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

[ammaraziz]

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

[j23414]

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.

[Rohit-Satyam]

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.

1. A new lineage nomenclature to aid genomic surveillance of dengue virus

2. Proposing a Systematic Lineage Classification Below the Genotype Level for Dengue Serotypes 1 and 2