Phylodynamics analysis of the Human Immunodeficiency Virus type 1 (HIV-1) envelope gene in mother and child pairs (original) (raw)

Characterizing the impact of HIV transmission routes on viral genetic diversity can improve the understanding of the mechanisms of virus evolution and adaptation. The HIV vertical transmission can occur in utero, during delivery or while breastfeeding. The present study investigated the phylodynamics of the HIV-1 env gene in mother-to-child transmission, by analyzing one chronically infected pair from Brazil and three acutely infected pairs from Zambia, with three to five time points. Sequences from 25 clones from each sample were obtained and aligned using Clustal X. ML trees were constructed in PhyML using the best evolutionary model. Bayesian analyses testing the relaxed and strict molecular clock were performed using BEAST and Bayesian Skyline Plot (BSP) was construed. The genetic variability of previously described epitopes were investigated and compared between each individual time points and between mother and child sequences. The relaxed molecular clock was the best-fitted m...