title: Sequence diversity of the capsid gene and the nonstructural gene NS2B of dengue-3 virus in vivo.
abstract: Previously, we studied the envelope (E) gene of dengue virus and reported that dengue-3 virus is present as a quasispecies. To investigate the extent of intrahost sequence variation of other dengue viral genes, we examined in this study the capsid (C) gene and the nonstructural gene, NS2B, derived directly from plasma dengue viruses from 18 confirmed dengue-3 patients. Using reverse transcription-PCR, multiple clones of a 360-nucleotide region covering the C gene and of a 404-nucleotide region covering the NS2B gene from each patient were completely sequenced and analyzed. Our findings of the intrahost sequence variation of the C and the NS2B genes (mean pairwise p-distance: 0.12 to 1.02%, and 0.16 to 1.20%, respectively) demonstrate the quasispecies structure of dengue virus in vivo. A linear relationship was found between the extent of sequence variation of the C and NS2B proteins, suggesting that intrahost sequence variation of dengue-3 virus is likely to reflect genetic drift. The extent of intrahost sequence variation observed is in the same range as that of acute human immunodeficiency virus or hepatitis C virus infection, indicating that the random mutation frequency of dengue virus is similar to that of other RNA viruses in vivo. Consistent with a previous report of the E gene, the observations of genome-defective clones in both the C and the NS2B genes (3.9 and 5.0% of the clones, respectively) suggest a higher frequency of defective viruses in vivo. These findings would add to our understanding of the evolution of dengue-3 virus.
authors.affiliation: Institute of Microbiology, College of Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan. wwang60@yahoo.com
authors.forename: Wei Kung
authors.initials: WK
authors.lastname: Wang
authors.forename: Tzu Ling
authors.initials: TL
authors.lastname: Sung
authors.forename: Chun Nan
authors.initials: CN
authors.lastname: Lee
authors.forename: Tsai Yu
authors.initials: TY
authors.lastname: Lin
authors.forename: Chwan Chuen
authors.initials: CC
authors.lastname: King
mesh_terms: D000328:Adult; D000368:Aged; D000595:Amino Acid Sequence; D036022:Capsid Proteins / Q000235:genetics*; D003715:Dengue / Q000821:virology*; D003716:Dengue Virus / Q000737:chemistry / Q000235:genetics*; D005814:Genes, Viral; D014644:Genetic Variation; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D014766:Viremia
chemical_list: D036022:Capsid Proteins; C080102:NS2B protein, flavivirus; D017361:Viral Nonstructural Proteins