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Late human immunodeficiency virus (HIV) diagnosis after severe co-morbidity remains common in resource-limited settings. Neurodevelopmental recovery during antiretroviral therapy (ART) for late-diagnosed children is understudied. We determined 6-month neurodevelopmental trajectories in HIV-infected children initiating ART during hospitalization.HIV-infected children initiated ART after HIV diagnosis during hospitalization in Kenya. The Malawi Developmental Assessment Tool was administered after clinical stabilization within 1 month and at 6 months post-ART initiation. Baseline versus 6-month Z scores for each developmental domain were compared; cofactors for change in Z scores were evaluated using linear regression.Among 74 children, median age was 1.7 years (interquartile range, 0.8–2.4) and median Z scores for gross motor, fine motor, social and language domains were −1.34, −1.04, −0.53 and −0.95, respectively. At baseline, children with higher plasma viremia had lower social Z scores (P = 0.008). Better nourished (weight-for-age Z score [WAZ] ≥−2) children had higher Z scores in all developmental domains (all P values ≤0.05). After 6 months on ART (n = 58), gross and fine motor Z scores improved significantly (mean change 0.39; P = 0.007 and 0.43; P = 0.001, respectively), but social and language did not. Children with better immune and growth response to ART had higher gains in gross motor (0.05 per unit-gain CD4%; P = 0.04; 0.34 per unit-gain WAZ; P = 0.006 and 0.44 per unit-gain height-for-age Z score; P = 0.005), social (0.37 per unit-gain WAZ; P = 0.002) and language (0.25 per unit-gain height-for-age Z score; P = 0.01).Children had significant neurodevelopmental gains during 6 months of ART, and children with better growth and immune recovery had greater improvement. Prompt commencement of ART may improve neurodevelopment in addition to immunity and growth.