The conversion of a gene-edited cell compartment is rate-limited by host cell turnover, not by the engineered graft

Abstract

This deposit contains the complete computational model and analysis code for a within-host study of autologous CCR5 gene-edited HIV cure. The work shows that the conversion of a patient's CD4 T cell pool to an HIV-resistant state is rate-limited by the turnover of the patient's own unedited cells rather than by any property of the engineered graft, so the edited fraction sets where conversion ends while host cell lifespan sets how fast it arrives. The repository includes the five-compartment within-host model, three independent implementations used for verification by differential testing, and every analysis reported in the manuscript, including the invariance of the conversion rate to graft-side parameters established both symbolically and by full-model linearization, the engineered survival advantage as the only controllable rate lever, the required cytotoxic killing rate, global sensitivity and practical identifiability analyses, the effect of host-turnover heterogeneity and age-dependent thymic involution, and the finding that conversion does not measurably accelerate latent reservoir clearance. All code needed to reproduce the results and figures is included, with a README describing each file and the order in which to run them.