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Predicting antigenic changes of influenza viruses using text data assimilation.

Research Project

Project/Area Number 25280080
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Intelligent informatics
Research InstitutionHokkaido University

Principal Investigator

Kimihito Ito  北海道大学, 人獣共通感染症リサーチセンター, 教授 (60396314)

Co-Investigator(Renkei-kenkyūsha) TAKADA Ayato  北海道大学, 人獣共通感染症リサーチセンター, 教授 (10292062)
IGARASHI Manabu  北海道大学, 人獣共通感染症リサーチセンター, 准教授 (10374240)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
Fiscal Year 2015: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2014: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2013: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Keywordsインフルエンザ / 抗原変異予測 / データ同化 / ワクチン / 変異予測 / ベイズ推定 / 粒子フィルタ
Outline of Final Research Achievements

Human influenza viruses mutate from time to time, causing annual epidemics worldwide. Given the high mutation rate of the viral gene, influenza vaccine strains need to be updated every two to three years. In order to prepare an effective vaccine strain prior to each influenza season, we investigated text data assimilation methods that allow us to predict the evolution of viral amino acid sequences. As a result, we developed a mathematical model consisting of human herd immunity, the number of infections, and population of circulating vires. The model provides a mathematical basis of bioinformatics methods to prepare an effective vaccine strain prior to influenza seasons.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (29 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (1 results) Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 5 results,  Acknowledgement Compliant: 4 results) Presentation (15 results) (of which Int'l Joint Research: 1 results,  Invited: 9 results) Funded Workshop (1 results)

  • [Int'l Joint Research] Icahn School of Medicine at Mount Sinai(米国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review2016

    • Author(s)
      Kim K, Omori R, Ueno K, Iida S, Ito K
    • Journal Title

      PLoS One

      Volume: 11(1) Issue: 1 Pages: e0147021-e0147021

    • DOI

      10.1371/journal.pone.0147021

    • NAID

      120005740331

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] インフルエンザの流行予測はどこまで可能か?2016

    • Author(s)
      渡邉真治,伊藤公人
    • Journal Title

      感染症

      Volume: 46巻1号 Pages: 13-23

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Efficient isolation of Swine influenza viruses by age-targeted specimen collection.2015

    • Author(s)
      Ozawa M, Matsuu A, Yonezawa K, Igarashi M, Okuya K, Kawabata T, Ito K, Tsukiyama-Kohara K, Taneno A, Deguchi E.
    • Journal Title

      J Clin Microbiol. 2015 Apr;53(4):1331-8.

      Volume: 53 Issue: 4 Pages: 1331-1338

    • DOI

      10.1128/jcm.02941-14

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Seroepidemiological prevalence of multiple species of filoviruses in fruit bats (Eidolon helvum) migrating in Africa.2015

    • Author(s)
      Hirohito Ogawa, Hiroko Miyamoto, Eri Nakayama, Reiko Yoshida, Ichiro Nakamura, Hirofumi Sawa, Akihiro Ishii, Yuka Thomas, Emiko Nakagawa, Keita Matsuno, Masahiro Kajihara, Junki Maruyama, Manabu Igarashi, Kimihito Ito, Ayato Takada et al
    • Journal Title

      Journal of Infectious Diseases

      Volume: jiv063 Issue: suppl 2 Pages: S101-S108

    • DOI

      10.1093/infdis/jiv063

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses.2015

    • Author(s)
      Sasaki M, Orba Y, Ueno K, Ishii A, Moonga L, Hang'ombe BM, Mweene AS, Ito K, Sawa H.
    • Journal Title

      Journal of General Virology

      Volume: 96 Issue: 2 Pages: 440-452

    • DOI

      10.1099/vir.0.071209-0

    • NAID

      120005697198

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset2014

    • Author(s)
      Ueno K, Ishii A, Ito K
    • Journal Title

      BMC Bioinform

      Volume: 28(15) Issue: 1 Pages: 254-254

    • DOI

      10.1186/1471-2105-15-254

    • NAID

      120005476099

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice.2014

    • Author(s)
      Ishii A, Ueno K, Orba Y, Sasaki M, Moonga L, Hang'ombe BM, Mweene AS, Umemura T, Ito K, Hall WW, Sawa H
    • Journal Title

      Nat Commun

      Volume: 5 Issue: 1 Pages: 1-11

    • DOI

      10.1038/ncomms6651

    • NAID

      120005540294

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] 計算機科学によるインフルエンザウイルスの抗原変異予測2014

    • Author(s)
      伊藤公人
    • Journal Title

      化学療法の領域

      Volume: 30巻12号 Pages: 68-74

    • Related Report
      2014 Annual Research Report
  • [Journal Article] 自然界から見る人獣共通感染症2014

    • Author(s)
      伊藤公人
    • Journal Title

      みんぱく

      Volume: 38 Pages: 4-5

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Antiviral activity of stachyflin on influenza A viruses of different hemagglutinin subtypes2013

    • Author(s)
      Motohashi Y, Igarashi M, Okamatsu M, Noshi T, Sakoda Y, Yamamoto N, Ito K, Yoshida R, Kida H
    • Journal Title

      Virol J

      Volume: 10 Issue: 1 Pages: 118-118

    • DOI

      10.1186/1743-422x-10-118

    • NAID

      120005323601

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent.2013

    • Author(s)
      Kyoko Hayashida, Takashi Abe, William Weir, Ryo Nakao, Kimihito Ito, Kiichi Kajino, Yutaka Suzuki, Frans Jongejan, Dirk Geysen, and Chihiro Sugimoto.
    • Journal Title

      DNA Research

      Volume: 20 Issue: 3 Pages: 209-220

    • DOI

      10.1093/dnares/dst003

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heterosubtypic antiviral activity of hemagglutinin-specific antibodies induced by intranasal immunization with inactivated influenza viruses in mice.2013

    • Author(s)
      Muramatsu M. et al.
    • Journal Title

      PLoS One

      Volume: 8 Issue: 8 Pages: e71534-e71534

    • DOI

      10.1371/journal.pone.0071534

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] インフルエンザウイルスの抗原変異とその予測可能性2015

    • Author(s)
      伊藤公人
    • Organizer
      国立感染症研究所 学友会シンポジウム
    • Place of Presentation
      国立感染症研究所(東京都)
    • Year and Date
      2015-12-14
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Combining Population Genetics of Pathogens and Epidemiology of Infectious Diseases2015

    • Author(s)
      Kimihito Ito
    • Organizer
      数学WEEK
    • Place of Presentation
      あきばホール(東京都)
    • Year and Date
      2015-09-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Prediction of amino acid substitutions on the hemagglutinin molecules of H3N2 seasonal influenza viruses using gamma distribution2015

    • Author(s)
      Kimihito Ito
    • Organizer
      The ARI conference in The U.S-Japan's Cooperative Medical Sciences Program
    • Place of Presentation
      Academia Sinica (Taipei, Taiwan)
    • Year and Date
      2015-01-28
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] コンピューターは季節性インフルエンザウイルスの抗原変異を予測できるか? (基調講演)2014

    • Author(s)
      伊藤公人
    • Organizer
      第15回IPABシンポジウム/感染症とコンピュータ創薬
    • Place of Presentation
      NEC本社ビル(東京都)
    • Year and Date
      2014-12-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Predicting the evolution of influenza A viruses through data assimilation (Keynote Lecture)2014

    • Author(s)
      Kimihito Ito
    • Organizer
      International Workshop on Information Search, Integration & Personalization (ISIP 2014)
    • Place of Presentation
      Help University (Kuala Lumpur, Malaysia)
    • Year and Date
      2014-10-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Predicting antigenic changes of influenza viruses through data assimilation2014

    • Author(s)
      Kimihito Ito
    • Organizer
      平成26年度 九州大学マス・フォア・インダストリ研究所 共同利用研究集会,感染症数理モデルの実用化と産業および政策での活用-問題解決型の数理モデリング-
    • Place of Presentation
      JR博多シティ会議場(福岡市)
    • Year and Date
      2014-10-02
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] コンピューターでインフルエンザウイルスの変異を予測する2014

    • Author(s)
      伊藤公人
    • Organizer
      第157回日本獣医学会学術集会 特別企画「人獣共通感染症の先回り対策策定に向けた情報戦略」
    • Place of Presentation
      北海道大学(札幌市)
    • Year and Date
      2014-09-11
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Data Structure and Parallel Algorithms for Big Data Assimilation in Meteorology2014

    • Author(s)
      Kimihito Ito
    • Organizer
      Mathematical Science on Big Data Assimilation in Meteorology
    • Place of Presentation
      京都大学(京都市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Tracking Zoonotic Outbreaks Using Bioinformatics Techniques2014

    • Author(s)
      Heidi Tessmer, Kimihito Ito
    • Organizer
      Mathematical Science on Big Data Assimilation in Meteorology
    • Place of Presentation
      京都大学(京都市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Towards data assimilation of Malaria epidemics in Zambia2014

    • Author(s)
      Mayumbo Nyirenda, Hiroki Arimura, Kimihito Ito
    • Organizer
      Mathematical Science on Big Data Assimilation in Meteorology
    • Place of Presentation
      京都大学(京都市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Inferring the population structure of viruses with Tajima’s D and its application to global surveillance2014

    • Author(s)
      Kiyeon Kim, Kimihito Ito
    • Organizer
      第3回感染症若手フォーラム
    • Place of Presentation
      やすらぎ伊王島海の見えるホテル(長崎市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] A large-scale analysis of interspecies transmission of influenza A viruses in pigs2014

    • Author(s)
      Nipawit Karnbunchob, Keisuke Ueno, Manabu Igarashi, Kimihito Ito
    • Organizer
      第3回感染症若手フォーラム
    • Place of Presentation
      やすらぎ伊王島海の見えるホテル(長崎市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Inferring the population structure of viruses with Tajima’s D and its application to global surveillance2013

    • Author(s)
      Kiyeon Kim, Kimihito Ito
    • Organizer
      The 1st Sapporo Summer Seminar for One Health
    • Place of Presentation
      北海道大学(札幌市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] コンピューターはインフルエンザの流行株を 予測できるか?2013

    • Author(s)
      伊藤公人
    • Organizer
      人工知能学会 第90回 人工知能基本問題研究会 (SIG-FPAI)
    • Place of Presentation
      稚内市日ロ友好会館(稚内市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] A formula on the number of amino acid substitutions on the hemagglutinin molecules of H3N2 seasonal influenza viruses2013

    • Author(s)
      Kimihito Ito, Manabu Igarashi, Ayato Takada
    • Organizer
      15th International Negative Strand Virus Meeting
    • Place of Presentation
      Palacio de Exposiciones y Congresos Granada (Spain)
    • Related Report
      2013 Annual Research Report
  • [Funded Workshop] Innovative Mathematical Modeling for the Analysis of Infectious Disease Data (IMAID2015)2015

    • Place of Presentation
      Hokkaido University
    • Year and Date
      2015-11-29
    • Related Report
      2015 Annual Research Report

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Published: 2013-05-21   Modified: 2022-01-27  

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