title: Genomic analysis of the Chinese genotype 1F rubella virus that disappeared after 2002 in China.
abstract: Genotype 1F was likely localized geographically to China as it has not been reported elsewhere. In this study, whole genome sequences of two rubella 1F virus isolates were completed. Both viruses contained 9,761 nt with a single nucleotide deletion in the intergenic region, compared to the NCBI rubella reference sequence (NC 001545). No evidence of recombination was found between 1F and other rubella viruses. The genetic distance between 1F viruses and 10 other rubella virus genotypes (1a, 1B, 1C, 1D, 1E, 1G, 1J 2A, 2B, and 2C) ranged from 3.9% to 8.6% by pairwise comparison. A region known to be hypervariable in other rubella genotypes was also the most variable region in the 1F genomes. Comparisons to all available rubella virus sequences from GenBank identified 22 nucleotide variations exclusively in 1F viruses. Among these unique variations, C9306U is located within the recommended molecular window for rubella virus genotyping assignment, could be useful to confirm 1F viruses. Using the Bayesian Markov Chain Monte Carlo (MCMC) method, the time of the most recent common ancestor for the genotype 1F was estimated between 1976 and 1995. Recent rubella molecular surveillance suggests that this indigenous strain may have circulated for less than three decades, as it has not been detected since 2002.
authors: WHO WPRO Regional Reference Measles/Rubella Laboratory and Ministry of Health Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
authors: Zhen
authors: Z
authors: Zhu
authors: Min-Hsin
authors: MH
authors: Chen
authors: Emily
authors: E
authors: Abernathy
authors: Shujie
authors: S
authors: Zhou
authors: Changyin
authors: C
authors: Wang
authors: Joseph
authors: J
authors: Icenogle
authors: Wenbo
authors: W
authors: Xu
mesh_terms: D002681:China; D016000:Cluster Analysis; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D012412:Rubella virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral
keywords: Rubella virus; genotype 1F; whole genome sequence, molecular clock