IDENTIFICATION OF STRAIN-SPECIFIC NUCLEOTIDE-SEQUENCES IN THE RA-27 3RUBELLA-VIRUS VACCINE/

A polymerase chain reaction-based protocol was developed for determina tion of the sequence of 1300 nucleotides in the El coding region of th e genomes of multiple strains of rubella virus. From a collection of s equences of 9 independent strains and isolates, characteristic nucleot ides were identified that distinguished the RA 27/3 strain, which is t he currently used attenuated vaccine strain. These characteristic nucl eotides were maintained in virus recovered from recent vaccinees. Both the assay and the knowledge of these characteristic nucleotides shoul d be of use in determining the origin of virus isolated from individua ls who have suspected vaccine-associated complications. The nucleotide sequences of the independent rubella virus strains differed by 0.7%-3 .6%. Phylogenetic tree analysis of the sequences indicated the existen ce of at least three distinct genetic lineages.