Fingerprints of the oligonucleotides generated by RNase T1 digestion of the equine virulent Venezuelan equine encephalitis virus, Trinidad donkey (TRD), intracellular 26 S RNA were similar to those of its vaccine derivative, TC-83 virus. Three oligonucleotides present in the fingerprint of TRD virus 26 S RNA were missing from that of the TC-83 26 S RNA which had three new oligonucleotides. To determine if these genetic changes are expressed in the three structural proteins of the two VEE viruses, we compared the individual proteins from each virus by peptide mapping the trypsin fragments by high-performance liquid chromatography. The nucleocapsid proteins and E, envelope glycoprotein from both viruses produced identical peptide maps; however, analysis of the peptide fragments of the E2 envelope glycoproteins revealed four different peptide fragments between the two viruses.
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