title: The genomic analysis of rubella virus detected from outbreak and sporadic cases in Rio de Janeiro state, Brazil.
abstract: BACKGROUND
  The molecular epidemiology of rubella virus (RV) based on the analysis of the viral E1 gene sequences indicated the existence of two genotypes that differ from each other by 8 to 10% in their nucleotide sequences: genotype I is present in Europe, North America and Asia; and genotype II is present only in Asia.
  
  
  OBJECTIVE
  The purpose of the study was to identify the RV genotypes circulating in Brazil.
  
  
  METHODS
  In this study, we analysed 86 clinical samples collected between 1996 and 1999 during a rubella outbreak and from sporadic cases of rubella in Rio de Janeiro State. For the molecular characterisation of RV strains we have used PCR/nested amplification and direct sequencing of a 513-nucleotide region of the E1 gene.
  
  
  RESULTS
  The E1 gene sequences of 14 RVs were obtained and were assigned to two lineages, both within genotype I. The percentage divergence of nucleotide sequence ranged from 3.4 to 5.1% between these two lineages. These results were in agreement with the pattern of variation observed among the sequences obtained from other lineages of RV.
  
  
  CONCLUSIONS
  This work demonstrated that two new lineages of RV circulated simultaneously between the years 1996 and 1999 in the state of Rio de Janeiro. These results provided new approaches for monitoring the progress of vaccination efforts in Brazil.
authors.affiliation: Department of Virology, Instituto Oswaldo Cruz, FIOCRUZ, Avenida Brasil, 4365, Rio de Janeiro, 21045-900, Brazil.
authors.forename: Flávia F
authors.initials: FF
authors.lastname: Donadio
authors.forename: Marilda M
authors.initials: MM
authors.lastname: Siqueira
authors.forename: Andrew
authors.initials: A
authors.lastname: Vyse
authors.forename: Li
authors.initials: L
authors.lastname: Jin
authors.forename: Solange A
authors.initials: SA
authors.lastname: Oliveira
mesh_terms: D000293:Adolescent; D001938:Brazil / Q000453:epidemiology; D002648:Child; D002675:Child, Preschool; D004196:Disease Outbreaks; D005814:Genes, Viral; D006801:Humans; D017720:Molecular Epidemiology; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis; D012409:Rubella / Q000453:epidemiology*; D012412:Rubella virus / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D012367:RNA, Viral