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Yamaguchi Japan Tamiflu Resistant Sequence Released

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  • Cyril
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    It's clearly different from osaka/180.

    HA relates to what is found in new york.
    NA has a polimorphism (254 AAA) that is found in the following h1n1 sequences:
    A/Akita/1/2009(H1N1)
    A/Distrito Federal/2611/2009(H1N1)
    A/Iwate/1/2009(H1N1)
    A/New York/3413/2009(H1N1)
    A/Shiga/3/2009(H1N1)
    A/Shizuoka/759/2009(H1N1)
    A/Yamaguchi/22/2009(H1N1)
    A/Yokohama/1/2009(H1N1)
    A/Zhejiang/1/2009(H1N1)
    hong kong/2369, osaka/180 and yamaguchi/22 all share this polymorphism (H274Y) but have different genetic backgrounds.

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Quebec finds first, Japan finds second cases of Tamiflu-resistant swine flu
    By Helen Branswell (CP) ? 1 hour ago
    TORONTO ? Canada has recorded a case of Tamiflu-resistant swine flu virus, in a Quebec man who had been given the drug to prevent infection.
    Meanwhile, Japan revealed Tuesday it had found a second such case of Tamiflu resistance, in a person who has no ties to the country's earlier reported case.
    The cases are the fourth and fifth globally since the new H1N1 virus was discovered in April.
    The Quebec man, 60, was given the flu antiviral after his son fell ill with the pandemic virus. It's believed the resistance arose in the man and there is no evidence he transmitted resistant virus to anyone else.
    "It appears to be an isolated case," said Jirina Vlk, spokesperson for the Public Health Agency of Canada.
    "Although the strain does not appear to have spread beyond the reported individual case we continue to be vigilant on this front."
    Use of Tamiflu to prevent infection - a procedure called prophylaxis - has been seen on occasion to give rise to resistant viruses.
    "We know that it was going to happen and it's not good news that it's happening," said Dr. Allison McGeer, an influenza expert at Toronto's Mount Sinai Hospital.
    But she said given the amount of Tamiflu being used in the world right now, such cases are bound to arise.
    "It's the problem with influenza, right? Either we're going to see small numbers of these and they're just going to kind of appear periodically and we're all going to worry or it's going to go big," McGeer said.
    "There's probably not going to be much in between."
    Another such case cropped up in Japan, in the city of Yamaguchi. Japan's National Institute of Infectious Diseases logged genetic sequence data for the virus on Tuesday in Genbank, a repository for genetic sequences used by flu researchers.
    The lab's director, Dr. Masato Tashiro, confirmed the case in an email containing details provided to the World Health Organization.
    The new case was a person who had been given the antiviral drug as post-exposure prophylaxis - an attempt to prevent illness in a person exposed to the pandemic virus.
    The person has since recovered, and it appears that there has been no spread, the email stated. The virus was sensitive to Relenza, a second drug in the same class as Tamiflu.
    The earlier Japanese case had occurred in a person in the city of Osaka.
    Other cases have been reported by Denmark and Hong Kong. Four of the five cases arose in people who had been taking the drug.
    One, however, was recorded in a girl from San Francisco who travelled while sick to Hong Kong. Health inspectors at the airport there pulled her aside and tested her for swine flu.
    She was positive, but told doctors there she hadn't taken Tamiflu. That suggests the virus that caused her infection was already resistant. U.S. officials have intensified surveillance for resistant viruses in the San Francisco area but say they have not found other cases.
    The Public Health Agency says the Quebec man recovered from his bout of swine flu without complications and never needed hospitalization.
    Vlk said the agency recommends using Tamiflu for treatment only, adding prudent use of the drug could stave off the development of resistance.

    Follow Canadian Press Medical Writer Helen Branswell's flu updates on Twitter at CP-Branswell

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Updated travel log

    gb|GQ397279.1| Influenza A virus (A/Yamaguchi/22/2009(H1N1)) ... 31.9 0.093
    gb|GQ368668.1| Influenza A virus (A/Distrito Federal/2611/200... 31.9 0.093
    gb|GQ365427.1| Influenza A virus (A/Iwate/1/2009(H1N1)) segme... 31.9 0.093
    gb|GQ365412.1| Influenza A virus (A/Akita/1/2009(H1N1)) segme... 31.9 0.093
    gb|GQ334348.1| Influenza A virus (A/Shizuoka/759/2009(H1N1)) ... 31.9 0.093
    gb|CY041760.1| Influenza A virus (A/New York/3413/2009(H1N1))... 31.9 0.093
    gb|GQ287628.1| Influenza A virus (A/Yokohama/1/2009(H1N1)) se... 31.9 0.093
    gb|GQ287624.1| Influenza A virus (A/Shiga/3/2009(H1N1)) segme... 31.9 0.093
    gb|GQ225351.1| Influenza A virus (A/Zhejiang/1/2009(H1N1)) se... 31.9 0.093
    gb|DQ432046.1| Influenza A virus (A/swine/Fujian/2003(H5N1)) ... 31.9 0.093
    gb|DQ432038.1| Influenza A virus (A/swine/Fujian/2001(H5N1)) ... 31.9 0.093
    gb|AY651473.2| Influenza A virus (A/teal/China/2978.1/2002(H5... 31.9 0.093
    gb|AY575883.2| Influenza A virus (A/Gs/HK/739.2/02 (H5N1)) ne... 31.9 0.093
    gb|CY029169.1| Influenza A virus (A/quail/Shantou/3846/2002(H... 31.9 0.093
    gb|CY029120.1| Influenza A virus (A/goose/Shantou/157/2002(H5... 31.9 0.093
    gb|CY029085.1| Influenza A virus (A/duck/Shantou/5526/2001(H5... 31.9 0.093
    gb|EF541469.1| Influenza A virus (A/Hong Kong/213/2003(H5N1))... 31.9 0.093
    gb|EF541468.1| Influenza A virus (A/chicken/Viet Nam/Ncvd8/20... 31.9 0.093
    gb|EF541465.1| Influenza A virus (A/duck/Viet Nam/Ncvd1/2002(... 31.9 0.093
    gb|EF467813.1| Influenza A virus (A/teal/Hong Kong/2978/03(H5... 31.9 0.093
    gb|EF124325.1| Influenza A virus (A/goose/Shantou/3624/2006(H... 31.9 0.093
    gb|EF124312.1| Influenza A virus (A/goose/Shantou/2086/2006(H... 31.9 0.093
    gb|EF124311.1| Influenza A virus (A/goose/Shantou/239/2006(H5... 31.9 0.093
    gb|DQ997385.1| Influenza A virus (A/swine/Anhui/ca/2004(H5N1)... 31.9 0.093
    gb|DQ997411.1| Influenza A virus (A/duck/Zhejiang/bj/2002(H5N... 31.9 0.093
    gb|DQ997397.1| Influenza A virus (A/chicken/Hunan/fg/2004(H5N... 31.9 0.093
    gb|DQ997183.1| Influenza A virus (A/chicken/Jiangsu/cz1/2002(... 31.9 0.093
    gb|DQ191691.1| Influenza A virus (A/golden mountain thrush/Fu... 31.9 0.093
    gb|DQ191690.1| Influenza A virus (A/curlew/Shandong/61/04(H5N... 31.9 0.093
    gb|DQ188911.1| Influenza A virus (A/black bulbul/Fujian/439/0... 31.9 0.093
    gb|DQ188910.1| Influenza A virus (A/slaty-backed gull/Shandon... 31.9 0.093
    gb|DQ188909.1| Influenza A virus (A/babbler/Fujian/320/04(H5N... 31.9 0.093
    gb|AY623431.1| Influenza A virus (A/chicken/Yichang/lung-1/04... 31.9 0.093
    gb|AY747610.2| Influenza A virus (A/swine/Fujian/1/2003(H5N1)... 31.9 0.093
    gb|AY747618.1| Influenza A virus (A/swine/Fujian/F1/2001(H5N1... 31.9 0.093
    gb|AY585419.1| Influenza A virus (A/duck/Zhejiang/52/2000(H5N... 31.9 0.093
    gb|AY575884.1| Influenza A virus (A/Eg/HK/757.3/02 (H5N1)) ne... 31.9 0.093
    gb|AY575882.1| Influenza A virus (A/HK/213/03 (H5N1)) neurami... 31.9 0.093
    gb|AY575881.1| Influenza A virus (A/HK/212/03 (H5N1)) neurami... 31.9 0.093
    gb|DQ321057.1| Influenza A virus (A/Chinese pond heron/Hong K... 31.9 0.093
    gb|DQ321055.1| Influenza A virus (A/grey heron/Hong Kong/728/... 31.9 0.093
    gb|DQ321026.1| Influenza A virus (A/chicken/Guangxi/2448/2004... 31.9 0.093
    gb|DQ321025.1| Influenza A virus (A/chicken/Guangxi/2439/2004... 31.9 0.093
    gb|DQ321024.1| Influenza A virus (A/duck/Guangxi/2396/2004(H5... 31.9 0.093
    gb|DQ321023.1| Influenza A virus (A/goose/Guangxi/2383/2004(H... 31.9 0.093
    gb|DQ321022.1| Influenza A virus (A/duck/Guangxi/2291/2004(H5... 31.9 0.093
    gb|DQ321021.1| Influenza A virus (A/goose/Guangxi/2112/2004(H... 31.9 0.093
    gb|DQ321020.1| Influenza A virus (A/goose/Guangxi/1832/2004(H... 31.9 0.093
    gb|DQ321019.1| Influenza A virus (A/duck/Guangxi/1793/2004(H5... 31.9 0.093
    gb|DQ321018.1| Influenza A virus (A/duck/Guangxi/1681/2004(H5... 31.9 0.093
    gb|DQ321017.1| Influenza A virus (A/duck/Guangxi/1586/2004(H5... 31.9 0.093
    gb|DQ321016.1| Influenza A virus (A/duck/Guangxi/1378/2004(H5... 31.9 0.093
    gb|DQ321015.1| Influenza A virus (A/duck/Guangxi/1311/2004(H5... 31.9 0.093
    gb|DQ321014.1| Influenza A virus (A/goose/Guangxi/1198/2004(H... 31.9 0.093
    gb|DQ321013.1| Influenza A virus (A/goose/Guangxi/1097/2004(H... 31.9 0.093
    gb|DQ321012.1| Influenza A virus (A/goose/Guangxi/914/2004(H5... 31.9 0.093
    gb|DQ321011.1| Influenza A virus (A/goose/Guangxi/668/2004(H5... 31.9 0.093
    dbj|AB212056.1| Influenza A virus (A/Hong Kong/213/2003(H5N1)... 31.9 0.093
    dbj|AB212282.1| Influenza A virus (A/duck/Yokohama/aq10/2003(... 31.9 0.093
    gb|AY676042.1| Influenza A virus (A/egret/Hong Kong/757.2/03(... 31.9 0.093

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Anti-flu drug "Tamiflu" avian flu virus was found to be resistant gene variant (A/H1N1) for confirmation of
    平成21年 (2009年) 7月 17日
    July 17, 2009
    本県で確認された患者から、「タミフル」耐性を示す遺伝子変異を持つ新型インフルエンザウイルスが確認され 、国に報告しましたので、お知らせします。
    Chiayi County has been identified in patients, "Tamiflu" was confirmed with a mutated avian flu virus showing resistance gene, have been reported in the country, and then let us know.
    なお、厚生労働省によれば、タミフルに対する耐性を持つ遺伝子変異は、ウイルスの重篤度(病原性)には直接 影響を及ぼすものではないとされています。
    However, according to the ministry, with the mutant gene are resistant to Tamiflu, the severity of the virus (pathogenic) is a direct influence is not.


    ウイルス検出の概要
    Overview of viral detection


    ○ 山口県で確認された患者から、タミフル耐性を示す遺伝子変異を持つ新型インフルエンザウイルスが検出さ れた。
    ○ from a patient who was confirmed in Yamaguchi Prefecture, was found with avian flu virus resistant to Tamiflu indicates the gene mutation.


    その後、この患者から周囲への感染拡大は認められていない。
    Then, to spread around the patient is not approved.


    ○ 国立感染症研究所によって実施された検査結果は、以下のとおりである。
    ○ test results conducted by the National Institute of Infectious Diseases, is as follows.


    遺伝子解析
    Genome


    ノイラミニダーゼ(NA)遺伝子の一部に、H275Yの突然変異を確認した。
    Neuraminidase (NA) of the gene, H275Y mutation was confirmed.
    季節性インフルエンザ(A/H1N1:ソ連型) との交雑は認めない。
    Seasonal influenza (A/H1N1: Soviet-type) and do not cross.


    薬剤感受性試験
    Drug susceptibility testing


    ・ オセルタミビル(商品名:タミフル):薬剤耐性あり(感受性低下を認める)
    Oseltamivir (product name: Tamiflu): with drug resistance (decreased sensitivity to admit)
    ・ ザ ナ ミ ビ ル(商品名:リレンザ):薬剤感受性あり
    The Big Le Mi Na (Product name: Relenza): In drug-sensitive

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Originally posted by mixin View Post
    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).

    Leave a comment:


  • mixin
    replied
    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.

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

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



    None listed developed H1N1 while on Tamiflu.

    Leave a comment:


  • HenryN
    replied
    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.

    Leave a comment:


  • AlaskaDenise
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Originally posted by niman View Post
    ........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.

    .

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Originally posted by AlaskaDenise View Post
    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.

    Leave a comment:


  • HenryN
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Originally posted by AlaskaDenise View Post
    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.

    Leave a comment:


  • AlaskaDenise
    replied
    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?

    .

    Leave a comment:


  • AlaskaDenise
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

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

    .

    Leave a comment:


  • HenryN
    replied
    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

    Leave a comment:


  • wotan
    replied
    Re: Yamaguchi Japan Tamiflu Resistant Sequence Released

    Originally posted by Rwilmer View Post
    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?

    Leave a comment:

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