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Trends Mol Med. 2014 Jul;20(7):394-404. doi: 10.1016/j.molmed.2014.04.002. Epub 2014 May 1.

Clinical applications of pathogen phylogenies.

Author information

1
Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France. Electronic address: matt.hartfield@gmail.com.
2
Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France.

Abstract

Innovative sequencing techniques now allow the routine access of whole genomes of pathogens, generating vast amounts of data. Phylogenetic trees are a common method for synthesizing this information. Unfortunately, these trees are often seen only as a visual support to guide researchers, thus neglecting the value of employing phylogenetic techniques to perform hypothesis testing on clinical questions. These include investigating how a pathogen spreads within a patient, or whether the infection severity (often measured by virus load) is controlled by viral genetics. Advances in methodology mean the time is ripe for combining phylogenies with clinical data to better understand and fight infectious diseases.

KEYWORDS:

HCV; HIV; immune escape; phylogenetic analysis; transmission network

PMID:
24794010
DOI:
10.1016/j.molmed.2014.04.002
[Indexed for MEDLINE]

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