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.
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Acknowledgments
We wish to acknowledge Jan Albert and Tomas Leitner for their supportive comments and suggestions about this study and Constantinos-Simos Nistiotis for statistical advice. D.P. was supported by a Marie Curie fellowship from the European Commission (QLK2-CT2001-51062) and by the Hellenic Center for Infectious Disease Control (KEEL). P.L. was supported by the Flemish Institute for Scientific-Technological Research in Industry (IWT). This work was supported by the Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases and in part by the Flemish Fonds voor Wetenschappelijk Onderzoek (FWO G.0288.01).
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Reviewing Editor: Dr. Lauren Ancel-Meyers
Isolated sequences from patients belonging to the CRF04_cpx transmission network always correspond to partially characterized gag, env, and gag+env genomic regions.
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Paraskevis, D., Magiorkinis, E., Magiorkinis, G. et al. Phylogenetic Reconstruction of a Known HIV-1 CRF04_cpx Transmission Network Using Maximum Likelihood and Bayesian Methods. J Mol Evol 59, 709–717 (2004). https://doi.org/10.1007/s00239-004-2651-6
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DOI: https://doi.org/10.1007/s00239-004-2651-6