Dynamic DEVILS (Dengue Evolutionary Viral Intra-genotype Lineage System) - A Systematic Lineage Classification Below the Genotype Level for Dengue Serotypes (1, 2, 3 and 4)
This repository contains the result of using a semi-automatic workflow for classifying Dengue virus (DENV) based on complete genome sequences. It addresses the current limitations in sub-genotype classification, offering a more granular and standardized system compared to traditional methods. Check our preprint at https://doi.org/10.1101/2024.03.25.586629
See the lattest version of DyDEVILS on our lab repository page!
To promote the widespread adoption of the proposed DENV lineage classification system, dedicated Nextclade datasets for DENV-1, DENV-2, DENV-3, and DENV-4 were constructed.
Users can download the datasets from this repository, located in the folder Nextclade_V3_data, to perform offline analysis using Nextclade CLI V3.3.1.
Users can propose new lineages following these steps.
- Apply the proposed DENV lineage classification system to DENV-3 and DENV-4. This expansion will create a comprehensive framework for DENV lineage designation encompassing all four serotypes.
- Integration with the Viral Identification Pipeline for Emergency Response (VIPER) assembly pipeline is planned.
- Upgrade datasets to ensure compatibility with Nextclade V3.
- Add lineage cladogram for better lineage system visualization.
Dynamic DEVILS was developed by CeVIVAS bioinformatics team at the Butantan Institute:
- James Siqueira Pereira
- Vinicius Carius De Souza
- Gabriela Ribeiro
- Isabela Carvalho Brcko
- Igor Santana Ribeiro
- Iago Trezena Tavares De Lima
Suppervised by:
- Alex Ranieri J. Lima
- Svetoslav Nanev Slavov
- Maria Carolina Quartim Barbosa Elias Sabbaga
- Sandra Coccuzzo Sampaio
Dynamic DEVILS was developed using free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
Dynamic DEVILS is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details: http://www.gnu.org/licenses/.
Funding for this work was provided by Fundação Butantan and the São Paulo Research Foundation (FAPESP) through grant number 21/11944-6, titled "Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS)". We express our sincere gratitude to all researchers who deposited their sequences on GISAID, particularly those affiliated with the Central Public Health Laboratories (LACEN) from the Brazilian States of Alagoas, Minas Gerais, Pará, and Paraná. We are also grateful to São Paulo City Hall. These partners are instrumental to the success of the CeVIVAS project.