A new lineage nomenclature to aid genomic surveillance of dengue virus
| Main Author: | |
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| Publication Date: | 2024 |
| Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | eng |
| Source: | Repositório Institucional da FIOCRUZ (ARCA) |
| DOI: | 10.1101/2024.05.16.24307504 |
| Download full: | https://arca.fiocruz.br/handle/icict/64650 |
Summary: | Department of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA. |
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Hill, VerityCleemput, SaraFonseca, VagnerTegally, HouriiyahBrito, Anderson F.Gifford, RobertTran, Vi ThuyKien, Duong Thi HueHuynh, TuyenYacoub, SophieDieng, IdrissaNdiaye, MignaneBalde, DiamilatouDiagne, Moussa M.Faye, OumarSalvato, RichardWallau, Gabriel LuzGregianini, Tatiana S.Godinho, Fernanda M. S.Vogels, Chantal B. F.Breban, Mallery I.Leguia, MarianaJagtap, SurajRoy, RahulHapuarachchi, ChandithaMwanyika, GasparyGiovanetti, MartaAlcantara, Luiz C. J.Faria, Nuno R.Carrington, Christine V. F.Hanley, Kathryn A.Holmes, Edward C.Dumon, WimOliveira, Tulio deGrubaugh, Nathan D.2024-06-25T15:43:21Z2024-06-25T15:43:21Z2024HILL, Verity et al. A new lineage nomenclature to aid genomic surveillance of dengue virus. medRxiv, p. 2024-2025, May 2024.https://arca.fiocruz.br/handle/icict/6465010.1101/2024.05.16.24307504engCold Spring Harbor LaboratoryA new lineage nomenclature to aid genomic surveillance of dengue virusinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleDepartment of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA.Emweb bv. Herent, Belgium.Department of Exact and Earth Sciences. University of the State of Bahia. Salvador, BA, Brazil / Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R. Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa.Instituto Todos pela Saúde. São Paulo, SP, Brazil.Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa / MRC-University of Glasgow Centre for Virus Research. Bearsden, Glasgow, UK.Oxford University Clinical Research Unit. Ho Chi Minh City, Vietnam.Oxford University Clinical Research Unit. Ho Chi Minh City, Vietnam.Oxford University Clinical Research Unit. Ho Chi Minh City, Vietnam.Oxford University Clinical Research Unit. Ho Chi Minh City, Vietnam.Arboviruses and Haemorrhagic Fever Viruses Unit. Virology Department. Institut Pasteur de Dakar. Dakar, Senegal.Arboviruses and Haemorrhagic Fever Viruses Unit. Virology Department. Institut Pasteur de Dakar. Dakar, Senegal.Arboviruses and Haemorrhagic Fever Viruses Unit. Virology Department. Institut Pasteur de Dakar. Dakar, Senegal.Arboviruses and Haemorrhagic Fever Viruses Unit. Virology Department. Institut Pasteur de Dakar. Dakar, Senegal.Arboviruses and Haemorrhagic Fever Viruses Unit. Virology Department. Institut Pasteur de Dakar. Dakar, Senegal.Estado do Rio Grande do Sul. Secretaria Estadual de Saúde. Centro de Vigilância em Saúde. Porto Alegre, RS, Brazil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Entomologia. Recife, PE, Brazil / Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine. WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference. Hamburg, Germany / National Reference Center for Tropical Infectious Diseases. Bernhard, Hamburg, Germany.Estado do Rio Grande do Sul. Secretaria Estadual de Saúde. Centro de Vigilância em Saúde. Porto Alegre, RS, Brazil.Estado do Rio Grande do Sul. Secretaria Estadual de Saúde. Centro de Vigilância em Saúde. Porto Alegre, RS, Brazil.Department of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA.Department of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA.Genomics Laboratory. Pontificia Universidad Católica del Peru. Lima, Peru.Department of Chemical Engineering. Indian Institute of Science. Bengaluru, Karnataka, India.Department of Chemical Engineering. Indian Institute of Science. Bengaluru, Karnataka, India/Center for BioSystems Science and Engineering. Indian Institute of Science. Bengaluru, Karnataka, India.Environmental Health Institute. National Environment Agency. Singapore.Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa / Department of Applied Sciences. Mbeya University of Science and Technology. Mbeya, Tanzania.Department of Sciences and Technologies for Sustainable Development and One Health. Universita Campus Bio-Medico. Roma, Italy / Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Climate Amplified Diseases and Epidemics. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil / Climate Amplified Diseases and Epidemics. Belo Horizonte, MG, Brazil.MRC Centre for Global Infectious Disease Analysis. Jameel Institute. Imperial College London. London, UK / Instituto de Medicina Tropical. Faculdade de Medicina da Universidade de São Paulo. São Paulo, SP, Brazil.Department of Preclinical Sciences. The University of the West Indies. St. Augustine, Trinidad and Tobago.Department of Biology. New Mexico State University. Las Cruces, New Mexico, USA.Sydney Institute for Infectious Diseases. School of Medical Sciences. The University of Sydney. Sydney, Australia.Emweb bv. Herent, Belgium.Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa / KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R. Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa / Department of Global Health. University of Washington. Seattle, WA, USA.Department of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA / Public Health Modeling Unit. Yale School of Public Health. New Haven, CT, USA / Department of Ecology and Evolutionary Biology. Yale University. New Haven, CT, USA.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 two 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 sub-national 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.Dengue virusDengue virus (DENV)Genomic surveillanceVirus classificationinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://arca.fiocruz.br/bitstreams/4a958d7e-405e-465a-9c9b-4799fb7b1855/download5a560609d32a3863062d77ff32785d58MD51falseAnonymousREADORIGINALA new lineage nomenclature to aid genomic.pdfA new lineage nomenclature to aid genomic.pdfapplication/pdf3047031https://arca.fiocruz.br/bitstreams/0a63a4e8-1ee9-4448-a8fe-9dc7c1d1975f/download259a180fb0b1d076ceb352e7dde2f8dfMD52trueAnonymousREAD2150-12-31TEXTA new lineage nomenclature to aid genomic.pdf.txtA new lineage nomenclature to aid genomic.pdf.txtExtracted texttext/plain100799https://arca.fiocruz.br/bitstreams/d5cef24b-0fc6-4a64-9284-c8487b84b7c2/download177f1a0260d35d95b76e71b6bd40b5bdMD57falseAnonymousREAD2150-12-31THUMBNAILA new lineage nomenclature to aid genomic.pdf.jpgA new lineage nomenclature to aid genomic.pdf.jpgGenerated Thumbnailimage/jpeg5568https://arca.fiocruz.br/bitstreams/96f4321d-ed27-455b-8439-6eed6ab44376/downloadf47004123dcabd16670d3c02a46dcdf0MD58falseAnonymousREAD2150-12-31icict/646502025-08-04 23:45:36.226embargo2150-12-31oai:arca.fiocruz.br:icict/64650https://arca.fiocruz.brRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352025-08-05T02:45:36Repositório Institucional da FIOCRUZ (ARCA) - 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A new lineage nomenclature to aid genomic surveillance of dengue virus |
| title |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| spellingShingle |
A new lineage nomenclature to aid genomic surveillance of dengue virus Hill, Verity Dengue virus Dengue virus (DENV) Genomic surveillance Virus classification |
| title_short |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| title_full |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| title_fullStr |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| title_full_unstemmed |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| title_sort |
A new lineage nomenclature to aid genomic surveillance of dengue virus |
| author |
Hill, Verity |
| author_facet |
Hill, Verity Cleemput, Sara Fonseca, Vagner Tegally, Houriiyah Brito, Anderson F. Gifford, Robert Tran, Vi Thuy Kien, Duong Thi Hue Huynh, Tuyen Yacoub, Sophie Dieng, Idrissa Ndiaye, Mignane Balde, Diamilatou Diagne, Moussa M. Faye, Oumar 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 Oliveira, Tulio de Grubaugh, Nathan D. |
| author_role |
author |
| author2 |
Cleemput, Sara Fonseca, Vagner Tegally, Houriiyah Brito, Anderson F. Gifford, Robert Tran, Vi Thuy Kien, Duong Thi Hue Huynh, Tuyen Yacoub, Sophie Dieng, Idrissa Ndiaye, Mignane Balde, Diamilatou Diagne, Moussa M. Faye, Oumar 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 Oliveira, Tulio de Grubaugh, Nathan D. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Hill, Verity Cleemput, Sara Fonseca, Vagner Tegally, Houriiyah Brito, Anderson F. Gifford, Robert Tran, Vi Thuy Kien, Duong Thi Hue Huynh, Tuyen Yacoub, Sophie Dieng, Idrissa Ndiaye, Mignane Balde, Diamilatou Diagne, Moussa M. Faye, Oumar 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 Oliveira, Tulio de Grubaugh, Nathan D. |
| dc.subject.en.none.fl_str_mv |
Dengue virus Dengue virus (DENV) Genomic surveillance Virus classification |
| topic |
Dengue virus Dengue virus (DENV) Genomic surveillance Virus classification |
| description |
Department of Epidemiology of Microbial Diseases. Yale School of Public Health. New Haven, CT, USA. |
| publishDate |
2024 |
| dc.date.accessioned.fl_str_mv |
2024-06-25T15:43:21Z |
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2024-06-25T15:43:21Z |
| dc.date.issued.fl_str_mv |
2024 |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
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HILL, Verity et al. A new lineage nomenclature to aid genomic surveillance of dengue virus. medRxiv, p. 2024-2025, May 2024. |
| dc.identifier.uri.fl_str_mv |
https://arca.fiocruz.br/handle/icict/64650 |
| dc.identifier.doi.none.fl_str_mv |
10.1101/2024.05.16.24307504 |
| identifier_str_mv |
HILL, Verity et al. A new lineage nomenclature to aid genomic surveillance of dengue virus. medRxiv, p. 2024-2025, May 2024. 10.1101/2024.05.16.24307504 |
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https://arca.fiocruz.br/handle/icict/64650 |
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eng |
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openAccess |
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Cold Spring Harbor Laboratory |
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Cold Spring Harbor Laboratory |
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