Time to Harmonize Dengue Nomenclature and Classification
Abstract
:1. Letter
- (a)
- The phylogenetic signal of the different DENV genes was assessed (see Supporting Information: Figure S1a). This signal is a measure of statistical dependence among species due to their phylogenetic relationships and is associated with the accuracy of phylogenetic studies [23]. The results of this analysis indicate that only parts of the DENV genome are suitable to classify sequences, at genotype and sub-genotype level, with high confidence. Although the envelope gene region is most often used for classification purposes, given its historical, diagnostic and functional importance, our evaluation shows that other genetic regions, such as NS1, NS3, and NS5 exhibit higher phylogenetic support. Whole-genome sequences provide superior classification precision and their availability is expected to increase in the near future when next-generation sequencing becomes routine practice, which will create an opportunity to harmonize DENV classification. Therefore, a detailed analysis of the classification potential of different genomic regions (as well as combinations of such genomic regions) is imperative to propose an adequate classification protocol.
- (b)
- We identified that particular clades are not clustering consistently over the entire genome and established these to be clades with a potential recombinant origin (see Supplementary Materials: Figure S1b). This highlights the need for any future classification protocol to assess the recombination signal of strains by identifying recombinant breakpoints prior to their classification. In addition, it illustrates the necessity to carefully select reference strains to perform consistent and sound classifications, in contrast to the widespread ad hoc classification in much of the current literature.
- (c)
- Certain whole-genome strains do not cluster with any known genotype. As we verified that these strains are not inter-genotypic recombinants (for details see Supplementary Materials: “Dataset and alignment” section), these strains appear to be outliers that the currently described genotypes fail to cover (see Supplementary Materials: Figure S1c and Table S1). To improve our understanding of their origin and whether these outliers indicate the source of novel genotypic or sub-genotypic clades, an in-depth analysis considering both a representative dataset and formal genotype definition is warranted.
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Cuypers, L.; Libin, P.J.K.; Simmonds, P.; Nowé, A.; Muñoz-Jordán, J.; Alcantara, L.C.J.; Vandamme, A.-M.; Santiago, G.A.; Theys, K. Time to Harmonize Dengue Nomenclature and Classification. Viruses 2018, 10, 569. https://doi.org/10.3390/v10100569
Cuypers L, Libin PJK, Simmonds P, Nowé A, Muñoz-Jordán J, Alcantara LCJ, Vandamme A-M, Santiago GA, Theys K. Time to Harmonize Dengue Nomenclature and Classification. Viruses. 2018; 10(10):569. https://doi.org/10.3390/v10100569
Chicago/Turabian StyleCuypers, Lize, Pieter J. K. Libin, Peter Simmonds, Ann Nowé, Jorge Muñoz-Jordán, Luiz Carlos Junior Alcantara, Anne-Mieke Vandamme, Gilberto A. Santiago, and Kristof Theys. 2018. "Time to Harmonize Dengue Nomenclature and Classification" Viruses 10, no. 10: 569. https://doi.org/10.3390/v10100569