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 identify 18 mutations in the HIV-1 Env protein that enhance resistance to the FDA-approved small-molecule therapeutic temsavir. We then examine their occurrence in HIV-infected individuals who developed resistance on therapy. Interestingly, only a subset of the resistance-enhancing mutations emerged in vivo. On-treatment mutation frequencies correlate with their emergence rates in temsavir-untreated individuals and are governed by two parameters: (1) probability of mutation appearance, determined by the number and type of nucleotide changes required, and (2) probability of mutation persistence, determined by Env functional and immune fitness. Notably, non-neutralizing antibodies commonly elicited in HIV-infected individuals restrict 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.