Rhiza Labs FluTracker Forum

several Hongkong poultry H6N1,H6N2 genomes from 2001-2003 were released.
e.g. A/Ck/HK/SF3/2001(H6N1)
It is similar in 7 segments to HK-flu from 1997, so apparantly reassorted
with H5N1 by exchanging HA.
Did this reassortment happen before the 1997 outbreak in Hongkong,
is it the reassortment which led to that outbreak ?
It seems so. E.g. the PB1 of SF3 is closer to A/Dk/HK/562/1979(H10N9),
the best matching PB1 from the 70s, than A/H//156/1997.
But I'm not so sure yet since we had these periods of low mutation
in China which can corrupt normal molecular-clock analyis.

Anyway, I think that probably there was H6N1 in HK poultry all the time
before 1997 and then it just picked up the HA from A/Gs/Gd/1996(H5N1),
so to form a strain much more virulent to chickens.

They should have deep-frozen some sick-chicken/duck-tissues from HK
from the 80s or 90s. We do have some HK-sequences from the 70s,
but almost nothing from 1980-1996.

The 2004 tree-parrows study shoud be redone.
Find the places,species in China where flu
survives without mutating.

_________________
no patents on genes, publish the GISAID sequences !

Reassortment in 1997 isolates was described in 1997. You are a decade behind the literature.

_________________
www.twitter.com/hniman

AFAIK no precursor virus was found so far which matched the 1997 virus
in 7 segments so well.
It was assumed that several reassortments had happened in wild birds
and then had jumped from wild birds to poultry in 1997.
But now we see matching H6N1 poultry viruses from 2001,
possibly existing in this or similar forms before 1997.

However, this is only for the 1997 outbreak, which was controlled.
Later outbreaks did happen by other viruses.

_________________
no patents on genes, publish the GISAID sequences !

4 Qinghai genomes from 2010 meanwhile at genbank with
236,233,250,229 diferences from the original
A/Gs/Index/Qinghai/2005(H1N1)

47 mutations per year fits well to what we saw in 2005-2007


http://magictour.free.fr/panflu/qh94a.GIF
http://magictour.free.fr/panflu/qht4.GIF
_________________

p0 e0 f1 h0 s2
maxl=54
#differences
                                                        1   2   3   4   5   PB2 PB1  PA  HA  NP  NA   M  NS
---------------------------------------------------------------------------------------------------------------------
  1 >Index Qinghai                                      0 236 233 250 229   135 113 153 207 128 173 118 147   146#  189   12920   5467      1:>Index Qinghai                                   
  2 >A/chicken/West Bengal/239020/2010(H5N1/01/12/    236   0  11 319 304   119 114 160 149 121 170 112 122   134#  174   12920   5486      2:>A/chicken/West Bengal/239020/2010(H5N1/01/12/   
  3 >A/chicken/West Bengal/239022/2010(H5N1/01/12/    233  11   0 315 300   119 117 169 149 121 161 112 122   135#  171   12709   5496      3:>A/chicken/West Bengal/239022/2010(H5N1/01/12/   
  4 >A/chicken/Bangladesh/1151-9/2010(H5N1///         250 319 315   0 166   181 135 188 195 139 155 155 140   164#  210   12766   5519      4:>A/chicken/Bangladesh/1151-9/2010(H5N1///        
  5 >A/chicken/Bangladesh/1151-11/2010(H5N1///        229 304 300 166   0   139 151 185 168 133 191 117 140   156#  199   12785   5497      5:>A/chicken/Bangladesh/1151-11/2010(H5N1///       
--------------------------------------------------------------------------------------------------------------------------------
                                                        1   2   3   4   5   138 126 171 173 128 170 122 134


#differences in total to index
#differences in total to index , considering only polymorphisms that occur more than once in this table
#differences in total to index, where defined
#differences in total to index, where defined, considering only polymorphisms that occur more than once in this table


                                                      0000000000000001111111111111111111111122222 000000000000000000000011111111111111122222 0000000000000000000000000000000111111111111111111111112 00000000000000000000000000000000000011111111111111111111 000000000000000000000000011111111111 000000000000000000000000001111111111 0000000000000000000 00000000000000000000 
                                                      0123455566677880000123333444456666778900112 000011235566667778999900000134556788800112 0122222344456666666777788888999002223333334445566778880 00011112222223334555566666777888899900122223334444555556 000000122333335555678889901112223344 001111111223333445567999990000122223 0011111335557777889 00123344566666667778 
                                                      6260948955947772388420159112614789037927392 127959844424590169148955789959145216749782 3301155112950033458067802378588005692344560340826071390 03377880234992260013711146066347934623123790481168113793 235689756002471157540592384893663788 390122238491369286719035561359725782 4501126674491678123 18250125302234793582 
                                                      6673832778375466239042462892157768712850637 515992950574445582254008105114229683537540 7594658476896708549877664468707687030514051443198492076 81514034270171917813145858208706265635913292790915584502 861447481381226950748511090806397158 340912350906960604188637937868494266 5194703323677000390 54336916812666222193 
-codon-position---------------------------------------         1  11           2                1       1  2 2 1 1 1     2    1    1         1 21   2   1 1 2  2 2  22    2 1            1        12 212           21211212   2 1    1                   1    1  1 1    2         1       2   2     11212    21      1     2     12  2    1   1      12  1     1 11 1112 1 2 1 1 
---Index----------------------------------------------ACGGCAATGGAATAAGGGCGTCTAATGAAACCTAGTCCAAAGA GATGGCGAGCGAGGACACATCAAGCGAAGCTGGCCGTACCTT ATCTGGGTAGGCAGCGCTGCGAGGCGCTGATCGCGTTTAGACATCTTCACAGAAC AGGCCATATGCGCCATGGAGCGGCCAGGCATCATCGAGCTTAACACAGTGCGGACA TGAGTAGGGCAGGCCGGGTTGGTTCTACACAGGAGT AAGCGGGAGCTCTCATACATCCACCCCTACCGCTAG CAATCGCCCGCACTGGTCA TTGCCACGCACTTAACAGAA 
   1 >Index Qinghai                                   ........................................... .......................................... ....................................................... ........................................................ .................................... .................................... ................... ....................        0      0 ,      0      0       1:>Index Qinghai                                   
   2 >A/chicken/West Bengal/239020/2010(H5N1/01/12/   G.A...CAAATG.GC.TATACACGGCAGG.T..GTCTTGTGAC AGC.AT.G.TA.A.G.G..ATTG.T.G.T.C.ATT.CGTTCC GC..AA.C.AATG....C.T.G..T.T.AG.TT.ACCCGA.T.GTCCTGTGAG.T CA.TTGCGCAT.ATC.AAGTT....TA.T.CT.CAAGATCCGGTG.G.CA..TGT. CATA..A.A.GAAT.AA.CCAAC..CGTGT..A.AC .GATAAATTTCTCTCG..GCTTGTTTTGGTTATCGA TC.CTAT.AAAGAC.A.TT AC.TT.TT.GAACGGAC.TG      236    228 ,    236    228       2:>A/chicken/West Bengal/239020/2010(H5N1/01/12/   
   3 >A/chicken/West Bengal/239022/2010(H5N1/01/12/   G.A...CAAATG.GC.TATACACGGCAGG.T..GTCTTGTGAC AGC.AT.G.TA.A.G.G..ATTG.T.G.T.C.ATT.CGTTCC GC..AA.C.AATG....C.T.G..T.T.AG.TT.ACCCGA.T.GTCCTGTGAG-- CA.TTGCGCAT.ATC.AAGTT....TA.T.CT.CAAGATCCGGTG.G.CA..TGT. CATA..A.A.GAAT.AA.CCAAC..CGTGT..A.AC .GATAAATTTCTCTCG..GCTTGTTTTGGTTATCGA TC.CTAT.AAAGAC.A.TT AC.TT.TT.GAACGGAC.TG      240    229 ,    233    227       3:>A/chicken/West Bengal/239022/2010(H5N1/01/12/   
   4 >A/chicken/Bangladesh/1151-9/2010(H5N1///        .TAAAG..A...C..A.AT....G.CA.GTTTCG..T.GT... A.CA..R.ATAG.RGA.AG....R.R.GTA.A...A....C. .CTCA.A.G.AT.RTRT.R.R.RR.ATC..C..A...C..G.G...C....A.GT .AA.T.CG..TAT.GC.AGTTAATTTAATGC.G.A...T.CG.T.T.AC.TTTGTG ..T.AG.A.A....T..ACC.ACAT...GTGA.G-- G...AA....C.CT..GT.C....T.T...TAT..A ..G.T.TT.AA...AAC.. A.ATTT..TG..C..A.A.-      253    165 ,    250    162       4:>A/chicken/Bangladesh/1151-9/2010(H5N1///        
   5 >A/chicken/Bangladesh/1151-11/2010(H5N1///       GTAAAG..A...C..A.AT....G.CA.GTTTCG..T.GT... A.CA..R.ATAG.RGA.AG....R.R.GTA.A..TA....C. .CTCA.A.G.AT.RTRT.R.R.RR.ATC..C..A...C..G.G...C....A.GT .AA.T.CG..TA...C.AGTTAATTTAATGC.G.A...T.CG.T.T.AC.TTTGTG ..T.AG.A.A....T..ACC.ACAT....TGA.G-- G...A.....C..T..GT.C....T.T...TAT..A ..G.T.TT.AA...A.C.. A.ATTT..TG..C..A.A.-      233    161 ,    229    158       5:>A/chicken/Bangladesh/1151-11/2010(H5N1///       
                                                                                                                                                                                                                                                                                                                                                                                 
---Index----------------------------------------------ACGGCAATGGAATAAGGGCGTCTAATGAAACCTAGTCCAAAGA GATGGCGAGCGAGGACACATCAAGCGAAGCTGGCCGTACCTT ATCTGGGTAGGCAGCGCTGCGAGGCGCTGATCGCGTTTAGACATCTTCACAGAAC AGGCCATATGCGCCATGGAGCGGCCAGGCATCATCGAGCTTAACACAGTGCGGACA TGAGTAGGGCAGGCCGGGTTGGTTCTACACAGGAGT AAGCGGGAGCTCTCATACATCCACCCCTACCGCTAG CAATCGCCCGCACTGGTCA TTGCCACGCACTTAACAGAA 
-codon-position---------------------------------------         1  11           2                1       1  2 2 1 1 1     2    1    1         1 21   2   1 1 2  2 2  22    2 1            1        12 212           21211212   2 1    1                   1    1  1 1    2         1       2   2     11212    21      1     2     12  2    1   1      12  1     1 11 1112 1 2 1 1 
                                                      0000000000000001111111111111111111111122222 000000000000000000000011111111111111122222 0000000000000000000000000000000111111111111111111111112 00000000000000000000000000000000000011111111111111111111 000000000000000000000000011111111111 000000000000000000000000001111111111 0000000000000000000 00000000000000000000 
                                                      0123455566677880000123333444456666778900112 000011235566667778999900000134556788800112 0122222344456666666777788888999002223333334445566778880 00011112222223334555566666777888899900122223334444555556 000000122333335555678889901112223344 001111111223333445567999990000122223 0011111335557777889 00123344566666667778 
                                                      6260948955947772388420159112614789037927392 127959844424590169148955789959145216749782 3301155112950033458067802378588005692344560340826071390 03377880234992260013711146066347934623123790481168113793 235689756002471157540592384893663788 390122238491369286719035561359725782 4501126674491678123 18250125302234793582 
                                                      6673832778375466239042462892157768712850637 515992950574445582254008105114229683537540 7594658476896708549877664468707687030514051443198492076 81514034270171917813145858208706265635913292790915584502 861447481381226950748511090806397158 340912350906960604188637937868494266 5194703323677000390 54336916812666222193 
.
.

.
.

_________________
no patents on genes, publish the GISAID sequences !

3524 H5N1-HA only since 1997, Asian HP (genbank,2011/07/22)

http://magictour.free.fr/panflu/h5ha11a.GIF

I printed it on 8 normal sized paper-sheets
and glued it together
compare with the phylo-tree (link ?)

the lower 9 sequences are LP,
will be removed in the next version

Indo - splits in 3 areas (one of 40 just above the LP)
to be corrected

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

biggest subpart (~30%) is "Qinghai" which starts in the middle
I count ~19 markers

Thailand,Vietnam,old 6 markers top

Thailand,Vietnam, 15 additional markers

Indonesia, 11 markers

Korea,Japan 2003 overlaps with Indo in the pic

2008ff Korea,Japan,Mongolia 12 markers above Qinghai

China 5 markers

lower part (below Qingha) : 4 markers


I'm planning to list all the markers and group more correctly

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

2nd version , no green for printing, Qinghai splits
http://magictour.free.fr/panflu/h5ha11b.GIF

_________________
no patents on genes, publish the GISAID sequences !

I make it 12 HA-substrains of Asian HP H5N1 :
markers relative to the China-2003 bottleneck

markers,strain
--------
29,Qinghai
32,VNM
19,IDN
87,MNG08
75,VNM08
48,HK97
78,Hebei05
11,Yunnam03
(26 Fujian05)
29,243...
18,1581...
50,Xinjiang05
30,rest

_________________
no patents on genes, publish the GISAID sequences !

new human H5N1 sequences from China, 2008-2010

looks like a lot of reassortment and mixing,
hard to track the evolution.

I don't see that _one_ new dominant strain

_________________
no patents on genes, publish the GISAID sequences !