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A New Algorithm for Analysis of Within-host Viral Evolution

Research Project

Project/Area Number 13680758
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Molecular biology
Research InstitutionTokyo Medical and Dental University

Principal Investigator

REN Fengrong  Tokyo Medical and Dental University, Research assistant, 難治疾患研究所, 教務職員 (60280989)

Co-Investigator(Kenkyū-buntansha) SUZUKI Yasuhiro  Tokyo Medical and Dental University, Research associate, 難治疾患研究所, 助手 (50292983)
TANAKA Hiroshi  Tokyo Medical and Dental University, Professor, 難治疾患研究所, 教授 (60155158)
Project Period (FY) 2001 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 2002: ¥1,000,000 (Direct Cost: ¥1,000,000)
Fiscal Year 2001: ¥1,500,000 (Direct Cost: ¥1,500,000)
KeywordsWithin-host viral evolution / Neutral evolution / Positive selection / Codon-based model / Sequential-linking algorithm / Serial viral samples / Longitudinal phylogenetic reconstruction / Sequential-linkingアルゴリズム
Research Abstract

The purpose of this study is to develop a computational method that would be simple and easy to use for the analysis of within-host viral evolution. Our method has two important features: noncontemporaneous viral samples can be dealt with by a simple computing algorithm, and both neutral and adaptive evolution patterns occurring during the process of viral evolution can be estimated. In the beginning stage of this research, we proposed a preliminary formulation of this algorithm that was based on the maximum likelihood method. However, it was difficult to use because the calculation of the likelihood required an extremely large amount of time and the number of possible tree topologies increased exponentially according to the increase in the number of viral variants. Therefore, we proposed another new algorithm, referred to as a distance-based sequential-linking algorithm, in which the neighbor-joining method is employed. This algorithm is applied to a longitudinal data set of the env gene (V3 region) of HIV-1 obtained over seven years after the infection of a single patient. The results suggest that this method can successfully reconstruct a longitudinal phylogenetic tree from noncontemporaneous viral samples within a reasonable calculation time.
Further development of this method would include an incorporation of the merits of the sUPGMA, which would allow for an estimation of the Ne and the internal sample times ; we would also like to use densely serial samples of HIV-1 with this method for further verification of its efficiency. Collaborative research with the NIID (National Institute of Infectious Diseases) of Japan applying our method to a large data set of the pol gene of HIV-1 is in progress.

Report

(3 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • Research Products

    (14 results)

All Other

All Publications (14 results)

  • [Publications] Fengrong Ren (任鳳蓉): "Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples : a distance-based sequential-linking method"GENE. (in press). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fengrong Ren (任鳳蓉): "A New Algorithm for Analysis of Within-host HIV-1 Evolution"Biocomputing PubMed Identifier : 11262976. PSB(6). 595-605 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Hiroshi Tanaka: "Analysis of Within-host Viral Evolution by Reconstructing the Longitudinal Phylogenetic Tree of HIV-1"Bulletin of the International Statistical Institute. Book(1). 355-358 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Soichi Ogishima: "Reconstruction and Analysis of Within-host Longitudinal HIV-1 Evolution by a Distance-based Sequential-linking Algorithm"Chem-Bio Informatics Journal. 1(2). 73-83 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fengrong Ren: "Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples : a distance-based sequential-linking method"GENE. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fengrong Ren: "A New Algorithm for Analysis of Within-host HlV-1 Evolution"Biocomputing PubMed Identifier. 11262976. PSB(6). 596-605 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Soichi Ogishima: "Reconstruction and Analysis of Within-host Longitudinal HIV-1 Evolution by a Distance-based Sequential-linking Algorithm"Chem-Bio Informatics Journal. 1(2). 73-83 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Hiroshi Tanaka: "Analysis of Within-host Viral Evolution by Reconstructing the Longitudinal Phylogenetic Tree of HIV-1"the International Statistical Institute. Book(1) (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 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. (In press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Fengrong Ren: "Inference and Prediction of Courses Courses of the Diseases Caused by Pathologic Viruses by Estimating Molecular Evolution of Within-host Virus"MEDINFO Pub Med Identifier : in preparation. 10(11). 979-983 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Fengrong Ren: "A New Algorith for Analysis of Within-host HIV-1 Evolution"Biocomputing PubMED Identifier : 11262976. PSB(6). 595-605 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Akihito Tsubota: "Genotype May Correlate with Liver Carcinogenesis and Tumor Characteristics in Cirrhotic Patients Infected with Hepatitis B Virus Subtype adw"Journal of Medical Virology. 65. 257-265 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Hiroshi Tanaka: "Analysis of Within-host Viral Evoluton by Reconstructing the Longitudinal Phylogenetic Tree of HIV-1"Bulletin of the International Statistical Institute. Book(1). 355-358 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Soichi Ogishima: "Reconstruction and Anaysis of Within-host Longitudinal HIV-1 Evolution by a Distance-based Sequential-linking Algorithm"Chem-Bio Informatics Journal. 1(2). 73-83 (2001)

    • Related Report
      2001 Annual Research Report

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Published: 2001-04-01   Modified: 2016-04-21  

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