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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
Matranga C.B.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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
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
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
Winnicki S.M.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
West K.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
Qu J.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
Baniecki M.L.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
Gladden-Young A.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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
Tomkins-Tinch C.H.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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
Park D.J.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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
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
Shah R.R.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
6Harvard University Extension School, Cambridge, MA, USA
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
Barbosa-Lima G.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
Delatorre E.
8Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro RJ, Brazil
Vieira Y.R.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
Paul L.M.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Tan A.L.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Barcellona C.M.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Porcelli M.C.
10Miami-Dade County Mosquito Control, Miami FL, USA
Vasquez C.
10Miami-Dade County Mosquito Control, Miami FL, USA
Cannons A.C.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Cone M.R.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Hogan K.N.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Kopp E.W.
11Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
Anzinger J.J.
12Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
Garcia K.F.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Parham L.A.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Gélvez Ramírez R.M.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Miranda Montoya M.C.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Rojas D.P.
15Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville FL, USA
Brown C.M.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
Hennigan S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
Sabina B.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
Scotland S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
Gangavarapu K.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Grubaugh N.D.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Oliveira G.
18Scripps Translational Science Institute, La Jolla CA, USA
Robles-Sikisaka R.
17Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Rambaut A.
19University of Edinburgh, Edinburgh, UK
20Fogarty International Center, National Institutes of Health, Bethesda MD, USA
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
Smole S.
16Massachusetts Department of Public Health, Jamaica Plain MA, USA
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
Villar Centeno L.A.
14Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
Mattar S.
25Institute for Tropical Biology Research, Universidad de Córdoba, Colombia
Lorenzana I.
13Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Honduras
Cerbino-Neto J.
7National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
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
Degrave W.
27Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro RJ, Brazil
Bozza P.T.
28Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro RJ, Brazil
Gnirke A.
1Broad Institute of MIT and Harvard, Cambridge MA, USA
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
Isern S.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
Michael S.F.
9Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
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
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
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
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
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
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
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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