCGCAAATGA TTAAGCCGTTCATGAGTTAATGGGGACA TGACGCACCGCAGGGCCAGTTGCCGTCTT AACTTATAAGCAAGCAGTCG [/FONT]
[FONT=Arial].................T.......G.... ........C................... ..C.......A.....T............ -.........T.......T. [/FONT]
[FONT=Arial].................T.......G.... ........C................... ..C.......A.....T............ ..........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.......C....AA..... ..C........G......A.......... -G........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.......C....AA..... ..C........G......A.......... -G........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.......C....AA..... ..C........G................. ..........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.T.....C....AAA.... ..C........G................. ..........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. [/FONT]
[FONT=Arial]G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. [/FONT]
[FONT=Arial].C.C.....C...A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. [/FONT]
[FONT=Arial].C.C.........A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. [/FONT]
[FONT=Arial].C.C.....C...A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. [/FONT]
[FONT=Arial].C.C.........A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. [/FONT]
[FONT=Arial].C...........A..C....T.T.....G ............C......G........ ..C.......................... -.................T. [/FONT]
[FONT=Arial].C..............C......T.....G ............C......G........ ..C.......................... -................... [/FONT]
[FONT=Arial].C..............C......T.....G ............C......G........ ..C.......................... -............A...... [/FONT]
[FONT=Arial].C..........C...C......T.....G ............................ ..C.......................... -................... [/FONT]
[FONT=Arial].C..............C......T.....G ............C......G........ ..C......A................... --.................. [/FONT]
[FONT=Arial].G............................ ......T.C................... ......C..........C.......C... -................... [/FONT]
[FONT=Arial].............................. ......T.C.........G........C C....TC..........C...AT..C... -..C................ [/FONT]
[FONT=Arial]......G....................... ......T.C.........G........C C....TC..........C...AT..C... -..C................ [/FONT]
[FONT=Arial].............................. ......T.C.........G........C C....TC..........C...AT..C... -..C................ [/FONT]
[FONT=Arial]......G............T.......... ......T.C.........G........C C....TC..A.......C.......C... -................... [/FONT]
[FONT=Arial]......G............T.......... ......T.C.........G........C C....TC..A.......C.......C... -................... [/FONT]
[FONT=Arial]...........T.................. ............................ ......C..........C.......C..C -G.................. [/FONT]
[FONT=Arial]...........T..............G... .............A.............. ......CT.........C.......CT.C -...C............... [/FONT]
[FONT=Arial]...........T..............G... .............A.............. ......CT.........C.......CT.C -...C............... [/FONT]
[FONT=Arial]...........T..............G... .............A.............. ......CT.........C.......CT.C -...C............... [/FONT]
[FONT=Arial]..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A [/FONT]
[FONT=Arial]..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A [/FONT]
[FONT=Arial]..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A [/FONT]
[FONT=Arial]..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A [/FONT]
[FONT=Arial]..A........T...T....T.....GC.. ............................ ......C.T...A....C.CC....CT.C ..T.C...........A..A [/FONT]
[FONT=Arial]..A.....A..T..TT....T.....GC.. ....AA.........A.C........T. ....A.C.T...A....C.CC..T.CTCC T.T.C.........A.A..A [/FONT]
[FONT=Arial]..A.....A..T..TT....T.....GC.. ....AA.........A.C........T. ....A.C.T...A....C.CC..T.CTCC T.T.C.........A.A..A [/FONT]
[FONT=Arial]..A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A [/FONT]
[FONT=Arial]..A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A [/FONT]
[FONT=Arial]..A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A [/FONT]
[FONT=Arial]..A.TC.GA.GT...T....T.....GC.. C..G...A.C..C......G....AG.. ..CT.......G................. .....G......GA.G.G.. [/FONT]
[FONT=Arial]..A.TC.GA.GT...T....T.....GC.. C..G...A.C..C......G....AG.. ..CT.......G................. .....G......GA.G.G.. [/FONT]
 
 
 
[FONT=Arial]00000000000000 0[/FONT]
[FONT=Arial]01222223444445 0[/FONT]
[FONT=Arial]85344694023344 0[/FONT]
[FONT=Arial]67325221474633 0[/FONT]
 
[FONT=Arial]2122211221212 0[/FONT]
[FONT=Arial]AGGGCACGAAAAAA 0[/FONT]
[FONT=Arial]....TT..G.G... 38[/FONT]
[FONT=Arial]....TT..G.G... 54[/FONT]
[FONT=Arial]....TT..G.G... 46[/FONT]
[FONT=Arial]....TT..G.G... 44[/FONT]
[FONT=Arial]....TT..G.G... 57[/FONT]
[FONT=Arial]....TT..G.G... 56[/FONT]
[FONT=Arial]....TT..G.G... 68[/FONT]
[FONT=Arial]....TT..G.G..G 62[/FONT]
[FONT=Arial]....TT..G.G..G 63[/FONT]
[FONT=Arial].....T....GG.. 48[/FONT]
[FONT=Arial].....T....GG.. 50[/FONT]
[FONT=Arial].....T....GG.. 47[/FONT]
[FONT=Arial].....T....G... 44[/FONT]
[FONT=Arial].....T....G... 43[/FONT]
[FONT=Arial].....T....G... 43[/FONT]
[FONT=Arial].....T....G... 45[/FONT]
[FONT=Arial]..........G... 30[/FONT]
[FONT=Arial].....T....G... 62[/FONT]
[FONT=Arial].............. 39[/FONT]
[FONT=Arial].............. 39[/FONT]
[FONT=Arial].............. 39[/FONT]
[FONT=Arial].............. 37[/FONT]
[FONT=Arial].............. 42[/FONT]
[FONT=Arial].............. 41[/FONT]
[FONT=Arial].A............ 40[/FONT]
[FONT=Arial].A............ 26[/FONT]
[FONT=Arial].A............ 30[/FONT]
[FONT=Arial].A............ 29[/FONT]
[FONT=Arial].A............ 73[/FONT]
[FONT=Arial].A............ 70[/FONT]
[FONT=Arial].A............ 74[/FONT]
[FONT=Arial].A............ 70[/FONT]
[FONT=Arial].A............ 70[/FONT]
[FONT=Arial]GA.A..GA....G. 81[/FONT]
[FONT=Arial]GA.A..GA....G. 85[/FONT]
[FONT=Arial]GAAA..GA.G.... 98[/FONT]
[FONT=Arial]GAAA..GA.G.... 101[/FONT]
[FONT=Arial]GAAA..GA.G.... 98[/FONT]
[FONT=Arial]GA.A..GA...... 98[/FONT]
[FONT=Arial]GA.A..GA...... 94[/FONT]

human sequences from Indonesia:
-------------------------------
2005/07/08 5/2005,38M
2005/09/29 CDC7/2005,25M
2005/11/12 CDC194P/2005,20F
2005/11/08 CDC184/2005,16F
2005/12/13 CDC287E/2005,39M
2005/12/13 CDC287T/2005,39M
2005/12/15 CDC292N/2005,8M
2005/12/15 CDC292T/2005,8M
2006/01/14 CDC329/2006,13F
2006/01/15 CDC326/2006,4M
2006/01/15 CDC326N2/2006,4M
2006/01/16 CDC326T/2006,4M
2006/01/17 CDC326N/2006,4M
2006/01/30 CDC357/2006,15M
2006/02/10 CDC370/2006,23M
2006/02/10 CDC370E/2006,23M
2006/02/10 CDC370P/2006,23M
2006/02/10 CDC370T/2006,23M
2006/02/20 CDC390/2006,27F
2006/03/23 CDC523/2006,1F
2006/03/23 CDC523E/2006,1F
2006/03/23 CDC523T/2006,1F
2006/04/26 CDC582/2006,30M
2006/05/10 CDC596/2006,25M
2006/05/10 CDC597/2006,18M
2006/05/11 CDC599/2006,10M
2006/05/11 CDC610/2006,12M
2006/05/12 CDC599N/2006,10M
2006/05/18 CDC623/2006,18M
2006/05/19 CDC623E/2006,18M
2006/05/19 CDC624/2006,39M
2006/05/19 CDC624E/2006,39M
2006/05/21 CDC625/2006,32M
2006/05/22 CDC625L/2006,32M
2006/05/23 CDC634/2006,10F
2006/05/23 CDC634P/2006,10F
2006/05/23 CDC634T/2006,10F
2006/05/29 CDC644T/2006,15M
2006/05/30 CDC644/2006,15M
2006/05/09 CDC594/2006,19M
2006/05/09 CDC595/2006,29F
2006/06/13 CDC669/2006,14M
2006/06/13 CDC669P/2006,14M
2006/07/06 CDC699/2006,3F
2006/08/05 CDC739/2006,16M
2006/08/07 CDC742/2006,17F
2006/09/22 CDC835/2006,9M
2006/09/24 CDC836/2006,20M
2006/09/24 CDC836T/2006,20M
2006/10/14 CDC887/2006,12M
2006/11/10 CDC938/2006,35F
2006/11/10 CDC938E/2006,35F
2006/11/12 CDC940/2006,2.5M
2006 CDC759/2006,35F
2007/01/11 CDC1046/2007,22F
2007/01/11 CDC1046T/2007,22F
2007/01/12 CDC1047/2007,26F
2007/01/12 CDC1047S/2007,26F
2007/01/05 CDC1031/2007,14M
2007/01/05 CDC1031RE2/2007,14M
2007/01/05 CDC1031T/2007,14M
2007/01/06 CDC1031T2/2007,14M
2007/01/06 CDC1032/2007,37F
2007/01/07 CDC1032N/2007,37F

[gsgs]

Re: reassortment in Indonesia

here a hopefully better formatted table (long lines, I hope it works)
segments PB2,PB1,PA,HA,NP,NA,M,NS separated by a blank-column

[FONT=Fixedsys]                         0000000000000000000000000000000000001111111111111111111111111111222222222 0000000000000000000001111111111111111111112222 000000000000000000000111111111111111111111111111111222 000000000000000000000000000000011111111111111111111 0000000000000000000001111111 00000000000000000000000011111 00000000000000000000 00000000000000   0[/FONT]
[FONT=Fixedsys]                         1122233333444444556677777788888899990000012222334444455666678899000111122 1112344445666667889990001122334567788889990011 133334444566788899999011222344455566667777788999999000 000011222333445666777777778888900111122334444555666 0000111224455666777790001223 11122223335677777888899912223 00123355566778888899 01222223444445   0[/FONT]
[FONT=Fixedsys]                         3405544599037899793612223800257835574467801589254668905035535702066456622 0692424890036672670773784537496852911991571215 322390357525802724689789556904905723780345638035689289 456847389258243223156688890479907234836692366279347 5999199151418228037983690128 33300383492334579567917890892 06101801509260358803 85344693023344   0[/FONT]
[FONT=Fixedsys]                         5475746306551948041314695048893634721481912119033285761700374390904577903 8289201977030886499583509599444798278034346521 857335201814912710215598370596707865191460867456238284 557749624177310592702903687462341879833855415729877 4369728984742451234272221810 15705780591338728283494141100 34715471836954995667 45103009252411   0[/FONT]
 
[FONT=Fixedsys]                             2212      2   1  1     1 1 1                 11    21    11 22   1       1    2    2       11    1 2    12            1             1 12 21112   2            11  2          11  22       2122   1     1 1 2            1                  1  1  1           2 221     2 1111  1  12  1     1     1      21 1 1  2   22  2 2 1   0[/FONT]
[FONT=Fixedsys]                         AAGGCCACGTACATGTAGTGGTGTTGTATCGATGTATCACACTGTACCAGGGCGGGTCTGGAGAAACACCGTG TACAGATAAAGAGGACTCTGTTTGCTTCAAGCGCTTGCAGTGTTCT AACAGACGCCAATAATGTAGTAAAGACCACACCGGGGAGACAAAGAGAATGGTA GGCTGAGCTGGCATTGCCAACAATTCTAAGTAATGCCTCTCCCGCAAATGA TTAAGCCGTTCATGAGTTAATGGGGACA TGACGCACCGCAGGGCCAGTTGCCGTCTT AACTTATAAGCAAGCAGTCG AGGGCACGAAAAAA   0[/FONT]
[FONT=Fixedsys]IDN/CDC610/06            .......................C.....................G..............A............ .........T...........C..T..T.........A........ .G...........G.C............G.GAT..............GG..... ---........T..........................T.......G.... ........C................... ..C.......A.....T............ -.........T.......T. ....TT..G.G...   38[/FONT]
[FONT=Fixedsys]IDN/CDC835/06            ...A...................C....................................A............ ....T....T...........C..T..T.........A........ .G...........GTC............G.GAT...........A..GG..... ...........T..........................T.......G.... ........C................... ..C.......A.....T............ ..........T.......T. ....TT..G.G...   54[/FONT]
[FONT=Fixedsys]IDN/CDC669/06            ............G..........CC..................A................A............ .........T...........C.A...T.................. .GT.......G..G.C............G.GAT..............GG..... R..........T.........G...........C....T....A.....A. ........C.......C....AA..... ..C........G......A.......... -G........T.......T. ....TT..G.G...   46[/FONT]
[FONT=Fixedsys]IDN/CDC669P/06           ............G..........CC..................A................A............ .........T...........C.A...T.......C.......... .GT.......G..G.C............G.GAT..............GG..... ...........T.........G...........C....T....A.....A. ........C.......C....AA..... ..C........G......A.......... -G........T.......T. ....TT..G.G...   44[/FONT]
[FONT=Fixedsys]IDN/CDC739/06            .......................CC..................A.G..........C...A............ .........T...........C.A...T.................. .GT..........G.C............G.GAT..............GG..... .....G.....T.........G...........C....T....A.....A. ........C.......C....AA..... ..C........G................. ..........T.......T. ....TT..G.G...   57[/FONT]
[FONT=Fixedsys]IDN/CDC759/06            .......................CC..................A..T.............A.A.......... A..GA...G.....G...............A.A..CAT.A.....C .GT..........G.C............G.GAT..............GG..... ...........T.........G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. ....TT..G.G...   56[/FONT]
[FONT=Fixedsys]IDN/CDC940/06            .......................CC..................A................A............ A..GA...G.....G...............A.A...AT.A.....C .GT..........G.C........A...G.GAT..............GG..... ...........T.........G...........C....T....A.....A. ........C.T.....C....AAA.... ..C........G................. ..........T.......T. ....TT..G.G...   68[/FONT]
[FONT=Fixedsys]IDN/CDC836/06            ...............C.....C.CC......GC..........A.......A........A.........A.. A..GA...G.A.T.G........A......A.A...AT.A.....C .GTG.........GTC........AG..GTGAT..............GG..... ..T........T.C.......G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. ....TT..G.G..G   62[/FONT]
[FONT=Fixedsys]IDN/CDC836T/06           ...............C.....C.CC......GC..........A.......A........A.........A.. A..GA...G.A.T.G........A......A.A...AT.A.....C .GTG.........GTC........AG..GTGAT..............GG..... ..T........T.C.......G...........C....T....A.....A. ........C.T.....C....AA..... ..C........G................. ..........T.......T. ....TT..G.G..G   63[/FONT]
[FONT=Fixedsys]IDN/CDC326/06            .........................T..........CT....C.............C................ .G............G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A...........C.C.....C...A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. .....T....GG..   48[/FONT]
[FONT=Fixedsys]IDN/CDC326N/06           .........................T..........CT....C.............................. .G............G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A...........C.C.........A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. .....T....GG..   50[/FONT]
[FONT=Fixedsys]IDN/CDC326T/06           .........................T..........CT....C.............C................ .G............G....A..........A.A...A.GA...... .G...........G.C...A..........GA..........G....GG..... ---.......A...........C.C.....C...A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. .....T....GG..   47[/FONT]
[FONT=Fixedsys]IDN/CDC329/06            .........................T..........CT....C.............................. ..............G...............A.A...A..A...... .G...........G.C..............GA..........G....GG..... ---.......A...........C.C.........A..C....T.T.....G ...........GC......G........ ..C...........A............C. -.................T. .....T....G...   44[/FONT]
[FONT=Fixedsys]feline/IDN/CDC1/06       .........................T..........C.....C.............................. ..............G........................AC..... .G...........G.C..............GA..........G....GG..... ---.......A...........C...........A..C....T.T.....G ............C......G........ ..C.......................... -.................T. .....T....G...   43[/FONT]
[FONT=Fixedsys]IDN/CDC292T/05           ................G..A................C.....C......................C....... ..............G............................... .G.....A.....G.C.C............GA..........G....GG..... ---...................C..............C......T.....G ............C......G........ ..C.......................... -................... .....T....G...   43[/FONT]
[FONT=Fixedsys]IDN/CDC357/06            ................G...................C.....C.............C................ ..............G............................... .G...........G.C..............GA..........G....GG..... ---.......A.........T.C..............C......T.....G ............C......G........ ..C.......................... -............A...... .....T....G...   45[/FONT]
[FONT=Fixedsys]IDN/CDC742/06            .......................C....................................A............ ..............G............................... .G.........G.G.C..............GA..........G.A..GG..... ---.......A...........C..............C......T.....G ............C......G........ ..C......A................... --.................. .....T....G...   62[/FONT]
[FONT=Fixedsys]IDN/CDC287E/05           ......................................................................... ..............G............................... .G...........G.C..............GA..........G....GG..... ---.......A...........C..........C...C......T.....G ............................ ..C.......................... -................... ..........G...   30[/FONT]
[FONT=Fixedsys]IDN/CDC582/06            ......G.............A.....C..........................A........A.......... .........T............C....................... .....................................................G ---...................G............................ ......T.C................... ......C..........C.......C... -................... ..............   39[/FONT]
[FONT=Fixedsys]IDN/CDC634/06            G.....G....T........A.....C.............G............A................T.A .........T........C...C........T.............. ............C.....G..C..................T............G ---...............G................................ ......T.C.........G........C C....TC..........C...AT..C... -..C................ ..............   39[/FONT]
[FONT=Fixedsys]IDN/CDC634P/06           G.....G....T........A.....C.............G............A................T.A .........T........C...C........T.............. ............C.....G..C..................T............G ---...............G........G....................... ......T.C.........G........C C....TC..........C...AT..C... -..C................ ..............   39[/FONT]
[FONT=Fixedsys]IDN/CDC634T/06           G.....G....T........A.....C.............G............A................T.A .........T........C...C........T.............. ............C.....G..C..................T............G ---...............G................................ ......T.C.........G........C C....TC..........C...AT..C... -..C................ ..............   37[/FONT]
[FONT=Fixedsys]IDN/CDC644/06            ......G....T..A.....A.....C.............G............AA.........G.T...T.. .........T...........C.A...T.......C.......... ............C.....G.C...................T............G ---........................G............T.......... ......T.C.........G........C C....TC..A.......C.......C... -................... ..............   42[/FONT]
[FONT=Fixedsys]IDN/CDC644T/06           ......G....T..A.....A.....C.............G............AA.........G.T...T.. .........T............C.................G..... ............C.....G.C...................T............G ---........................G............T.......... ......T.C.........G........C C....TC..A.......C.......C... -................... ..............   41[/FONT]
[FONT=Fixedsys]IDN/CDC699/06            ....T............A....................................................... .............................................. ...........G..............T...................A....... .....G..........................T.................. ............................ ......C..........C.......C..C -G.................. .A............   40[/FONT]
[FONT=Fixedsys]IDN/CDC523/06            .................A.............................TT............G........... ................C...........G.............C... ..........................T...................A....... ...A...........A................T..............G... .............A.............. ......CT.........C.......CT.C -...C............... .A............   26[/FONT]
[FONT=Fixedsys]IDN/CDC523E/06           .................A.............................TT............G........... ................C...........G.............C... .......A..................T...................A....... ---A...T.......A................T..............G... .............A.............. ......CT.........C.......CT.C -...C............... .A............   30[/FONT]
[FONT=Fixedsys]IDN/CDC523T/06           .................A.............................TT............G........... ................C...........G.............C... ..........................T...................A....... ---A...T.......A................T..............G... .............A.............. ......CT.........C.......CT.C -...C............... .A............   29[/FONT]
[FONT=Fixedsys]IDN/CDC1031/07           ..AA......G......A.........G.....T..............T.A......T....A..G...T... .....G.G...G...T.T.......C...T...TC......CC.T. C.....A..T.......C......A.T.......TA.G.T......A..KAA.. ---.....C...G..AA...T..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A .A............   73[/FONT]
[FONT=Fixedsys]IDN/CDC1031RE2/07        ..AA......G......A.........G.....T..............T.A......T.......G...T... .....G.G...G...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. .T......C...G..AA...T..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A .A............   70[/FONT]
[FONT=Fixedsys]IDN/CDC1031T/07          ..AA......G......A.........G.....T..............T.A...R..T.......G...T... .....G.G...G...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. ---.....C...G..AA...T..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A .A............   74[/FONT]
[FONT=Fixedsys]IDN/CDC1031T2/07         ..AA......G......A.........G.....T..............T.A......T.......G...T... .....G.G...G...T.T.......C...T...TC......CC.T. C.....A..T.......C........T.......TA.G.T......A..GAA.. ---.....C...G..AA...T..A........T...T....T...G.GC.. ..............G........A.... ......C.T..GA....C.C....T.T.C ..T.C..C.A......A..A .A............   70[/FONT]
[FONT=Fixedsys]IDN/CDC887/06            ..AA...........C.A......................G.......T.A..............G...T... .......G...G...T.............T...TC.......C.T. ........T........C.....GAG.......AT...........A...AA.. AT......C...G..AA......A........T...T....T.....GC.. ............................ ......C.T...A....C.CC....CT.C ..T.C...........A..A .A............   70[/FONT]
[FONT=Fixedsys]IDN/CDC938/06            ..AA.G..T........A...........T....CT........C...T.A.A......A.....G...T... .......G...G...T..........C..T...TC......CC.T. ........T........C.....G..TT.....AT.T.........A...AA.. .T......CA..G.CAA......A.....A..T..TT....T.....GC.. ....AA.........A.C........T. ....A.C.T...A....C.CC..T.CTCC T.T.C.........A.A..A GA.A..GA....G.   81[/FONT]
[FONT=Fixedsys]IDN/CDC938E/06           ..AA.G..T........A...........T....CT....G...C...T.A.A......A.....G...T... .......G...G...T..........C..T...TC......CC.T. ........T........C.....GA.TT.....AT.T.........A...AA.. .T......CA..G.CAA......A.....A..T..TT....T.....GC.. ....AA.........A.C........T. ....A.C.T...A....C.CC..T.CTCC T.T.C.........A.A..A GA.A..GA....G.   85[/FONT]
[FONT=Fixedsys]IDN/CDC1032/07           ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G.A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G...A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A GAAA..GA.G....   98[/FONT]
[FONT=Fixedsys]IDN/CDC1032N/07          ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G.A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G...A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A GAAA..GA.G....   101[/FONT]
[FONT=Fixedsys]IDN/CDC1032T/07          ..AA.G..T........A...........T.....T........C...TAA.A.....CA.....G...T... ..T...CG...G.A.T....C........T...TC......CCCT. .....G..T........C....GG..T......AT......C....A...AAC. ---.....CA..G..AAA.G...A..C..A.GT...T..C.T.....GC.. .GG.AA.........A.C..C.....T. .A....C.T...AA.A.C.CC....CT.C ..T.C.C.G..T....A..A GAAA..GA.G....   98[/FONT]
[FONT=Fixedsys]IDN/CDC1046/07           .G..T..T.A...C..G.CA..A.....C.T.....C.GT.TC...T........A.......G.C.GT..C. ..T...CG...G.A.T....C........T...TC......CCCT. ..A.AG..T.......AC.....G..T......AT...A....G.GA...AAC. .T..A.A.CA..G..AAA.G...A.TC.GA.GT...T....T.....GC.. C..G...A.C..C......G....AG.. ..CT.......G................. .....G......GA.G.G.. GA.A..GA......   98[/FONT]
[FONT=Fixedsys]IDN/CDC1047/07           .G..T..T.A...C..G.CA..A.....C.T.....C.GT.TC...T........A.......G.C.GT..C. ......CG...G...T....C........T...TC......CC.T. ..A.AG..T.......AC.....G..T......AT...A....G.GA...AAC. .T..A.A.CA..G..AAA.G...A.TC.GA.GT...T....T.....GC.. C..G...A.C..C......G....AG.. ..CT.......G................. .....G......GA.G.G.. GA.A..GA......   94[/FONT]

Reason for Editing:

[Sharpe]

Re: reassortment in Indonesia

Thanks gsgs. Very interesting. 1046/1047 are quite different from the others. Any idea which patients they came from? Since they are probably the most recent isolates from the last few weeks, considering what a big change has occurred in the sequence (probably by either reassortment or a large recombination event like you say), it might begin to explain why the number of suspected cases has skyrocketed recently.

[aardvark]

Re: reassortment in Indonesia

This recent post by Laidback Al correlates the strains under discussion with specific patients:

http://www.flutrackers.com/forum/showpost.php?p=61217&postcount=4

[gsgs]

Re: reassortment in Indonesia

I hadn't yet included the date,age,sex in the table, so I posted it separately, see above.

1046 is from 11.Jan 2007, 22F
1047 is from 12.Jan.2007, 26F

you should be able to see the differences in segments 1,5,6,7 but not 2,3,4,8


column 5 with the 2s and 1s is the position within the codon, BTW.
Most are position 3 (blank) , which is synonymous when A is
exchanged with G or C with T.

The number on the right is the number of differences from the artificial reference sequence,
remember, that polymorphisms which only occur once were omitted in the table
but included in that number.

[aardvark]

Re: reassortment in Indonesia

Perhaps most importantly, these two particular cases (1046/1047) do not seem to be geographically linked. Coupled with your observation, gsgs, this definitely warrants very close attention.

Some related discussion here:

http://www.planforpandemic.com/viewtopic.php?p=45018

and here:

http://web.mac.com/monotreme1/iWeb/Pandemic%20Influenza%20Information/Blog/49605FC2-C8F2-408B-B38E-1C96C8CFE2C9.html

[gsgs]

Re: reassortment in Indonesia

thanks Aardvark I hadn't yet seen these.
1046 and 1047 are almost identical and both contain this
reassorted PB2-segment, they are very much related to each other.
Probably only 1 or 2 host-generations.
However, in PB1 there are 3 differences and the strange thing is,
that both variants do occur in other sequences, so these
differences are probably not just random.
Also 1046 and 1047 are both very similar to 1032 in PB1 and other genes,
but then we also have this reassortment, so PB2 is very different from 1032.
I'm not sure how to interpret this.

[scottmcpherson]

Re: reassortment in Indonesia

gsgs,
This is WAY beyond my pay grade, but is it possible this is due to recombination as opposed to reassortment? Are these segments the province of another A-type influenza? Or B?

Is this also why I shudder when I hear Thai or Indonesian authorities say "Nothing to see here, no bird flu here, just a few people dying of "human" flu, move along!" ?

Isn't PB1 a governor over virulence? Could these changes explain why the virus is apparently gaining lethality in Indonesia?

[gsgs]

Re: reassortment in Indonesia

scottmcpherson, doesn't look like recombination, more like 4 complete
segments being swapped. No other flu-A or even flu-B, it's
still H5N1, still Indonesian stains, although quite different
in PB2,NP.
This is from another unknown virus in Indonesia different from
the others , so this is a little surprising but not so much
different as that it could have come from elsewhere or even
a different serotype.
The Karo sequences e.g. were much more unusual and different
from typical Indo-H5N1 then this one in PB2,NP,

I can't say anything about gain in lethality. Well, we have this PB2-E627K,
...checking... no, nothing happening at this position.

[Mamabird]

Re: reassortment in Indonesia

I can't say anything about gain in lethality. Well, we have this PB2-E627K,
...checking... no, nothing happening at this position.

Just a heads up folks from my earlier posts on another thread when these isolates were first made available.

Isolate CDC1031 bears close scrutiny. It not only has 627K in the PB2 segment, but also has the S409N mutation in PA. This is a very human like characteristic and all the seasonal flu viruses have these two mutations, as did the 57 and 68 pandemic strains. Suggests either a mammalian source or that these mutations are becoming set within the Indonesian strains.

[gsgs]

Re: reassortment in Indonesia

my enumeration is probably nonstandard, but I found nothing remarcable
in the region. Either they all have 627K or none (including 1031)
will check this....

...OK, subtract 30 from my PB2-numbers. So 1909 is the critical position
for E627K. A G-nucleotide is E and a A-nucleotide is K, the virulence mutation.
3 sequences in my list have this: 759,582,1031.
But 1031RE2,1031T,1031T2 don't have it.

...and subtract 27 from my PA-numbers, so S409N corresponds to position 1253.
These have the N-mutation: 940,836,836T,1031,887,938E (but not 938)
940,836,938,887 were also sequences with particularly high mammelean score, see here:

http://www.flutrackers.com/forum/showthread.php?p=62370

[Mamabird]

Re: reassortment in Indonesia

3 sequences in my list have this: 759,582,1031.
But 1031RE2,1031T,1031T2 don't have it.

Yes, and 582 was the 30M from Jakarta whose viral sample was taken on April 26 of last year at his time of death. It is difficult to say how he acquired 627K since no bird isolates seem to match.

[Sharpe]

Re: reassortment in Indonesia

What this major reassortment means in regard to all the negative PCR tests being produced in Indonesia is a very interesting question.

[scottmcpherson]

Re: reassortment in Indonesia

Sharpe, that exactly was going to be my next question. Has the virus evolved beyond the PCR test's capability of detecting it?

[gsgs]

Re: reassortment in Indonesia

is there any example of such a virus , any serotype ?
I never heard it. With these mice or ferrets in labs,
they should have such examples, where there was dicease
but PCR failed.