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INFERENCE OF EVOLUTIONARY CHANGES OF WITHIN-HOST VIRUS

Research Project

Project/Area Number 15510157
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 基礎ゲノム科学
Research InstitutionTokyo Medical and Dental University

Principal Investigator

REN Fengrong  Tokyo Medical and Dental University, Guest Associate Professor, 情報処理センター, 客員助教授 (60280989)

Co-Investigator(Kenkyū-buntansha) TANAKA Hiroshi  Tokyo Medical and Dental University, Professor, 難治疾患研究所, 教授 (60155158)
Project Period (FY) 2003 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 2004: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2003: ¥1,400,000 (Direct Cost: ¥1,400,000)
KeywordsWithin-patient viral evolution / Anti-HIV therapy / Serial viral samples / Sequential-linking algorithm / Longitudinal phylogenetic tree / Mutual information criterion / Positive selection / 情報量基準 / 淘汰進化 / HIV-1 / 経時的な連続サンプル / 正の淘汰進化 / 抗HIV多剤併用療法 / 耐性サイト
Research Abstract

We have previously proposed an algorithm, distance-based sequential-linking method, for longitudinal analysis of within-host viral evolution and successfully reconstructed a longitudinal phylogenetic tree of 24 HIV-1 env gene sequences obtained from patients who had not received drug treatment. However, viral evolution in patients who are undergoing drug therapy, especially HARRT (Highly Active Anti-Retroviral Therapy), is much more complicated because of the selective pressure from the anti-viral drugs. To estimate this complicated process, we largely improved the previous algorithm by introducing information criterion into our method. We employed C4.5 (software package, Quinlan, 1993), which is developed based on mutual information criterion, to obtain the decision tree that identifies the relations between virus samples and drug combinations administered. We applied the revised algorithm to a large data set (189 sequences) of HIV-1 protease gene serially sampled from a single patient under HAART over three years. The obtained decision tree showed that there were always two or more viral subpopulations with different frequencies and also different characteristic mutations during the whole observation period. Moreover, by estimating the synonymous (ds) and nonsynonymous (d_N) substitution rates of each viral subpopulation classified by the decision tree, we found that the selective pressure exerted on the virus is highly variable over time when different drugs are administered, but the virus may often be under positive Darwinian selection to evolve.
The above results have been presented at several meetings including international meetings (SMBE2004, ISMB2004), and received the "Excellent Theme Prize" from the 18th annual meeting of the Japanese society for AIDS research

Report

(3 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • Research Products

    (4 results)

All 2003 Other

All Journal Article (3 results) Publications (1 results)

  • [Journal Article] Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples : a distance-based sequential-linking method2003

    • Author(s)
      Ren F, S Ogishima, H Tanaka
    • Journal Title

      Gene 317

      Pages: 89-95

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction

    • Author(s)
      Ren F, H Tanaka, Z Yang
    • Journal Title

      Systematic Biology (Accepted)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction

    • Author(s)
      Ren F, H Tanaka, Z Yang
    • Journal Title

      Systematic Biology (accepted)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Fengrong Ren(任鳳蓉): "Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples : a distance-based sequential-linking method"GENE. 317. 89-95 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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