Fig. 1

Maximum likelihood phylogenetic tree constructed on the pol gene sequences of 102 isolates and additional 4 subtype C references. The tree was rooted using the midpoint rooting method. Branch lenghts were estimated with the best fitting nucleotide substitution model (GTR + G + I) according to a hierarchical likelihood ratio test. The bar at the bottom indicating 0.03 nucleotide substitution per site. The astericks (*) along a branch represent bootstrap support >85%. The 4 C sequences belonged to mother to child transmission chain are shown in red and the cluster involving them is in the gray box. The cartoon summarizes the timing of sampling