We have examined the molecular basis for the observed antigenic differences between isolates of western equine encephalomyelitis (WEE) virus and those of a serologically related alphavirus from the eastern United States designated Highlands J (HJ). The structural proteins of WEE virus isolates have mol. wt. of 55 x 103 (E1), 47 x 103 (E2) and 33 x 103 for the nucleocapsid. The E1 glycoprotein had an isoelectric point (pI) of 6.4 and induced haemagglutination-inhibiting (HI) antibody which was specific for WEE virus. The E2 glycoprotein of WEE virus had a pI of 8.4 and induced antibody which was virus specific by neutralization (PRNT) but cross-reacted with HJ virus in the radioimmune precipitation (RIP) test. Envelope glycoproteins of HJ virus isolates had mol.wt. of 58 x 103 (E1) and 49 x 103 (E2) respectively. The E1 glycoprotein from HJ virus had a pI of 6.8 and induced antibody which reacted specifically in the HI, PRNT and RIP tests. Isolated E2 protein of HJ virus had a pI of 9.1 and induced antibodies which were reactive at equal titre with both WEE and HJ viruses by RIP. Two-dimensional gel electrophoresis of RNase T1 oligonucleotides of WEE virus and HJ virus genome RNase T1 oligonucleotides revealed that the primary structures of the RNAs of these two serologically related alphaviruses were very distant. The fingerprints of the oligonucleotides from 16 WEE viruses from western and central North America, Mexico and South America were similar to each other and easily distinguished from those of the eight HJ viruses isolated in the eastern United States from Massachusetts to Louisiana.
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