A new lineage nomenclature to aid genomic surveillance of dengue virus

• Verity Hill ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: verity.hill@yale.edu (VH); alex.lima@fundacaobutantan.org.br (ARJL); grubauglab@gmail.com (NDG)

  Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

  https://orcid.org/0000-0002-3509-8146

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• Sara Cleemput ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Software, Validation, Writing – original draft, Writing – review & editing

  Affiliation Emweb bv, Herent, Belgium

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• James Siqueira Pereira ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Software, Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Robert J. Gifford,

  Roles Software, Writing – review & editing

  Affiliations MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom, Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa

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• Vagner Fonseca,

  Roles Software

  Affiliations Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa, Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil

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• Houriiyah Tegally,

  Roles Writing – review & editing

  Affiliation KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa

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• Anderson F. Brito,

  Roles Resources, Writing – review & editing

  Affiliation Instituto Todos pela Saúde, São Paulo, Brazil

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• Gabriela Ribeiro,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Vinicius Carius de Souza,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Isabela Carvalho Brcko,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Igor Santana Ribeiro,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

  ⨯
• Iago Trezena Tavares De Lima,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Svetoslav Nanev Slavov,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

  ⨯
• Sandra Coccuzzo Sampaio,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Maria Carolina Elias,

  Roles Writing – review & editing

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

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• Vi Thuy Tran,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliation Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

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• Duong Thi Hue Kien,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliation Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

  ⨯
• Tuyen Huynh,

  Roles Data curation, Investigation, Resources

  Affiliation Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

  ⨯
• Sophie Yacoub,

  Roles Investigation, Resources, Writing – review & editing

  Affiliation Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

  ⨯
• Idrissa Dieng,

  Roles Writing – review & editing

  Affiliation Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal

  ⨯
• Richard Salvato,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliation Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil

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• Gabriel Luz Wallau,

  Roles Data curation, Investigation, Resources, Writing – review & editing

  Affiliations Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, 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

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• Tatiana S. Gregianini,

  Roles Data curation, Investigation, Resources

  Affiliation Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil

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• Fernanda M. S. Godinho,

  Roles Data curation, Investigation, Resources

  Affiliation Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil

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• Chantal B. F. Vogels,

  Roles Data curation, Investigation, Writing – review & editing

  Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

  ⨯
• Mallery I. Breban,

  Roles Data curation, Investigation

  Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

  ⨯
• Mariana Leguia,

  Roles Writing – review & editing

  Affiliation Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru

  ⨯
• Suraj Jagtap,

  Roles Writing – review & editing

  Affiliation Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India

  ⨯
• Rahul Roy,

  Roles Writing – review & editing

  Affiliations Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India, Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India

  ⨯
• Chanditha Hapuarachchi,

  Roles Writing – review & editing

  Affiliation Environmental Health Institute, National Environment Agency, Singapore

  ⨯
• Gaspary Mwanyika,

  Roles Writing – review & editing

  Affiliations Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa, Department of Applied Sciences, Mbeya University of Science and Technology (MUST), Mbeya, Tanzania

  ⨯
• Marta Giovanetti,

  Roles Writing – review & editing

  Affiliations Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Roma, Italy, Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil, Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil

  ⨯
• Luiz C. J. Alcantara,

  Roles Writing – review & editing

  Affiliations Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil, Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil

  ⨯
• Nuno R. Faria,

  Roles Writing – review & editing

  Affiliations MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, United Kingdom, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil

  ⨯
• Christine V. F. Carrington,

  Roles Writing – review & editing

  Affiliation Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago

  ⨯
• Kathryn A. Hanley,

  Roles Writing – review & editing

  Affiliation Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America

  ⨯
• Edward C. Holmes,

  Roles Writing – review & editing

  Affiliation Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia

  ⨯
• Wim Dumon ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Software, Supervision, Validation, Writing – review & editing

  Affiliation Emweb bv, Herent, Belgium

  ⨯
• Alex Ranieri Jerônimo Lima ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Software, Supervision, Writing – review & editing

  * E-mail: verity.hill@yale.edu (VH); alex.lima@fundacaobutantan.org.br (ARJL); grubauglab@gmail.com (NDG)

  Affiliation Centro para Vigilância Viral e Avaliação Sorológica (CeVIVAS), Instituto Butantan, São Paulo, Brazil

  ⨯
• Tulio de Oliveira ,

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Supervision, Writing – review & editing

  Affiliations Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa, KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa, Department of Global Health, University of Washington, Seattle, Washington, United States of America

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•  [ ... ],
• Nathan D. Grubaugh

  Contributed equally to this work with: Verity Hill, Sara Cleemput, James Siqueira Pereira, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

  Roles Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: verity.hill@yale.edu (VH); alex.lima@fundacaobutantan.org.br (ARJL); grubauglab@gmail.com (NDG)

  Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America

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