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ZIKA VIRUS EVOLUTION AND SPREAD IN THE AMERICAS: MANUSCRIPT AUTHOR
https://www.arca.fiocruz.br/handle/icict/19083
Edson Delatorre. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, Rio de Janeiro, Brasil.
Wim Degrave. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, Rio de Janeiro, Brasil.
Patricia T. Bozza. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Imunofarmacologia. Rio de Janeiro, RJ, Brasil.
Thiago M. L. Souza. Fundação Oswaldo Cruz. Instituto Nacional de Ciência e Tecnologia sobre Inovação em Doenças Negligenciadas. Rio de Janeiro, RJ, Brasil.
Thiago M. L. Souza. Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil.
AUTHORS: Hayden C. Metsky1,2,*, Christian B. Matranga1,*, Shirlee Wohl1,3,*, Stephen F. Schaffner1,3,4,*, Catherine A. Freije1,3, Sarah M. Winnicki1, Kendra West1, James Qu1, Mary Lynn Baniecki1, Adrianne Gladden-Young1, Aaron E. Lin1,3, Christopher H. Tomkins-Tinch1, Simon H. Ye1,5, Daniel J. Park1, Cynthia Y. Luo1,3, Kayla G. Barnes1,3,4, Rickey R. Shah1,6, Bridget Chak1,3, Giselle Barbosa-Lima7, Edson Delatorre8, Yasmine R. Vieira7, Lauren M. Paul9, Amanda L. Tan9, Carolyn M. Barcellona9, Mario C. Porcelli10, Chalmers Vasquez10, Andrew C. Cannons11, Marshall R. Cone11, Kelly N. Hogan11, Edgar W. Kopp IV11, Joshua J. Anzinger12, Kimberly F. Garcia13, Leda A. Parham13, Rosa M. Gélvez Ramírez14, Maria C. Miranda Montoya14, Diana P. Rojas15, Catherine M. Brown16, Scott Hennigan16, Brandon Sabina16, Sarah Scotland16, Karthik Gangavarapu17, Nathan D. Grubaugh17, Glenn Oliveira18, Refugio Robles-Sikisaka17, Andrew Rambaut19,20, Lee Gehrke21,22, Sandra Smole16, M. Elizabeth Halloran23,24, Luis Villar14, Salim Mattar25, Ivette Lorenzana13, Jose Cerbino-Neto7, Clarissa Valim4,26, Wim Degrave27, Patricia T. Bozza28, Andreas Gnirke1, Kristian G. Andersen17,18,29,§, Sharon Isern9,§, Scott F. Michael9,§, Fernando A. Bozza7,30,§, Thiago M. L.Souza31,32,§, Irene Bosch21,§, Nathan L. Yozwiak1,3,§, Bronwyn L. MacInnis1,4,§, and Pardis C. Sabeti1,3,4,33,§ - AFFILIATIONS: Affiliations1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA2Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA5Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA6Harvard University Extension School, Cambridge, Massachusetts, USA7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil8Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA10Miami-Dade County Mosquito Control, Miami, Florida, USA11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA12Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia15Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA16Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA18Scripps Translational Science Institute, La Jolla, California, USA19Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK, 20Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA21Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA22Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA23Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA24Department of Biostatistics, University of Washington, Seattle, Washington, USA25Institute for Tropical Biology Research, Universidad de Córdoba, Montería, Córdoba, Colombia26Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michegan, USA27FIOCRUZ, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, Rio de Janeiro, Brazil28Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil29Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA30D’Or Institute for Research and Education, Rio de Janeiro, Brazil31National Institute for Science and Technology on Innovation on Neglected Diseases, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil32Center for Technological Development in Health, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil33Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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Abstract
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.
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Nature Research
Later version
Citation
METSKY, Hayden C. et al. Zika virus evolution and spread in Americas: manuscript author. Nature, v. 546, n. 7658, p. 411-415, June 2017.DOI
10.1038/nature22402ISSN
0028-0836Notes
Giselle Barbosa-Lima; Yasmine R. Vieira; Fernando A. Bozza. Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, Brasil.Edson Delatorre. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, Rio de Janeiro, Brasil.
Wim Degrave. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, Rio de Janeiro, Brasil.
Patricia T. Bozza. Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Imunofarmacologia. Rio de Janeiro, RJ, Brasil.
Thiago M. L. Souza. Fundação Oswaldo Cruz. Instituto Nacional de Ciência e Tecnologia sobre Inovação em Doenças Negligenciadas. Rio de Janeiro, RJ, Brasil.
Thiago M. L. Souza. Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil.
AUTHORS: Hayden C. Metsky1,2,*, Christian B. Matranga1,*, Shirlee Wohl1,3,*, Stephen F. Schaffner1,3,4,*, Catherine A. Freije1,3, Sarah M. Winnicki1, Kendra West1, James Qu1, Mary Lynn Baniecki1, Adrianne Gladden-Young1, Aaron E. Lin1,3, Christopher H. Tomkins-Tinch1, Simon H. Ye1,5, Daniel J. Park1, Cynthia Y. Luo1,3, Kayla G. Barnes1,3,4, Rickey R. Shah1,6, Bridget Chak1,3, Giselle Barbosa-Lima7, Edson Delatorre8, Yasmine R. Vieira7, Lauren M. Paul9, Amanda L. Tan9, Carolyn M. Barcellona9, Mario C. Porcelli10, Chalmers Vasquez10, Andrew C. Cannons11, Marshall R. Cone11, Kelly N. Hogan11, Edgar W. Kopp IV11, Joshua J. Anzinger12, Kimberly F. Garcia13, Leda A. Parham13, Rosa M. Gélvez Ramírez14, Maria C. Miranda Montoya14, Diana P. Rojas15, Catherine M. Brown16, Scott Hennigan16, Brandon Sabina16, Sarah Scotland16, Karthik Gangavarapu17, Nathan D. Grubaugh17, Glenn Oliveira18, Refugio Robles-Sikisaka17, Andrew Rambaut19,20, Lee Gehrke21,22, Sandra Smole16, M. Elizabeth Halloran23,24, Luis Villar14, Salim Mattar25, Ivette Lorenzana13, Jose Cerbino-Neto7, Clarissa Valim4,26, Wim Degrave27, Patricia T. Bozza28, Andreas Gnirke1, Kristian G. Andersen17,18,29,§, Sharon Isern9,§, Scott F. Michael9,§, Fernando A. Bozza7,30,§, Thiago M. L.Souza31,32,§, Irene Bosch21,§, Nathan L. Yozwiak1,3,§, Bronwyn L. MacInnis1,4,§, and Pardis C. Sabeti1,3,4,33,§ - AFFILIATIONS: Affiliations1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA2Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA5Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA6Harvard University Extension School, Cambridge, Massachusetts, USA7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil8Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA10Miami-Dade County Mosquito Control, Miami, Florida, USA11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA12Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia15Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA16Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA18Scripps Translational Science Institute, La Jolla, California, USA19Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK, 20Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA21Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA22Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA23Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA24Department of Biostatistics, University of Washington, Seattle, Washington, USA25Institute for Tropical Biology Research, Universidad de Córdoba, Montería, Córdoba, Colombia26Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michegan, USA27FIOCRUZ, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, Rio de Janeiro, Brazil28Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil29Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA30D’Or Institute for Research and Education, Rio de Janeiro, Brazil31National Institute for Science and Technology on Innovation on Neglected Diseases, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil32Center for Technological Development in Health, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil33Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
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