Antigenic variation and lentivirus persistence: Variations in envelope gene sequences during EIAV infection resemble changes reported for sequential isolates of HIV

The extent and nature of genomic variation among nine antigenically distinct EIAV isolates recovered during sequential clinical episodes from two experimentally infected ponies were examined by restriction fragment analysis and nucleotide sequencing. Only minor variations in restriction enzyme patterns were observed among the viral genomes. In contrast, env gene sequences of four isolates from one pony revealed numerous clustered base substitutions. Divergence in env gene nucleotide and deduced amino acid sequences between pairs of virus isolates ranged from 0.62 to 3.4%. env gene mutation rates for isolates recovered during sequential febrile episodes were calculated to be greater than 10 −2 base substitutions per site per year. The degree and nature of env gene variation in EIAV is remarkably similar to the human immunodeficiency virus, suggesting common mechanisms for env gene variation among lentiviruses.