A new lineage nomenclature to aid genomic surveillance of dengue virus
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 assignment tools 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.
Authors
- James Siqueira Pereira (ORCID: https://orcid.org/0000-0003-1893-8956)
- Maria Carolina Elias (ORCID: https://orcid.org/0000-0002-0501-8280)
- Mariana Leguía (ORCID: https://orcid.org/0000-0002-7297-0263)
- Nathan D. Grubaugh (ORCID: https://orcid.org/0000-0003-2031-1933)
- Anderson Fernandes Brito (ORCID: https://orcid.org/0000-0001-5785-7222)
- Gabriel Luz Wallau (ORCID: https://orcid.org/0000-0002-1419-5713)
- Verity Hill (ORCID: https://orcid.org/0000-0002-3509-8146)
- Richard Steiner Salvato (ORCID: https://orcid.org/0000-0002-5701-9437)
- Chantal B. F. Vogels (ORCID: https://orcid.org/0000-0003-0027-6480)
- Igor Santana Ribeiro
- Idrissa Dieng (ORCID: https://orcid.org/0000-0002-8584-5592)
- Fernanda Marques de Souza Godinho (ORCID: https://orcid.org/0000-0002-2211-192X)
- Tatiana Schäffer Gregianini (ORCID: https://orcid.org/0000-0002-9912-9060)
- Gaspary Mwanyika (ORCID: https://orcid.org/0000-0001-5549-8393)
- Robert J. Gifford (ORCID: https://orcid.org/0000-0003-4028-9884)
- Mallery I. Breban (ORCID: https://orcid.org/0000-0002-8976-9988)
- Sophie Yacoub (ORCID: https://orcid.org/0000-0002-2910-7819)
- Túlio de Oliveira (ORCID: https://orcid.org/0000-0002-3027-5254)
- Vi Tran (ORCID: https://orcid.org/0000-0003-2901-3692)
- Chanditha Hapuarachchi
- Svetoslav Nanev Slavov (ORCID: https://orcid.org/0000-0003-0805-6140)
- Isabela Carvalho Brcko (ORCID: https://orcid.org/0000-0002-6036-520X)
- Sara Cleemput
- Christine V. F. Carrington (ORCID: https://orcid.org/0000-0001-6533-9302)
- Wim Dumon
- Luíz Carlos Júnior Alcântara (ORCID: https://orcid.org/0000-0002-6769-9931)
- Duong Thi Hue Kien
- Marta Giovanetti (ORCID: https://orcid.org/0000-0002-5849-7326)
- Nuno R. Faria
- Vagner Fonseca (ORCID: https://orcid.org/0000-0001-5521-6448)
- Suraj Jagtap (ORCID: https://orcid.org/0000-0002-3022-7236)
- Alex Ranieri Jerônimo Lima (ORCID: https://orcid.org/0000-0002-5283-7502)
- Rahul Roy (ORCID: https://orcid.org/0000-0003-3329-8803)
- Gabriela Ribeiro (ORCID: https://orcid.org/0000-0003-2987-2243)
- Edward Charles Holmes (ORCID: https://orcid.org/0000-0001-9596-3552)
- Sandra Coccuzzo Sampaio (ORCID: https://orcid.org/0000-0001-6257-3531)
- Vinícius Carius de Souza (ORCID: https://orcid.org/0000-0001-8075-3253)
- Iago Trezena Tavares De Lima
- Tuyen Huynh (ORCID: https://orcid.org/0009-0009-4878-8953)
- Kathryn A. Hanley
- Houriiyah Tegally
Institutions
- New Mexico State University (US)
- The University of Sydney (AU)
- Universidade do Estado da Bahia (BR)
- National Environment Agency (SG)
- Università Campus Bio-Medico (IT)
- Universidade de São Paulo (BR)
- University of Washington (US)
- Stellenbosch University (ZA)
- Instituto Butantan (BR)
- Taronga Conservation Society Australia (AU)
- Mbeya University of Science and Technology (TZ)
- Yale University (US)
- University of the West Indies (TT)
- Yale New Haven Health System (US)
- Emweb (Belgium) (BE)
- Instituto de Saúde (BR)
- Secretaria da Saúde (BR)
- Institut Pasteur de Dakar (SN)
- MRC University of Glasgow Centre for Virus Research (GB)
- Oxford University Clinical Research Unit (VN)
- Imperial College London (GB)
- Fundação Oswaldo Cruz (BR)
- Indian Institute of Science Bangalore (IN)
- Pontificia Universidad Católica del Perú (PE)
- Bernhard Nocht Institute for Tropical Medicine (DE)
- University of KwaZulu-Natal (ZA)
Publication Details
- Journal
- PLoS Biology
- Published
- 2024-09-16
- DOI
- https://doi.org/10.1371/journal.pbio.3002834
- Citations
- 57
- Primary Topic
- Mosquito-borne diseases and control
- Type
- article
- Field-Weighted Citation Impact
- 30.95
Funders
- American Society of Tropical Medicine and Hygiene
- Georgia Clinical and Translational Science Alliance
- European Commission
- Fundação de Amparo à Pesquisa do Estado de São Paulo
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul
- Fundação Oswaldo Cruz
- National Institutes of Health
- Horizon 2020 Framework Programme
- Pan American Health Organization
- Medical Research Council
- National Institute of Allergy and Infectious Diseases
- National Center for Advancing Translational Sciences