Diversity within natural populations of eastern equine encephalomyelitis virus.

We evaluated genetic and phenotypic diversity within natural populations of the alphavirus, Eastern equine encephalomyelitis (EEE) virus. RNA fingerprinting revealed that most populations within infected hosts (unpassaged isolates) contained a consensus genotype along with minority genotypes differing in one to three T1-resistant oligonucleotides. Mutation frequencies appeared to be similar to those reported for other RNA viruses, suggesting that the slow rate of EEE virus evolution is not limited by fidelity of genome replication. Within a given year, genetic diversity was generally greater among geographically distant isolates than among those from the same transmission focus, suggesting that dispersal among EEE viruses in North America is not complete annually. Two of three bird isolates from Maryland and New York contained relatively distantly related genotypes, differing in 15-19 oligonucleotides. A 1985 mosquito isolate from Maryland contained stable, small plaque variants which comprised the majority of that population. These small plaque variants differed by up to eight T1-resistant oligonucleotides when compared with their large plaque counterparts. Temperature sensitive virus was not detected in six unpassaged mosquito isolates from Maryland and New York.