SUMMARYThe genomes of diabetogenic and non-diabetogenic variants of encephalomyocarditis virus were analysed by nucleic acid hybridization and RNA fingerprinting. Hybridization and thermal elution profiles failed to show any difference between the RNAs of the two variants, whereas fingerprinting of the T 1-digested RNAs revealed at least one oligonucleotide, 20 to 25 nucleotides long, missing in the non-diabetogenic variant.Encephalomyocarditis (EMC) virus produces diabetes in mice by infecting and destroying pancreatic beta cells (Notkins, 1977). Recently, we showed that our virus pool contained two antigenically similar variants which could not be distinguished by hyperimmune sera (Yoon et al., 1980). One of the variants, designated D, produced diabetes, whereas the other variant, designated B, failed to produce diabetes. The present study was initiated to analyse the genomes of these two variants by nucleic acid hybridization and RNA fingerprinting. We found that both viral cDNA probes hybridized equally well to homologous and heterologous RNAs, but that the RNAs differed by at least one spot in the unique sequence region of their oligonucleotide fingerprints.Viruses were purified from infected L929 cells by sucrose and CsCI gradient centrifugation . RNA was obtained from purified virions after phenol-cresolchloroform extraction and ethanol precipitation (Kacian & Myers, 1976). The viral RNA was treated with methylmercury hydroxide to enhance transcription according to the method of Payvar & Schimke (1979). Then, labelled cDNA was synthesized using [~-32p]dCTP and avian myeloblastosis virus reverse transcriptase. Oligo(dT) and oligo(dG) were used as primers and the cDNA was purified by Sephadex G-75 and DEAE column chromatography. Foldback sequences were removed by hydroxylapatite column chromatography as previously outlined by Aulakh & GaUo (1977). The single-stranded cDNA probes of EMC-D and EMC-B were shown to be representative of the complete viral genomes by their ability to protect the labelled viral RNAs from digestion with ribonucleases A and T1. The respective homologous cDNAs protected greater than 94~o of EMC-D-and 95~ of EMC-B-labelled RNAs.Hybridizations were performed using 20 ~tg/ml viral RNA and approximately 0-05 ~tg/ml cDNA probe (50000 ct/min) in 0.48 M-sodium phosphate buffer pH 6.8, 3 mM-EDTA, and 0.4~ SDS. After denaturing at 105 °C for 5 min, the hybrids were allowed to anneal at 65 °C for 10 h. Hybrids were separated from unhybridized strands by hydroxylapatite chromatography.When EMC-D cDNA was hybridized with EMC-D and EMC-B RNA, 90~o and 91~, respectively, of the cDNA formed hybrids. Similarly, when EMC-B cDNA was hybridized with homologous and heterologous viral RNA, 90~ and 89~ of the cDNA formed hybrids. The hybrids were also analysed for thermal stability to evaluate mismatching in base pairing.