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Genome sequencing reveals Zika virus diversity and spread in the Americas
View ORCID ProfileMetsky H.C., View ORCID ProfileMatranga C.B., Wohl S., View ORCID ProfileSchaffner S.F., Freije C.A., Winnicki S.M., West K., View ORCID ProfileQu J., Baniecki M.L., Gladden-Young A., View ORCID ProfileLin A.E., View ORCID ProfileTomkins-Tinch C.H., View ORCID ProfileYe S.H., View ORCID ProfilePark D.J., Luo C.Y., Barnes K.G., Shah R.R., Chak B., View ORCID ProfileBarbosa-Lima G., Delatorre E., Vieira Y.R., Paul L.M., Tan A.L., Barcellona C.M., Porcelli M.C., Vasquez C., Cannons A.C., Cone M.R., Hogan K.N., Kopp E.W., Anzinger J.J., Garcia K.F., Parham L.A., Gélvez Ramírez R.M., Miranda Montoya M.C., Rojas D.P., Brown C.M., Hennigan S., Sabina B., Scotland S., Gangavarapu K., View ORCID ProfileGrubaugh N.D., Oliveira G., Robles-Sikisaka R., Rambaut A., View ORCID ProfileGehrke L., Smole S., View ORCID ProfileHalloran M.E., Villar Centeno L.A., View ORCID ProfileMattar S., Lorenzana I., Cerbino-Neto J., Valim C., View ORCID ProfileDegrave W., View ORCID ProfileBozza P.T., Gnirke A., View ORCID ProfileAndersen K.G., Isern S., Michael S.F., Bozza F.A., View ORCID ProfileSouza T.M.L., Bosch I., View ORCID ProfileYozwiak N.L., MacInnis B.L., Sabeti P.C.
doi: https://doi.org/10.1101/109348
Metsky H.C.
Broad Institute of MIT and Harvard, Cambridge MA, USADepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA, USA
Matranga C.B.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Wohl S.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Schaffner S.F.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USADepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
Freije C.A.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Winnicki S.M.
Broad Institute of MIT and Harvard, Cambridge MA, USA
West K.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Qu J.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Baniecki M.L.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Gladden-Young A.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Lin A.E.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Tomkins-Tinch C.H.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Ye S.H.
Broad Institute of MIT and Harvard, Cambridge MA, USAHarvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge MA, USA
Park D.J.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Luo C.Y.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Barnes K.G.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Shah R.R.
Broad Institute of MIT and Harvard, Cambridge MA, USAHarvard University Extension School, Cambridge, MA, USA
Chak B.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Barbosa-Lima G.
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
Delatorre E.
Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro RJ, Brazil
Vieira Y.R.
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
Paul L.M.
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Tan A.L.
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Barcellona C.M.
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Porcelli M.C.
Miami-Dade County Mosquito Control, Miami FL, USA
Vasquez C.
Miami-Dade County Mosquito Control, Miami FL, USA
Cannons A.C.
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Cone M.R.
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Hogan K.N.
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Kopp E.W.
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Anzinger J.J.
Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
Garcia K.F.
Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Parham L.A.
Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Gélvez Ramírez R.M.
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Miranda Montoya M.C.
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Rojas D.P.
Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville FL, USA
Brown C.M.
Massachusetts Department of Public Health, Jamaica Plain MA, USA
Hennigan S.
Massachusetts Department of Public Health, Jamaica Plain MA, USA
Sabina B.
Massachusetts Department of Public Health, Jamaica Plain MA, USA
Scotland S.
Massachusetts Department of Public Health, Jamaica Plain MA, USA
Gangavarapu K.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Grubaugh N.D.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Oliveira G.
Scripps Translational Science Institute, La Jolla CA, USA
Robles-Sikisaka R.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Rambaut A.
University of Edinburgh, Edinburgh, UKFogarty International Center, National Institutes of Health, Bethesda MD, USA
Gehrke L.
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USADepartment of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
Smole S.
Massachusetts Department of Public Health, Jamaica Plain MA, USA
Halloran M.E.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA, USADepartment of Biostatistics, University of Washington, Seattle WA, USA
Villar Centeno L.A.
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Mattar S.
Institute for Tropical Biology Research, Universidad de Córdoba, Colombia
Lorenzana I.
Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Cerbino-Neto J.
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
Valim C.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USADepartment of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
Degrave W.
Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro RJ, Brazil
Bozza P.T.
Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro RJ, Brazil
Gnirke A.
Broad Institute of MIT and Harvard, Cambridge MA, USA
Andersen K.G.
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USAScripps Translational Science Institute, La Jolla CA, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla CA, USA
Isern S.
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Michael S.F.
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Bozza F.A.
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, BrazilD'Or Institute for Research and Education, Brazil
Souza T.M.L.
National Institute for Science and Technology on Innovation on Neglected Diseases, Fiocruz, Rio de Janeiro RJ, BrazilCenter for Technological Development in Health, Fiocruz, Rio de Janeiro RJ, Brazil
Bosch I.
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USADepartment of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
Yozwiak N.L.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
MacInnis B.L.
Broad Institute of MIT and Harvard, Cambridge MA, USADepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
Sabeti P.C.
Broad Institute of MIT and Harvard, Cambridge MA, USACenter for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USADepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
Abstract
Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas, much remains unknown about its epidemiology and evolution, in part due to a lack of genomic data. We applied 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 analyzed 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 US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted April 23, 2017.
Genome sequencing reveals Zika virus diversity and spread in the Americas
Metsky H.C., Matranga C.B., Wohl S., Schaffner S.F., Freije C.A., Winnicki S.M., West K., Qu J., Baniecki M.L., Gladden-Young A., Lin A.E., Tomkins-Tinch C.H., Ye S.H., Park D.J., Luo C.Y., Barnes K.G., Shah R.R., Chak B., Barbosa-Lima G., Delatorre E., Vieira Y.R., Paul L.M., Tan A.L., Barcellona C.M., Porcelli M.C., Vasquez C., Cannons A.C., Cone M.R., Hogan K.N., Kopp E.W., Anzinger J.J., Garcia K.F., Parham L.A., Gélvez Ramírez R.M., Miranda Montoya M.C., Rojas D.P., Brown C.M., Hennigan S., Sabina B., Scotland S., Gangavarapu K., Grubaugh N.D., Oliveira G., Robles-Sikisaka R., Rambaut A., Gehrke L., Smole S., Halloran M.E., Villar Centeno L.A., Mattar S., Lorenzana I., Cerbino-Neto J., Valim C., Degrave W., Bozza P.T., Gnirke A., Andersen K.G., Isern S., Michael S.F., Bozza F.A., Souza T.M.L., Bosch I., Yozwiak N.L., MacInnis B.L., Sabeti P.C.
bioRxiv 109348; doi: https://doi.org/10.1101/109348
Genome sequencing reveals Zika virus diversity and spread in the Americas
Metsky H.C., Matranga C.B., Wohl S., Schaffner S.F., Freije C.A., Winnicki S.M., West K., Qu J., Baniecki M.L., Gladden-Young A., Lin A.E., Tomkins-Tinch C.H., Ye S.H., Park D.J., Luo C.Y., Barnes K.G., Shah R.R., Chak B., Barbosa-Lima G., Delatorre E., Vieira Y.R., Paul L.M., Tan A.L., Barcellona C.M., Porcelli M.C., Vasquez C., Cannons A.C., Cone M.R., Hogan K.N., Kopp E.W., Anzinger J.J., Garcia K.F., Parham L.A., Gélvez Ramírez R.M., Miranda Montoya M.C., Rojas D.P., Brown C.M., Hennigan S., Sabina B., Scotland S., Gangavarapu K., Grubaugh N.D., Oliveira G., Robles-Sikisaka R., Rambaut A., Gehrke L., Smole S., Halloran M.E., Villar Centeno L.A., Mattar S., Lorenzana I., Cerbino-Neto J., Valim C., Degrave W., Bozza P.T., Gnirke A., Andersen K.G., Isern S., Michael S.F., Bozza F.A., Souza T.M.L., Bosch I., Yozwiak N.L., MacInnis B.L., Sabeti P.C.
bioRxiv 109348; doi: https://doi.org/10.1101/109348
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