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Phylogenetically resolving epidemiologic linkage.

Ethan O Romero-Severson1, Ingo Bulla1, Thomas Leitner2

  • 1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545.

Proceedings of the National Academy of Sciences of the United States of America
|February 24, 2016
PubMed
Summary
This summary is machine-generated.

Phylogenetic trees can reliably infer human immunodeficiency virus (HIV) transmission history. This study provides a framework for interpreting phylogenetic relationships to determine transmission direction and identify potential intermediary links or common sources.

Keywords:
HIV-1coalescentparaphylyphylogenytransmission

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Area of Science:

  • Epidemiology
  • Phylogenetics
  • Computational Biology

Background:

  • Phylogenetic trees are increasingly used in epidemiological investigations.
  • Systematic evaluation of phylogenetic interpretation in epidemiology is lacking.

Purpose of the Study:

  • To probabilistically evaluate HIV-1 transmission histories using a within-host coalescent model.
  • To systematically assess the epidemiological interpretation of phylogenetic trees.

Main Methods:

  • Utilized an HIV-1 within-host coalescent model to analyze transmission histories of linked hosts.
  • Classified phylogenetic relationships into six tree types based on cladistics and consistency with transmission history.
  • Evaluated predictions of tree topology based on transmission direction, intermediary links, and common sources.

Main Results:

  • Direction of transmission can be inferred when paraphyly exists.
  • Intermediary links can be excluded if multiple lineages were transmitted.
  • Monophyletic HIV populations in sampled hosts suggest a common source.
  • Robust results typically require 20 or more sequences per subject.
  • Inconsistent phylogenetic interpretations suggesting incorrect transmission direction were rare.

Conclusions:

  • Phylogenetic tree interpretation can reliably establish HIV transmission direction.
  • The framework aids in excluding intermediary links and identifying common sources.
  • Findings support the use of phylogenetic trees in epidemiological investigations with appropriate interpretation.