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Review
. 2018 Aug:62:279-295.
doi: 10.1016/j.meegid.2018.04.032. Epub 2018 Apr 25.

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

S Pollett  1 , M C Melendrez  2 , I Maljkovic Berry  2 , S Duchêne  3 , H Salje  4 , D A T Cummings  5 , R G Jarman  2
Affiliations
Review

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development

S Pollett et al. Infect Genet Evol. 2018 Aug.

Abstract

Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.

Keywords: Dengue virus; Evolution; Molecular epidemiology; Phylogenetics.

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Conflict of interest statement

Conflicts of interest

The authors declare no conflicts of interest

Figures

Figure 1.
Figure 1.. Dengue virus genome protein structures with corresponding proteome diversity across serotypes 1 −4.
Vertical axis represents Shannon entropy values, as derived from curated DENV proteomes published at FlaviDB (http://cvc.dfci.harvard.edu/flavi/). Figure abbreviations: C = capsid protein, prM = pre-cursor membrane protein, E = envelope protein, NS1 = non-structural protein 1, NS2A = non-structural protein 2A, NS2B = non-structural protein 2B, NS3 = non-structural protein 3, NS4A = non-structural protein 4A, 2K = 2K fragment at C-terminus of NS4A, NS4B = non-structural protein 4B, NS5 = non-structural protein 5.
Fig 2.
Fig 2.. Taxonomy and population structure of DENV serotype 1.
Legend indicates genotypes. Inferred by maximum likelihood method using RAxML and all published full env-gene sequences from DENV infections occurring 1943 through 2016 (n = 4018). Rooted by sylvatic genotype. Scale refers to nucleotide substitutions/site. Numbers correspond to bootstrap values for genotype-defining branch support. Recombinants and highly divergent sequences suggestive of dating/sequencing errors or laboratory contaminants were removed after analysis by RDP4 and Temp_est respectively.
Fig 3.
Fig 3.. Taxonomy and population structure of DENV serotype 2.
Legend indicates genotypes. Inferred by maximum likelihood method using PhyML using 3112 full env-gene sequences from infections occurring 1944 through 2016. Rooted by sylvatic genotype. Scale refers to nucleotide substitutions/site. Numbers correspond to aLRT values for genotype-defining branch support. Recombinants and highly divergent sequences suggestive of dating/sequencing errors or laboratory contaminants were removed after analysis by RDP4 and Temp-est respectively.
Fig 4.
Fig 4.. Taxonomy and population structure of DENV serotype 3.
Legend indicates genotypes. Inferred by maximum likelihood method using PhyML and all full env-gene sequences from infections occurring 1956 through 2016 (n = 1840). Rooted by genotype IV. Scale refers to nucleotide substitutions/site. Numbers correspond to aLRT values for genotype-defining branch support. Recombinants and highly divergent sequences suggestive of dating/sequencing errors or laboratory contaminants were removed after analysis by RDP4 and Temp_est respectively.
Fig 5.
Fig 5.. Taxonomy and population structure of DENV serotype 4.
Legend indicates genotypes. Inferred by maximum likelihood method using PhyML and all published full env-gene sequences from infections across 1956 through 2016 (n = 1297). Rooted by sylvatic genotype. Scale refers to nucleotide substitutions/site. Numbers correspond to aLRT values for genotype-defining branch support. Recombinants and highly divergent sequences suggestive of dating/sequencing errors or laboratory contaminants were removed after analysis by RDP4 and Temp_est respectively.
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