  Mutational escape from vaccine induced immune responses has thwarted the
development of a successful vaccine against AIDS, whose causative agent is HIV,
a highly mutable virus. Knowing the virus' fitness as a function of its
proteomic sequence can enable rational design of potent vaccines, as this
information can focus vaccine induced immune responses to target mutational
vulnerabilities of the virus. Spin models have been proposed as a means to
infer intrinsic fitness landscapes of HIV proteins from patient-derived viral
protein sequences. These sequences are the product of non-equilibrium viral
evolution driven by patient-specific immune responses, and are subject to
phylogenetic constraints. How can such sequence data allow inference of
intrinsic fitness landscapes? We combined computer simulations and variational
theory \'{a} la Feynman to show that, in most circumstances, spin models
inferred from patient-derived viral sequences reflect the correct rank order of
the fitness of mutant viral strains. Our findings are relevant for diverse
viruses.
