title: Clinical applications of pathogen phylogenies.
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.
authors.affiliation: 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.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hartfield
authors.affiliation: Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Carmen Lía
authors.initials: CL
authors.lastname: Murall
authors.affiliation: Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Alizon
mesh_terms: D000890:Anti-Infective Agents / Q000627:therapeutic use*; D005075:Biological Evolution; D016000:Cluster Analysis; D003141:Communicable Diseases / Q000188:drug therapy* / Q000235:genetics; D015195:Drug Design; D054884:Host-Pathogen Interactions / Q000187:drug effects*; D006801:Humans; D007239:Infections / Q000188:drug therapy* / Q000235:genetics; D064307:Microbiota / Q000187:drug effects* / Q000235:genetics; D010802:Phylogeny
chemical_list: D000890:Anti-Infective Agents
keywords: HCV; HIV; immune escape; phylogenetic analysis; transmission network