Thesis (MMed (Medical Microbiology))--University of Stellenbosch, 2006. / One of the major routes of transmission of human immunodeficiency virus (HIV) in the developing world is vertical transmission from mother to infant – pre-, intra-, or post-partum. In the Western Cape, HIV-1 subtype C is the predominant subtype in the heterosexual population, and this trend was expected to be seen amongst cases of mother-to-child transmission of HIV. The aim of this study was to perform genetic characterisation and phylogenetic analysis of the HIV-1 genome in positive serum/plasma samples obtained from children (age 0 to 18 months) from 2000-2002, and temporally related specimens from their mothers. We obtained 27 suitable pairs of samples taken within 6 months of delivery. From this pool, we obtained 21 infant DNA sequences and 17 maternal sequences, resulting in 16 mother-infant pairs. All patient sequences were identified as HIV-1 subtype C, and, as expected, mother and infant viral sequences clustered together. In some cases where a mother was suspected to have two dominant quasispecies based on the electropherogram, only one sequence was detectable in the infant. Single or multiple amino acid deletions were consistent between mothers and infants, and some pairs showed the same amino acid deletions seen in other pairs.