Molecular genotyping of dengue viruses by phylogenetic analysis of the sequences of individual genes

The prevalence of four serotypes of dengue virus (DENV) has risen dramatically in recent years accompanied by an increase in viral genetic diversity. The evolution of DENV has had a major impact on their virulence for humans and on the epidemiology of dengue disease around the world. In order to per...

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Bibliographic Details
Published in:Journal of virological methods 2008-12, Vol.154 (1), p.175-181
Main Authors: Klungthong, C., Putnak, R., Mammen, M.P., Li, T., Zhang, C.
Format: Article
Language:English
Subjects:
3' Untranslated Regions
Biological and medical sciences
Cluster Analysis
Dengue virus
Dengue Virus - classification
Dengue Virus - genetics
Dengue viruses
Diversity
Fundamental and applied biological sciences. Psychology
Genotype
Genotyping
Humans
Individual genes
Microbiology
Phylogeny
RNA, Viral - genetics
Sequence Analysis, DNA
Techniques used in virology
Viral Proteins - genetics
Virology
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Summary:The prevalence of four serotypes of dengue virus (DENV) has risen dramatically in recent years accompanied by an increase in viral genetic diversity. The evolution of DENV has had a major impact on their virulence for humans and on the epidemiology of dengue disease around the world. In order to perform disease surveillance and understand DENV evolution and its effects on virus transmission and disease, an efficient and accurate method for genotype identification is required. Phylogenetic analysis of viral gene sequences is the method used most commonly, with envelope (E) gene the most frequently selected target. To determine which gene might be suitable targets for genotyping DENV, phylogenetic analysis was performed on 10 individual coding genes plus the 3′-non-translated region (3′NTR) for 56 geographically divergent DENV strains representing all identified genotypes. These were reflected in eleven maximum likelihood phylogenetic trees. Based on the bootstrap values (over 90%) supporting the major nodes, the best target genes were identified for each serotype: for DENV-1, the sequences of all coding genes except non-structural gene 4A (NS4A), for DENV-2, PrM/M, E, NS1, NS3, NS4A and NS5, for DENV-3, all coding genes and the 3′NTR, and for DENV-4, C, PrM/M, E, NS1, NS2A, NS2B, NS4A and NS5.
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2008.07.021