NOVEL AND DYNAMIC EVOLUTION OF EQUINE INFECTIOUS-ANEMIA VIRUS GENOMICQUASI-SPECIES ASSOCIATED WITH SEQUENTIAL DISEASE CYCLES IN AN EXPERIMENTALLY INFECTED PONY

We have investigated the genetic evolution of three functionally disti nct regions of the equine infectious anemia virus (EIAV) genome (env, rev, and long terminal repeat) during recurring febrile episodes in a pony experimentally infected with a well-characterized reference biolo gical clone designated EIAV(PV). Viral populations present in the plas ma of an EIAV(PV)-infected pony during sequential febrile episodes (18 , 34, 80, 106, and 337 days postinfection) were amplified from viral R NA, analyzed, and compared to the inoculated strain. The comparison of the viral quasispecies showed that the inoculated EIAV(PV) quasispeci es were all represented during the first febrile episode, but entirely replaced at the time of the second febrile episode, and that new pred ominant quasispecies were associated with each subsequent cycle of dis ease. One of the more surprising results was the in vivo generation of large deletion (up to 15 amino acids) in the principal neutralizing d omain (PND) of gp90 during the third febrile episode. This deletion di d not alter the competence for in vitro replication as shown by the an alysis of a env chimeric clone with a partially deleted PND and did no t altered the fitness of the virus in vivo, since this partially delet ed envelope became the major population during the fourth febrile epis ode. Finally, we showed that the amino acid mutations were not randoml y distributed but delineated eight variables regions, V1 to V8, with V 3 containing the PND region. These studies provide the first detailed description of the evolution of EIAV genomic quasispecies during persi stent infection and reveal new insights into the genetics and potentia l mechanisms of lentivirus genomic variation.