Subtype variability and phylogenetic analyses in HIV

Origin and spread of HIV infection has been modeled by an array of phylogenetic tools. The phylogenetic modeling has been used to calculate the time of transmission of HIV from primates to humans, trace the spread of HIV subtypes and calculate ancestries in the modern epidemics. These techniques are constantly used for the molecular surveillance of antiretroviral drug resistance especially from the perspective of transmitted mutations and spread of recombinant and mutated clades. Molecular clock based models allow to seek the index cases and trace the origin of the local epidemics, including nosocomial transmissions. It is also possible to design therapeutic interventions based on the phylogeny defined risk groups. In phylogeography the local spread and site of infection import of may be visualized. Phylogenetic models created with bioinformatic inference are a valuable and well developed tool in modern HIV medicine.