title: Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.
abstract: Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals.
authors.affiliation: National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, Athens, Greece.
authors.forename: Apostolos
authors.initials: A
authors.lastname: Beloukas
authors.forename: Emmanouil
authors.initials: E
authors.lastname: Magiorkinis
authors.forename: Gkikas
authors.initials: G
authors.lastname: Magiorkinis
authors.forename: Asimina
authors.initials: A
authors.lastname: Zavitsanou
authors.forename: Timokratis
authors.initials: T
authors.lastname: Karamitros
authors.forename: Angelos
authors.initials: A
authors.lastname: Hatzakis
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Paraskevis
mesh_terms: D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D010802:Phylogeny; D012680:Sensitivity and Specificity; D014773:Virology / Q000379:methods*
chemical_list: D054303:HIV Reverse Transcriptase; D016333:HIV Protease