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Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
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Defining HIV-1 transmission clusters based on sequence data.

Amin S Hassan1, Oliver G Pybus, Eduard J Sanders

  • 1aKEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research (Coast), Kilifi, Kenya bDepartment of Laboratory Medicine, Lund University, Lund, Sweden cDepartment of Zoology dNuffield Department of Medicine, University of Oxford, Oxford, UK eDepartment of Clinical Microbiology, Karolinska University Hospital fDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.

AIDS (London, England)
|March 30, 2017
PubMed
Summary
This summary is machine-generated.

Understanding human immunodeficiency virus type 1 (HIV-1) transmission requires clear methods for defining transmission clusters. This review clarifies common molecular epidemiology techniques for tracking HIV-1 spread and offers guidance for accurate cluster definition.

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Area of Science:

  • Molecular epidemiology
  • Virology
  • Public health

Background:

  • Understanding HIV-1 transmission dynamics is crucial for effective screening and intervention strategies.
  • Current methods for defining HIV-1 transmission chains rely on sequence similarity analysis and phylogenetic tree inference.

Purpose of the Study:

  • To introduce and explain methodologies for defining HIV-1 transmission clusters.
  • To systematically review common methods and definitions used in HIV-1 molecular epidemiology studies.
  • To provide guidance on selecting appropriate cluster definitions for specific research questions and datasets.

Main Methods:

  • Systematic review of 105 HIV-1 molecular epidemiology studies.
  • Analysis of sequence similarity assessments and phylogenetic tree inference methods.
  • Literature synthesis of common cluster definition approaches.

Main Results:

  • Identified and summarized the most frequently used methods and definitions for HIV-1 transmission clusters in published literature.
  • Highlighted variations in cluster definition approaches across different studies.
  • Provided an overview of established practices in the field.

Conclusions:

  • Standardized definitions and clear methodologies are essential for accurate HIV-1 transmission cluster identification.
  • Guidance is provided to aid researchers in choosing optimal methods for their specific HIV-1 transmission studies.
  • Improved understanding of transmission dynamics can enhance public health interventions.