title: Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing.
abstract: Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009-0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.
authors.affiliation: Menzies Health Institute Queensland, Griffith University, Brisbane, Australia.|Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
authors.forename: Md Abu
authors.initials: MA
authors.lastname: Choudhury
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.|School of Chemistry, Physics, and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia.
authors.forename: William B
authors.initials: WB
authors.lastname: Lott
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
authors.forename: Shahera
authors.initials: S
authors.lastname: Banu
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
authors.forename: Anthony Youzhi
authors.initials: AY
authors.lastname: Cheng
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.|Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.|Life Sciences Institute, National University of Singapore, Singapore, Singapore.|Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.
authors.forename: Yik-Ying
authors.initials: YY
authors.lastname: Teo
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
authors.forename: Rick Twee-Hee
authors.initials: RT
authors.lastname: Ong
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Aaskov
mesh_terms: D003715:Dengue / Q000821:virology*; D003716:Dengue Virus / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014759:Viral Envelope Proteins