Comprehensive Mapping of the Virus and Host Factors that Guide the Paths of HIV-1 Escape from a Therapeutic
HIV-1 resistance to therapeutics can emerge through diverse mutational routes, yet the determinants guiding pathway selection in vivo remain unclear. Through comprehensive screening, we identified 18 mutations in the HIV-1 Env protein that enhance resistance to the FDA-approved small-molecule therapeutic temsavir. We then examined their occurrence in HIV-infected individuals who developed resistance on therapy. Only a subset of the resistance-enhancing mutations emerged in vivo. On-treatment mutation frequencies correlated with their spontaneous emergence rates in temsavir-untreated individuals, and were governed by two parameters: (i) Probability of mutation appearance, determined by number and type of nucleotide changes required, and (ii) Probability of mutation persistence, determined by Env functional and immune fitness. Notably, non-neutralizing antibodies commonly-elicited in HIV-infected individuals restricted emergence of multiple resistant forms, driving convergence to a narrow set of escape routes. These findings establish a quantitative framework for predicting therapeutic resistance and reveal how host-immunity constrains viral evolution during treatment.