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Cell. 2019 Aug 22;178(5):1057-1071.e11. doi: 10.1016/j.cell.2019.07.018.

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.

Author information

1
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: nathan.grubaugh@yale.edu.
2
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
3
Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada.
4
Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA.
5
Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
6
Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA.
7
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
8
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
9
Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA.
10
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA.
11
Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, FL 33125, USA.
12
Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
13
Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA.
14
Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
15
Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA; Section of Infectious Diseases, Department of Medicine, Boston Medical Center, Boston, MA 02118, USA.
16
School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Department of Civil Engineering, Johns Hopkins University, Baltimore, MD 21287, USA.
17
Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
18
Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8, Canada.
19
Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA.
20
Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA. Electronic address: smichael@fgcu.edu.
21
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA. Electronic address: andersen@scripps.edu.

Abstract

The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Zika cases to identify transmission not captured by reporting. We uncovered an unreported outbreak in Cuba during 2017, a year after peak transmission in neighboring islands. By sequencing Zika virus, we show that the establishment of the virus was delayed by a year and that the ensuing outbreak was sparked by long-lived lineages of Zika virus from other Caribbean islands. Our data suggest that, although mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, such measures need to be maintained to be effective. Our study highlights how Zika virus may still be "silently" spreading and provides a framework for understanding outbreak dynamics. VIDEO ABSTRACT.

KEYWORDS:

Zika epidemic; Zika virus; clinical sequencing; genomic epidemiology; infectious disease genomics; phylogenetics; travel surveillance; virus sequencing

PMID:
31442400
PMCID:
PMC6716374
[Available on 2020-08-22]
DOI:
10.1016/j.cell.2019.07.018

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