Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3.
BACKGROUND
Although the previous study demonstrated the envelope protein of dengue viruses is under purifying selection pressure, little is known about the genetic differences of full-length viral genomes of DENV-3. In our study, complete genomic sequencing of DENV-3 strains collected from different geographical locations and isolation years were determined and the sequence diversity as well as selection pressure sites in the DENV genome other than within the E gene were also analyzed.


RESULTS
Using maximum likelihood and Bayesian approaches, our phylogenetic analysis revealed that the Taiwan's indigenous DENV-3 isolated from 1994 and 1998 dengue/DHF epidemics and one 1999 sporadic case were of the three different genotypes - I, II, and III, each associated with DENV-3 circulating in Indonesia, Thailand and Sri Lanka, respectively. Sequence diversity and selection pressure of different genomic regions among DENV-3 different genotypes was further examined to understand the global DENV-3 evolution. The highest nucleotide sequence diversity among the fully sequenced DENV-3 strains was found in the nonstructural protein 2A (mean +/- SD: 5.84 +/- 0.54) and envelope protein gene regions (mean +/- SD: 5.04 +/- 0.32). Further analysis found that positive selection pressure of DENV-3 may occur in the non-structural protein 1 gene region and the positive selection site was detected at position 178 of the NS1 gene.


CONCLUSIONS
Our study confirmed that the envelope protein is under purifying selection pressure although it presented higher sequence diversity. The detection of positive selection pressure in the non-structural protein along genotype II indicated that DENV-3 originated from Southeast Asia needs to monitor the emergence of DENV strains with epidemic potential for better epidemic prevention and vaccine development.
King
Chwan-Chuen
CC
Institute of Epidemiology, College of Public Health, National Taiwan University, Taipei, Taiwan(10020), PRoC. cc_king99@hotmail.com.tw
Chao
Day-Yu
DY
Chien
Li-Jung
LJ
Chang
Gwong-Jen J
GJ
Lin
Ting-Hsiang
TH
Wu
Yin-Chang
YC
Huang
Jyh-Hsiung
JH
D000595:Amino Acid Sequence; D001208:Asia / Q000453:epidemiology; D001483:Base Sequence; D003715:Dengue / Q000453:epidemiology / Q000821:virology*; D003716:Dengue Virus / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D020506:Untranslated Regions / Q000737:chemistry / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
D012367:RNA, Viral; D020506:Untranslated Regions; D014764:Viral Proteins