Dataset Information

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

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.

SUBMITTER: Grubaugh ND

PROVIDER: S-EPMC6716374 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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

Grubaugh Nathan D ND Saraf Sharada S Gangavarapu Karthik K Watts Alexander A Tan Amanda L AL Oidtman Rachel J RJ Ladner Jason T JT Oliveira Glenn G Matteson Nathaniel L NL Kraemer Moritz U G MUG Vogels Chantal B F CBF Hentoff Aaron A Bhatia Deepit D Stanek Danielle D Scott Blake B Landis Vanessa V Stryker Ian I Cone Marshall R MR Kopp Edgar W EW Cannons Andrew C AC Heberlein-Larson Lea L White Stephen S Gillis Leah D LD Ricciardi Michael J MJ Kwal Jaclyn J Lichtenberger Paola K PK Magnani Diogo M DM Watkins David I DI Palacios Gustavo G Hamer Davidson H DH Gardner Lauren M LM Perkins T Alex TA Baele Guy G Khan Kamran K Morrison Andrea A Isern Sharon S Michael Scott F SF Andersen Kristian G KG

Cell 20190801 5

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, ...[more]

PMID: 31442400

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Project description:In the realm of infectious disease control, accurate modeling of the transmission dynamics is pivotal. As human mobility and commuting patterns are key components of communicable disease spread, we introduce a novel travel time aware metapopulation model. Our model aims to enhance estimations of disease transmission. By providing more reliable assessments on the efficacy of interventions, curtailing personal rights or human mobility behavior through interventions can be minimized. The proposed model is an advancement over traditional compartmental models, integrating explicit transmission on travel and commute, a factor available in agent-based models but often neglected with metapopulation models. Our approach employs a multi-edge graph ODE-based (Graph-ODE) model, which represents the intricate interplay between mobility and disease spread. This granular modeling is particularly important when assessing the dynamics in densely connected urban areas or when heterogeneous structures across entire countries have to be assessed. The given approach can be coupled with any kind of ODE-based model. In addition, we propose a novel multi-layer waning immunity model that integrates waning of different paces for protection against mild and severe courses of the disease. As this is of particular interest for late-phase epidemic or endemic scenarios, we consider the late-phase of SARS-CoV-2 in Germany. The results of this work show that accounting for resolved mobility significantly influences the pattern of outbreaks. The improved model provides a refined tool for predicting outbreak trajectories and evaluating intervention strategies in relation to mobility by allowing us to assess the transmission that result on traveling. The insights derived from this model can serve as a basis for decisions on the implementation or suspension of interventions, such as mandatory masks on public transportation. Eventually, our model contributes to maintaining mobility as a social good while reducing exuberant disease dynamics potentially driven by travel activities.

Project description:BackgroundZika virus (ZIKV) is an emerging mosquito-borne arbovirus that can produce serious public health consequences. In 2016, ZIKV caused an epidemic in many countries around the world, including the United States. ZIKV surveillance and vector control is essential to combating future epidemics. However, challenges relating to the timely publication of case reports significantly limit the effectiveness of current surveillance methods. In many countries with poor infrastructure, established systems for case reporting often do not exist. Previous studies investigating the H1N1 pandemic, general influenza and the recent Ebola outbreak have demonstrated that time- and geo-tagged Twitter data, which is immediately available, can be utilized to overcome these limitations.MethodsIn this study, we employed a recently developed system called Cloudberry to filter a random sample of Twitter data to investigate the feasibility of using such data for ZIKV epidemic tracking on a national and state (Florida) level. Two auto-regressive models were calibrated using weekly ZIKV case counts and zika tweets in order to estimate weekly ZIKV cases 1 week in advance.ResultsWhile models tended to over-predict at low case counts and under-predict at extreme high counts, a comparison of predicted versus observed weekly ZIKV case counts following model calibration demonstrated overall reasonable predictive accuracy, with an R2 of 0.74 for the Florida model and 0.70 for the U.S.ModelTime-series analysis of predicted and observed ZIKV cases following internal cross-validation exhibited very similar patterns, demonstrating reasonable model performance. Spatially, the distribution of cumulative ZIKV case counts (local- & travel-related) and zika tweets across all 50 U.S. states showed a high correlation (r = 0.73) after adjusting for population.ConclusionsThis study demonstrates the value of utilizing Twitter data for the purposes of disease surveillance. This is of high value to epidemiologist and public health officials charged with protecting the public during future outbreaks.

Dataset Information

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

Publications

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

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