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.

[1]  S. Emerson,et al.  Determination and analysis of the complete genomic sequence of avian hepatitis E virus (avian HEV) and attempts to infect rhesus monkeys with avian HEV. , 2004, The Journal of general virology.

[2]  M. Salemi,et al.  The phylogenetic handbook : a practical approach to DNA and protein phylogeny , 2003 .

[3]  S. Weaver,et al.  Molecular analysis of rubella virus epidemiology across three continents, North America, Europe, and Asia, 1961-1997. , 1998, The Journal of infectious diseases.

[4]  Ziheng Yang.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[5]  A. von Haeseler,et al.  Phylogenetic analysis of rubella virus including new genotype I isolates. , 2003, Virus research.

[6]  S. Katow.  Molecular epidemiology of rubella virus in Asia: Utility for reduction in the burden of diseases due to congenital rubella syndrome , 2004, Pediatrics international : official journal of the Japan Pediatric Society.

[7]  T. Frey,et al.  Sequence of the genome RNA of rubella virus: Evidence for genetic rearrangement during togavirus evolution☆ , 1990, Virology.

[8]  X. Xia,et al.  DAMBE: software package for data analysis in molecular biology and evolution. , 2001, The Journal of heredity.

[9]  G. Atkins,et al.  Sequence analysis of the avirulent, demyelinating A7 strain of Semliki Forest virus. , 1997, The Journal of general virology.

[10]  Xuhua Xia,et al.  Data Analysis in Molecular Biology and Evolution , 2002, Springer US.

[11]  Standardization of the nomenclature for genetic characteristics of wild-type rubella viruses. , 2005, Releve epidemiologique hebdomadaire.

[12]  E. Abernathy,et al.  Global Distribution of Rubella Virus Genotypes , 2003, Emerging infectious diseases.

[13]  P. Roques,et al.  Phylogenetic analysis of the first complete hepatitis E virus (HEV) genome from Africa. , 2003, FEMS immunology and medical microbiology.

[14]  E. Koonin,et al.  Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Hersh,et al.  Rubella and congenital rubella syndrome: global update. , 2003, Revista panamericana de salud publica = Pan American journal of public health.

[16]  T. Frey.  Molecular Biology of Rubella Virus , 1994, Advances in Virus Research.

[17]  S. Emerson,et al.  Phylogenetic analysis of hepatitis E virus isolates from India (1976-1993). , 1999, The Journal of general virology.

[18]  Dirk Husmeier,et al.  TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments , 2004, Bioinform..

[19]  T. Frey,et al.  Infectious cDNA clone of the RA27/3 vaccine strain of Rubella virus. , 2000, Virology.

[20]  S. Katow,et al.  Identification of strain-specific nucleotide sequences in E1 and NS4 genes of rubella virus vaccine strains in Japan. , 1997, Vaccine.

[21]  G. Gerna,et al.  Phylogenetic analysis of rubella virus isolated during a period of epidemic transmission in Italy, 1991-1997. , 2003, The Journal of infectious diseases.

[22]  K. Strimmer,et al.  Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies , 1996 .

[23]  J. Chantler,et al.  Mapping of Genetic Determinants of Rubella Virus Associated with Growth in Joint Tissue , 2000, Journal of Virology.

[24]  J. Best,et al.  Nucleotide sequence analysis of a major antigenic domain of the E1 glycoprotein of 22 rubella virus isolates. , 1996, The Journal of general virology.

[25]  V. Gouvea,et al.  Hepatitis E virus: complete genome sequence and phylogenetic analysis of a Nepali isolate. , 1998, Virus research.

[26]  E. Koonin,et al.  Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses. , 1992, The Journal of general virology.

[27]  A. von Haeseler,et al.  Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. , 1999, Genetics.

[28]  A. Vyse,et al.  The genomic analysis of rubella virus detected from outbreak and sporadic cases in Rio de Janeiro state, Brazil. , 2003, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[29]  E. Abernathy,et al.  Genetic analysis of rubella viruses found in the United States between 1966 and 2004: evidence that indigenous rubella viruses have been eliminated. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[30]  E. Abernathy,et al.  Genomic sequence of the RA27/3 vaccine strain of rubella virus. , 1997, Archives of Virology.

[31]  H. Ushijima,et al.  Mutations of rubella virus vaccine TO-336 strain occurred in the attenuation process of wild progenitor virus. , 2001, Vaccine.

[32]  Masahiko Kato,et al.  Phylogenetic Analysis of Envelope Glycoprotein (E1) Gene of Rubella Viruses Prevalent in Japan in 2004 , 2006, Microbiology and immunology.

[33]  J. Roehrig,et al.  Nucleotide sequences of the 26S mRNAs of the viruses defining the Venezuelan equine encephalitis antigenic complex. , 1998, The American journal of tropical medicine and hygiene.

[34]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[35]  P. Chong,et al.  Nucleotide sequence and in vitro expression of rubella virus 24S subgenomic messenger RNA encoding the structural proteins E1, E2 and C. , 1987, Nucleic acids research.

[36]  T. Frey,et al.  Characterization of genotype II Rubella virus strains , 2003, Archives of Virology.

[37]  J. Gilsdorf,et al.  The Changing Epidemiology of Rubella in the 1990s: On the Verge of Elimination and New Challenges for Control and Prevention , 2002 .

[38]  Choi-Kyu Park,et al.  Molecular characterization of PL97-1, the first Korean isolate of the porcine reproductive and respiratory syndrome virus , 2004, Virus Research.

[39]  T. Nishizawa,et al.  Characterization of Japanese swine and human hepatitis E virus isolates of genotype IV with 99 % identity over the entire genome. , 2003, The Journal of general virology.

[40]  G. Duverlie,et al.  rubella virus , 2022 .

[41]  M. Lindsay,et al.  Complete Genomic Sequence of the Australian South-West Genotype of Sindbis Virus: Comparisons with Other Sindbis Strains and Identification of a Unique Deletion in the 3′-Untranslated Region , 2004, Virus Genes.

[42]  S. Mishiro,et al.  Full-Length Sequences of Six Hepatitis E Virus Isolates of Genotypes III and IV from Patients with Sporadic Acute or Fulminant Hepatitis in Japan , 2003, Intervirology.

[43]  J. Kwon,et al.  Molecular characterization of full-length genome of Japanese encephalitis virus (KV1899) isolated from pigs in Korea. , 2004, Journal of veterinary science.

[44]  S. Henikoff,et al.  Position-based sequence weights. , 1994, Journal of molecular biology.

[45]  S. Katow,et al.  Molecular epidemiology of rubella by nucleotide sequences of the rubella virus E1 gene in three East Asian countries. , 1997, The Journal of infectious diseases.