title: Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.
abstract: The CRF04_cpx strains of HIV-1 accounts for approximately 2-10% of the infected population in Greece, across different transmission risk groups. CRF04_cpx was the lineage documented in an HIV-1 transmission network in Thessalonica, northern Greece. Most of the transmissions occurred through unprotected heterosexual contacts between 1989 and 1993. Blood samples were available for six patients, obtained 6-10 years later, except for one patient sampled in 1991. Our objective was to examine whether the transmission history is compatible with the evolutionary tree of the virus, in partial gag, partial env, and partial gag+env. The inferred phylogenetic tree obtained using maximum likelihood and Bayesian methods in partial gag+env was much closer to the transmission tree than that using either env or gag separately. Our findings suggest that the epidemiological relationships among patients who have been infected by a common source correspond almost exactly to the evolutionary trees of the virus, given that enough phylogenetic signal is present in the alignment. Moreover, we found evidence that recombination is not the most parsimonious explanation for the phylogenetic incongruence between gag and env. For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates.
authors.affiliation: National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece. dimitris.paraskevis@uz.kuleuven.ac.be
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Paraskevis
authors.forename: Emmanouil
authors.initials: E
authors.lastname: Magiorkinis
authors.forename: Gkikas
authors.initials: G
authors.lastname: Magiorkinis
authors.forename: Vassilios G
authors.initials: VG
authors.lastname: Kiosses
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.forename: Anne-Mieke
authors.initials: AM
authors.lastname: Vandamme
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.forename: Angelos
authors.initials: A
authors.lastname: Hatzakis
mesh_terms: D001499:Bayes Theorem; D019143:Evolution, Molecular; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015683:Gene Products, gag / Q000235:genetics; D016679:Genome, Viral; D006115:Greece / Q000453:epidemiology; D015658:HIV Infections / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D010802:Phylogeny; D013997:Time Factors
chemical_list: D015686:Gene Products, env; D015683:Gene Products, gag