Dengue Virus Typing Tool

Start using our new user interface: Genome Detective Platform

Introduction

This tool provides three levels of classification of dengue virus: serotype, genotype and major lineage. The serotype is determined based on a blast analysis against the reference sequences for the different serotypes. The genotype and major lineage are determined based on phylogenetic analysis.

The definition of a dengue genotype is based on a diversity of variables, e.g., monophyly, pairwise distance within and between groups, net genetic diversity within groups, etc. For each genotype we have carefully selected reference sequences that represent its diversity. In addition, we performed extensive testing to be sure that our reference strains accurately classify other sequences. Since tool version 4.0 we have slightly expanded the genotypes by pulling back the defining node closer to the root, so that less sequences are unassigned.

We include serotypes 1, 2, 3 and 4.
Serotype 1 includes 1I ,1II, 1III, 1IV and 1V genotypes, and a newly defined 1 VI genotype.
Serotype 2 includes 2I, 2II, 2III, 2IV, 2V and 2VI genotypes.
Serotype 3 includes 3I, 3II, 3III and 3V genotypes.
Serotype 4 includes 4I, 4II, 4III and 4IV genotypes.

In addition to the genotypes, we have also added an additional layer of classification, proposed in a manuscript currently under preparation. Major lineages are based on phylogenetic distance, monophyly, and the size of the clade. There are a handful of major lineages in most (not all) genotypes, denoted using latin letters, e.g. 2II_A is major lineage A in genotype II serotype 2. We do skip I and V to avoid confusion because these are used in genotype designations. Importantly these lineages are neutral descriptors of diversity, and aim to provide additional temporal and spatial granularity to the spread of dengue virus globally, as well as standardise the discussion of important diversity. There are also minor lineages in this system, denoted by dots and numbers (e.g. 2II_A.1.2), but these are not yet identified by the current version of the Genome Detective dengue tool.

Serotype 1

Genotype I: A-K
Genotype III: A and B
Genotype IV: A-C
Genotype V: A-G
Genotype VI: A and B

Serotype 2

Genotype II: A-F
Genotype III: A-D
Genotype V: A-E

Serotype 3

Genotype I: A-C
Genotype II: A and B
Genotype III: A-C

Serotype 4

Genotype I: A and B
Genotype II: A and B

Fig. 1. Dengue virus 1 phylogenetic tree

Fig. 2. Dengue virus 2 phylogenetic tree

Fig. 3. Dengue virus 3 phylogenetic tree

Fig. 4. Dengue virus 4 phylogenetic tree

This lineage system has been a wide global collaborative effort, and so we thank everyone who has provided input, feedback and data.

There is broad consensus that the envelope glycoprotein gene (E) is suitable for phylogenetic classification, since it contains sufficient phylogenetic signal (1,485bp) to distinguish dengue from other viruses and differentiate between serotypes and genotypes. Phylogenetic trees inferred with E gene sequence data generate topologies very similar to whole genome trees. Therefore, investigators working with dengue sequences can expect similar classification accuracy when using either WGS or E gene for both genotype and major lineage.

In past versions of the Genome Detective dengue tool DENV-2 genotypes were also named based on geographic associations. Since dengue has spread considerably beyond the old geographic association, we find that using only roman numerals (i.e. I, II, III, etc.) is more appropriate. Moreover, a numeral system helps to stay in structure with new diverging lineages and genotypes. For reference, the geographic association names for DENV-2 correspond to the currently used genotype names as follows:

Genotype I - American
Genotype II - Cosmopolitan
Genotype III - Southern Asian-American
Genotype IV - Asian II
Genotype V - Asian I
Genotype VI - Sylvatic

Acknowledgements

Developed by: FIOCRUZ, Brazil (Vagner Fonseca, Marta Giovanetti, Maria Inês Restovic, Murilo Freire, Luiz Alcantara), KU Leuven, Belgium (Kristof Theys, Pieter Libin, Lize Cuypers, Ana Abecasis, Anne-Mieke Vandamme), University of Oxford, U.K. (Nuno Faria and Oliver Pybus), Evandro Chagas Institute, Pará, Brazil (Marcio Roberto Teixeira Nunes), CDC/OID/NCEZID (Gilberto A. Santiago), Emweb bvba, Belgium (Koen Deforche, Sara Cleemput), Krisp/UKZN, South Africa (Tulio de Oliveira), and Yale School of Public Health, USA (Verity Hill, Nathan Grubaugh).

Software: Genome Detective

Contact: Vagner Fonseca, Dr. Luiz Alcantara and/or Prof. Tulio de Oliveira