Hill, V and Cleemput, S and Pereira, JS and Gifford, RJ and Fonseca, V and Tegally, H and Brito, AF and Ribeiro, G and de Souza, VC and Brcko, IC and Ribeiro, IS and De Lima, ITT and Slavov, SN and Sampaio, SC and Elias, MC and Tran, VT and Kien, DTH and Huynh, T and Yacoub, S and Dieng, I and Salvato, R and Wallau, GL and Gregianini, TS and Godinho, FMS and Vogels, CBF and Breban, MI and Leguia, M and Jagtap, S and Roy, R and Hapuarachchi, C and Mwanyika, G and Giovanetti, M and Alcantara, LCJ and Faria, NR and Carrington, CVF and Hanley, KA and Holmes, EC and Dumon, W and Jerônimo Lima, AR and de Oliveira, T and Grubaugh, ND (2024) A new lineage nomenclature to aid genomic surveillance of dengue virus. In: PLoS Biology, 22 (9).
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Abstract
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org. © 2024 Hill et al.
| Item Type: | Journal Article |
|---|---|
| Publication: | PLoS Biology |
| Publisher: | Public Library of Science |
| Additional Information: | The copyright for this article belongs to authors. |
| Keywords: | dengue vaccine, aid genomic surveillance; Article; bioinformatics; dengue; genetic distance; genetic variability; genome; genotype; human; lineage nomenclature; medical procedures; monophyly; nomenclature; phylogeny; serotype; whole genome sequencing |
| Department/Centre: | Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering Division of Mechanical Sciences > Chemical Engineering |
| Date Deposited: | 16 Oct 2024 07:54 |
| Last Modified: | 16 Oct 2024 07:54 |
| URI: | http://eprints.iisc.ac.in/id/eprint/86333 |
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