A new lineage nomenclature to aid genomic surveillance of dengue virus

Author(s):Show less -

Hill, Verity ; Cleemput, Sara ; Pereira, James Siqueira ; Gifford, Robert J. ; Fonseca, Vagner ; Tegally, Houriiyah ; Brito, Anderson F. ; Ribeiro, Gabriela ; de Souza, Vinicius Carius ; Brcko, Isabela Carvalho ; Ribeiro, Igor Santana ; De Lima, Iago Trezena Tavares ; Slavov, Svetoslav Nanev ; Sampaio, Sandra Coccuzzo ; Elias, Maria Carolina ; Tran, Vi Thuy ; Kien, Duong Thi Hue ; Huynh, Tuyen ; Yacoub, Sophie ; Dieng, Idrissa ; Salvato, Richard ; Wallau, Gabriel Luz ; Gregianini, Tatiana S. ; Godinho, Fernanda M. S. ; Vogels, Chantal B. F. ; Breban, Mallery I. ; Leguia, Mariana ; Jagtap, Suraj ; Roy, Rahul ; Hapuarachchi, Chanditha ; Mwanyika, Gaspary ; Giovanetti, Marta ; Alcantara, Luiz C. J. ; Faria, Nuno R. ; Carrington, Christine V. F. ; Hanley, Kathryn A. ; Holmes, Edward C. ; Dumon, Wim ; Lima, Alex Ranieri Jeronimo ; De Oliveira, Tulio ; Grubaugh, Nathan D.

• Document type: Journal article
• Source: PLOS BIOLOGY; v. 22, n. 9, p. 27-pg., 2024-09-01.

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. (AU)

• FAPESP's process: 18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 21/11944-6 - Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS)
• Grantee: Sandra Coccuzzo Sampaio Vessoni
• Support Opportunities: Research Grants - Science Centers for Development