Thailand, H5N1 found in chickens

[gsgs]

Re: Thailand, H5N1 found in chickens

A/chicken/Thailand/ST-351/2008(H5N1)
http://www.ncbi.nlm.nih.gov/nuccore/226425692?report=genbank

all 8 segments, submitted Oct.01,2009
no date or location given


this virus is remarkable, it is close to the original Vietnam virus from 2003,
but more distant from other more recent viruses

8,5,5,8,2,14,3,5 nucleotide-differences to Index-Vietnam/2003(H5N1)
17,17,14,28,10,27,8,8 nucleotide-differences to Index-genotype-Z/~2001(H5N1)
19,16,15,26,10,17,7,9 nucleotide-differences of Vietnam to genotype_Z

(genotype-Z is the ancestor of all modern H5N1, including Indonesia,Vietnam,
Thailand,Qinghai,Japan,Henan,Fujian(except segment 3),...)

0,2,0,6,1,5,1,2 differences to A/little grebe/Thailand/Phichit-01/2004(H5N1)
which in turn has 8,7,5,6,1,11,2,7 differences to Index-Vietnam/2003
http://www.tm.mahidol.ac.th/seameo/2008_39_3/01-4106.pdf



2006-outbreak Phichit:
http://www.flutrackers.com/forum/showthread.php?t=8463

2004-outbreak Phichit: ?

                                                      0000000111111111122222 000000001111111111122 00000000001111111 000000000000000000000000000111111111111 00000000011 000000000000000000000011111111 000000000 0000000000000 
                                                      0333349023356677901112 234557790001256788802 01335678992225688 001122333344444555666778899022455566666 00223455911 000000111222355677799900011223 225567788 1122333444578 
                                                      2112936182374555780551 135792592457694123915 50053400598992967 221209023411368137138260923459645813458 35572834114 155578123588689634502317846476 482716878 7827669049600 
                                                      2352953683387358439141 906010610119338043036 12047558701361598 278045586989470241463057470219400610793 01834379569 305765743145039327717381654380 652934085 7033455837870 
-codon-position---------------------------------------11 1   21 1      1            1  1   1              1          1 1  121 11222 2 12 2      1   122 1                121 11 1122  12   11  1  2 1 1     12 2    1 122 22122 
---Index----------------------------------------------AAGATTACCCCGCATACCAAAG AGGAAAGGCATACGCGGGGTG GACTACATGAATTAGAA CAGTAGCACCGACGCAACGCAACAGCACTACTACAGGTG TAGAGCCGTAT CTAAAAGACCGCGAACTGTATGCTCGGTAA TGGGGCGTA TGGAACTAAGTCG 
   1 >A/Ck/Thailand/ST-351/2008(H5N1)                 CG.G..TA.T.ATGCGTTGGGA GAAG.G..T.CGTATAAAACA .GTCGAGC.T.CAGAGG T.A.G.TGTTAGTA.GG.ATG..G.T.TCGTCGTT.AC. CGAGAA.ACGC ACGG.TCGAAATAG.TCTCC.ATCAAACGG .AAAAAAGC CAA.GT.G..AA.
   2 >A/little grebe/Thailand/Phichit-01/2004(H5N1)   CG.G..TA.T.ATGCGTTGGGA GAAG.G.ATGCGTATAAAACA .GTCGAGC.T.CAGAGG T...G.TGTTAGTA.GG.A.G....T.TCGTC.TTAACA .GAGAA.ACGC AC.G.TC.AAATA.GTCTCC..TCAAACGG ..AAAAAGC .AAGGT.G..AA.
   3 >Index Vietnam                                   CGAGCGTAATTA.GC..TGGGA ...GGGC.T.CGTATAAAACA AGTCGA.CA.GCAGAGG TG..G.TGTTAGTA.GGAA.GG...T.TCGT..TT.AC. .GAGAATACGC .C..G.C..AA.....CTCCC.TC.AACGG C.A.AAAGC CAA...CGG.AAA
   4 >A/Index-se9agbi.26                              ...................... ..................... ................. ...C.A.G......T.G.....A.A.C............ ........... .............................. ......... .........A...
   5 >Index-se9agbi.51                                ...................... ..................... ................. ....................................... ........... .............................. ......... .............

 

[gsgs]

Re: Thailand, H5N1 found in chickens

6 mutations (wrt. the genotype-Z index) from the little grebe 2004 were "undone"
while 12 new ones were generated.
So this doesn't look like a lab-error, a contamination with the little-grebe-virus
or another virus.
The sample could still have been stored and then intermixed with othe samples
and thus given a wrong collection-year

We also had this with 3 viruses from Vietnam 2005 that had the genes from
HK/1997 in almost unchanged form. A/duck/Vietnam/8/05(H5N1) ...

And the Hungary-Suffolk virus from 2007 that had only as many mutations
as similar viruses from >one year before.

H5N1 may in rare cases (<5%) survive unchanged in grebes or other animals
or in the environment without replicating, without mutating.

Maybe in immunodeficient animals in certain organs or organelles.
Maybe inside sandcorns or dust or bacteria or small holes protected
rom chemicals and radiation


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


HA,Thailand,2008
---------------------
A/chicken/Thailand/ICRC-V586/2008(H5N1)
A/chicken/Thailand/ICRC-618/2008(H5N1)
A/brown-head gull/Thailand/vsmu-4/2008(H5N1)
A/duck/Thailand/ICRC-V629/2008(H5N1)
A/Kalij pheasant/Thailand/vsmu-1/2008(H5N1)
A/chicken/Thailand/NS-341/2008(H5N1)
A/chicken/Thailand/NS-342/2008(H5N1)
A/chicken/Thailand/NS-339/2008(H5N1)
A/chicken/Thailand/PC-340/2008(H5N1)
A/chicken/Uthaithani/NIAH115067/2008(H5N1)
A/chicken/Sukhothai/NIAH114843/2008(H5N1)
A/chicken/Thailand/ST-351/2008(H5N1)
A/chicken/Phichit/NIAH600674/2008/01(H5N1))
A/chicken/Nakhonsawan/NIAH6006587/2008/01(H5N1)
A/chicken/Sukhothai/NIAH114843/2008/11(H5N1)
A/chicken/Uthaithani/NIAH115067/2008/11(H5N1)
A/chicken/Thailand/CU-354/2008/11/14(H5N1)


NIAH: Department of Livestock Development, National Institute of Animal Health
, Kasetklang, Chatuchak, Bangkok 10900, Thailand
ICRC: Molecular Biology and Virology Unit,
Faculty of Veterinary Science, Mahidol University,
Putthamontol-4, Salaya, Nakornpatom 73170, Thailand
vsmu: Molecular Biology and Virology Unit,
Faculty of Veterinary Science, Mahidol University,
Puthamontol-4 Rd., Salaya, Nakornpathom 73170, Thailand
NS-: Pediatric, Chulalongkorn University,
Pratumwan, Bangkok, Bangkok 10330, Thailand
ST-: Chulalongkorn University,
Pratumwan, Bangkok 10330, Thailand
PC-: Pediatrics, Chulalongkorn University,
Pratumwan, Bangkok, Bangkok 10330, Thailand
CU: Faculty of Veterinary Science, Veterinary Public Health Department,
Chulalongkorn University, Pathumwan,
Bangkok 10330, Thailand


no google-hits, no info where that st-351 sequence was from, no date (only 2008),
no location. Nor the circumstances nor any mentioning let alone speculation why
that virus was conserved for 4 years.