Osaka Japan Tamiflu Resistant Sequence Released

[HenryN]

Japan has released the NA sequence with H274Y

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

LOCUS GQ365445 1410 bp cRNA linear VRL 08-JUL-2009
DEFINITION Influenza A virus (A/Osaka/180/2009(H1N1)) segment 6 neuraminidase
(NA) gene, complete cds.
ACCESSION GQ365445
VERSION GQ365445.1 GI:251833645
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Osaka/180/2009(H1N1))
ORGANISM Influenza A virus (A/Osaka/180/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1410)
AUTHORS Ujike,M., Obuchi,M., Tashiro,M., Horikawa,H., Kato,Y., Oguchi,A.,
Fujita,N. and Odagiri,T.
TITLE Human infection with novel swine H1N1 influenza
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1410)
AUTHORS Horikawa,H., Kato,Y., Oguchi,A. and Fujita,N.
TITLE Direct Submission
JOURNAL Submitted (08-JUL-2009) National Institute of Technology and
Evaluation (NITE), Tokyo, Japan
REFERENCE 3 (bases 1 to 1410)
AUTHORS Ujike,M., Obuchi,M., Tashiro,M. and Odagiri,T.
TITLE Direct Submission
JOURNAL Submitted (08-JUL-2009) National Institute of Infectious Diseases,
4-7-1, Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..1410
/organism="Influenza A virus (A/Osaka/180/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Osaka/180/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:653902"
/segment="6"
/country="Japan"
/collection_date="2009"
/note="lineage: swl
passage history: MDCK1; resistance to Oseltamivir"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="ACT22016.1"
/db_xref="GI:251833646"
/translation="MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHS IQLGNQN
QIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPV SGWAIYSK
DNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDR SPYRTLMS
CPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNG IITDTIKS
WRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVE MNAPNYYY
EECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNP RPNDKTGS
CGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTD NNFSIKQD
IVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSS ISFCGVNS
DTVGWSWPDGAELPFTIDK"
ORIGIN
1 atgaatccaa accaaaagat aataaccatt ggttcggtct gtatgacaat tggaatggct
61 aacttaatat tacaaattgg aaacataatc tcaatatgga ttagccactc aattcaactt
121 gggaatcaaa atcagattga aacatgcaat caaagcgtca ttacttatga aaacaacact
181 tgggtaaatc agacatatgt taacatcagc aacaccaact ttgctgctgg acagtcagtg
241 gtttccgtga aattagcggg caattcctct ctctgccctg ttagtggatg ggctatatac
301 agtaaagaca acagtataag aatcggttcc aagggggatg tgtttgtcat aagggaacca
361 ttcatatcat gctccccctt ggaatgcaga accttcttct tgactcaagg ggccttgcta
421 aatgacaaac attccaatgg aaccattaaa gacaggagcc catatcgaac cctaatgagc
481 tgtcctattg gtgaagttcc ctctccatac aactcaagat ttgagtcagt cgcttggtca
541 gcaagtgctt gtcatgatgg catcaattgg ctaacaattg gaatttctgg cccagacaat
601 ggggcagtgg ctgtgttaaa gtacaacggc ataataacag acactatcaa gagttggaga
661 aacaatatat tgagaacaca agagtctgaa tgtgcatgtg taaatggttc ttgctttact
721 gtaatgaccg atggaccaag taatggacag gcctcataca agatcttcag aatagaaaag
781 ggaaagatag tcaaatcagt cgaaatgaat gcccctaatt attactatga ggaatgctcc
841 tgttatcctg attctagtga aatcacatgt gtgtgcaggg ataactggca tggctcgaat
901 cgaccgtggg tgtctttcaa ccagaatctg gaatatcaga taggatacat atgcagtggg
961 attttcggag acaatccacg ccctaatgat aagacaggca gttgtggtcc agtatcgtct
1021 aatggagcaa atggagtaaa aggattttca ttcaaatacg gcaatggtgt ttggataggg
1081 agaactaaaa gcattagttc aagaaacggt tttgagatga tttgggatcc gaacggatgg
1141 actgggacag acaataactt ctcaataaag caagatatcg taggaataaa tgagtggtca
1201 ggatatagcg ggagttttgt tcagcatcca gaactaacag ggctggattg tataagacct
1261 tgcttctggg ttgaactaat cagagggcga cccaaagaga acacaatctg gactagcggg
1321 agcagcatat ccttttgtgg tgtaaacagt gacactgtgg gttggtcttg gccagacggt
1381 gctgagttgc catttaccat tgacaagtaa

[Rwilmer]

Re: Osaka Japan Tamiflu Resistant Sequence Released

So Dr. Niman this means that tami resistant flu is widespread?

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Exact NA matches (other than H274Y)

gb|GQ287622.1| Influenza A virus (A/Shiga/2/2009(H1N1)) segme... 2538 0.0
gb|GQ261276.1| Influenza A virus (A/Sakai/2/2009(H1N1)) segme... 2538 0.0
gb|GQ261274.1| Influenza A virus (A/Sakai/1/2009(H1N1)) segme... 2538 0.0
gb|GQ261273.1| Influenza A virus (A/Himeji/1/2009(H1N1)) segm... 2538 0.0
gb|GQ220732.2| Influenza A virus (A/Hyogo/2/2009(H1N1)) segme... 2538 0.0
gb|GQ220737.1| Influenza A virus (A/Osaka-C/2/2009(H1N1)) seg... 2538 0.0
gb|GQ220736.1| Influenza A virus (A/Osaka-C/1/2009(H1N1)) seg... 2538 0.0
gb|GQ220735.1| Influenza A virus (A/Osaka/2/2009(H1N1)) segme... 2538 0.0
gb|GQ220734.1| Influenza A virus (A/Osaka/1/2009(H1N1)) segme... 2538 0.0
gb|GQ220733.1| Influenza A virus (A/Kobe/1/2009(H1N1)) segmen... 2538 0.0
gb|GQ220730.1| Influenza A virus (A/Amagasaki/1/2009(H1N1)) s... 2538 0.0
gb|GQ220729.1| Influenza A virus (A/Amagasaki/2/2009(H1N1)) s... 2538 0.0

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

HA match

gb|GQ219578.1| Influenza A virus (A/Osaka/1/2009(H1N1)) segme... 3068 0.0

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

HA travel log

gb|GQ365444.1| Influenza A virus (A/Osaka/180/2009(H1N1)) seg... 38.2 0.18
gb|GQ219578.1| Influenza A virus (A/Osaka/1/2009(H1N1)) segme... 38.2 0.18
gb|EU798784.1| Influenza A virus (A/swine/Korea/Asan04/2006(H... 38.2 0.18

[Cyril]

Re: Osaka Japan Tamiflu Resistant Sequence Released

So it's not genetically related to the previous strain to bear this marker (HK/2369), and the acquisition of H274Y in both those isolates are distinct events.

This isolate seems to be part of a "family" of japanese strains that share a set of very specific markers, although none of these markers are on HA or NA (which are the only genes published).

[gsgs]

Re: Osaka Japan Tamiflu Resistant Sequence Released

see here for Japanese markers:

http://www.flutrackers.com/forum/showthread.php?t=113542

[Cyril]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Thanks, very interesting! I was actually looking forward to mapping the japanese isolates.

[gsgs]

Re: Osaka Japan Tamiflu Resistant Sequence Released

we can always need a confirmation.
So many people here who distrust me...

[Cyril]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Well we seem to be using the same kind of approach (studying polymorphisms at the nucleotides level) and have a similar background (we're both programmers... although I'm far from being academic).

At first glance your observations regarding the japanese strains match what I noticed, but I haven't been that far into the details. I don't see how they can in themselves cause "distrust" - they're just observations, factual information.

Interpreting the facts is another matter - I don't myself have the background for that.

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Well we seem to be using the same kind of approach (studying polymorphisms at the nucleotides level) and have a similar background (we're both programmers... although I'm far from being academic).

At first glance your observations regarding the japanese strains match what I noticed, but I haven't been that far into the details. I don't see how they can in themselves cause "distrust" - they're just observations, factual information.

Interpreting the facts is another matter - I don't myself have the background for that.

Facts are facts and interpretaions are interpretations (like the jumping polymorphisms representing recombination which is far from random).

Speaking of Japan, NA of Osaka/1 matches the Jersey girl (New Jersey/1), which matches Hong Kong prior to acquistion of H274Y.

[Cyril]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Very sorry, but I fail to see what you mean?

I find two SNP when I compare the NA genes from Osaka/1 and NJ/1:

cgg@cgg-laptop:~/code/h1n1$ ./genecmp bank/Osaka-1_NA bank/NewJersey-01_NA
 248 AAT -> GAT
 291 GTG -> GTA
2 mutations

[HenryN]

Re: Osaka Japan Tamiflu Resistant Sequence Released

Very sorry, but I fail to see what you mean?

I find two SNP when I compare the NA genes from Osaka/1 and NJ/1:

cgg@cgg-laptop:~/code/h1n1$ ./genecmp bank/Osaka-1_NA bank/NewJersey-01_NA
 248 AAT -> GAT
 291 GTG -> GTA
2 mutations

Sorry. I posted on the wrong H274Y thread (was supposed to be on Hong Kong thread). The identity is between Sapporo/1 and New Jersey/1 (and Hong Kong/2369 only differs from both because of H274Y).