Background:  Virus replication under selective pressure of protease inhibitors (PI) often results in CD4 T-cell reconstitution despite viral rebound, suggesting that PI-resistant viruses are attenuated for pathogenesis in vivo. This study compares the relationship between the extent of thymic output and T-cell activation among a cohort of HIV-infected children with sustained viral replication.

Methods:  We followed over 96 weeks, a prospective cohort of 36 HIV-infected subjects (ages 2 to 24 years) receiving PI-based ART who, following treatment, either:  successfully suppressed viral replication (viral success) and reconstituted CD4 T cells (immune success); failed to optimally suppress virus (viral failure), but were immune successes ; or failed to suppress virus and failed to reconstitute CD4 T cells and were switched to a new treatment. The proportion of activated T cells was measured using multi-color flow cytometry analysis to enumerate CD8CD45RA CD11a^bright effector T cells. Thymic output was assessed by competitive PRC-based analysis of T-cell receptor excisional circles (TREC) within peripheral blood mononuclear cells (PBMC).

Results:  Pre-therapy TREC levels were similar in the viral success/immune success (median 9024 copies/Lx10⁶ PBMC, 25 to 75 quartile, 3731 to 22,237) and the viral failure/immune success (median 11,984; 7957 to 23,181) groups (p = 0.7); but were significantly lower in the viral failure/immune failure group (median 851; 553 to 1247) (p = 0.03). Despite similar levels of viremia before and after therapy (median pre-viral RNA, 5.1 log copies/mL and post-viral RNA, 4.7 log copies/mL, p = 0.2), viral failure/immune success patients exhibited sustained increases in TREC (median 30,376; 21,472 to 44,504) similar to viral success/immune success (median 38,764; 24,150 to 56,624) (p = 0.6). TREC levels in viral failure/immune failure patients remained depressed (median 2034; 1643 to 2144) (p = 0.001). Decrease in CD8 activation, as determined by proportion of CD8CD45RACD11a^bright T cells, correlated with improvement of TREC levels. Post-therapy, there was a shift from activated effector phenotype to greater percentage of naive CD8 T cells in viral success/immune success and viral failure/immune success patients. CD8 T-cell activation persisted in the viral failure/immune failure group.

Conclusions:  Among children and adolescents receiving PI-containing ART and whose CD4 T cells reconstitute in spite of viral load rebounds to pre-therapy levels, increases in thymic output and declines in T-cell activation indicate that drug-resistant viruses are attenuated for pathogenesis independent of their replication capacity.