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The Complete Genome Phylogeny of Geographically Distinct Dengue Virus Serotype 2 Isolates (1944-2013) Supports Further Groupings within the Cosmopolitan Genotype.

Ali A, Ali I - PLoS ONE (2015)

Bottom Line: A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes.Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes.Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, The University of Tulsa, Tulsa Oklahoma, 74104, United States of America.

ABSTRACT
Dengue virus serotype 2 (DENV-2) isolates have been implicated in deadly outbreaks of dengue fever (DF) and dengue hemorrhagic fever (DHF) in several regions of the world. Phylogenetic analysis of DENV-2 isolates collected from particular countries has been performed using partial or individual genes but only a few studies have examined complete whole-genome sequences collected worldwide. Herein, 50 complete genome sequences of DENV-2 isolates, reported over the past 70 years from 19 different countries, were downloaded from GenBank. Phylogenetic analysis was conducted and evolutionary distances of the 50 DENV-2 isolates were determined using maximum likelihood (ML) trees or Bayesian phylogenetic analysis created from complete genome nucleotide (nt) and amino acid (aa) sequences or individual gene sequences. The results showed that all DENV-2 isolates fell into seven main groups containing five previously defined genotypes. A Cosmopolitan genotype showed further division into three groups (C-I, C-II, and C-III) with the C-I group containing two subgroups (C-IA and C-IB). Comparison of the aa sequences showed specific mutations among the various groups of DENV-2 isolates. A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes. Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes. Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic maximum-likelihood trees of DENV-2 ORF nucleotide sequences.Trees were constructed using MEGAV5.05 software with bootstrap support of 1000 replicates. All sequences of the ORF were manually separated from the whole-genome sequences that were downloaded from the GenBank database for analysis. The phylogenetic tree was constructed using the GTR model.
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pone.0138900.g003: Phylogenetic maximum-likelihood trees of DENV-2 ORF nucleotide sequences.Trees were constructed using MEGAV5.05 software with bootstrap support of 1000 replicates. All sequences of the ORF were manually separated from the whole-genome sequences that were downloaded from the GenBank database for analysis. The phylogenetic tree was constructed using the GTR model.

Mentions: Phylogenetic analysis of all 50 isolates based on complete ORFs showed almost exactly the same results as obtained on the basis of entire genome nucleotide sequences (Fig 3). The topology of the ORF-based tree was highly similar to the complete genome nt or aa trees and showed the same distribution of DENV-2 types (Fig 3).


The Complete Genome Phylogeny of Geographically Distinct Dengue Virus Serotype 2 Isolates (1944-2013) Supports Further Groupings within the Cosmopolitan Genotype.

Ali A, Ali I - PLoS ONE (2015)

Phylogenetic maximum-likelihood trees of DENV-2 ORF nucleotide sequences.Trees were constructed using MEGAV5.05 software with bootstrap support of 1000 replicates. All sequences of the ORF were manually separated from the whole-genome sequences that were downloaded from the GenBank database for analysis. The phylogenetic tree was constructed using the GTR model.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4587552&req=5

pone.0138900.g003: Phylogenetic maximum-likelihood trees of DENV-2 ORF nucleotide sequences.Trees were constructed using MEGAV5.05 software with bootstrap support of 1000 replicates. All sequences of the ORF were manually separated from the whole-genome sequences that were downloaded from the GenBank database for analysis. The phylogenetic tree was constructed using the GTR model.
Mentions: Phylogenetic analysis of all 50 isolates based on complete ORFs showed almost exactly the same results as obtained on the basis of entire genome nucleotide sequences (Fig 3). The topology of the ORF-based tree was highly similar to the complete genome nt or aa trees and showed the same distribution of DENV-2 types (Fig 3).

Bottom Line: A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes.Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes.Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, The University of Tulsa, Tulsa Oklahoma, 74104, United States of America.

ABSTRACT
Dengue virus serotype 2 (DENV-2) isolates have been implicated in deadly outbreaks of dengue fever (DF) and dengue hemorrhagic fever (DHF) in several regions of the world. Phylogenetic analysis of DENV-2 isolates collected from particular countries has been performed using partial or individual genes but only a few studies have examined complete whole-genome sequences collected worldwide. Herein, 50 complete genome sequences of DENV-2 isolates, reported over the past 70 years from 19 different countries, were downloaded from GenBank. Phylogenetic analysis was conducted and evolutionary distances of the 50 DENV-2 isolates were determined using maximum likelihood (ML) trees or Bayesian phylogenetic analysis created from complete genome nucleotide (nt) and amino acid (aa) sequences or individual gene sequences. The results showed that all DENV-2 isolates fell into seven main groups containing five previously defined genotypes. A Cosmopolitan genotype showed further division into three groups (C-I, C-II, and C-III) with the C-I group containing two subgroups (C-IA and C-IB). Comparison of the aa sequences showed specific mutations among the various groups of DENV-2 isolates. A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes. Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes. Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.

No MeSH data available.


Related in: MedlinePlus