{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T03:29:02Z","timestamp":1787887742964,"version":"build-2784847793"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T00:00:00Z","timestamp":1481587200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T00:00:00Z","timestamp":1481587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Rubella viruses of genotypes 1E and 2B are currently the most frequently detected wild-type viruses in the world. Genotype 1E viruses from China have been genetically distinct from genotype 1E viruses found elsewhere, while genotype 2B viruses found in China are not distinguishable from genotype 2B viruses from other areas. Genetic clusters of viruses of both genotypes were defined previously using sequences of the 739-nt genotyping window. Here we report phylogenic analysis using whole genomic sequences from seven genotype 1E and three genotype 2B viruses which were isolated in China between 2000 and 2013 and confirm the subgrouping of current circulating genotypes 1E and 2B viruses. In addition, the whole genomic characterization of Chinese rubella viruses was clarified. The results indicated that the Chinese rubella viruses were highly conserved at the genomic level, and no predicted amino acid variations were found at positions where functional domains of the proteins were identified. Therefore, it gives us the idea that the rubella control and elimination goal should be achieved if vaccine immunization coverage continues maintaining at the high level.<\/jats:p>","DOI":"10.1038\/srep39025","type":"journal-article","created":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T14:45:06Z","timestamp":1481640306000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Analysis of complete genomes of the rubella virus genotypes 1E and 2B which circulated in China, 2000\u20132013"],"prefix":"10.1038","volume":"6","author":[{"given":"Zhen","family":"Zhu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-hsin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Abernathy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Icenogle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shujie","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changyin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunfang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyun","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Si","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenbo","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,12,13]]},"reference":[{"key":"BFsrep39025_CR1","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/S0065-3527(08)60328-0","volume":"44","author":"TK Frey","year":"1994","unstructured":"Frey, T. K. Molecular biology of rubella virus. Adv Virus Res 44, 69\u2013160 (1994).","journal-title":"Adv Virus Res"},{"key":"BFsrep39025_CR2","unstructured":"WHO. Rubella vaccines: WHO position paper. Wkly Epidemiol Rec 86, 301\u2013316 (2011)."},{"key":"BFsrep39025_CR3","doi-asserted-by":"publisher","first-page":"1052","DOI":"10.15585\/mmwr.mm6437a5","volume":"64","author":"GB Grant","year":"2015","unstructured":"Grant, G. B., Reef, S. E., Dabbagh, A., Gacic-Dobo, M. & Strebel, P. M. Global Progress Toward Rubella and Congenital Rubella Syndrome Control and Elimination \u2013 2000\u20132014. MMWR Morb Mortal Wkly Rep 64, 1052\u20131055 (2015).","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"BFsrep39025_CR4","doi-asserted-by":"publisher","first-page":"8259","DOI":"10.1073\/pnas.89.17.8259","volume":"89","author":"EV Koonin","year":"1992","unstructured":"Koonin, E. V. 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. Proc Natl Acad Sci USA 89, 8259\u20138263 (1992).","journal-title":"Proc Natl Acad Sci USA"},{"key":"BFsrep39025_CR5","doi-asserted-by":"publisher","first-page":"2129","DOI":"10.1099\/0022-1317-73-8-2129","volume":"73","author":"MN Rozanov","year":"1992","unstructured":"Rozanov, M. N., Koonin, E. V. & Gorbalenya, A. E. Conservation of the putative methyltransferase domain: a hallmark of the \u2018Sindbis-like\u2019 supergroup of positive-strand RNA viruses. J Gen Virol 73 (Pt 8), 2129\u20132134 (1992).","journal-title":"J Gen Virol"},{"key":"BFsrep39025_CR6","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1743-422X-10-32","volume":"10","author":"E Abernathy","year":"2013","unstructured":"Abernathy, E. et al. Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961\u20132009. Virol J 10, 32 (2013).","journal-title":"Virol J"},{"key":"BFsrep39025_CR7","doi-asserted-by":"crossref","first-page":"4707","DOI":"10.1128\/jvi.70.7.4707-4713.1996","volume":"70","author":"JP Chen","year":"1996","unstructured":"Chen, J. P., Strauss, J. H., Strauss, E. G. & Frey, T. K. Characterization of the rubella virus nonstructural protease domain and its cleavage site. J Virol 70, 4707\u20134713 (1996).","journal-title":"J Virol"},{"key":"BFsrep39025_CR8","doi-asserted-by":"publisher","first-page":"586","DOI":"10.1006\/viro.1994.1070","volume":"198","author":"LD Marr","year":"1994","unstructured":"Marr, L. D., Wang, C. Y. & Frey, T. K. Expression of the rubella virus nonstructural protein ORF and demonstration of proteolytic processing. Virology 198, 586\u2013592 (1994).","journal-title":"Virology"},{"key":"BFsrep39025_CR9","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1006\/viro.1996.0125","volume":"217","author":"C Gros","year":"1996","unstructured":"Gros, C. & Wengler, G. Identification of an RNA-stimulated NTPase in the predicted helicase sequence of the Rubella virus nonstructural polyprotein. Virology 217, 367\u2013372 (1996).","journal-title":"Virology"},{"key":"BFsrep39025_CR10","first-page":"337","volume":"88","author":"WHO. Rubella virus nomenclature upd","year":"2013","unstructured":"WHO. Rubella virus nomenclature update : 2013. Wkly Epidemiol Rec 88, 337\u2013343 (2013).","journal-title":"Wkly Epidemiol Rec"},{"key":"BFsrep39025_CR11","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1099\/vir.0.82495-0","volume":"88","author":"Y Zhou","year":"2007","unstructured":"Zhou, Y., Ushijima, H. & Frey, T. K. Genomic analysis of diverse rubella virus genotypes. J Gen Virol 88, 932\u2013941 (2007).","journal-title":"J Gen Virol"},{"key":"BFsrep39025_CR12","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1128\/JCM.02055-09","volume":"48","author":"Z Zhu","year":"2010","unstructured":"Zhu, Z. et al. Rubella virus genotypes in the People\u2019s Republic of China between 1979 and 2007: a shift in endemic viruses during the 2001 Rubella Epidemic. J Clin Microbiol 48, 1775\u20131781 (2010).","journal-title":"J Clin Microbiol"},{"key":"BFsrep39025_CR13","doi-asserted-by":"publisher","first-page":"7999","DOI":"10.1038\/srep07999","volume":"5","author":"Z Zhu","year":"2015","unstructured":"Zhu, Z. et al. Evolutionary analysis of rubella viruses in mainland China during 2010\u20132012: endemic circulation of genotype 1E and introductions of genotype 2B. Scientific reports 5, 7999 (2015).","journal-title":"Scientific reports"},{"key":"BFsrep39025_CR14","doi-asserted-by":"publisher","first-page":"e0139173","DOI":"10.1371\/journal.pone.0139173","volume":"10","author":"Z Zhu","year":"2015","unstructured":"Zhu, Z. et al. Imported Genotype 2B Rubella Virus Caused the 2012 Outbreak in Anqing City, China. PLoS One 10, e0139173 (2015).","journal-title":"PLoS One"},{"key":"BFsrep39025_CR15","doi-asserted-by":"publisher","first-page":"438","DOI":"10.15585\/mmwr.mm6517a3","volume":"65","author":"MN Mulders","year":"2016","unstructured":"Mulders, M. N. et al. Global Measles and Rubella Laboratory Network Support for Elimination Goals, 2010\u20132015. MMWR Morb Mortal Wkly Rep 65, 438\u2013442 (2016).","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"BFsrep39025_CR16","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1128\/JCM.00289-07","volume":"45","author":"Z Zhu","year":"2007","unstructured":"Zhu, Z. et al. Comparison of four methods using throat swabs to confirm rubella virus infection. J Clin Microbiol 45, 2847\u20132852 (2007).","journal-title":"J Clin Microbiol"},{"key":"BFsrep39025_CR17","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1093\/molbev\/mst197","volume":"30","author":"K Tamura","year":"2013","unstructured":"Tamura, K. et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30, 2725\u20132729 (2013).","journal-title":"Mol Biol Evol"},{"key":"BFsrep39025_CR18","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/1471-2148-7-214","volume":"7","author":"AJ Drummond","year":"2007","unstructured":"Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214 (2007).","journal-title":"BMC Evol Biol"},{"key":"BFsrep39025_CR19","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","volume":"73","author":"KS Lole","year":"1999","unstructured":"Lole, K. S. et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152\u2013160 (1999).","journal-title":"J Virol"},{"key":"BFsrep39025_CR20","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1006\/viro.2001.0939","volume":"285","author":"X Wang","year":"2001","unstructured":"Wang, X. & Gillam, S. Mutations in the GDD motif of rubella virus putative RNA-dependent RNA polymerase affect virus replication. Virology 285, 322\u2013331 (2001).","journal-title":"Virology"},{"key":"BFsrep39025_CR21","doi-asserted-by":"publisher","first-page":"5949","DOI":"10.1128\/JVI.74.13.5949-5956.2000","volume":"74","author":"X Liu","year":"2000","unstructured":"Liu, X., Yang, J., Ghazi, A. M. & Frey, T. K. Characterization of the zinc binding activity of the rubella virus nonstructural protease. J Virol 74, 5949\u20135956 (2000).","journal-title":"J Virol"},{"key":"BFsrep39025_CR22","doi-asserted-by":"publisher","first-page":"7517","DOI":"10.1128\/JVI.00605-07","volume":"81","author":"Y Zhou","year":"2007","unstructured":"Zhou, Y. et al. Identification of a Ca2+-Binding Domain in the Rubella Virus Nonstructural Protease. J Virol 81, 7517\u20137528 (2007).","journal-title":"J Virol"},{"key":"BFsrep39025_CR23","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1099\/0022-1317-80-2-327","volume":"80","author":"RY Forng","year":"1999","unstructured":"Forng, R. Y. & Atreya, C. D. Mutations in the retinoblastoma protein-binding LXCXE motif of rubella virus putative replicase affect virus replication. J Gen Virol 80 (Pt 2), 327\u2013332 (1999).","journal-title":"J Gen Virol"},{"key":"BFsrep39025_CR24","doi-asserted-by":"publisher","first-page":"3041","DOI":"10.1093\/nar\/15.7.3041","volume":"15","author":"DM Clarke","year":"1987","unstructured":"Clarke, D. M., Loo, T. W., Hui, I., Chong, P. & Gillam, S. Nucleotide sequence and in vitro expression of rubella virus 24S subgenomic messenger RNA encoding the structural proteins E1, E2 and C. Nucleic acids research 15, 3041\u20133057 (1987).","journal-title":"Nucleic acids research"},{"key":"BFsrep39025_CR25","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/S0168-1702(01)00374-4","volume":"81","author":"M Ramanujam","year":"2001","unstructured":"Ramanujam, M., Hofmann, J., Nakhasi, H. L. & Atreya, C. D. Effect of site-directed asparagine to isoleucine substitutions at the N-linked E1 glycosylation sites on rubella virus viability. Virus Res 81, 151\u2013156 (2001).","journal-title":"Virus Res"},{"key":"BFsrep39025_CR26","doi-asserted-by":"crossref","unstructured":"Chen, M. H. & Icenogle, J. B. Molecular virology of rubella virus. Rubella Viruses. J. Banatvala and C. Peckham. Oxford, UK, Elsevier, 1\u201318 (2007).","DOI":"10.1016\/S0168-7069(06)15001-6"},{"key":"BFsrep39025_CR27","doi-asserted-by":"publisher","first-page":"2530","DOI":"10.1128\/JCM.00181-10","volume":"48","author":"C Vauloup-Fellous","year":"2010","unstructured":"Vauloup-Fellous, C. et al. Phylogenetic analysis of rubella viruses involved in congenital rubella infections in France between 1995 and 2009. J Clin Microbiol 48, 2530\u20132535 (2010).","journal-title":"J Clin Microbiol"},{"key":"BFsrep39025_CR28","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1128\/JCM.01264-11","volume":"50","author":"Z Zhu","year":"2012","unstructured":"Zhu, Z. et al. Emergence and Continuous Evolution of Genotype 1E Rubella Viruses in China. J Clin Microbiol 50, 353\u2013363 (2012).","journal-title":"J Clin Microbiol"},{"key":"BFsrep39025_CR29","doi-asserted-by":"publisher","first-page":"S524","DOI":"10.1093\/infdis\/jir099","volume":"204","author":"ES Abernathy","year":"2011","unstructured":"Abernathy, E. S. et al. Status of global virologic surveillance for rubella viruses. J Infect Dis 204 Suppl 1, S524\u2013532 (2011).","journal-title":"J Infect Dis"},{"key":"BFsrep39025_CR30","doi-asserted-by":"crossref","unstructured":"Zhu, Z. et al. Genomic analysis of the Chinese genotype 1F rubella virus that disappeared after 2002 in China. J Med Virol (2014).","DOI":"10.1002\/jmv.23936"},{"key":"BFsrep39025_CR31","doi-asserted-by":"publisher","first-page":"6035","DOI":"10.1038\/srep06035","volume":"4","author":"L Hu","year":"2014","unstructured":"Hu, L. et al. Phylogenetic evidence for multiple intertypic recombinations in enterovirus B81 strains isolated in Tibet, China. Scientific reports 4, 6035 (2014).","journal-title":"Scientific reports"},{"key":"BFsrep39025_CR32","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1099\/vir.0.057455-0","volume":"95","author":"M Karlsen","year":"2014","unstructured":"Karlsen, M., Gjerset, B., Hansen, T. & Rambaut, A. Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture. J Gen Virol 95, 52\u201359 (2014).","journal-title":"J Gen Virol"},{"key":"BFsrep39025_CR33","doi-asserted-by":"publisher","first-page":"e73374","DOI":"10.1371\/journal.pone.0073374","volume":"8","author":"S Xu","year":"2013","unstructured":"Xu, S. et al. Genetic characterization of the hemagglutinin genes of wild-type measles virus circulating in china, 1993\u20132009. PLoS One 8, e73374 (2013).","journal-title":"PLoS One"},{"key":"BFsrep39025_CR34","doi-asserted-by":"publisher","first-page":"4429","DOI":"10.1128\/JVI.02354-07","volume":"82","author":"J Jorba","year":"2008","unstructured":"Jorba, J., Campagnoli, R., De, L. & Kew, O. Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range. J Virol 82, 4429\u20134440 (2008).","journal-title":"J Virol"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep39025.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep39025","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep39025.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T01:38:09Z","timestamp":1672882689000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep39025"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12,13]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12,23]]}},"alternative-id":["BFsrep39025"],"URL":"https:\/\/doi.org\/10.1038\/srep39025","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,13]]},"assertion":[{"value":"26 July 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 November 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 December 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"39025"}}