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Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing.

Choudhury MA, Lott WB, Banu S, Cheng AY, Teo YY, Ong RT, Aaskov J - PLoS ONE (2015)

Bottom Line: The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene.No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5).The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

View Article: PubMed Central - PubMed

Affiliation: Menzies Health Institute Queensland, Griffith University, Brisbane, Australia.

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.

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Distribution of polymorphic sites in the E genes of haplotypes of DENV-1 Lineage A, B, C and D.Changes from the most prevalent haplotypes/consensus are shown as A: green, T: red, G: orange, C: light blue. The percentage of each haplotype in the population is shown in parenthesis.
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pone.0142473.g003: Distribution of polymorphic sites in the E genes of haplotypes of DENV-1 Lineage A, B, C and D.Changes from the most prevalent haplotypes/consensus are shown as A: green, T: red, G: orange, C: light blue. The percentage of each haplotype in the population is shown in parenthesis.

Mentions: The distribution and the nature of the changes (relative to the sequence of the most common haplotype/consensus) within the E gene are shown in Fig 3. Few strains in either lineage displayed polymorphisms in their complete E genes. Overall, only 1 to 5 variable sites were observed. No polymorphic positions between extinct and extant lineages were conserved, and there were no conserved substitutions (e.g., A or T or G or C) that were exclusive to either extinct or extant lineages. The most polymorphic sites were observed between nucleotides 800 to 1100 in an extinct lineage; however, the frequency of these polymorphisms between extinct and extant lineages was not significantly different (p>0.69, t test). Studies have shown that the DENV E domain (D) II contains the highest diversity of all viral genome domains [21]. However, in this study, no domain (DI-DIII) bias in conservative and non-conservative changes between extinct and extant lineages was observed.


Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing.

Choudhury MA, Lott WB, Banu S, Cheng AY, Teo YY, Ong RT, Aaskov J - PLoS ONE (2015)

Distribution of polymorphic sites in the E genes of haplotypes of DENV-1 Lineage A, B, C and D.Changes from the most prevalent haplotypes/consensus are shown as A: green, T: red, G: orange, C: light blue. The percentage of each haplotype in the population is shown in parenthesis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643897&req=5

pone.0142473.g003: Distribution of polymorphic sites in the E genes of haplotypes of DENV-1 Lineage A, B, C and D.Changes from the most prevalent haplotypes/consensus are shown as A: green, T: red, G: orange, C: light blue. The percentage of each haplotype in the population is shown in parenthesis.
Mentions: The distribution and the nature of the changes (relative to the sequence of the most common haplotype/consensus) within the E gene are shown in Fig 3. Few strains in either lineage displayed polymorphisms in their complete E genes. Overall, only 1 to 5 variable sites were observed. No polymorphic positions between extinct and extant lineages were conserved, and there were no conserved substitutions (e.g., A or T or G or C) that were exclusive to either extinct or extant lineages. The most polymorphic sites were observed between nucleotides 800 to 1100 in an extinct lineage; however, the frequency of these polymorphisms between extinct and extant lineages was not significantly different (p>0.69, t test). Studies have shown that the DENV E domain (D) II contains the highest diversity of all viral genome domains [21]. However, in this study, no domain (DI-DIII) bias in conservative and non-conservative changes between extinct and extant lineages was observed.

Bottom Line: The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene.No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5).The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

View Article: PubMed Central - PubMed

Affiliation: Menzies Health Institute Queensland, Griffith University, Brisbane, Australia.

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.

Show MeSH
Related in: MedlinePlus