Identification of strain-specific nucleotide sequences in E1 and NS4 genes of rubella virus vaccine strains in Japan

Phylogenetic Analysis of Envelope Glycoprotein (E1) Gene of Rubella Viruses Prevalent in Japan in 2004

We performed a molecular epidemiological study on the envelope glycoprotein gene (E1 gene) obtained by PCR amplification from specimens of 17 rubella patients in certain areas (Gunma, Saitama, and Kagoshima prefectures, and Tokyo metropolitan area) in Japan in 2004. In these sequences of partially amplified DNAs (283 bases) within the E1 gene, no nucleotide substitution was observed. They were classified into genotype 1D of clade 1 in the constructed phylogenetic tree. One amino acid substitution was found between the amino acid sequence predicted from these DNAs and those of Japanese strains [To-336 vaccine strain (To-336 vac) and its wild progenitor (To-336 wt)]. The results suggest that the rubella viruses (RV) prevalent in certain areas of Japan in 2004 were highly homologous and were closely related with Japanese vaccine strain.

Co-circulation of multiple rubella virus strains in Belarus forming novel genetic groups within clade 1

Although the WHO recommends a comprehensive genetic characterization, little is known about circulating strains and genotypes of rubella virus (RUBV) for many European countries. Studies investigating the genetic diversity of a sizeable number of strains from a certain location are rare. This study presents the first molecular characterization of isolates from Belarus. Throat swab and urine samples were collected between 2004 and 2005 from patients presenting in two infectious disease hospitals and three outpatient clinics in and around Minsk. In total, 14 isolates were obtained from this clinical material. Phylogenetic analysis of the E1 gene sequence of these isolates showed that three distinct groups of RUBV strains co-circulated. One group of isolates was assigned to genotype 1E, whereas the other two did not group with any of the recognized genotypes but grouped with a strain belonging to the provisional genotype 1g. Detailed analysis showed that the group comprising 1g strains also contained sequences formerly attributed to genotype 1B and could be divided into four subgroups, one of which might represent a putative novel provisional genotype of clade 1. These findings show that three distinct strains with limited variability are present in Belarus, suggesting independent introductory events. As there currently seem to be misattributions of strains to genotypes and unclear phylogenetic relationships, criteria for genotyping of RUBV should be clarified further.

Genomic analysis of diverse rubella virus genotypes

Based on the sequence of the E1 glycoprotein gene, two clades and ten genotypes of Rubella virus have been distinguished; however, genomic sequences have been determined for viruses in only two of these genotypes. In this report, genomic sequences for viruses in an additional six genotypes were determined. The genome was found to be well conserved. The viruses in all eight of these genotypes had the same number of nucleotides in each of the two open reading frames (ORFs) and the untranslated regions (UTRs) at the 5' and 3' ends of the genome. Only the UTR between the ORFs (the junction region) exhibited differences in length. Of the nucleotides in the genome, 78% were invariant. The greatest observed distance between viruses in different genotypes was 8.74% and the maximum calculated genetic distance was 14.78 substitutions in 100 sites. This degree of variability was similar among regions of the genome with two exceptions, both within the P150 non-structural protein gene: the N-terminal region that encodes the methyl/guanylyltransferase domain was less variable, whereas the hypervariable domain in the middle of the gene was more divergent. Comparative phylogenetic analysis of different regions of the genome was done, using sequences from 43 viruses of the non-structural protease (near the 5' end of the genome), the junction region (the middle) and the E1 gene (the 3' end). Phylogenetic segregation of sequences from these three genomic regions was similar with the exception of genotype 1B viruses, among which a recombinational event near the junction region was identified.

Vaccine adverse events reported in post-marketing study of the Kitasato Institute from 1994 to 2004

General physicians, pediatricians and parents realize that serious adverse events occur with an extremely rare incidence, but have no information on the incidences of vaccine-associated adverse events. A proper understanding of vaccine adverse events would be helpful in promoting an immunization strategy. Causal association can rarely be determined in adverse events through laboratory examinations. We examined the cases reported in the post-marketing surveillance of the Kitasato Institute, categorizing them into two groups: allergic reactions and severe systemic illnesses. Anaphylactic patients with gelatin allergy after immunization with live measles, rubella and mumps monovalent vaccines have been reported since 1993, but the number of reported cases with anaphylaxis dramatically decreased after 1999 when gelatin was removed from all brands of DPT. The incidence of anaphylactic reaction was estimated to be 0.63 per million for Japanese encephalitis virus (JEV) vaccine, 0.95 for DPT and 0.68 for Influenza vaccine, but the causative component has not yet been specified. Among 67.2 million immunization practices, 6 cases with encephalitis or encephalopathy, 7 with acute disseminated encephalomyelitis (ADEM), 10 with Guillain-Barré syndrome and 12 with idiopathic thrombocytopenic purpura (ITP) were reported. The wild-type measles virus genome was detected in a patient with encephalitis and in two of four bone marrow aspirates obtained from ITP after measles vaccination. Enterovirus infection was identified in two patients after mumps vaccination (one each with encephalitis and ADEM), one patient with encephalitis after immunization with JEV vaccine, and one with aseptic meningitis after immunization with influenza vaccine. The total estimated incidence of serious neurological illness after vaccination was 0.1-0.2 per million immunization practices. We found that enterovirus or wild-type measles virus infection was coincidentally associated with vaccination in several cases suspected of being vaccine adverse events.

Mutations of rubella virus vaccine TO-336 strain occurred in the attenuation process of wild progenitor virus

The sequences of the genomes in the TO-336 vaccine strain (TO-336vac) of rubella virus and its wild progenitor virus (TO-336wt) have been determined and compared with each other. There were 21 differences in the nucleotide sequences between the TO-336vac and the TO-336wt: 13 in the nonstructural protein open reading frame (NSP-ORF), five in the structural protein open reading frame (SP-ORF) and three in the untranslated regions (UTRs) (one in each three UTRs). These mutations resulted in amino acid substitutions at ten residues. Of the ten substitutions, eight were in NSP-ORF and two were in the SP-ORF. Of the eight substitutions in NSP-ORF, four (amino acids (aa) 320, 501, 573 and 704) were in the regions of unknown function, two (aa 1154 and 1159) were within the protease motif, and two (aa 1351 and 1559) were within the helicase motif. Both of the two residues (aa 890 and 954) in the SP-ORF were within the E1 gene. The predicted second structure of the 5'UTR of the TO-336vac was identical to that of TO-336wt. Comparing the TO-336 sequences with other four strains, Therien and M33 (wild viruses), and RA27/3 and Cendehill (vaccine viruses), the mutations responsible for attenuation are thought to differ with each vaccine strain. This is the first report of sequencing in a pair of live attenuated rubella vaccines and their wild-type parent.