Switch DENV2 genotypes to numeric to be consistent with DENV1, 3, and 4

nextstrain / dengue

Nextstrain build for dengue virus

https://nextstrain.org/dengue

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Switch DENV2 genotypes to numeric to be consistent with DENV1, 3, and 4 #32

Open j23414 opened 4 months ago

j23414 commented 4 months ago

Context

In response to comment: https://github.com/nextstrain/dengue/issues/28#issuecomment-1956937534

DENV2/AA --> DENV2/III
DENV2/AI --> DENV2/V 
DENV2/AM --> DENV2/I
DENV2/C --> DENV2/II
DENV2/S --> DENV2/VI
DENV4/S --> DENV4/IV

One modification is to keep the S groups, since S=Sylvatic.

Description

Transition to using numeric lineage labels, and less geography-tied naming conventions.

DENV2/AA --> DENV2/III
DENV2/AI --> DENV2/V 
DENV2/AM --> DENV2/I
DENV2/C --> DENV2/II

Before implementing this, check if this is standard in the literature or will cause any confusion.

Examples

Possible solution

(Optional)

j23414 commented 3 months ago

Thanks @ckikawa for pointing to the paper:

Cuypers, L., Libin, P.J., Simmonds, P., Nowé, A., Muñoz-Jordán, J., Alcantara, L.C.J., Vandamme, A.M., Santiago, G.A. and Theys, K., 2018. Time to harmonize dengue Nomenclature and classification. Viruses, 10(10), p.569.

ammaraziz commented 3 months ago

Hi @j23414

I've only just started working on Dengue viruses very recently. Looking for a genotyping tool I came across the unreleased nextclade dataset and also another tool (Genome Detective).

So we're all on the same page, these:

DENV2/AA --> DENV2/III
DENV2/AI --> DENV2/V 
DENV2/AM --> DENV2/I
DENV2/C --> DENV2/II

Are referred to as genotypes.

The reason for the correction is because there are 'major' lineages ('subgenotypes') referenced in the literature: https://www.mdpi.com/1999-4915/12/8/829

If this is within scope of this project, I could assist with generating lineages.

Thanks,

Ammar

Rohit-Satyam commented 3 weeks ago

Hi, there are two recent publications that I read recently that are proposing to extend the dengue classification further from serotype and genotype by splitting genotypes into major and minor lineages. Please take out time to read these two and if we can adopt this nomenclature to avoid confusion in future.