Rhiza Labs FluTracker Forum

similar to Shianxi/2/06 are the environment/Hunan sequences from 2007

Xinjiang/1/2009 is similar to human/GD02/2006
Shandong,Beijing are the Fujian strain
the other 5 are

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no patents on genes, publish the GISAID sequences !

WRONG. The original sequence, deposited in 2006 had no deletion

LOCUS DQ914814 1779 bp cRNA linear VRL 01-DEC-2008
DEFINITION Influenza A virus (A/chicken/Shanxi/2/2006(H5N1)) segment 4,
complete sequence.
ACCESSION DQ914814
VERSION DQ914814.1 GI:117414797
KEYWORDS .
SOURCE Influenza A virus (A/chicken/Shanxi/2/2006(H5N1))
ORGANISM Influenza A virus (A/chicken/Shanxi/2/2006(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1779)
AUTHORS Chen,H., Li,Y., Shi,J. and Zhao,H.
TITLE Direct Submission
JOURNAL Submitted (22-AUG-2006) National Avian Influenza Reference
Laboratory, Harbin Veterinary Research Institute, No. 427 Maduan
Street, Nangang District, Harbin, Heilongjiang 150001, China
COMMENT [WARNING] On Feb 9, 2009 this sequence was replaced by
gi:223006846.
GenBank Accession Numbers DQ914811-DQ914818 represent the complete
genome of Influenza A virus (A/chicken/Shanxi/2/2006(H5N1)).
FEATURES Location/Qualifiers
source 1..1779
/organism="Influenza A virus
(A/chicken/Shanxi/2/2006(H5N1))"
/mol_type="viral cRNA"
/strain="A/chicken/Shanxi/2/2006"
/serotype="H5N1"
/isolation_source="egg"
/db_xref="taxon:404408"
/segment="4"
/country="China"
gene 29..1735
/gene="HA"
CDS 29..1735
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABK34764.1"
/db_xref="GI:117414798"
/translation="MEKIVLLLAIIGLVKSDQICVGYHANNSTEQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLDGVKPLILKDCSVAGWLLGNPMCDEFINVSEWSYIVEKASPA
NGLCYPGDFNDYEELKHLLSRINHFEKIKIIPKSSWSNHEASSGVSSACSYLGKPSFF
RNVVWLIKKNNTYPPIKVNYTNTNQEDLLVLWGIHHPNDETEQIKIYQNPTTYISVGT
STLNQRLVPKIATKSQVNGQSGRMEFFWTILKPNDAINFDSNGNFIAPEYAYKIVKKG
DSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLR
NAPQREGRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYSADKESTQKAID
GVTNKVNSIIDKMNTQFEGVVREINNLERRIENLNKKMEDGFLDVWTYNAELLVLMEN
ERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYPQY
SEEARLNREEISGVKLESMVTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCRI
CI"
ORIGIN
1 agcaaaagca ggggtataat ctgtcaaaat ggagaaaata gtgcttcttc ttgcaataat
61 cggtcttgtt aaaagtgatc agatttgcgt tggttaccat gcaaacaact caacagagca
121 ggttgacaca ataatggaaa agaacgttac tgttacacat gctcaagaca tactggagaa
181 gacacacaac gggaagctct gcgacctaga tggagtgaag cctctcattt tgaaagattg
241 tagtgtagct ggatggctcc tcggaaaccc tatgtgtgac gaatttatca atgtgtcgga
301 atggtcttac atagtggaga aggccagtcc agccaatggc ctctgttacc caggggattt
361 caatgactat gaagaactga aacacctatt gagcagaata aaccattttg agaaaattaa
421 gatcatcccc aaaagttctt ggtccaatca tgaagcctca tcaggggtga gctcagcatg
481 ttcctatctg gggaagccct cctttttcag aaatgtggta tggcttatca aaaagaataa
541 tacataccca ccaataaagg tgaactacac caataccaac caagaagatc ttttggtact
601 gtgggggatt caccatccca acgatgagac agagcagata aagatctatc aaaacccaac
661 cacctatatt tccgttggaa catcaacact aaaccagaga ttggtaccaa aaatagctac
721 taaatcccaa gtgaacgggc aaagtggaag aatggagttc ttctggacaa ttttaaagcc
781 gaatgatgct atcaatttcg atagtaatgg aaatttcatt gctccagaat atgcatacaa
841 aattgtcaag aaaggggact cagcgattat gaaaagtgaa ttggaatatg gtaactgcaa
901 caccaagtgt caaactccaa tgggggcgat aaattctagt atgccattcc acaacataca
961 ccctctcacc atcggggaat gccccaaata tgtgaaatca aacagattag tcctcgcgac
1021 tggactcaga aatgcccctc aaagagaggg aagaagaaaa aagagaggac tatttggagc
1081 catagcaggg tttatagagg gaggatggca gggaatggta gatggttggt atgggtacca
1141 ccatagcaat gagcagggga gtggatactc tgcagacaaa gaatccactc aaaaggcaat
1201 agatggagtc accaataagg tcaactcgat cattgacaaa atgaacactc agtttgaggg
1261 cgttgttagg gaaattaata acttagaaag gagaatagag aatttaaaca aaaagatgga
1321 agacggattc ctagatgtct ggacttataa cgctgaactt ctggttctca tggaaaatga
1381 gagaactcta gactttcatg actcaaatgt caagaacctt tacgacaagg tccgactgca
1441 gcttagggat aatgcaaagg agctgggtaa cggttgtttc gaattctatc acaaatgtga
1501 taatgaatgt atggaaagtg taaaaaacgg aacgtatgac tacccgcagt attcagaaga
1561 agcaagacta aacagagagg aaataagtgg agtaaaattg gaatcaatgg taacttacca
1621 aatactgtca atttattcaa cagtggcgag ttccctagca ttggcaatca tggtggctgg
1681 tctatcttta tggatgtgct ccaatggatc gttacaatgc agaatttgca tttgaatttg
1741 tgagttcaga ttgtagttaa aaacaccctt gtttctact

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www.twitter.com/hniman

You are confused. In 2006 the original sequence was placed on deposit at Genbank. It had no deletion (did not have 125del).
http://www.ncbi.nlm.nih.gov/nuccore/117414797
On February 9, 2009, after the December, 2008 outbreak at Jiangsu, as well as the human cases in early, 2009, the 2006 submission was replaced with a new submission that had the deletion. The following month, the latest version appeared, which also has the deletion.

Thus, the deletion problem in Shanxi/2/2006 was "discovered" right after the Jiangsu outbreak, which was reported to OIE, and the relationship to Shanxi/2 was noted.

The sequences from the Jiangsu outbreak, which almost certainly have the 3 BP deletion (125del), have not been made public (and reports of human cases in China abruptly stopped in Feb/Mar 2009).

Those paying attention to the 3 BP deletion are well aware of this sequence of sequences.

_________________
www.twitter.com/hniman

how can they "discover" it


they sequenced it and there was no deletion

or they uploaded a wrong sequence

or it was mixed

or contamination


they must know this, (but won't tell us (yet))

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no patents on genes, publish the GISAID sequences !

Please. The Shanxi sequence is quite unique and they probbaly didn't believe the deletion. When they saw the deletion in Jiangsu and the close relationship with Shanxi, they looked at the Shanxi sequence again and saw the deletion.

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www.twitter.com/hniman

so, you think the sequencing did show the deletion but they thought
it was an error and deleted the deletion by hand ???

_________________
no patents on genes, publish the GISAID sequences !

I'm sure the deletion was there in 2006. Maybe they had more than one sequence and just selected the one without the deletion.

_________________
www.twitter.com/hniman

the same virus, once with deletion and once without -
that seems to imply the deletion first happened
in that very chicken (or very closely related).

unlikely

_________________
no patents on genes, publish the GISAID sequences !

Please. Mixtures are VERY common and transmitted as mixtures.
Your "unlikely" comment remains PURE fanatasy.

_________________
www.twitter.com/hniman

that "very old" Shanxi/2/06 has 23 differences in HA
from the "old" Shanxi/2/06


and it's again that Harbin laboratory, where we had probable errors before

_________________
no patents on genes, publish the GISAID sequences !