Yamaguchi Japan Tamiflu Resistant Sequence Released

[HenryN]

The sequence of a second example of H274Y in Japan has been released'

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

LOCUS GQ397279 1410 bp cRNA linear VRL 21-JUL-2009
DEFINITION Influenza A virus (A/Yamaguchi/22/2009(H1N1)) segment 6
neuraminidase (NA) gene, complete cds.
ACCESSION GQ397279
VERSION GQ397279.1 GI:254548843
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Yamaguchi/22/2009(H1N1))
ORGANISM Influenza A virus (A/Yamaguchi/22/2009(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JOURNAL Unpublished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 Toda,S. and Sirabe,S.
TITLE Direct Submission
JOURNAL Submitted (21-JUL-2009) Yamaguchi Prefectural Institute of Public
Health and Environment, Yamagauchi, Japan
REFERENCE 3 (bases 1 to 1410)
AUTHORS Ujike,M., Obuchi,M., Tashiro,M. and Odagiri,T.
TITLE Direct Submission
JOURNAL Submitted (21-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/Yamaguchi/22/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Yamaguchi/22/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:660652"
/segment="6"
/country="Japan"
/collection_date="2009"
/note="lineage: swl; passage history: MDCK2; resistance to
oseltamivir"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="ACT67256.1"
/db_xref="GI:254548844"
/translation="MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHS IQLGNQN
QIETCNQSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPV SGWAIYSK
DNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDR SPYRTLMS
CPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNG IITDTIKS
WRNNILRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVE 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 tgatggacag gcctcataca aaatcttcag 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: Yamaguchi Japan Tamiflu Resistant Sequence Released

So does this, coupled with the quebec resistance, indicate that there is a circulating strain with H274Y?

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

So does this, coupled with the quebec resistance, indicate that there is a circulating strain with H274Y?

The circumstances surrounding this sequence are unclear. The Quebec sequence appears to be from a contact taking a prophylactic dose of Tamiflu. This sequence has H274Y and it is assumed that the Quebec sequence also has H274Y, but on a different genetic background.

[wotan]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

So does this, coupled with the quebec resistance, indicate that there is a circulating strain with H274Y?

The Quebec case seems to imply infection from a family member. We would need at least a sequence from the family member who may have been the source of the older man's infection. But there is the question being raised in that thread: did the man with the known resistant strain spread it?

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

NA travel log

gb|GQ368668.1| Influenza A virus (A/Distrito Federal/2611/200... 34.2 2.9
gb|GQ365427.1| Influenza A virus (A/Iwate/1/2009(H1N1)) segme... 34.2 2.9
gb|GQ365412.1| Influenza A virus (A/Akita/1/2009(H1N1)) segme... 34.2 2.9
gb|GQ334348.1| Influenza A virus (A/Shizuoka/759/2009(H1N1)) ... 34.2 2.9
gb|CY041760.1| Influenza A virus (A/New York/3413/2009(H1N1))... 34.2 2.9
gb|GQ287628.1| Influenza A virus (A/Yokohama/1/2009(H1N1)) se... 34.2 2.9
gb|GQ287624.1| Influenza A virus (A/Shiga/3/2009(H1N1)) segme... 34.2 2.9
gb|GQ225351.1| Influenza A virus (A/Zhejiang/1/2009(H1N1)) se... 34.2 2.9
gb|DQ432046.1| Influenza A virus (A/swine/Fujian/2003(H5N1)) ... 34.2 2.9
gb|DQ432038.1| Influenza A virus (A/swine/Fujian/2001(H5N1)) ... 34.2 2.9
gb|AY651473.2| Influenza A virus (A/teal/China/2978.1/2002(H5... 34.2 2.9
gb|AY575883.2| Influenza A virus (A/Gs/HK/739.2/02 (H5N1)) ne... 34.2 2.9
gb|CY029169.1| Influenza A virus (A/quail/Shantou/3846/2002(H... 34.2 2.9
gb|CY029120.1| Influenza A virus (A/goose/Shantou/157/2002(H5... 34.2 2.9
gb|CY029085.1| Influenza A virus (A/duck/Shantou/5526/2001(H5... 34.2 2.9
gb|EF541469.1| Influenza A virus (A/Hong Kong/213/2003(H5N1))... 34.2 2.9
gb|EF541468.1| Influenza A virus (A/chicken/Viet Nam/Ncvd8/20... 34.2 2.9
gb|EF541465.1| Influenza A virus (A/duck/Viet Nam/Ncvd1/2002(... 34.2 2.9
gb|EF467813.1| Influenza A virus (A/teal/Hong Kong/2978/03(H5... 34.2 2.9
gb|EF124325.1| Influenza A virus (A/goose/Shantou/3624/2006(H... 34.2 2.9
gb|EF124312.1| Influenza A virus (A/goose/Shantou/2086/2006(H... 34.2 2.9
gb|EF124311.1| Influenza A virus (A/goose/Shantou/239/2006(H5... 34.2 2.9
gb|DQ997385.1| Influenza A virus (A/swine/Anhui/ca/2004(H5N1)... 34.2 2.9
gb|DQ997411.1| Influenza A virus (A/duck/Zhejiang/bj/2002(H5N... 34.2 2.9
gb|DQ997397.1| Influenza A virus (A/chicken/Hunan/fg/2004(H5N... 34.2 2.9
gb|DQ997183.1| Influenza A virus (A/chicken/Jiangsu/cz1/2002(... 34.2 2.9
gb|DQ191691.1| Influenza A virus (A/golden mountain thrush/Fu... 34.2 2.9
gb|DQ191690.1| Influenza A virus (A/curlew/Shandong/61/04(H5N... 34.2 2.9
gb|DQ188911.1| Influenza A virus (A/black bulbul/Fujian/439/0... 34.2 2.9
gb|DQ188910.1| Influenza A virus (A/slaty-backed gull/Shandon... 34.2 2.9
gb|DQ188909.1| Influenza A virus (A/babbler/Fujian/320/04(H5N... 34.2 2.9
gb|AY623431.1| Influenza A virus (A/chicken/Yichang/lung-1/04... 34.2 2.9
gb|AY747610.2| Influenza A virus (A/swine/Fujian/1/2003(H5N1)... 34.2 2.9
gb|AY747618.1| Influenza A virus (A/swine/Fujian/F1/2001(H5N1... 34.2 2.9
gb|AY585419.1| Influenza A virus (A/duck/Zhejiang/52/2000(H5N... 34.2 2.9
gb|AY575884.1| Influenza A virus (A/Eg/HK/757.3/02 (H5N1)) ne... 34.2 2.9
gb|AY575882.1| Influenza A virus (A/HK/213/03 (H5N1)) neurami... 34.2 2.9
gb|AY575881.1| Influenza A virus (A/HK/212/03 (H5N1)) neurami... 34.2 2.9
gb|DQ321057.1| Influenza A virus (A/Chinese pond heron/Hong K... 34.2 2.9
gb|DQ321055.1| Influenza A virus (A/grey heron/Hong Kong/728/... 34.2 2.9
gb|DQ321026.1| Influenza A virus (A/chicken/Guangxi/2448/2004... 34.2 2.9
gb|DQ321025.1| Influenza A virus (A/chicken/Guangxi/2439/2004... 34.2 2.9
gb|DQ321024.1| Influenza A virus (A/duck/Guangxi/2396/2004(H5... 34.2 2.9
gb|DQ321023.1| Influenza A virus (A/goose/Guangxi/2383/2004(H... 34.2 2.9
gb|DQ321022.1| Influenza A virus (A/duck/Guangxi/2291/2004(H5... 34.2 2.9
gb|DQ321021.1| Influenza A virus (A/goose/Guangxi/2112/2004(H... 34.2 2.9
gb|DQ321020.1| Influenza A virus (A/goose/Guangxi/1832/2004(H... 34.2 2.9
gb|DQ321019.1| Influenza A virus (A/duck/Guangxi/1793/2004(H5... 34.2 2.9
gb|DQ321018.1| Influenza A virus (A/duck/Guangxi/1681/2004(H5... 34.2 2.9
gb|DQ321017.1| Influenza A virus (A/duck/Guangxi/1586/2004(H5... 34.2 2.9
gb|DQ321016.1| Influenza A virus (A/duck/Guangxi/1378/2004(H5... 34.2 2.9
gb|DQ321015.1| Influenza A virus (A/duck/Guangxi/1311/2004(H5... 34.2 2.9
gb|DQ321014.1| Influenza A virus (A/goose/Guangxi/1198/2004(H... 34.2 2.9
gb|DQ321013.1| Influenza A virus (A/goose/Guangxi/1097/2004(H... 34.2 2.9
gb|DQ321012.1| Influenza A virus (A/goose/Guangxi/914/2004(H5... 34.2 2.9
gb|DQ321011.1| Influenza A virus (A/goose/Guangxi/668/2004(H5... 34.2 2.9
dbj|AB212056.1| Influenza A virus (A/Hong Kong/213/2003(H5N1)... 34.2 2.9
dbj|AB212282.1| Influenza A virus (A/duck/Yokohama/aq10/2003(... 34.2 2.9
gb|AY676042.1| Influenza A virus (A/egret/Hong Kong/757.2/03(... 34.2 2.9

[AlaskaDenise]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Do all the sequences in the NA travel log have H274Y?

.

[AlaskaDenise]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Since there is no New Jersey in that travel log, can we assume it is not the same NA as the 274Y-infected HK girl flying from San Francisco?

.

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Do all the sequences in the NA travel log have H274Y?

.

No, all of the sequences in the travel log have a recently acquired polymorphism found in Yamaguchi/22.

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Since there is no New Jersey in that travel log, can we assume it is not the same NA as the 274Y-infected HK girl flying from San Francisco?

.

Correct. This is H274Y on a different genetic background than the Hong Kong / San Francisco sequence or the Osaka sequence. The sequences from Denmark and Quebec have not been released.

Thus, at this time H274Y is on five isolates and no evidence has been presented to show that any of the five match each other.

[AlaskaDenise]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

........at this time H274Y is on five isolates and no evidence has been presented to show that any of the five match each other.

There shouldn't be any doubt influenza knows what it's doing.

.

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Today, June 2nd, the first case of H1N1 influenza was confirmed in Yamaguchi Prefecture.
We are taking all possible measures as a prefecture in order to prevent the spread of infection, so we ask that everyone please act in a calm manner and act based upon accurate information.

http://www.pref.yamaguchi.lg.jp/cms/a12900/Pandemic-Influen/urgentmessage.html

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

A PDF (in English) for each confirmed case in Yamaguchi is here

http://www.pref.yamaguchi.lg.jp/cms/a12900/Pandemic-Influen/infection.html

None listed developed H1N1 while on Tamiflu.

[mixin]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Niman,
Thanks for that link. They did a good job of including details on the patients; I wish more reports were like that.

[HenryN]

Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

Niman,
Thanks for that link. They did a good job of including details on the patients; I wish more reports were like that.

I think Japan and Hong Kong provide that type of detail (at least on the initial cases).