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Objective: To evaluate efficiency of HAART in the prevention of mother to child HIV transmission. Methods: A longitudinal study was conducted on 1 300 women attending the antenatal service at Saint Camille Medical Centre from September 2010 to July 2011. The HIV status of mothers was determined by rapid tests and ELISA. Discordant results were confirmed by real-time PCR. PCR was used to determine HIV status of children b from HIV-positive mothers. Results: Among 1 300 pregnant women tested for HIV, 378 were seropositive. Mothers were predominantly housewives (69.7%), and their mean age was (28.32±0.15) years. The overall prevalence of HIV transmission from mother to child was 4.8% (18/378). This prevalence differed significantly from 0.0% (0/114) to 6.8% (18/264) in children b from mothers under HAART and those with mothers under New Prophylactic Protocol (AZT + 3TC + NVP), respectively (P<0.01). Children’s mortality rate during the medical follow up was 1.3% (5/378). Among 16 women with HIV dubious status by ELISA, the Real Time PCR confirmed 2/16 (12.5%) as HIV positive. Conclusions: The protocol of prevention of mother to children HIV transmission (PMTCT) is effective. The rate of HIV vertical transmission is significantly reduced. Early diagnosis determined by PCR of children b from HIV- positive mother is necessary and recommended in the context of PMTCT in Burkina Faso. We also found that PCR is an effective tool to confirm HIV status in pregnant women.