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Genome sequencing reveals Zika virus diversity and spread in the Americas
View ORCID ProfileH.C. Metsky, C.B. Matranga, S. Wohl, S.F. Schaner, C.A. Freije, S. M. Winnicki, K. West, J. Qu, M.L. Baniecki, A. Gladden-Young, A.E. Lin, C.H. Tomkins-Tinch, D.J. Park, C.Y. Luo, K.G. Barnes, B. Chak, G. Barbosa-Lima, E. Delatorre, Y.R. Vieira, L.M. Paul, A.L. Tan, M.C. Porcelli, C. Vasquez, A.C. Cannons, M.R. Cone, K.N. Hogan, E.W. Kopp IV, J.J. Anzinger, K.F. Garcia, L.A. Parham, R.M. Gélvez Ramírez, M.C. Miranda Montoya, D.P. Rojas, C.M. Brown, S. Hennigan, B. Sabina, S. Scotland, K. Gangavarapu, N.D. Grubaugh, G. Oliveira, R. Robles-Sikisaka, A. Rambaut, L. Gehrke, S. Smole, M.E. Halloran, L.A. Villar Centeno, S. Mattar, I. Lorenzana, J. Cerbino-Neto, W. Degrave, P.T. Bozza, A. Gnirke, K.G. Andersen, S. Isern, S. Michael, F. Bozza, T.M.L. Souza, I. Bosch, N.L. Yozwiak, B.L. MacInnis, P.C. Sabeti
doi: https://doi.org/10.1101/109348
H.C. Metsky
Broad Institute of MIT and Harvard, Cambridge MA, USA
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge MA, USA
C.B. Matranga
Broad Institute of MIT and Harvard, Cambridge MA, USA
S. Wohl
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
S.F. Schaner
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
C.A. Freije
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
S. M. Winnicki
Broad Institute of MIT and Harvard, Cambridge MA, USA
K. West
Broad Institute of MIT and Harvard, Cambridge MA, USA
J. Qu
Broad Institute of MIT and Harvard, Cambridge MA, USA
M.L. Baniecki
Broad Institute of MIT and Harvard, Cambridge MA, USA
A. Gladden-Young
Broad Institute of MIT and Harvard, Cambridge MA, USA
A.E. Lin
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
C.H. Tomkins-Tinch
Broad Institute of MIT and Harvard, Cambridge MA, USA
D.J. Park
Broad Institute of MIT and Harvard, Cambridge MA, USA
C.Y. Luo
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
K.G. Barnes
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
B. Chak
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
G. Barbosa-Lima
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
E. Delatorre
Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro RJ, Brazil
Y.R. Vieira
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
L.M. Paul
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
A.L. Tan
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
M.C. Porcelli
Miami-Dade County Mosquito Control, Miami FL, USA
C. Vasquez
Miami-Dade County Mosquito Control, Miami FL, USA
A.C. Cannons
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
M.R. Cone
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
K.N. Hogan
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
E.W. Kopp IV
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa FL, USA
J.J. Anzinger
Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
K.F. Garcia
Instituto de Investigacion en Microbiologia (IIM) - Universidad Nacional Autónoma de Honduras, Honduras
L.A. Parham
Instituto de Investigacion en Microbiologia (IIM) - Universidad Nacional Autónoma de Honduras, Honduras
R.M. Gélvez Ramírez
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
M.C. Miranda Montoya
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
D.P. Rojas
Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville FL, USA
C.M. Brown
Massachusetts Department of Public Health, Jamaica Plain MA, USA
S. Hennigan
Massachusetts Department of Public Health, Jamaica Plain MA, USA
B. Sabina
Massachusetts Department of Public Health, Jamaica Plain MA, USA
S. Scotland
Massachusetts Department of Public Health, Jamaica Plain MA, USA
K. Gangavarapu
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
N.D. Grubaugh
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
G. Oliveira
Scripps Translational Science Institute, La Jolla CA, USA
R. Robles-Sikisaka
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
A. Rambaut
University of Edinburgh, Edinburgh EH9 3FL, UK
Fogarty International Center, National Institutes of Health, Bethesda MD, USA
L. Gehrke
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USA
Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
S. Smole
Massachusetts Department of Public Health, Jamaica Plain MA, USA
M.E. Halloran
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
Department of Biostatistics, University of Washington, Seattle WA, USA
L.A. Villar Centeno
Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
S. Mattar
Institute for Tropical Biology Research, Universidad de Córdoba, Colombia
I. Lorenzana
Instituto de Investigacion en Microbiologia (IIM) - Universidad Nacional Autónoma de Honduras, Honduras
J. Cerbino-Neto
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
W. Degrave
Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro RJ, Brazil
P.T. Bozza
Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
A. Gnirke
Broad Institute of MIT and Harvard, Cambridge MA, USA
K.G. Andersen
Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA, USA
Scripps Translational Science Institute, La Jolla CA, USA
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla CA, USA
S. Isern
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
S. Michael
Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers FL, USA
F. Bozza
National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro RJ, Brazil
D’Or Institute for Research and Education (IDOR), Brazil
T.M.L. Souza
National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Fiocruz, Rio de Janeiro RJ, Brazil
Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro RJ, Brazil
I. Bosch
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge MA, USA
N.L. Yozwiak
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
B.L. MacInnis
Broad Institute of MIT and Harvard, Cambridge MA, USA
Harvard T.H. Chan School of Public Health, Harvard University, Boston MA, USA
P.C. Sabeti
Broad Institute of MIT and Harvard, Cambridge MA, USA
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
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 100 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, confirming phylogenetic evidence for the origin and rapid expansion of the outbreak in Brazil1, and for multiple introductions from Brazil into Honduras, Colombia, Puerto Rico, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in many regions of the Americas for up to a year before the first locally transmitted cases were confirmed, highlighting the challenge of effective surveillance for this virus. We further characterize genetic variation across the outbreak to identify mutations with possible functional implications for ZIKV biology and pathogenesis.
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 February 18, 2017.
Genome sequencing reveals Zika virus diversity and spread in the Americas
H.C. Metsky, C.B. Matranga, S. Wohl, S.F. Schaner, C.A. Freije, S. M. Winnicki, K. West, J. Qu, M.L. Baniecki, A. Gladden-Young, A.E. Lin, C.H. Tomkins-Tinch, D.J. Park, C.Y. Luo, K.G. Barnes, B. Chak, G. Barbosa-Lima, E. Delatorre, Y.R. Vieira, L.M. Paul, A.L. Tan, M.C. Porcelli, C. Vasquez, A.C. Cannons, M.R. Cone, K.N. Hogan, E.W. Kopp IV, J.J. Anzinger, K.F. Garcia, L.A. Parham, R.M. Gélvez Ramírez, M.C. Miranda Montoya, D.P. Rojas, C.M. Brown, S. Hennigan, B. Sabina, S. Scotland, K. Gangavarapu, N.D. Grubaugh, G. Oliveira, R. Robles-Sikisaka, A. Rambaut, L. Gehrke, S. Smole, M.E. Halloran, L.A. Villar Centeno, S. Mattar, I. Lorenzana, J. Cerbino-Neto, W. Degrave, P.T. Bozza, A. Gnirke, K.G. Andersen, S. Isern, S. Michael, F. Bozza, T.M.L. Souza, I. Bosch, N.L. Yozwiak, B.L. MacInnis, P.C. Sabeti
bioRxiv 109348; doi: https://doi.org/10.1101/109348
Genome sequencing reveals Zika virus diversity and spread in the Americas
H.C. Metsky, C.B. Matranga, S. Wohl, S.F. Schaner, C.A. Freije, S. M. Winnicki, K. West, J. Qu, M.L. Baniecki, A. Gladden-Young, A.E. Lin, C.H. Tomkins-Tinch, D.J. Park, C.Y. Luo, K.G. Barnes, B. Chak, G. Barbosa-Lima, E. Delatorre, Y.R. Vieira, L.M. Paul, A.L. Tan, M.C. Porcelli, C. Vasquez, A.C. Cannons, M.R. Cone, K.N. Hogan, E.W. Kopp IV, J.J. Anzinger, K.F. Garcia, L.A. Parham, R.M. Gélvez Ramírez, M.C. Miranda Montoya, D.P. Rojas, C.M. Brown, S. Hennigan, B. Sabina, S. Scotland, K. Gangavarapu, N.D. Grubaugh, G. Oliveira, R. Robles-Sikisaka, A. Rambaut, L. Gehrke, S. Smole, M.E. Halloran, L.A. Villar Centeno, S. Mattar, I. Lorenzana, J. Cerbino-Neto, W. Degrave, P.T. Bozza, A. Gnirke, K.G. Andersen, S. Isern, S. Michael, F. Bozza, T.M.L. Souza, I. Bosch, N.L. Yozwiak, B.L. MacInnis, P.C. Sabeti
bioRxiv 109348; doi: https://doi.org/10.1101/109348
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