Article

Archives of Virology

, Volume 142, Issue 6, pp 1165-1180

Genomic sequence of the RAff27/3 vaccine strainof rubella virus

  • K. V. PugachevAffiliated withDepartment of Biology, Georgia State University, Atlanta, Georgia, U.S.A.
  • , E. S. AbernathyAffiliated withDepartment of Biology, Georgia State University, Atlanta, Georgia, U.S.A.
  • , T. K. FreyAffiliated withDepartment of Biology, Georgia State University, Atlanta, Georgia, U.S.A.

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Summary

The sequence of the genome of the RAff27/3 vaccine strain of rubella virus (RUB) was determined. In the process, several discrepancies between the previously reported genomic sequences of two wild RUB strains (Therien and M33) were resolved. The genomes of all three strains contain 9 762 nucleotides (nts), exclusive of the 3′ poly A tract. In all three strains, the genome contains (5′ to 3′), a 40 nt 5′ untranslated region (UTR), an open reading frame (ORF) of 6 348 nts that encodes nonstructural proteins, a 123 nt UTR between the two genomic ORFs, a 3 189 nt ORF that encodes the structural proteins, and a 62 nt 3′ UTR. The 5′ end of the subgenomic RNA was found to correspond to a uridine residue at nt 6 436 of the genomic RNA. At the nucleotide level, the sequence of the three strains varied by 1.0 to 2.8%, while at the amino acid level, the sequence varied by 1.1 to 2.4% over both ORFs. The RAff27/3 sequence will be of use in identification of the determinants of its attenuation, in vaccine production control and in development of second generation RUB vaccines based on recombinant DNA technology.