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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.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
2Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA, USA
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Matranga C.B.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Wohl S.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Schaffner S.F.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
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  • ORCID record for Schaffner S.F.
Freije C.A.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Winnicki S.M.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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West K.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Qu J.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Baniecki M.L.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Gladden-Young A.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Lin A.E.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Tomkins-Tinch C.H.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Ye S.H.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
5Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge MA, USA
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Park D.J.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Luo C.Y.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Barnes K.G.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Shah R.R.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
6Harvard University Extension School, Cambridge, MA, USA
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Chak B.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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Barbosa-Lima G.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
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Delatorre E.
8Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro RJ, Brazil
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Vieira Y.R.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
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Paul L.M.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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Tan A.L.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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Barcellona C.M.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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Porcelli M.C.
10Miami-Dade County Mosquito Control, Miami FL, USA
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Vasquez C.
10Miami-Dade County Mosquito Control, Miami FL, USA
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Cannons A.C.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
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Cone M.R.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
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Hogan K.N.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
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Kopp E.W.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
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Anzinger J.J.
12Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
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Garcia K.F.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
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Parham L.A.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
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Gélvez Ramírez R.M.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
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Miranda Montoya M.C.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
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Rojas D.P.
15Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville FL, USA
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Brown C.M.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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Hennigan S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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Sabina B.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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Scotland S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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Gangavarapu K.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
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Grubaugh N.D.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
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Oliveira G.
18Scripps Translational Science Institute, La Jolla CA, USA
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Robles-Sikisaka R.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
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Rambaut A.
19University of Edinburgh, Edinburgh, UK
20Fogarty International Center, National Institutes of Health, Bethesda MD, USA
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Gehrke L.
21Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USA
22Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
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Smole S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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Halloran M.E.
23Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
24Department of Biostatistics, University of Washington, Seattle WA, USA
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Villar Centeno L.A.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
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Mattar S.
25Institute for Tropical Biology Research, Universidad de Córdoba, Colombia
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Lorenzana I.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
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Cerbino-Neto J.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
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Valim C.
4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
26Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
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Degrave W.
27Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro RJ, Brazil
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Bozza P.T.
28Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro RJ, Brazil
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Gnirke A.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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Andersen K.G.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
18Scripps Translational Science Institute, La Jolla CA, USA
29Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla CA, USA
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Isern S.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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Michael S.F.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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Bozza F.A.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
30D'Or Institute for Research and Education, Brazil
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Souza T.M.L.
31National Institute for Science and Technology on Innovation on Neglected Diseases, Fiocruz, Rio de Janeiro RJ, Brazil
32Center for Technological Development in Health, Fiocruz, Rio de Janeiro RJ, Brazil
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  • For correspondence: bronwyn@broadinstitute.org tmoreno@cdts.fiocruz.br
Bosch I.
21Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USA
22Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
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Yozwiak N.L.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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  • ORCID record for Yozwiak N.L.
MacInnis B.L.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
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  • For correspondence: bronwyn@broadinstitute.org tmoreno@cdts.fiocruz.br
Sabeti P.C.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
3Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
4Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
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  • Abstract
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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.

Footnotes

  • ↵* co-first author

  • ↵† co-senior author

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.
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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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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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