In September, 2009, a 74-day-old infant presented to a local hospital in Bloemfontein, South Africa, in broncho- pneumonia related respiratory distress. She appeared pale, cyanosed, and had palpable axillary lymph nodes, hepatomegaly, and oropharyngeal candidosis. She had received all scheduled vaccinations and had been exclusively breastfed. Cytomegalovirus was isolated from a respiratory sample by shell vial culture, and a paired blood sample showed a cytomegalovirus viral load of 12 600 copies per mL. She was positive for HIV by ELISA and DNA PCR. However, the baby?s mother said that she tested HIV negative during pregnancy, which was confirmed by fourth generation ELISA test. The baby?s CD4 cell count was 2189 cells per mL (40% lymphocytes) and antiretroviral therapy was started. The mother reported that her sister had breastfed the baby inter- mittently from 6 weeks of age. The sister and her 5-month-old child were subsequently found to be HIV positive by ELISA and DNA PCR. Laboratory records confirmed the sister's positive HIV status in February, 2008, excluding recent seroconversion. At final follow-up in April, 2010, our patient was well with an undetectable HIV viral load.
Plasma samples from the sister and both infants were used for partial sequencing of the HIV pol gene with the TRUGENE HIV-1 genotyping kit (Siemens Healthcare Diagnostics, Tarrytown, NY, USA). We analysed the data with the same approach used to identify the source of the nosocomial HIV-1 CRFO2_AG outbreak in the Al-Fateh Hospital, Libya.1 We collated 100 HIV-1 reference strains from the Free State Province, South Africa, closely related to the three case sequences, and then estimated and assessed phylogenies using algorithmic, Bayesian, and maximum-likelihood methods. The case sequences form a well-supported monophyletic cluster within the HIV-1 subtype C clade. The linkage is supported with 100% bootstrap in the algorithm and maximum-likelihood methods and with 100% posterior probability in the Bayesian phylogenies.