Only slight impact of predicted replicative capacity for therapy response prediction

BACKGROUND: Replication capacity (RC) of specific HIV isolates is occasionally blamed for unexpected treatment responses. However, the role of viral RC in response to antiretroviral therapy is not yet fully understood. MATERIALS AND METHODS: We developed a method for predicting RC from genotype using support vector machines (SVMs) trained on about 300 genotype-RC pairs. Next, we studied the impact of predicted viral RC (pRC) on the change of viral load (VL) and CD4(+) T-cell count (CD4) during the course of therapy on about 3,000 treatment change episodes (TCEs) extracted from the EuResist integrated database. Specifically, linear regression models using either treatment activity scores (TAS), the drug combination, or pRC or any combination of these covariates were trained to predict change in VL and CD4, respectively. RESULTS: The SVM models achieved a Spearman correlation (rho) of 0.54 between measured RC and pRC. The prediction of change in VL (CD4) was best at 180 (360) days, reaching a correlation of rho = 0.45 (rho = 0.27). In general, pRC was inversely correlated to drug resistance at treatment start (on average rho = -0.38). Inclusion of pRC in the linear regression models significantly improved prediction of virological response to treatment based either on the drug combination or on the TAS (t-test; p-values range from 0.0247 to 4 10(-6)) but not for the model using both TAS and drug combination. For predicting the change in CD4 the improvement derived from inclusion of pRC was not significant. CONCLUSION: Viral RC could be predicted from genotype with moderate accuracy and could slightly improve prediction of virological treatment response. However, the observed improvement could simply be a consequence of the significant correlation between pRC and drug resistance.