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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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Related in: MedlinePlus

Phylogenetic analysis of the E gene haplotype and consensus sequences of DENV-1.Consensus sequences for each strain have been highlighted. Bootstrap values (100 replications) for key nodes are shown. A distance bar is shown below the tree. Lineage A became extinct in 1998 about the same time lineages B and C appeared. No examples of lineage B have been recovered since 2002, but lineage C still circulated in 2008. Lineage D, first detected in 2006, also still circulated in 2008. For the purposes of analysis, lineages A and B are considered to have become extinct in 1998 and 2002, respectively. Lineages C and D were deemed to be still circulating in 2008.
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pone.0142473.g001: Phylogenetic analysis of the E gene haplotype and consensus sequences of DENV-1.Consensus sequences for each strain have been highlighted. Bootstrap values (100 replications) for key nodes are shown. A distance bar is shown below the tree. Lineage A became extinct in 1998 about the same time lineages B and C appeared. No examples of lineage B have been recovered since 2002, but lineage C still circulated in 2008. Lineage D, first detected in 2006, also still circulated in 2008. For the purposes of analysis, lineages A and B are considered to have become extinct in 1998 and 2002, respectively. Lineages C and D were deemed to be still circulating in 2008.

Mentions: A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences obtained from Sanger sequencing and the sequences of each constructed haplotype obtained through Roche/454 pyrosequencing, to determine any disparities (Fig 1). With the exception of the M47317 strain, each haplotype segregated with the Sanger consensus sequence of the population from which it was drawn (Fig 1). The intermediate position of the M47317consensus sequence in this tree suggests that it might have been derived from a recombinant genome (Fig 2). Alignment of the consensus nucleotide sequences of representative strains from lineage B and C with the consensus sequence for M47317 and the sequences of M47317 haplotypes, suggested a recombination break point at about nucleotide 1087. Phylogenetic trees constructed with sequences from either side of this point supported this conclusion [i.e., nt 1–1087 of the consensus sequence of M47317 segregated with those from lineage C viruses (Fig 2), while sequences 3/ to this point segregated more closely with lineage B viruses and the M47317 haplotypes]. There was no recombination observed within the sequences of M47317 haplotypes with strains from lineage A or D.


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)

Phylogenetic analysis of the E gene haplotype and consensus sequences of DENV-1.Consensus sequences for each strain have been highlighted. Bootstrap values (100 replications) for key nodes are shown. A distance bar is shown below the tree. Lineage A became extinct in 1998 about the same time lineages B and C appeared. No examples of lineage B have been recovered since 2002, but lineage C still circulated in 2008. Lineage D, first detected in 2006, also still circulated in 2008. For the purposes of analysis, lineages A and B are considered to have become extinct in 1998 and 2002, respectively. Lineages C and D were deemed to be still circulating in 2008.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142473.g001: Phylogenetic analysis of the E gene haplotype and consensus sequences of DENV-1.Consensus sequences for each strain have been highlighted. Bootstrap values (100 replications) for key nodes are shown. A distance bar is shown below the tree. Lineage A became extinct in 1998 about the same time lineages B and C appeared. No examples of lineage B have been recovered since 2002, but lineage C still circulated in 2008. Lineage D, first detected in 2006, also still circulated in 2008. For the purposes of analysis, lineages A and B are considered to have become extinct in 1998 and 2002, respectively. Lineages C and D were deemed to be still circulating in 2008.
Mentions: A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences obtained from Sanger sequencing and the sequences of each constructed haplotype obtained through Roche/454 pyrosequencing, to determine any disparities (Fig 1). With the exception of the M47317 strain, each haplotype segregated with the Sanger consensus sequence of the population from which it was drawn (Fig 1). The intermediate position of the M47317consensus sequence in this tree suggests that it might have been derived from a recombinant genome (Fig 2). Alignment of the consensus nucleotide sequences of representative strains from lineage B and C with the consensus sequence for M47317 and the sequences of M47317 haplotypes, suggested a recombination break point at about nucleotide 1087. Phylogenetic trees constructed with sequences from either side of this point supported this conclusion [i.e., nt 1–1087 of the consensus sequence of M47317 segregated with those from lineage C viruses (Fig 2), while sequences 3/ to this point segregated more closely with lineage B viruses and the M47317 haplotypes]. There was no recombination observed within the sequences of M47317 haplotypes with strains from lineage A or D.

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