A new lineage nomenclature to aid genomic surveillance of dengue virus


Publication in PLoS Biology, new website & tools to better classify Dengue genomes for public health response.

The new nomenclaure system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals.

The system aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system.

Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. We designated an initial set of lineages based on all publicly available whole genome sequences with coverage greater than 70% in mid-2023.

We envision two ways of generating new lineage suggestions. The first is through community effort via a github repo, which is what this page is designed to help with. Here, members of the dengue research/public health community can suggest new lineages to help with their surveillance efforts. These will be reviewed with some regularity and given a 'putative' name.

The second method is an annual review, where all publicly available whole genome data is run through custom scripts to ensure that all new lineages have been identified, including appropriate putative ones suggested throughout the year. These will then be reviewed by an advisory board and assignment tools are updated.

Open Publication:

- Hill et al. PLoS Bioology 2024

Website with classification system & sequencing protocols:

- https://dengue-lineages.org/


This news piece was published in the gem, Oct/Nov 2024

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News date: 2024-10-31

Links:

https://issuu.com/the.gem/docs/3rdedition_the_gem_newsletter_a4_v2?fr=xKAE9_zU1NQ