A series of 57 Saint Louis encephalitis (SLE) virus isolates from humans, birds, rodents, and mosquitoes showed extensive variability in their RNase T1 oligonucleotide fingerprints. The fingerprints of virion RNA did not contain an obvious poly(A) tract and were identical when the virus was grown in either mosquito or mammalian cells. Analysis and comparison of long oligonucleotides, representing approximately 10% of the genome of SLE isolates from the Central and Atlantic states, indicated the viruses share at least 80% of their long oligonucleotides. Analysis of the large T1-resistant oligonucleotides by RNase A digestion revealed chemical similarities in the composition of common oligonucleotides derived from the genomes of four isolates. Analysis of 57 SLE strains from North America indicated that on the basis of the similarity of the oligonucleotide fingerprints, SLE isolates could be divided into genotypic sets representing different geographic regions in North America. These geographic varieties, designated "topotypes," represent isolates from: (1) the Central/Atlantic states, (2) Florida, (3) and the Western United States. Variants of each "topotype" have been characterized whose oligonucleotide fingerprints are similar to that of the "topotype" but are sufficiently distinct to permit separation of the highly and less virulent SLE strains.
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