A highly effective attenuated equine infectious anemia virus (EIAV) vaccine (EIAV D9)). An inverse correlation between challenge strain Env variation and vaccine protection from disease was observed. Given the striking differences in protective immunity, we hypothesized that analysis of the humoral and cellular immune responses to the Env protein could reveal potential determinants of vaccine protection. Neutralization activity against the homologous Env or challenge strain-specific Env in immune sera from the vaccinated ponies did not correlate with protection from disease. Cellular analysis with Env peptide pools did not reveal an association with vaccine protection from disease. However, when individual vaccinespecific Env peptides were utilized, eight cytotoxic-T-lymphocyte (CTL) peptides were found to associate closely with vaccine protection. One of these peptides also yielded the only lymphoproliferative response associated with protective immunity. The identified peptides spanned both variable and conserved regions of gp90. Amino acid divergence within the principal neutralization domain and the identified peptides profoundly affected immune recognition, as illustrated by the inability to detect cross-reactive neutralizing antibodies and the observation that certain peptide-specific CTL responses were altered. In addition to identifying potential Env determinants of EIAV vaccine efficacy and demonstrating the profound effects of defined Env variation on immune recognition, these data also illustrate the sensitivity offered by individual peptides compared to peptide pools in measuring cellular immune responses in lentiviral vaccine trials.Equine infectious anemia virus (EIAV) is a macrophagetropic equine lentivirus that has been used extensively as a model for human immunodeficiency virus type 1 (HIV-1) persistence and pathogenesis and for AIDS vaccine development (8,18,24,25,29,36,(48)(49)(50)55). Compared to other progressively degenerative lentiviral infections, EIAV is characterized by three distinct phases of infection, namely, acute, chronic, and inapparent. By 2 months post-EIAV exposure, most horses experience an acute disease episode characterized by high fever, a drop in platelets, and a high viral load. The horse then enters a chronic stage of infection characterized by recurrent disease episodes, which typically progress to the inapparent carrier stage of disease for the life span of the animal (48). During the inapparent phase, the horse has gained immunologic control of the virulent and constantly evolving lentivirus, as demonstrated by the fact that whole blood transfers from inapparent carriers to naïve horses can cause an acute episode within 2 months (31,43,48). Additionally, if the inapparent carrier is immunosuppressed or stressed, there can be recrudescing disease associated with a new viral quasispecies. Inapparent carriers of EIAV appear to be resistant to additional exposure to EIAV variant strains, indicating that the horse has gained a high level of prophylactic immunity (48). Th...