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Meyer AD, Guerrero SM, Dean NE, Anderson KB, Stoddard ST, Perkins TA. Model-based estimates of chikungunya epidemiological parameters and outbreak risk from varied data types. Epidemics 2023; 45:100721. [PMID: 37890441 DOI: 10.1016/j.epidem.2023.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Assessing the factors responsible for differences in outbreak severity for the same pathogen is a challenging task, since outbreak data are often incomplete and may vary in type across outbreaks (e.g., daily case counts, serology, cases per household). We propose that outbreaks described with varied data types can be directly compared by using those data to estimate a common set of epidemiological parameters. To demonstrate this for chikungunya virus (CHIKV), we developed a realistic model of CHIKV transmission, along with a Bayesian inference method that accommodates any type of outbreak data that can be simulated. The inference method makes use of the fact that all data types arise from the same transmission process, which is simulated by the model. We applied these tools to data from three real-world outbreaks of CHIKV in Italy, Cambodia, and Bangladesh to estimate nine model parameters. We found that these populations differed in several parameters, including pre-existing immunity and house-to-house differences in mosquito activity. These differences resulted in posterior predictions of local CHIKV transmission risk that varied nearly fourfold: 16% in Italy, 28% in Cambodia, and 62% in Bangladesh. Our inference method and model can be applied to improve understanding of the epidemiology of CHIKV and other pathogens for which outbreaks are described with varied data types.
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Affiliation(s)
- Alexander D Meyer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | | | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kathryn B Anderson
- Department of Microbiology and Immunology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven T Stoddard
- Bavarian Nordic Inc., 6275 Nancy Ridge Drive Suite 110/120, San Diego, CA 92121, USA; Division of Health Promotion and Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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2
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Gardini Sanches Palasio R, Marques Moralejo Bermudi P, Luiz de Lima Macedo F, Reis Santana LM, Chiaravalloti-Neto F. Zika, chikungunya and co-occurrence in Brazil: space-time clusters and associated environmental-socioeconomic factors. Sci Rep 2023; 13:18026. [PMID: 37865641 PMCID: PMC10590386 DOI: 10.1038/s41598-023-42930-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/16/2023] [Indexed: 10/23/2023] Open
Abstract
Chikungunya and Zika have been neglected as emerging diseases. This study aimed to analyze the space-time patterns of their occurrence and co-occurrence and their associated environmental and socioeconomic factors. Univariate (individually) and multivariate (co-occurrence) scans were analyzed for 608,388 and 162,992 cases of chikungunya and Zika, respectively. These occurred more frequently in the summer and autumn. The clusters with the highest risk were initially located in the northeast, dispersed to the central-west and coastal areas of São Paulo and Rio de Janeiro (2018-2021), and then increased in the northeast (2019-2021). Chikungunya and Zika demonstrated decreasing trends of 13% and 40%, respectively, whereas clusters showed an increasing trend of 85% and 57%, respectively. Clusters with a high co-occurrence risk have been identified in some regions of Brazil. High temperatures are associated with areas at a greater risk of these diseases. Chikungunya was associated with low precipitation levels, more urbanized environments, and places with greater social inequalities, whereas Zika was associated with high precipitation levels and low sewage network coverage. In conclusion, to optimize the surveillance and control of chikungunya and Zika, this study's results revealed high-risk areas with increasing trends and priority months and the role of socioeconomic and environmental factors.
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Affiliation(s)
- Raquel Gardini Sanches Palasio
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil.
| | - Patricia Marques Moralejo Bermudi
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil
| | - Fernando Luiz de Lima Macedo
- Epidemiological Surveillance Center (CVE) Prof. Alexandre Vranjac, Coordination of Disease Control, Health Department of the State of São Paulo, São Paulo, SP, Brazil
| | - Lidia Maria Reis Santana
- Epidemiological Surveillance Center (CVE) Prof. Alexandre Vranjac, Coordination of Disease Control, Health Department of the State of São Paulo, São Paulo, SP, Brazil
- Federal University of Sao Paulo (Unifesp), São Paulo, SP, Brazil
| | - Francisco Chiaravalloti-Neto
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil
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3
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López L, Dommar C, San José A, Meyers L, Fox S, Castro L, Rodó X. Changing risk of arboviral emergence in Catalonia due to higher probability of autochthonous outbreaks. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Mac PA, Airiohuodion PE, Zubair S, Tadele M, Aighobahi JO, Anyaike C, Kroeger A, Panning M. Antibody seropositivity and endemicity of chikungunya and Zika viruses in Nigeria. ANIMAL DISEASES 2023; 3:7. [PMID: 36968287 PMCID: PMC10034229 DOI: 10.1186/s44149-023-00070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/16/2023] [Indexed: 03/25/2023] Open
Abstract
Mosquito-borne infections are of global health concern because of their rapid spread and upsurge, which creates a risk for coinfections. chikungunya virus (CHIKV), an arbovirus disease transmitted by Aedes aegypti or A. albopictus, and malaria, a parasitic disease transmitted by Anopheles gambiae, are prevalent in Nigeria and neighbouring countries, but their burden and possible coinfections are poorly understood. In this study, we investigated the antibody seropositivity and endemicity of chikungunya and Zika viruses (ZIKV) in three regions of Nigeria. A cross-sectional sero-survey was conducted on 871 participants. Samples were collected from outpatients by simple random sampling. Analyses of the samples were performed using recomLine Tropical Fever for the presence of antibody serological marker IgG immunoblot with CHIKV VLP (virus like particle), ZIKV NS1 and ZIKV Equad according to manufacturers’ instructions and malaria RDT for malaria parasite. There was a significantly higher antibody seropositivity against CHIKV in the central region than in the northern and southern regions (69.5%, 291/419), while ZIKV-seropositivity (22.4%, 34/152) and CHIKV-ZIKV co-circulating antibody seropositivity (17.8%, 27/152) were notably higher in the southern region than in the central and northern regions. This investigation revealed an unexpectedly high antibody seropositivity and concealed endemicity of CHIKV and ZIKV in three Nigerian regions. The seropositivity of detectable antibodies differed among the three geographical locations.
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Affiliation(s)
- Peter Asaga Mac
- Institute of Virology, University Medical Freiburg, Hermann Herder Str, 11, 79104 Freiburg, Germany
| | - Philomena E. Airiohuodion
- grid.3575.40000000121633745World Health Organization, Special Programme for Research and Training in Tropical Diseases (TDR), Avenue Appia 20, 1211 Geneva 27, Switzerland
| | - Shaistha Zubair
- grid.3575.40000000121633745World Health Organization, WHO/NTD Unit, Avenue Appia 20, 1211 Geneva 27, Switzerland
- grid.449054.80000 0004 0426 5233Maldives National University, Buruzu, Magu, Male, Maldives
| | - Markos Tadele
- grid.463251.70000 0001 2195 6683Ethiopian Institute Of Agricultural Research/EIAR, Addis Ababa, Ethiopia
| | - Jude, O. Aighobahi
- Icon Clinical Research, Heinrich-Hertz Starsse 26, 63225 Langen Hessen, Berlin, Germany
| | - Chukwuma Anyaike
- grid.434433.70000 0004 1764 1074Federal Ministry of Health, National Tuberculosis and Leprosy ControlProgramme, Abuja, Nigeria
| | - Axel Kroeger
- grid.5963.9Centre for Medicine and Society, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, University Medical Freiburg, Hermann Herder Str, 11, 79104 Freiburg, Germany
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5
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Modeling the spread of the Zika virus by sexual and mosquito transmission. PLoS One 2022; 17:e0270127. [PMID: 36584063 PMCID: PMC9803243 DOI: 10.1371/journal.pone.0270127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 06/05/2022] [Indexed: 12/31/2022] Open
Abstract
Zika Virus (ZIKV) is a flavivirus that is transmitted predominantly by the Aedes species of mosquito, but also through sexual contact, blood transfusions, and congenitally from mother to child. Although approximately 80% of ZIKV infections are asymptomatic and typical symptoms are mild, multiple studies have demonstrated a causal link between ZIKV and severe diseases such as Microcephaly and Guillain Barré Syndrome. Two goals of this study are to improve ZIKV models by considering the spread dynamics of ZIKV as both a vector-borne and sexually transmitted disease, and also to approximate the degree of under-reporting. In order to accomplish these objectives, we propose a compartmental model that allows for the analysis of spread dynamics as both a vector-borne and sexually transmitted disease, and fit it to the ZIKV incidence reported to the National System of Public Health Surveillance in 27 municipalities of Colombia between January 1 2015 and December 31 2017. We demonstrate that our model can represent the infection patterns over this time period with high confidence. In addition, we argue that the degree of under-reporting is also well estimated. Using the model we assess potential viability of public health scenarios for mitigating disease spread and find that targeting the sexual pathway alone has negligible impact on overall spread, but if the proportion of risky sexual behavior increases then it may become important. Targeting mosquitoes remains the best approach of those considered. These results may be useful for public health organizations and governments to construct and implement suitable health policies and reduce the impact of the Zika outbreaks.
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Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Alex Perkins T, Cavany SM. Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220829. [PMID: 36277835 PMCID: PMC9579765 DOI: 10.1098/rsos.220829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/27/2022] [Indexed: 05/11/2023]
Abstract
Though instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the environmental and biological conditions that make co-infections more likely to occur. To understand this, we developed a mathematical model of co-circulation of two arboviruses, with transmission parameters approximating dengue, Zika and/or chikungunya viruses, and co-infection possible in both humans and mosquitoes. We examined the influence of seasonal timing of arbovirus co-circulation on the extent of co-infection. By undertaking a sensitivity analysis of this model, we examined how biological factors interact with seasonality to determine arbovirus co-infection transmission and prevalence. We found that temporal synchrony of the co-infecting viruses and average temperature were the most influential drivers of co-infection incidence. Our model highlights the synergistic effect of co-transmission from mosquitoes, which leads to more than double the number of co-infections than would be expected in a scenario without co-transmission. Our results suggest that appreciable numbers of co-infections are unlikely to occur except in tropical climates when the viruses co-occur in time and space.
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Affiliation(s)
- Marya L. Poterek
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - T. Alex Perkins
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sean M. Cavany
- Eck Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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7
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McAndrew T, Reich NG. Adaptively stacking ensembles for influenza forecasting. Stat Med 2021; 40:6931-6952. [PMID: 34647627 PMCID: PMC8671371 DOI: 10.1002/sim.9219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/01/2023]
Abstract
Seasonal influenza infects between 10 and 50 million people in the United States every year. Accurate forecasts of influenza and influenza-like illness (ILI) have been named by the CDC as an important tool to fight the damaging effects of these epidemics. Multi-model ensembles make accurate forecasts of seasonal influenza, but current operational ensemble forecasts are static: they require an abundance of past ILI data and assign fixed weights to component models at the beginning of a season, but do not update weights as new data on component model performance is collected. We propose an adaptive ensemble that (i) does not initially need data to combine forecasts and (ii) finds optimal weights which are updated week-by-week throughout the influenza season. We take a regularized likelihood approach and investigate this regularizer's ability to impact adaptive ensemble performance. After finding an optimal regularization value, we compare our adaptive ensemble to an equal-weighted and static ensemble. Applied to forecasts of short-term ILI incidence at the regional and national level, our adaptive model outperforms an equal-weighted ensemble and has similar performance to the static ensemble using only a fraction of the data available to the static ensemble. Needing no data at the beginning of an epidemic, an adaptive ensemble can quickly train and forecast an outbreak, providing a practical tool to public health officials looking for a forecast to conform to unique features of a specific season.
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Affiliation(s)
- Thomas McAndrew
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States,College of Health, Lehigh University, Bethlehem, Pennsylvania, United States,Correspondence: Thomas McAndrew, Lehigh University Bethlehem, Pennsylvania, United States of America.
| | - Nicholas G. Reich
- College of Health, Lehigh University, Bethlehem, Pennsylvania, United States
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8
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Pollett S, Johansson MA, Reich NG, Brett-Major D, Del Valle SY, Venkatramanan S, Lowe R, Porco T, Berry IM, Deshpande A, Kraemer MUG, Blazes DL, Pan-ngum W, Vespigiani A, Mate SE, Silal SP, Kandula S, Sippy R, Quandelacy TM, Morgan JJ, Ball J, Morton LC, Althouse BM, Pavlin J, van Panhuis W, Riley S, Biggerstaff M, Viboud C, Brady O, Rivers C. Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines. PLoS Med 2021; 18:e1003793. [PMID: 34665805 PMCID: PMC8525759 DOI: 10.1371/journal.pmed.1003793] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. METHODS AND FINDINGS We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. CONCLUSIONS These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.
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Affiliation(s)
- Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, United States of America
| | - Nicholas G. Reich
- University of Massachusetts–Amherst, School of Public Health and Health Sciences, Amherst, Massachusetts, United States of America
| | - David Brett-Major
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sara Y. Del Valle
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases and Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Barcelona Institute for Global Health, Barcelona, Spain
| | - Travis Porco
- University of California at San Francisco, San Francisco, California, United States of America
| | - Irina Maljkovic Berry
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Alina Deshpande
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - David L. Blazes
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Wirichada Pan-ngum
- Mahidol-Oxford Tropical Medicine Research Unit and Department of Tropical Hygiene, Mahidol University, Thailand
| | - Alessandro Vespigiani
- Network Science Institute, Northeastern University, Boston, Massachusetts, United States of America
| | - Suzanne E. Mate
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sheetal P. Silal
- Modelling and Simulation Hub, Africa, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sasikiran Kandula
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, New York, United States of America
| | - Rachel Sippy
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Talia M. Quandelacy
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, United States of America
| | - Jeffrey J. Morgan
- Catholic University of America, Washington, DC, United States of America
| | - Jacob Ball
- U.S. Army Public Health Center, Edgewood, Maryland, United States of America
| | - Lindsay C. Morton
- Armed Forces Health Surveillance Division, Global Emerging Infections Surveillance, Silver Spring, Maryland, United States of America
- George Washington University, Milken Institute School of Public Health, Washington, DC, United States of America
| | - Benjamin M. Althouse
- University of Washington, Seattle, Washington, United States of America
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Julie Pavlin
- National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States of America
| | - Wilbert van Panhuis
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, United Kingdom
| | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control & Prevention, Atlanta, Georgia, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes for Health, Bethesda, Maryland, United States of America
| | - Oliver Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Caitlin Rivers
- Johns Hopkins Center for Health Security, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Oidtman RJ, Omodei E, Kraemer MUG, Castañeda-Orjuela CA, Cruz-Rivera E, Misnaza-Castrillón S, Cifuentes MP, Rincon LE, Cañon V, Alarcon PD, España G, Huber JH, Hill SC, Barker CM, Johansson MA, Manore CA, Reiner RC, Rodriguez-Barraquer I, Siraj AS, Frias-Martinez E, García-Herranz M, Perkins TA. Trade-offs between individual and ensemble forecasts of an emerging infectious disease. Nat Commun 2021; 12:5379. [PMID: 34508077 PMCID: PMC8433472 DOI: 10.1038/s41467-021-25695-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about human mobility, spatiotemporal variation in transmission potential, and the number of virus introductions. We found that which model assumptions had the most ensemble weight changed through time. We additionally identified a trade-off whereby some individual models outperformed ensemble models early in the epidemic, but on average the ensembles outperformed all individual models. Our results suggest that multiple models spanning uncertainty across alternative assumptions are necessary to obtain robust forecasts for emerging infectious diseases.
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Affiliation(s)
- Rachel J Oidtman
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
- UNICEF, New York, NY, USA.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
| | | | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | - Guido España
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - John H Huber
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Christopher M Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicince, University of California, Davis, CA, USA
| | - Michael A Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Carrie A Manore
- Information Systems and Modeling (A-1), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | | | - Amir S Siraj
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
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10
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Sadeghieh T, Sargeant JM, Greer AL, Berke O, Dueymes G, Gachon P, Ogden NH, Ng V. Zika virus outbreak in Brazil under current and future climate. Epidemics 2021; 37:100491. [PMID: 34454353 DOI: 10.1016/j.epidem.2021.100491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Zika virus (ZIKV) is primarily transmitted byAedes aegypti and Aedes albopictus mosquitoes between humans and non-human primates. Climate change may enhance virus reproduction in Aedes spp. mosquito populations, resulting in intensified ZIKV outbreaks. The study objective was to explore how an outbreak similar to the 2016 ZIKV outbreak in Brazil might unfold with projected climate change. METHODS A compartmental infectious disease model that included compartments for humans and mosquitoes was developed to fit the 2016 ZIKV outbreak data from Brazil using least squares optimization. To explore the impact of climate change, published polynomial relationships between temperature and temperature-sensitive mosquito population and virus transmission parameters (mosquito mortality, development rate, and ZIKV extrinsic incubation period) were used. Projections for future outbreaks were obtained by simulating transmission with effects of projected average monthly temperatures on temperature-sensitive model parameters at each of three future time periods: 2011-2040, 2041-2070, and 2071-2100. The projected future climate was obtained from an ensemble of regional climate models (RCMs) obtained from the Co-Ordinated Regional Downscaling Experiment (CORDEX) that used Representative Concentration Pathways (RCP) with two radiative forcing values, RCP4.5 and RCP8.5. A sensitivity analysis was performed to explore the impact of temperature-dependent parameters on the model outcomes. RESULTS Climate change scenarios impacted the model outcomes, including the peak clinical case incidence, cumulative clinical case incidence, time to peak incidence, and the duration of the ZIKV outbreak. Comparing 2070-2100 to 2016, using RCP4.5, the peak incidence was 22,030 compared to 10,473; the time to epidemic peak was 12 compared to 9 weeks, and the outbreak duration was 52 compared to 41 weeks. Comparing 2070-2100 to 2016, using RCP8.5, the peak incidence was 21,786 compared to 10,473; the time to epidemic peak was 11 compared to 9 weeks, and the outbreak duration was 50 compared to 41weeks. The increases are due to optimal climate conditions for mosquitoes, with the mean temperature reaching 28 °C in the warmest months. Under a high emission scenario (RCP8.5), mean temperatures extend above optimal for mosquito survival in the warmest months. CONCLUSION Outbreaks of ZIKV in locations similar to Brazil are expected to be more intense with a warming climate. As climate change impacts are becoming increasingly apparent on human health, it is important to quantify the effect and use this knowledge to inform decisions on prevention and control strategies.
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Affiliation(s)
- Tara Sadeghieh
- Population Medicine, University of Guelph, Guelph, Ontario, Canada; Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada; Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario and St. Hyacinthe, Québec, Canada.
| | - Jan M Sargeant
- Population Medicine, University of Guelph, Guelph, Ontario, Canada; Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amy L Greer
- Population Medicine, University of Guelph, Guelph, Ontario, Canada; Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Olaf Berke
- Population Medicine, University of Guelph, Guelph, Ontario, Canada; Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Guillaume Dueymes
- ESCER (Étude et Simulation du Climat à l'Échelle Régionale) Centre, Université du Québec à Montréal, Québec, Canada
| | - Philippe Gachon
- ESCER (Étude et Simulation du Climat à l'Échelle Régionale) Centre, Université du Québec à Montréal, Québec, Canada
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario and St. Hyacinthe, Québec, Canada
| | - Victoria Ng
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario and St. Hyacinthe, Québec, Canada
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Li Z, Wang J, Cheng X, Hu H, Guo C, Huang J, Chen Z, Lu J. The worldwide seroprevalence of DENV, CHIKV and ZIKV infection: A systematic review and meta-analysis. PLoS Negl Trop Dis 2021; 15:e0009337. [PMID: 33909610 PMCID: PMC8109817 DOI: 10.1371/journal.pntd.0009337] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 05/10/2021] [Accepted: 03/28/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND As the three major arthropod-borne viruses, dengue virus (DENV), chikungunya virus (CHIKV), and zika virus (ZIKV) are posing a growing threat to global public health and socioeconomic development. Our study aimed to systematically review the global seroprevalences of these arboviruses from existing publications. METHODS Articles published between Jan 01, 2000 and Dec 31, 2019 in the databases of Embase, Pubmed and Web of Science were searched and collected. Countries or areas with known local presence of Aedes vector mosquitoes were included. Random effects model was utilized to estimate the pooled seroprevalences and the proportion of inapparent infection. RESULTS Out of 1375, a total of 133 articles involving 176,001 subjects were included for our analysis. The pooled seroprevalences of DENV, CHIKV and ZIKV were 38%, 25% and 18%, respectively; and their corresponding proportions of inapparent infections were 80%, 40% and 50%. The South-East Asia Region had the highest seroprevalences of DENV and CHIKV, while the Region of the Americas had the highest seroprevalence of ZIKV. The seroprevalences of DENV and CHIKV were similar when comparing developed and developing countries, urban and rural areas, or among different populations. In addition, we observed a decreased global seroprevalences in the new decade (2010-2019) comparing to the decade before (2000-2009) for CHIKV. For ZIKV, the positive rates tested with the nucleic acid detection method were lower than those tested with the antibody detection method. Lastly, numerous cases of dual seropositivity for CHIKV and DENV were reported. CONCLUSIONS Our results revealed a varied prevalence of arbovirus infections in different geographical regions and countries, and the inapparent infection accounted an unneglected portion of infections that requires more attention. This study will shed lights on our understanding of the true burden of arbovirus infections and promote appropriate vaccination in the future.
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Affiliation(s)
- Zhihui Li
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Jin Wang
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Xiaomin Cheng
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Huan Hu
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, New York, United States of America
| | - Jingyi Huang
- Songgang People’s Hospital of Bao’an District, Shenzhen, Guangdong Province, China
| | - Zeliang Chen
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- * E-mail: (ZC); (JL)
| | - Jiahai Lu
- School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- * E-mail: (ZC); (JL)
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12
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Sadeghieh T, Sargeant JM, Greer AL, Berke O, Dueymes G, Gachon P, Ogden NH, Ng V. Yellow fever virus outbreak in Brazil under current and future climate. Infect Dis Model 2021; 6:664-677. [PMID: 33997536 PMCID: PMC8090996 DOI: 10.1016/j.idm.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/20/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction Yellow fever (YF) is primarily transmitted by Haemagogus species of mosquitoes. Under climate change, mosquitoes and the pathogens that they carry are expected to develop faster, potentially impacting the case count and duration of YF outbreaks. The aim of this study was to determine how YF virus outbreaks in Brazil may change under future climate, using ensemble simulations from regional climate models under RCP4.5 and RCP8.5 scenarios for three time periods: 2011–2040 (short-term), 2041–2070 (mid-term), and 2071–2100 (long-term). Methods A compartmental model was developed to fit the 2017/18 YF outbreak data in Brazil using least squares optimization. To explore the impact of climate change, temperature-sensitive mosquito parameters were set to change over projected time periods using polynomial equations fitted to their relationship with temperature according to the average temperature for years 2011–2040, 2041–2070, and 2071–2100 for climate change scenarios using RCP4.5 and RCP8.5, where RCP4.5/RCP8.5 corresponds to intermediate/high radiative forcing values and to moderate/higher warming trends. A sensitivity analysis was conducted to determine how the temperature-sensitive parameters impacted model results, and to determine how vaccination could play a role in reducing YF in Brazil. Results Yellow fever case projections for Brazil from the models varied when climate change scenarios were applied, including the peak clinical case incidence, cumulative clinical case incidence, time to peak incidence, and the outbreak duration. Overall, a decrease in YF cases and outbreak duration was observed. Comparing the observed incidence in 2017/18 to the projected incidence in 2070–2100, for RCP4.5, the cumulative case incidence decreased from 184 to 161, and the outbreak duration decreased from 21 to 20 weeks. For RCP8.5, the peak case incidence decreased from 184 to 147, and the outbreak duration decreased from 21 to 17 weeks. The observed decrease was primarily due to temperature increasing beyond that suitable for Haemagogus mosquito survival. Conclusions Climate change is anticipated to have an impact on mosquito-borne diseases. We found outbreaks of YF may reduce in intensity as temperatures increase in Brazil; however, temperature is not the only factor involved with disease transmission. Other factors must be explored to determine the attributable impact of climate change on mosquito-borne diseases.
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Affiliation(s)
- Tara Sadeghieh
- Population Medicine, University of Guelph, Guelph, Ontario, Canada.,Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.,Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, St. Hyacinthe, Québec, Canada
| | - Jan M Sargeant
- Population Medicine, University of Guelph, Guelph, Ontario, Canada.,Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amy L Greer
- Population Medicine, University of Guelph, Guelph, Ontario, Canada.,Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Olaf Berke
- Population Medicine, University of Guelph, Guelph, Ontario, Canada.,Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Guillaume Dueymes
- ESCER (Étude et Simulation du Climat à l'Échelle Régionale) Centre, Université du Québec à Montréal, Québec, Canada
| | - Philippe Gachon
- ESCER (Étude et Simulation du Climat à l'Échelle Régionale) Centre, Université du Québec à Montréal, Québec, Canada
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, St. Hyacinthe, Québec, Canada
| | - Victoria Ng
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, St. Hyacinthe, Québec, Canada
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Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region. Cell Rep 2021; 30:2275-2283.e7. [PMID: 32075736 DOI: 10.1016/j.celrep.2020.01.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/16/2019] [Accepted: 01/24/2020] [Indexed: 02/08/2023] Open
Abstract
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.
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14
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Eberle RJ, Olivier DS, Pacca CC, Avilla CMS, Nogueira ML, Amaral MS, Willbold D, Arni RK, Coronado MA. In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases. PLoS One 2021; 16:e0246319. [PMID: 33661906 PMCID: PMC7932080 DOI: 10.1371/journal.pone.0246319] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/15/2021] [Indexed: 11/19/2022] Open
Abstract
The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3pro of ZIKV and nsP2pro of CHIKV and, Hesperidin (HSD) against nsP2pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC50 values are in low µM range for HST against ZIKV NS2B/NS3pro (12.6 ± 1.3 µM) and against CHIKV nsP2pro (2.5 ± 0.4 µM). The IC50 for HSD against CHIKV nsP2pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.
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Affiliation(s)
- Raphael J. Eberle
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | | | - Carolina C. Pacca
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- FACERES Medical School, São José do Rio Preto, Brazil
| | - Clarita M. S. Avilla
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
| | - Mauricio L. Nogueira
- Faculdade de Medicina de São José do Rio Preto–FAMERP, São José do Rio Preto, Brazil
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, Jülich, Germany
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
| | - Monika A. Coronado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
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15
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Bedi JS, Vijay D, Dhaka P, Singh Gill JP, Barbuddhe SB. Emergency preparedness for public health threats, surveillance, modelling & forecasting. Indian J Med Res 2021; 153:287-298. [PMID: 33906991 PMCID: PMC8204835 DOI: 10.4103/ijmr.ijmr_653_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/04/2022] Open
Abstract
In the interconnected world, safeguarding global health security is vital for maintaining public health and economic upliftment of any nation. Emergency preparedness is considered as the key to control the emerging public health challenges at both national as well as international levels. Further, the predictive information systems based on routine surveillance, disease modelling and forecasting play a pivotal role in both policy building and community participation to detect, prevent and respond to potential health threats. Therefore, reliable and timely forecasts of these untoward events could mobilize swift and effective public health responses and mitigation efforts. The present review focuses on the various aspects of emergency preparedness with special emphasis on public health surveillance, epidemiological modelling and capacity building approaches. Global coordination and capacity building, funding and commitment at the national and international levels, under the One Health framework, are crucial in combating global public health threats in a holistic manner.
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Affiliation(s)
- Jasbir Singh Bedi
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Deepthi Vijay
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Pankaj Dhaka
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Jatinder Paul Singh Gill
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sukhadeo B. Barbuddhe
- Department of Meat Safety, ICAR-National Research Centre on Meat, Chengicherla, Hyderabad, Telangana, India
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16
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Badolato-Corrêa J, Carvalho FR, Paiva IA, Familiar-Macedo D, Dias HG, Pauvolid-Corrêa A, Fernandes-Santos C, Lima MDRQ, Gandini M, Silva AA, Baeta Cavalcanti SM, de Oliveira SA, de Oliveira Vianna RA, de Azeredo EL, Cardoso CAA, Grifoni A, Sette A, Weiskopf D, de-Oliveira-Pinto LM. Differential Longevity of Memory CD4 and CD8 T Cells in a Cohort of the Mothers With a History of ZIKV Infection and Their Children. Front Immunol 2021; 12:610456. [PMID: 33679748 PMCID: PMC7928292 DOI: 10.3389/fimmu.2021.610456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
Background: Zika virus (ZIKV) infection causes for mild and self-limiting disease in healthy adults. In newborns, it can occasionally lead to a spectrum of malformations, the congenital Zika syndrome (CZS). Thus, little is known if mothers and babies with a history of ZIKV infection were able to develop long-lasting T-cell immunity. To these issues, we measure the prevalence of ZIKV T-cell immunity in a cohort of mothers infected to the ZIKV during pregnancy in the 2016–2017 Zika outbreak, who gave birth to infants affected by neurological complications or asymptomatic ones. Results: Twenty-one mothers and 18 children were tested for IFN-γ ELISpot and T-cell responses for flow cytometry assays in response to CD4 ZIKV and CD8 ZIKV megapools (CD4 ZIKV MP and CD8 ZIKV MP). IFN-γ ELISpot responses to ZIKV MPs showed an increased CD4 and CD8 T-cell responses in mothers compared to children. The degranulation activity and IFN-γ-producing CD4 T cells were detected in most mothers, and children, while in CD8 T-cells, low responses were detected in these study groups. The total Temra T cell subset is enriched for IFN-γ+ CD4 T cells after stimulation of CD4 ZIKV MP. Conclusion: Donors with a history of ZIKV infection demonstrated long-term CD4 T cell immunity to ZIKV CD4 MP. However, the same was not observed in CD8 T cells with the ZIKV CD8 MP. One possibility is that the cytotoxic and pro-inflammatory activities of CD8 T cells are markedly demonstrated in the early stages of infection, but less detected in the disease resolution phase, when the virus has already been eliminated. The responses of mothers' T cells to ZIKV MPs do not appear to be related to their children's clinical outcome. There was also no marked difference in the T cell responses to ZIKV MP between children affected or not with CZS. These data still need to be investigated, including the evaluation of the response of CD8 T cells to other ZIKV peptides.
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Affiliation(s)
| | - Fabiana Rabe Carvalho
- Multiuser Laboratory for Research in Nephrology and Medical Science, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
| | - Iury Amancio Paiva
- Laboratory of Viral Immunology, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States.,Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | | | | | - Mariana Gandini
- Laboratory of Cellular Microbiology, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Andréa Alice Silva
- Multiuser Laboratory for Research in Nephrology and Medical Science, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
| | | | | | | | | | - Claudete Aparecida Araújo Cardoso
- Multiuser Laboratory for Research in Nephrology and Medical Science, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil.,Department of Maternal and Child, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), San Diego, CA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), San Diego, CA, United States.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), San Diego, CA, United States
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17
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Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas. PLoS Negl Trop Dis 2020; 14:e0008640. [PMID: 32986701 PMCID: PMC7544039 DOI: 10.1371/journal.pntd.0008640] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/08/2020] [Accepted: 07/25/2020] [Indexed: 12/22/2022] Open
Abstract
Several hundred thousand Zika cases have been reported across the Americas since 2015. Incidence of infection was likely much higher, however, due to a high frequency of asymptomatic infection and other challenges that surveillance systems faced. Using a hierarchical Bayesian model with empirically-informed priors, we leveraged multiple types of Zika case data from 15 countries to estimate subnational reporting probabilities and infection attack rates (IARs). Zika IAR estimates ranged from 0.084 (95% CrI: 0.067–0.096) in Peru to 0.361 (95% CrI: 0.214–0.514) in Ecuador, with significant subnational variability in every country. Totaling infection estimates across these and 33 other countries and territories, our results suggest that 132.3 million (95% CrI: 111.3-170.2 million) people in the Americas had been infected by the end of 2018. These estimates represent the most extensive attempt to determine the size of the Zika epidemic in the Americas, offering a baseline for assessing the risk of future Zika epidemics in this region. During the recent Zika epidemic in the Americas millions of people were likely infected, but the true size of the epidemic is unknown because of gaps in the surveillance system. The infection attack rate (IAR)—defined as the proportion of the population that was infected over the course of the epidemic—has important implications for the longer-term epidemiology of Zika in the region, such as the timing, location, and likelihood of future outbreaks. To estimate the IAR and the total number of people infected, we leveraged multiple types of Zika case data from 15 countries and territories where subnational data were publicly available. Datasets included confirmed and suspected Zika cases in pregnant women and in the total population, Zika-associated Guillan-Barré syndrome cases, and cases of congenital Zika syndrome. We used a hierarchical Bayesian model with empirically-informed priors that leveraged the different case report types to simultaneously estimate national and subnational reporting probabilities, the fraction of symptomatic infections, and subnational IARs. In these 15 countries and territories, estimates of Zika IAR ranged from 0.084 (95% CrI: 0.067–0.096) in Peru to 0.361 (95% CrI: 0.214–0.514) in Ecuador. Totaling these infection estimates across these and 33 other countries and territories in the region, our results suggest that 132.3 million (95% CrI: 111.3-170.2 million) people in the Americas were infected with ZIKV by the end of 2018.
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18
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Perkins TA, Cavany SM, Moore SM, Oidtman RJ, Lerch A, Poterek M. Estimating unobserved SARS-CoV-2 infections in the United States. Proc Natl Acad Sci U S A 2020; 117:22597-22602. [PMID: 32826332 PMCID: PMC7486725 DOI: 10.1073/pnas.2005476117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
By March 2020, COVID-19 led to thousands of deaths and disrupted economic activity worldwide. As a result of narrow case definitions and limited capacity for testing, the number of unobserved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during its initial invasion of the United States remains unknown. We developed an approach for estimating the number of unobserved infections based on data that are commonly available shortly after the emergence of a new infectious disease. The logic of our approach is, in essence, that there are bounds on the amount of exponential growth of new infections that can occur during the first few weeks after imported cases start appearing. Applying that logic to data on imported cases and local deaths in the United States through 12 March, we estimated that 108,689 (95% posterior predictive interval [95% PPI]: 1,023 to 14,182,310) infections occurred in the United States by this date. By comparing the model's predictions of symptomatic infections with local cases reported over time, we obtained daily estimates of the proportion of symptomatic infections detected by surveillance. This revealed that detection of symptomatic infections decreased throughout February as exponential growth of infections outpaced increases in testing. Between 24 February and 12 March, we estimated an increase in detection of symptomatic infections, which was strongly correlated (median: 0.98; 95% PPI: 0.66 to 0.98) with increases in testing. These results suggest that testing was a major limiting factor in assessing the extent of SARS-CoV-2 transmission during its initial invasion of the United States.
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Affiliation(s)
- T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556;
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
| | - Sean M Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
| | - Sean M Moore
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
| | - Rachel J Oidtman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
| | - Anita Lerch
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
| | - Marya Poterek
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
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19
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Viennet E, Frentiu FD, Williams CR, Mincham G, Jansen CC, Montgomery BL, Flower RLP, Faddy HM. Estimation of mosquito-borne and sexual transmission of Zika virus in Australia: Risks to blood transfusion safety. PLoS Negl Trop Dis 2020; 14:e0008438. [PMID: 32663213 PMCID: PMC7380650 DOI: 10.1371/journal.pntd.0008438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 07/24/2020] [Accepted: 06/01/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Since 2015, Zika virus (ZIKV) outbreaks have occurred in the Americas and the Pacific involving mosquito-borne and sexual transmission. ZIKV has also emerged as a risk to global blood transfusion safety. Aedes aegypti, a mosquito well established in north and some parts of central and southern Queensland, Australia, transmits ZIKV. Aedes albopictus, another potential ZIKV vector, is a threat to mainland Australia. Since these conditions create the potential for local transmission in Australia and a possible uncertainty in the effectiveness of blood donor risk-mitigation programs, we investigated the possible impact of mosquito-borne and sexual transmission of ZIKV in Australia on local blood transfusion safety. METHODOLOGY/PRINCIPAL FINDINGS We estimated 'best-' and 'worst-' case scenarios of monthly reproduction number (R0) for both transmission pathways of ZIKV from 1996-2015 in 11 urban or regional population centres, by varying epidemiological and entomological estimates. We then estimated the attack rate and subsequent number of infectious people to quantify the ZIKV transfusion-transmission risk using the European Up-Front Risk Assessment Tool. For all scenarios and with both vector species R0 was lower than one for ZIKV transmission. However, a higher risk of a sustained outbreak was estimated for Cairns, Rockhampton, Thursday Island, and theoretically in Darwin during the warmest months of the year. The yearly estimation of the risk of transmitting ZIKV infection by blood transfusion remained low through the study period for all locations, with the highest potential risk estimated in Darwin. CONCLUSIONS/SIGNIFICANCE Given the increasing demand for plasma products in Australia, the current strategy of restricting donors returning from infectious disease outbreak regions to source plasma collection provides a simple and effective risk management approach. However, if local transmission was suspected in the main urban centres of Australia, potentially facilitated by the geographic range expansion of Ae. aegypti or Ae. albopictus, this mitigation strategy would need urgent review.
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Affiliation(s)
- Elvina Viennet
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- Institute for Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
- * E-mail:
| | - Francesca D. Frentiu
- Institute for Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Craig R. Williams
- Australian Centre for Precision Health, University of South Australia, Adelaide, South Australia, Australia
| | - Gina Mincham
- Australian Centre for Precision Health, University of South Australia, Adelaide, South Australia, Australia
| | - Cassie C. Jansen
- Communicable Diseases Branch, Queensland Department of Health, Herston, Queensland, Australia
| | - Brian L. Montgomery
- Metro South Public Health Unit, Metro South Hospital and Health Service, Brisbane, Queensland, Australia
| | - Robert L. P. Flower
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- Institute for Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Helen M. Faddy
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- Institute for Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
- School of Health and Sport Sciences, University of the Sunshine Coast, Queensland, Australia
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20
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Pollett S, Johansson M, Biggerstaff M, Morton LC, Bazaco SL, Brett Major DM, Stewart-Ibarra AM, Pavlin JA, Mate S, Sippy R, Hartman LJ, Reich NG, Maljkovic Berry I, Chretien JP, Althouse BM, Myer D, Viboud C, Rivers C. Identification and evaluation of epidemic prediction and forecasting reporting guidelines: A systematic review and a call for action. Epidemics 2020; 33:100400. [PMID: 33130412 PMCID: PMC8667087 DOI: 10.1016/j.epidem.2020.100400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/24/2020] [Accepted: 06/25/2020] [Indexed: 01/26/2023] Open
Abstract
Introduction: High quality epidemic forecasting and prediction are critical to support response to local, regional and global infectious disease threats. Other fields of biomedical research use consensus reporting guidelines to ensure standardization and quality of research practice among researchers, and to provide a framework for end-users to interpret the validity of study results. The purpose of this study was to determine whether guidelines exist specifically for epidemic forecast and prediction publications. Methods: We undertook a formal systematic review to identify and evaluate any published infectious disease epidemic forecasting and prediction reporting guidelines. This review leveraged a team of 18 investigators from US Government and academic sectors. Results: A literature database search through May 26, 2019, identified 1467 publications (MEDLINE n = 584, EMBASE n = 883), and a grey-literature review identified a further 407 publications, yielding a total 1777 unique publications. A paired-reviewer system screened in 25 potentially eligible publications, of which two were ultimately deemed eligible. A qualitative review of these two published reporting guidelines indicated that neither were specific for epidemic forecasting and prediction, although they described reporting items which may be relevant to epidemic forecasting and prediction studies. Conclusions: This systematic review confirms that no specific guidelines have been published to standardize the reporting of epidemic forecasting and prediction studies. These findings underscore the need to develop such reporting guidelines in order to improve the transparency, quality and implementation of epidemic forecasting and prediction research in operational public health.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, MD, USA.
| | - Michael Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, USA
| | | | - Lindsay C Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; Cherokee Nation Strategic Programs, Tulsa, OK, USA; Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Sara L Bazaco
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; General Dynamics Information Technology, Falls Church, VA, USA
| | | | - Anna M Stewart-Ibarra
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, NY, USA; InterAmerican Institute for Global Change Research (IAI), Montevideo, Department of Montevideo, Uruguay
| | - Julie A Pavlin
- National Academies of Sciences, Engineering, and Medicine, DC, USA
| | - Suzanne Mate
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, MD, USA
| | - Rachel Sippy
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Laurie J Hartman
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; Cherokee Nation Strategic Programs, Tulsa, OK, USA
| | | | | | | | - Benjamin M Althouse
- University of Washington, WA, USA; Institute for Disease Modeling, Bellevue, WA, USA; New Mexico State University, Las Cruces, NM, USA
| | - Diane Myer
- Johns Hopkins Center for Health Security, MD, USA
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, MD, USA
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21
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Marques R, Krüger RF, Peterson AT, de Melo LF, Vicenzi N, Jiménez-García D. Climate change implications for the distribution of the babesiosis and anaplasmosis tick vector, Rhipicephalus (Boophilus) microplus. Vet Res 2020; 51:81. [PMID: 32546223 PMCID: PMC7298856 DOI: 10.1186/s13567-020-00802-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/29/2020] [Indexed: 11/10/2022] Open
Abstract
Climate change ranks among the most important issues globally, affecting geographic distributions of vectors and pathogens, and inducing losses in livestock production among many other damaging effects. We characterized the potential geographic distribution of the ticks Rhipicephalus (Boophilus) microplus, an important vector of babesiosis and anaplasmosis globally. We evaluated potential geographic shifts in suitability patterns for this species in two periods (2050 and 2070) and under two emissions scenarios (RCPs 4.5 and 8.5). Our results anticipate increases in suitability worldwide, particularly in the highest production areas for cattle. The Indo-Malayan region resulted in the highest cattle exposure under both climate change projections (2050), with increases in suitability of > 30%. This study illustrates how ecological niche modeling can be used to explore probable effects of climate change on disease vectors, and the possible consequences on economic dimensions.
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Affiliation(s)
- Roberta Marques
- Laboratório de Ecologia de Parasitos e Vetores, Programa de Pós Graduação em Microbiologia e Parasitologia, Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Rodrigo F. Krüger
- Laboratório de Ecologia de Parasitos e Vetores, Programa de Pós Graduação em Microbiologia e Parasitologia, Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | | | - Larissa F. de Melo
- Laboratório de Ecologia de Parasitos e Vetores, Programa de Pós Graduação em Microbiologia e Parasitologia, Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Natália Vicenzi
- Laboratório de Ecologia de Parasitos e Vetores, Programa de Pós Graduação em Microbiologia e Parasitologia, Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS Brazil
| | - Daniel Jiménez-García
- Centro de Agroecología y Ambiente, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla México
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22
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Modeling human migration across spatial scales in Colombia. PLoS One 2020; 15:e0232702. [PMID: 32379787 PMCID: PMC7205305 DOI: 10.1371/journal.pone.0232702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Human mobility, both short and long term, are important considerations in the study of numerous systems. Economic and technological advances have led to a more interconnected global community, further increasing the need for considerations of human mobility. While data on human mobility are better recorded in many developed countries, availability of such data remains limited in many low- and middle-income countries around the world, particularly at the fine temporal and spatial scales required by many applications. In this study, we used 5-year census-based internal migration microdata for 32 departments in Colombia (i.e., Admin-1 level) to develop a novel spatial interaction modeling approach for estimating migration, at a finer spatial scale, among the 1,122 municipalities in the country (i.e., Admin-2 level). Our modeling approach addresses a significant lack of migration data at administrative unit levels finer than those at which migration data are typically recorded. Due to the widespread availability of census-based migration microdata at the Admin-1 level, our modeling approach opens up for the possibilities of modeling migration patterns at Admin-2 and Admin-3 levels across many other countries where such data are currently lacking.
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23
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Abdur Rehman N, Salje H, Kraemer MUG, Subramanian L, Saif U, Chunara R. Quantifying the localized relationship between vector containment activities and dengue incidence in a real-world setting: A spatial and time series modelling analysis based on geo-located data from Pakistan. PLoS Negl Trop Dis 2020; 14:e0008273. [PMID: 32392225 PMCID: PMC7241855 DOI: 10.1371/journal.pntd.0008273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/21/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Increasing urbanization is having a profound effect on infectious disease risk, posing significant challenges for governments to allocate limited resources for their optimal control at a sub-city scale. With recent advances in data collection practices, empirical evidence about the efficacy of highly localized containment and intervention activities, which can lead to optimal deployment of resources, is possible. However, there are several challenges in analyzing data from such real-world observational settings. Using data on 3.9 million instances of seven dengue vector containment activities collected between 2012 and 2017, here we develop and assess two frameworks for understanding how the generation of new dengue cases changes in space and time with respect to application of different types of containment activities. Accounting for the non-random deployment of each containment activity in relation to dengue cases and other types of containment activities, as well as deployment of activities in different epidemiological contexts, results from both frameworks reinforce existing knowledge about the efficacy of containment activities aimed at the adult phase of the mosquito lifecycle. Results show a 10% (95% CI: 1-19%) and 20% reduction (95% CI: 4-34%) reduction in probability of a case occurring in 50 meters and 30 days of cases which had Indoor Residual Spraying (IRS) and fogging performed in the immediate vicinity, respectively, compared to cases of similar epidemiological context and which had no containment in their vicinity. Simultaneously, limitations due to the real-world nature of activity deployment are used to guide recommendations for future deployment of resources during outbreaks as well as data collection practices. Conclusions from this study will enable more robust and comprehensive analyses of localized containment activities in resource-scarce urban settings and lead to improved allocation of resources of government in an outbreak setting.
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Affiliation(s)
- Nabeel Abdur Rehman
- Computer Science and Engineering, Tandon School of Engineering, New York University, Brooklyn, New York, United States of America
| | | | | | | | - Umar Saif
- UNESCO Chair for ICTD, Lahore, Pakistan
| | - Rumi Chunara
- Computer Science and Engineering, Tandon School of Engineering, New York University, Brooklyn, New York, United States of America
- Department of Biostatistics, School of Global Public Health, New York University, New York, New York, United States of America
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24
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Mina MJ, Guterman LB, Allen KE, Omer SB. Comprehensive Profiling of Zika Virus Risk with Natural and Artificial Mitigating Strategies, United States. Emerg Infect Dis 2020; 26:700-710. [PMID: 32043959 PMCID: PMC7101119 DOI: 10.3201/eid2604.181739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Zika virus is transitioning to become a long-term public health challenge, and countries should remain informed of the risk for emergence. We developed a stochastic epidemiologic model to profile risk for Zika virus emergence, including trimester-specific fetal risk across time, in all 3,208 counties in the United States, including Puerto Rico. Validation against known transmission in North America demonstrated accuracy to predict epidemic dynamics and absolute case counts across scales (R2 = 0.98). We found that, although sporadic single transmission events could occur in most US counties, outbreaks will likely be restricted to the Gulf Coast region and to late spring through autumn. Seasonal fluctuations in birth rates will confer natural population-level protection against early-trimester infections. Overall, outbreak control will be more effective and efficient than prevention, and vaccination will be most effective at >70% coverage. Our county-level risk profiles should serve as a critical resource for resource allocation.
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25
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Olson MF, Ndeffo-Mbah ML, Juarez JG, Garcia-Luna S, Martin E, Borucki MK, Frank M, Estrada-Franco JG, Rodríguez-Pérez MA, Fernández-Santos NA, Molina-Gamboa GDJ, Carmona Aguirre SD, Reyes-Berrones BDL, Cortés-De la cruz LJ, García-Barrientos A, Huidobro-Guevara RE, Brussolo-Ceballos RM, Ramirez J, Salazar A, Chaves LF, Badillo-Vargas IE, Hamer GL. High Rate of Non-Human Feeding by Aedes aegypti Reduces Zika Virus Transmission in South Texas. Viruses 2020; 12:E453. [PMID: 32316394 PMCID: PMC7232486 DOI: 10.3390/v12040453] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
Mosquito-borne viruses are emerging or re-emerging globally, afflicting millions of people around the world. Aedes aegypti, the yellow fever mosquito, is the principal vector of dengue, Zika, and chikungunya viruses, and has well-established populations across tropical and subtropical urban areas of the Americas, including the southern United States. While intense arboviral epidemics have occurred in Mexico and further south in the Americas, local transmission in the United States has been minimal. Here, we study Ae. aegypti and Culex quinquefasciatus host feeding patterns and vertebrate host communities in residential environments of South Texas to identify host-utilization relative to availability. Only 31% of Ae. aegypti blood meals were derived from humans, while 50% were from dogs and 19% from other wild and domestic animals. In Cx. quinquefasciatus, 67% of blood meals were derived from chicken, 22% came from dogs, 9% from various wild avian species, and 2% from other mammals including one human, one cat, and one pig. We developed a model for the reproductive number, R0, for Zika virus (ZIKV) in South Texas relative to northern Mexico using human disease data from Tamaulipas, Mexico. We show that ZIKV R0 in South Texas communities could be greater than one if the risk of human exposure to Ae. aegypti bites in these communities is at least 60% that of Northern Mexico communities. The high utilization of non-human vertebrates and low risk of human exposure in South Texas diminishes the outbreak potential for human-amplified urban arboviruses transmitted by Ae. aegypti.
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Affiliation(s)
- Mark F. Olson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
| | - Martial L. Ndeffo-Mbah
- Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA;
| | - Jose G. Juarez
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
| | - Selene Garcia-Luna
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
| | - Estelle Martin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
| | - Monica K. Borucki
- Biosciences and Biotechnology Division, Chemistry, Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.K.B.); (M.F.)
| | - Matthias Frank
- Biosciences and Biotechnology Division, Chemistry, Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.K.B.); (M.F.)
| | - José Guillermo Estrada-Franco
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Cd. Reynosa 88710, Tamaulipas, Mexico; (J.G.E.-F.); (M.A.R.-P.); (N.A.F.-S.)
| | - Mario A. Rodríguez-Pérez
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Cd. Reynosa 88710, Tamaulipas, Mexico; (J.G.E.-F.); (M.A.R.-P.); (N.A.F.-S.)
| | - Nadia A. Fernández-Santos
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Cd. Reynosa 88710, Tamaulipas, Mexico; (J.G.E.-F.); (M.A.R.-P.); (N.A.F.-S.)
| | - Gloria de Jesús Molina-Gamboa
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Santos Daniel Carmona Aguirre
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Bernardita de Lourdes Reyes-Berrones
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Luis Javier Cortés-De la cruz
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Alejandro García-Barrientos
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Raúl E. Huidobro-Guevara
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Regina M. Brussolo-Ceballos
- Secretary of Health of the State of Tamaulipas, Epidemiology Directorate, Cd. Victoria 87000, Tamaulipas, Mexico; (G.d.J.M.-G.); (S.D.C.A.); (B.d.L.R.-B.); (L.J.C.-D.l.c.); (A.G.-B.); (R.E.H.-G.); (R.M.B.-C.)
| | - Josue Ramirez
- Health Department, City of Harlingen, TX 78550, USA;
| | - Aaron Salazar
- Hidalgo County Health & Human Services, Edinburg, TX 78539, USA;
| | - Luis F. Chaves
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Apartado Postal, Tres Ríos, Cartago 4-2250, Costa Rica;
| | - Ismael E. Badillo-Vargas
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
| | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (M.F.O.); (J.G.J.); (S.G.-L.); (E.M.); (I.E.B.-V.)
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26
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Sadeghieh T, Waddell LA, Ng V, Hall A, Sargeant J. A scoping review of importation and predictive models related to vector-borne diseases, pathogens, reservoirs, or vectors (1999-2016). PLoS One 2020; 15:e0227678. [PMID: 31940405 PMCID: PMC6961930 DOI: 10.1371/journal.pone.0227678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/25/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND As globalization and climate change progress, the expansion and introduction of vector-borne diseases (VBD) from endemic regions to non-endemic regions is expected to occur. Mathematical and statistical models can be useful in predicting when and where these changes in distribution may happen. Our objective was to conduct a scoping review to identify and characterize predictive and importation models related to vector-borne diseases that exist in the global literature. METHODS A literature search was conducted to identify publications published between 1999 and 2016 from five scientific databases using relevant keywords. All publications had to be in English or French, and include a predictive or importation model on VBDs, pathogens, reservoirs and/or vectors. Relevance screening and data characterization were performed by two reviewers using pretested forms. The data were analyzed using descriptive statistics. RESULTS The search initially identified 19 710 unique articles, reports, and conference abstracts. This was reduced to 428 relevant documents after relevance screening and data charting. About half of the models used mathematical techniques, and the remainder were statistical. Most of the models were predictive (87%), rather than importation (5%). The most commonly investigated diseases were malaria and dengue fever. Around 12% of the publications did not report all the parameters used in their model. Only 29% of the models incorporated the impacts of climate change. CONCLUSIONS A wide variety of mathematical and statistical models on vector-borne diseases exist. Researchers creating their own mathematical and/or statistical models may be able to use this scoping review to be informed about the diseases and/or regions, parameters, model types, and methodologies used in published models.
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Affiliation(s)
- Tara Sadeghieh
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Lisa A. Waddell
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victoria Ng
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Alexandra Hall
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jan Sargeant
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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27
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Bi Q, Goodman KE, Kaminsky J, Lessler J. What is Machine Learning? A Primer for the Epidemiologist. Am J Epidemiol 2019; 188:2222-2239. [PMID: 31509183 DOI: 10.1093/aje/kwz189] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 07/29/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022] Open
Abstract
Machine learning is a branch of computer science that has the potential to transform epidemiologic sciences. Amid a growing focus on "Big Data," it offers epidemiologists new tools to tackle problems for which classical methods are not well-suited. In order to critically evaluate the value of integrating machine learning algorithms and existing methods, however, it is essential to address language and technical barriers between the two fields that can make it difficult for epidemiologists to read and assess machine learning studies. Here, we provide an overview of the concepts and terminology used in machine learning literature, which encompasses a diverse set of tools with goals ranging from prediction to classification to clustering. We provide a brief introduction to 5 common machine learning algorithms and 4 ensemble-based approaches. We then summarize epidemiologic applications of machine learning techniques in the published literature. We recommend approaches to incorporate machine learning in epidemiologic research and discuss opportunities and challenges for integrating machine learning and existing epidemiologic research methods.
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Affiliation(s)
- Qifang Bi
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Katherine E Goodman
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Joshua Kaminsky
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Justin Lessler
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
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28
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Armstrong PM, Ehrlich HY, Magalhaes T, Miller MR, Conway PJ, Bransfield A, Misencik MJ, Gloria-Soria A, Warren JL, Andreadis TG, Shepard JJ, Foy BD, Pitzer VE, Brackney DE. Successive blood meals enhance virus dissemination within mosquitoes and increase transmission potential. Nat Microbiol 2019; 5:239-247. [PMID: 31819213 PMCID: PMC7199921 DOI: 10.1038/s41564-019-0619-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/23/2019] [Indexed: 01/07/2023]
Abstract
The recent Zika virus (ZIKV) and chikungunya virus (CHIKV) epidemics highlight the explosive nature of arthropod-borne (arbo)viruses transmitted by Aedes spp. mosquitoes1,2. Vector competence and the extrinsic incubation period (EIP) are two key entomological parameters used to assess the public health risk posed by arboviruses3. These are typically measured empirically by offering mosquitoes an infectious bloodmeal and temporally sampling mosquitoes to determine infection and transmission status. This approach has been used for the better part of a century; however, it does not accurately capture the biology and behavior of many mosquito vectors which refeed frequently (every 2–3 days)4. Here we demonstrate that acquisition of a second non-infectious bloodmeal significantly shortens the EIP of ZIKV-infected Ae. aegypti by enhancing virus dissemination from the mosquito midgut. Similarly, a second bloodmeal increases the competence of this species for dengue virus and CHIKV as well as Ae. albopictus for ZIKV, suggesting that this phenomenon may be common among other virus-vector pairings and that Ae. albopictus might be a more important vector than once thought. Bloodmeal-induced microperforations in the virus-impenetrable basal lamina which surrounds the midgut provide a mechanism for enhanced virus escape. Modeling of these findings reveals that a shortened EIP would result in a significant increase in the basic reproductive number, R0, estimated from experimental data. This helps explain how Ae. aegypti can sustain explosive epidemics like ZIKV despite relatively poor vector competence in single-feed laboratory trials. Together, these data demonstrate a direct and unrecognized link between mosquito feeding behavior, EIP, and vector competence.
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Affiliation(s)
- Philip M Armstrong
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
| | - Hanna Y Ehrlich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Tereza Magalhaes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Patrick J Conway
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA.,Department of Biomedical Sciences, Quinnipiac University, Hamden, CT, USA
| | - Angela Bransfield
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Michael J Misencik
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Andrea Gloria-Soria
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Theodore G Andreadis
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - John J Shepard
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Brian D Foy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Doug E Brackney
- Center for Vector-Borne and Zoonotic Diseases, Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
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Kamiya T, Greischar MA, Wadhawan K, Gilbert B, Paaijmans K, Mideo N. Temperature-dependent variation in the extrinsic incubation period elevates the risk of vector-borne disease emergence. Epidemics 2019; 30:100382. [PMID: 32004794 DOI: 10.1016/j.epidem.2019.100382] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying ecological drivers of disease transmission is central to understanding disease risks. For vector-borne diseases, temperature is a major determinant of transmission because vital parameters determining the fitness of parasites and vectors are highly temperature-sensitive, including the extrinsic incubation period required for parasites to develop within the vector. Temperature also underlies dramatic differences in the individual-level variation in the extrinsic incubation period, yet the influence of this variation in disease transmission is largely unexplored. We incorporate empirical estimates of dengue virus extrinsic incubation period and its variation across a range of temperatures into a stochastic model to examine the consequences for disease emergence. We find that such variation impacts the probability of disease emergence because exceptionally rapid, but empirically observed incubation - typically ignored by modelling only the average - increases the chance of disease emergence even at the limits of the temperature range for dengue transmission. We show that variation in the extrinsic incubation period causes the greatest proportional increase in the risk of disease emergence at cooler temperatures where the mean incubation period is long, and associated variation is large. Thus, ignoring EIP variation will likely lead to underestimation of the risk of vector-borne disease emergence in temperate climates.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Megan A Greischar
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Kiran Wadhawan
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Benjamin Gilbert
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Krijn Paaijmans
- Center for Evolution & Medicine, Biodesign Center for Immunotherapy, Vaccines and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
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A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern. PLoS Negl Trop Dis 2019; 13:e0007451. [PMID: 31584946 PMCID: PMC6805005 DOI: 10.1371/journal.pntd.0007451] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/22/2019] [Accepted: 08/27/2019] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016-2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was. METHODS To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers. RESULTS 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies. CONCLUSIONS Many ZIKV predictions were published during the 2016-2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics.
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Mordecai EA, Caldwell JM, Grossman MK, Lippi CA, Johnson LR, Neira M, Rohr JR, Ryan SJ, Savage V, Shocket MS, Sippy R, Stewart Ibarra AM, Thomas MB, Villena O. Thermal biology of mosquito-borne disease. Ecol Lett 2019; 22:1690-1708. [PMID: 31286630 PMCID: PMC6744319 DOI: 10.1111/ele.13335] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/22/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Mosquito-borne diseases cause a major burden of disease worldwide. The vital rates of these ectothermic vectors and parasites respond strongly and nonlinearly to temperature and therefore to climate change. Here, we review how trait-based approaches can synthesise and mechanistically predict the temperature dependence of transmission across vectors, pathogens, and environments. We present 11 pathogens transmitted by 15 different mosquito species - including globally important diseases like malaria, dengue, and Zika - synthesised from previously published studies. Transmission varied strongly and unimodally with temperature, peaking at 23-29ºC and declining to zero below 9-23ºC and above 32-38ºC. Different traits restricted transmission at low versus high temperatures, and temperature effects on transmission varied by both mosquito and parasite species. Temperate pathogens exhibit broader thermal ranges and cooler thermal minima and optima than tropical pathogens. Among tropical pathogens, malaria and Ross River virus had lower thermal optima (25-26ºC) while dengue and Zika viruses had the highest (29ºC) thermal optima. We expect warming to increase transmission below thermal optima but decrease transmission above optima. Key directions for future work include linking mechanistic models to field transmission, combining temperature effects with control measures, incorporating trait variation and temperature variation, and investigating climate adaptation and migration.
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Affiliation(s)
- Erin A. Mordecai
- Department of BiologyStanford University371 Serra MallStanfordCAUSA
| | | | - Marissa K. Grossman
- Department of Entomology and Center for Infectious Disease DynamicsPenn State UniversityUniversity ParkPA16802USA
| | - Catherine A. Lippi
- Department of Geography and Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Leah R. Johnson
- Department of StatisticsVirginia Polytechnic and State University250 Drillfield DriveBlacksburgVAUSA
| | - Marco Neira
- Center for Research on Health in Latin America (CISeAL)Pontificia Universidad Católica del EcuadorQuitoEcuador
| | - Jason R. Rohr
- Department of Biological SciencesEck Institute of Global HealthEnvironmental Change InitiativeUniversity of Notre Dame, Notre DameINUSA
| | - Sadie J. Ryan
- Department of Geography and Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Van Savage
- Department of Ecology and Evolutionary Biology and Department of BiomathematicsUniversity of California Los AngelesLos AngelesCA90095USA
- Santa Fe Institute1399 Hyde Park RdSanta FeNM87501USA
| | - Marta S. Shocket
- Department of BiologyStanford University371 Serra MallStanfordCAUSA
| | - Rachel Sippy
- Department of Geography and Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
- Institute for Global Health and Translational SciencesSUNY Upstate Medical UniversitySyracuseNY13210USA
| | - Anna M. Stewart Ibarra
- Institute for Global Health and Translational SciencesSUNY Upstate Medical UniversitySyracuseNY13210USA
| | - Matthew B. Thomas
- Department of Entomology and Center for Infectious Disease DynamicsPenn State UniversityUniversity ParkPA16802USA
| | - Oswaldo Villena
- Department of StatisticsVirginia Polytechnic and State University250 Drillfield DriveBlacksburgVAUSA
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Fox SJ, Bellan SE, Perkins TA, Johansson MA, Meyers LA. Downgrading disease transmission risk estimates using terminal importations. PLoS Negl Trop Dis 2019; 13:e0007395. [PMID: 31199809 PMCID: PMC6594658 DOI: 10.1371/journal.pntd.0007395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 06/26/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022] Open
Abstract
As emerging and re-emerging infectious arboviruses like dengue, chikungunya, and Zika threaten new populations worldwide, officials scramble to assess local severity and transmissibility, with little to no epidemiological history to draw upon. Indirect estimates of risk from vector habitat suitability maps are prone to great uncertainty, while direct estimates from epidemiological data are only possible after cases accumulate and, given environmental constraints on arbovirus transmission, cannot be widely generalized beyond the focal region. Combining these complementary methods, we use disease importation and transmission data to improve the accuracy and precision of a priori ecological risk estimates. We demonstrate this approach by estimating the spatiotemporal risks of Zika virus transmission throughout Texas, a high-risk region in the southern United States. Our estimates are, on average, 80% lower than published ecological estimates-with only six of 254 Texas counties deemed capable of sustaining a Zika epidemic-and they are consistent with the number of autochthonous cases detected in 2017. Importantly our method provides a framework for model comparison, as our mechanistic understanding of arbovirus transmission continues to improve. Real-time updating of prior risk estimates as importations and outbreaks arise can thereby provide critical, early insight into local transmission risks as emerging arboviruses expand their global reach.
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Affiliation(s)
- Spencer J. Fox
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Steven E. Bellan
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Gerogia, United States of America
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Michael A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Ancel Meyers
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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McHale TC, Romero-Vivas CM, Fronterre C, Arango-Padilla P, Waterlow NR, Nix CD, Falconar AK, Cano J. Spatiotemporal Heterogeneity in the Distribution of Chikungunya and Zika Virus Case Incidences during their 2014 to 2016 Epidemics in Barranquilla, Colombia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E1759. [PMID: 31109024 PMCID: PMC6572372 DOI: 10.3390/ijerph16101759] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022]
Abstract
Chikungunya virus (CHIKV) and Zika virus (ZIKV) have recently emerged as globally important infections. This study aimed to explore the spatiotemporal heterogeneity in the occurrence of CHIKV and ZIKV outbreaks throughout the major international seaport city of Barranquilla, Colombia in 2014 and 2016 and the potential for clustering. Incidence data were fitted using multiple Bayesian Poisson models based on multiple explanatory variables as potential risk factors identified from other studies and options for random effects. A best fit model was used to analyse their case incidence risks and identify any risk factors during their epidemics. Neighbourhoods in the northern region were hotspots for both CHIKV and ZIKV outbreaks. Additional hotspots occurred in the southwestern and some eastern/southeastern areas during their outbreaks containing part of, or immediately adjacent to, the major circular city road with its import/export cargo warehouses and harbour area. Multivariate conditional autoregressive models strongly identified higher socioeconomic strata and living in a neighbourhood near a major road as risk factors for ZIKV case incidences. These findings will help to appropriately focus vector control efforts but also challenge the belief that these infections are driven by social vulnerability and merit further study both in Barranquilla and throughout the world's tropical and subtropical regions.
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Affiliation(s)
- Thomas C McHale
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, London WCIE 7HT, UK.
| | | | - Claudio Fronterre
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, London WCIE 7HT, UK.
| | - Pedro Arango-Padilla
- Programa de Prevención y Control de Enfermedades Trasmitidas por Vectores, Secretaria de Salud Distrital, Barranquilla 081007, Colombia.
| | - Naomi R Waterlow
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, London WCIE 7HT, UK.
| | - Chad D Nix
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, London WCIE 7HT, UK.
| | - Andrew K Falconar
- Departamento de Medicina, Universidad del Norte, Barranquilla 081007, Colombia.
| | - Jorge Cano
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, London WCIE 7HT, UK.
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Global expansion and redistribution of Aedes-borne virus transmission risk with climate change. PLoS Negl Trop Dis 2019; 13:e0007213. [PMID: 30921321 PMCID: PMC6438455 DOI: 10.1371/journal.pntd.0007213] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022] Open
Abstract
Forecasting the impacts of climate change on Aedes-borne viruses-especially dengue, chikungunya, and Zika-is a key component of public health preparedness. We apply an empirically parameterized model of viral transmission by the vectors Aedes aegypti and Ae. albopictus, as a function of temperature, to predict cumulative monthly global transmission risk in current climates, and compare them with projected risk in 2050 and 2080 based on general circulation models (GCMs). Our results show that if mosquito range shifts track optimal temperature ranges for transmission (21.3-34.0°C for Ae. aegypti; 19.9-29.4°C for Ae. albopictus), we can expect poleward shifts in Aedes-borne virus distributions. However, the differing thermal niches of the two vectors produce different patterns of shifts under climate change. More severe climate change scenarios produce larger population exposures to transmission by Ae. aegypti, but not by Ae. albopictus in the most extreme cases. Climate-driven risk of transmission from both mosquitoes will increase substantially, even in the short term, for most of Europe. In contrast, significant reductions in climate suitability are expected for Ae. albopictus, most noticeably in southeast Asia and west Africa. Within the next century, nearly a billion people are threatened with new exposure to virus transmission by both Aedes spp. in the worst-case scenario. As major net losses in year-round transmission risk are predicted for Ae. albopictus, we project a global shift towards more seasonal risk across regions. Many other complicating factors (like mosquito range limits and viral evolution) exist, but overall our results indicate that while climate change will lead to increased net and new exposures to Aedes-borne viruses, the most extreme increases in Ae. albopictus transmission are predicted to occur at intermediate climate change scenarios.
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Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nat Microbiol 2019; 4:854-863. [PMID: 30833735 PMCID: PMC6522366 DOI: 10.1038/s41564-019-0376-y] [Citation(s) in RCA: 536] [Impact Index Per Article: 107.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 12/20/2022]
Abstract
The global population at risk from mosquito-borne diseases—including dengue, yellow fever, chikungunya and Zika—is expanding in concert with changes in the distribution of two key vectors: Aedes aegypti and Aedes albopictus. The distribution of these species is largely driven by both human movement and the presence of suitable climate. Using statistical mapping techniques, we show that human movement patterns explain the spread of both species in Europe and the United States following their introduction. We find that the spread of Ae. aegypti is characterized by long distance importations, while Ae. albopictus has expanded more along the fringes of its distribution. We describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. Global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and Zika viruses must consider the so far unabated spread of these mosquitos. Our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally. Statistical mapping techniques provide insights into the spread of two key arbovirus vectors in Europe and the United States, and predict the future distributions of both mosquitoes in response to accelerating urbanization, connectivity and climate change.
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Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. Arbovirus coinfection and co-transmission: A neglected public health concern? PLoS Biol 2019; 17:e3000130. [PMID: 30668574 PMCID: PMC6358106 DOI: 10.1371/journal.pbio.3000130] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/01/2019] [Indexed: 12/21/2022] Open
Abstract
Epidemiological synergy between outbreaks of viruses transmitted by Aedes aegypti mosquitoes, such as chikungunya, dengue, and Zika viruses, has resulted in coinfection of humans with multiple viruses. Despite the potential impact on public health, we know only little about the occurrence and consequences of such coinfections. Here, we review the impact of coinfection on clinical disease in humans, discuss the possibility for co-transmission from mosquito to human, and describe a role for modeling transmission dynamics at various levels of co-transmission. Solving the mystery of virus coinfections will reveal whether they should be viewed as a serious concern for public health.
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Affiliation(s)
- Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Claudia Rückert
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Sean M. Cavany
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail:
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Kao YH, Eisenberg MC. Practical unidentifiability of a simple vector-borne disease model: Implications for parameter estimation and intervention assessment. Epidemics 2018; 25:89-100. [PMID: 29903539 PMCID: PMC6264791 DOI: 10.1016/j.epidem.2018.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 12/25/2022] Open
Abstract
Mathematical modeling has an extensive history in vector-borne disease epidemiology, and is increasingly used for prediction, intervention design, and understanding mechanisms. Many studies rely on parameter estimation to link models and data, and to tailor predictions and counterfactuals to specific settings. However, few studies have formally evaluated whether vector-borne disease models can properly estimate the parameters of interest given the constraints of a particular dataset. Identifiability analysis allows us to examine whether model parameters can be estimated uniquely-a lack of consideration of such issues can result in misleading or incorrect parameter estimates and model predictions. Here, we evaluate both structural (theoretical) and practical identifiability of a commonly used compartmental model of mosquito-borne disease, using the 2010 dengue epidemic in Taiwan as a case study. We show that while the model is structurally identifiable, it is practically unidentifiable under a range of human and mosquito time series measurement scenarios. In particular, the transmission parameters form a practically identifiable combination and thus cannot be estimated separately, potentially leading to incorrect predictions of the effects of interventions. However, in spite of the unidentifiability of the individual parameters, the basic reproduction number was successfully estimated across the unidentifiable parameter ranges. These identifiability issues can be resolved by directly measuring several additional human and mosquito life-cycle parameters both experimentally and in the field. While we only consider the simplest case for the model, we show that a commonly used model of vector-borne disease is unidentifiable from human and mosquito incidence data, making it difficult or impossible to estimate parameters or assess intervention strategies. This work illustrates the importance of examining identifiability when linking models with data to make predictions and inferences, and particularly highlights the importance of combining laboratory, field, and case data if we are to successfully estimate epidemiological and ecological parameters using models.
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Affiliation(s)
- Yu-Han Kao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States
| | - Marisa C Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States; Department of Mathematics, University of Michigan, Ann Arbor, MI, United States.
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Alaniz AJ, Carvajal MA, Bacigalupo A, Cattan PE. Global spatial assessment of Aedes aegypti and Culex quinquefasciatus: a scenario of Zika virus exposure. Epidemiol Infect 2018; 147:e52. [PMID: 30474578 PMCID: PMC6518585 DOI: 10.1017/s0950268818003102] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/12/2018] [Accepted: 10/27/2018] [Indexed: 02/04/2023] Open
Abstract
Zika virus (ZIKV) is an arbovirus transmitted mainly by Aedes aegypti mosquitoes. Recent scientific evidence on Culex quinquefasciatus has suggested its potential as a vector for ZIKV, which may change the current risk zones. We aimed to quantify the world population potentially exposed to ZIKV in a spatially explicit way, considering the primary vector (A. aegypti) and the potential vector (C. quinquefasciatus). Our model combined species distribution modelling of mosquito species with spatially explicit human population data to estimate ZIKV exposure risk. We estimated the potential global distribution of C. quinquefasciatus and estimated its potential interaction zones with A. aegypti. Then we evaluated the risk zones for ZIKV considering both vectors. Finally, we quantified and compared the people under risk associated with each vector by risk level, country and continent. We found that C. quinquefasciatus had a more temperate distribution until 42° in both hemispheres, while the risk involving A. aegypti is concentrated mainly in tropical latitudes until 35° in both hemispheres. Globally, 4.2 billion people are under risk associated with ZIKV. Around 2.6 billon people are under very high risk associated with C. quinquefasciatus and 1 billion people associated with A. aegypti. Several countries could be exposed to ZIKV, which emphasises the need to clarify the competence of C. quinquefasciatus as a potential vector as soon as possible. The models presented here represent a tool for risk management, public health planning, mosquito control and preventive actions, especially to focus efforts on the most affected areas.
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Affiliation(s)
- Alberto J. Alaniz
- Centro de Estudios en Ecología Espacial y Medio Ambiente – Ecogeografía, Santiago, Chile
- Laboratorio de Ecología, Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Mario A. Carvajal
- Centro de Estudios en Ecología Espacial y Medio Ambiente – Ecogeografía, Santiago, Chile
| | - Antonella Bacigalupo
- Laboratorio de Ecología, Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Pedro E. Cattan
- Laboratorio de Ecología, Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Argüelles-Nava VG, Alvarez-Bañuelos MT, Córdoba-Suárez D, Sampieri CL, Ortiz-León MC, Riande-Juárez G, Montero H. Knowledge, Attitudes, and Practices about Zika among a University Community Located in an Endemic Zone in Mexico. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E2548. [PMID: 30441747 PMCID: PMC6267223 DOI: 10.3390/ijerph15112548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/04/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022]
Abstract
To assess the knowledge, attitudes, and practices about the Zika virus in both students and workers at the University of Veracruz, an online survey was conducted. The participants were divided into two groups: one according to sex, the other according to whether they were workers or students. Their answers were classified into knowledge, attitudes, and practices and they were rated as low, medium, and high. The results showed that knowledge about Zika prevailing among the university population is considered as medium in 79.4% of the study population. Most respondents know that the mosquito spreads the Zika virus (98.8%) and the clinical characteristics, while sexual transmission by the virus is little known (36.85%). Both the univariate analysis (OR (CI5) 0.227 (0.070⁻0.735), p = 0.013] and multivariate analysis (OR (CI95) 0.234 (0.071⁻778), p = 0.018] showed that belonging to the health sciences area is related to having a greater knowledge about Zika. Despite the existing knowledge, a low level of prevention practices prevails in the whole community (55%). A medium level of knowledge about Zika prevailed, while proper implementation of preventive measures for Zika is low, despite the fact that the state of Veracruz-the place where the University is located-is an endemic area.
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Affiliation(s)
| | | | - Daniel Córdoba-Suárez
- Licenciatura en Ciencias y Técnicas Estadísticas, Universidad Veracruzana, Xalapa 91000, Veracruz, Mexico.
| | - Clara L Sampieri
- Instituto de Salud Pública, Universidad Veracruzana, Xalapa 91190, Veracruz, Mexico.
| | - María C Ortiz-León
- Instituto de Salud Pública, Universidad Veracruzana, Xalapa 91190, Veracruz, Mexico.
| | - Gabriel Riande-Juárez
- Instituto de Salud Pública, Universidad Veracruzana, Xalapa 91190, Veracruz, Mexico.
| | - Hilda Montero
- Instituto de Salud Pública, Universidad Veracruzana, Xalapa 91190, Veracruz, Mexico.
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40
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Abstract
A growing number of infectious pathogens are spreading among geographic regions. Some pathogens that were previously not considered to pose a general threat to human health have emerged at regional and global scales, such as Zika and Ebola Virus Disease. Other pathogens, such as yellow fever virus, were previously thought to be under control but have recently re-emerged, causing new challenges to public health organisations. A wide array of new modelling techniques, aided by increased computing capabilities, novel diagnostic tools, and the increased speed and availability of genomic sequencing allow researchers to identify new pathogens more rapidly, assess the likelihood of geographic spread, and quantify the speed of human-to-human transmission. Despite some initial successes in predicting the spread of acute viral infections, the practicalities and sustainability of such approaches will need to be evaluated in the context of public health responses.
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Sun K, Zhang Q, Pastore-Piontti A, Chinazzi M, Mistry D, Dean NE, Rojas DP, Merler S, Poletti P, Rossi L, Halloran ME, Longini IM, Vespignani A. Quantifying the risk of local Zika virus transmission in the contiguous US during the 2015-2016 ZIKV epidemic. BMC Med 2018; 16:195. [PMID: 30336778 PMCID: PMC6194624 DOI: 10.1186/s12916-018-1185-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/28/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Local mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties in the contiguous United States (US), prompting the issuance of travel, prevention, and testing guidance across the contiguous US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transmission across different areas of the US. METHODS We present a framework for the projection of ZIKV autochthonous transmission in the contiguous US during the 2015-2016 epidemic using a data-driven stochastic and spatial epidemic model accounting for seasonal, environmental, and detailed population data. The model generates an ensemble of travel-related case counts and simulates their potential to have triggered local transmission at the individual level in the 2015-2016 ZIKV epidemic. RESULTS We estimate the risk of ZIKV introduction and local transmission at the county level and at the 0.025° × 0.025° cell level across the contiguous US. We provide a risk measure based on the probability of observing local transmission in a specific location during a ZIKV epidemic modeled after the epidemic observed during the years 2015-2016. The high spatial and temporal resolution of the model allows us to generate statistical estimates of the number of ZIKV introductions leading to local transmission in each location. We find that the risk was spatially heterogeneously distributed and concentrated in a few specific areas that account for less than 1% of the contiguous US population. Locations in Texas and Florida that have actually experienced local ZIKV transmission were among the places at highest risk according to our results. We also provide an analysis of the key determinants for local transmission and identify the key introduction routes and their contributions to ZIKV transmission in the contiguous US. CONCLUSIONS This framework provides quantitative risk estimates, fully captures the stochasticity of ZIKV introduction events, and is not biased by the under-ascertainment of cases due to asymptomatic cases. It provides general information on key risk determinants and data with potential uses in defining public health recommendations and guidance about ZIKV risk in the US.
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Affiliation(s)
- Kaiyuan Sun
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA
| | - Qian Zhang
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA
| | - Ana Pastore-Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA
| | - Dina Mistry
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA
| | - Natalie E Dean
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, 32611, USA
| | - Diana Patricia Rojas
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, 32611, USA
| | | | | | - Luca Rossi
- Institute for Scientific Interchange Foundation, 10126, Turin, Italy
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, USA
- Department of Biostatistics, University of Washington, Seattle, 98195, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, 32611, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, 02115, USA.
- Institute for Scientific Interchange Foundation, 10126, Turin, Italy.
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O'Reilly KM, Lowe R, Edmunds WJ, Mayaud P, Kucharski A, Eggo RM, Funk S, Bhatia D, Khan K, Kraemer MUG, Wilder-Smith A, Rodrigues LC, Brasil P, Massad E, Jaenisch T, Cauchemez S, Brady OJ, Yakob L. Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis. BMC Med 2018; 16:180. [PMID: 30285863 PMCID: PMC6169075 DOI: 10.1186/s12916-018-1158-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Zika virus (ZIKV) emerged in Latin America and the Caribbean (LAC) region in 2013, with serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and the lack of a comprehensive collation of data from affected countries. METHODS Our analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 90 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vectorial capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories. RESULTS There was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 would present within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (p < 0.05) with the reported peak in incidence. The reporting rate varied across countries, with lower reporting rates for those with only confirmed cases compared to those who reported both confirmed and suspected cases. CONCLUSIONS The findings suggest that the ZIKV epidemic is by and large over within LAC, with incidence projected to be low in most cities in 2018. Local low levels of transmission are probable, but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.
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Affiliation(s)
- Kathleen M O'Reilly
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK. .,Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.,Barcelona Institute for Global Health (ISGLOBAL), Barcelona, Spain
| | - W John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Philippe Mayaud
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Rosalind M Eggo
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Deepit Bhatia
- Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada.,Centre for Research on Inner City Health, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Toronto, ON, Canada
| | - Kamran Khan
- Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada.,Centre for Research on Inner City Health, Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Toronto, ON, Canada
| | - Moritz U G Kraemer
- Harvard Medical School, Harvard University, Boston, MA, USA.,Boston Children's Hospital, Boston, MA, USA.,Department of Zoology, University of Oxford, Oxford, UK
| | - Annelies Wilder-Smith
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK.,Department of Medicine and Public Health, Umea University, Umea, Sweden.,Institute of Public Health, University of Heidelberg, Heidelberg, Germany
| | - Laura C Rodrigues
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Patricia Brasil
- Instituto Nacional de Infectologia Evandro Chagas/Fiocruz, Rio de Janeiro, Brazil
| | - Eduardo Massad
- School of Applied Mathematics, Fundacao Getulio Vargas, Rio de Janeiro, Brazil
| | - Thomas Jaenisch
- Department for Infectious Diseases and Parasitology, Department for Infectious Diseases, University of Heidelberg, Heidelberg, Germany
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Oliver J Brady
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Laith Yakob
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK.,Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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43
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Arora N, Banerjee AK, Narasu ML. Zika outbreak aftermath: status, progress, concerns and new insights. Future Virol 2018. [DOI: 10.2217/fvl-2018-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika, a neurotrophic virus belonging to Flaviviridae family of viruses and transmitted by vector mosquitoes of Aedes species, took the world by storm during its recent outbreak. Its spread to newer territories, unprecedented pace of transmission, lack of existing therapeutic agents and vaccines and an empty drug pipeline raised an alarm. Uncertainty about full spectrum of diseases and its long-term consequences, newly discovered modes of transmission and controversies over vector status of mosquito species like Culex quinquefasciatus led to layers of complexity and presented new hurdles and challenges in Zika virus research. This review summarizes the progress and updates of efforts, concerns, financial burden and available resources in light of newly acquired knowledge in Zika virus research.
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Affiliation(s)
- Neelima Arora
- Centre for Biotechnology, Institute of Science & Technology (Autonomous), Jawaharlal Nehru Technological University-Hyderabad, Kukatpally, Hyderabad 500085, Telangana, India
| | - Amit K Banerjee
- Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India
| | - Mangamoori L Narasu
- Centre for Biotechnology, Institute of Science & Technology (Autonomous), Jawaharlal Nehru Technological University-Hyderabad, Kukatpally, Hyderabad 500085, Telangana, India
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44
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Kollars TM. Potential for the Invasive Species Aedes Albopictus and Arboviral Transmission through the Chabahar Port in Iran. IRANIAN JOURNAL OF MEDICAL SCIENCES 2018; 43:393-400. [PMID: 30046208 PMCID: PMC6055213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dengue, chikungunya, and Zika viruses are emerging infectious disease threats wherever suitable vectors, hosts, and habitat are present. The aim of the present study was to use the bioagent transport and environmental modeling system (BioTEMS) to identify the potential for arbovirus-infected Aedes species to invade the Chabahar area in southeastern Iran. METHODS ArcGIS geospatial analysis software, Statistica software, and BioTEMS were used to analyze geographic information and conduct data analysis. BioTEMS utilizes up to several hundred abiotic and biotic factors to produce risk and vulnerability assessments for biological agents and infectious diseases. The output of BioTEMS was validated using published predictive models, and most importantly published collection data of Aedes species in Iran. RESULTS There appears to have been two separate invasion events by Ae. albopictus into the southern region of Iran, first preceding 2009 and then again in 2013. BioTEMS identified two probable areas of introduction during the 2009 time frame, either through one or both the Chabahar ports or the Iranshahr airport with subsequent spread through vehicular transport. BioTEMS identified the port as an introduction zone for ZIKAV with high-risk zones and identifies gap zones during the 2013 time frame. Recommended surveillance sites are provided. CONCLUSION The air and maritime ports of Iran serve international customers, and are therefore vulnerable to import and invasion of mosquito vectors and arboviruses. Based on comparisons with other published low-resolution models, BioTEMS provides information for medical and public health professionals conducting integrated mosquito management, preventive medicine, and epidemiological surveillance.
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45
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Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG. Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico. Cell Host Microbe 2018; 23:855-864.e7. [PMID: 29805095 PMCID: PMC6006413 DOI: 10.1016/j.chom.2018.04.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tony Li
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mariateresa de Cesare
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Angel Balmaseda
- Laboratory Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rory Bowden
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | - Trevor Brooks
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medcine, Baltimore, MD, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - José E Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cesar R González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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Structural and Practical Identifiability Analysis of Zika Epidemiological Models. Bull Math Biol 2018; 80:2209-2241. [PMID: 29948883 DOI: 10.1007/s11538-018-0453-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
The Zika virus (ZIKV) epidemic has caused an ongoing threat to global health security and spurred new investigations of the virus. Use of epidemiological models for arbovirus diseases can be a powerful tool to assist in prevention and control of the emerging disease. In this article, we introduce six models of ZIKV, beginning with a general vector-borne model and gradually including different transmission routes of ZIKV. These epidemiological models use various combinations of disease transmission (vector and direct) and infectious classes (asymptomatic and pregnant), with addition to loss of immunity being included. The disease-induced death rate is omitted from the models. We test the structural and practical identifiability of the models to find whether unknown model parameters can uniquely be determined. The models were fit to obtain time-series data of cumulative incidences and pregnant infections from the Florida Department of Health Daily Zika Update Reports. The average relative estimation errors (AREs) were computed from the Monte Carlo simulations to further analyze the identifiability of the models. We show that direct transmission rates are not practically identifiable; however, fixed recovery rates improve identifiability overall. We found ARE is low for each model (only slightly higher for those that account for a pregnant class) and help to confirm a reproduction number greater than one at the start of the Florida epidemic. Basic reproduction number, [Formula: see text], is an epidemiologically important threshold value which gives the number of secondary cases generated by one infected individual in a totally susceptible population in duration of infectiousness. Elasticity of the reproduction numbers suggests that the mosquito-to-human ratio, mosquito life span and biting rate have the greatest potential for reducing the reproduction number of Zika, and therefore, corresponding control measures need to be focused on.
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Riou J, Poletto C, Boëlle PY. Improving early epidemiological assessment of emerging Aedes-transmitted epidemics using historical data. PLoS Negl Trop Dis 2018; 12:e0006526. [PMID: 29864129 PMCID: PMC6002135 DOI: 10.1371/journal.pntd.0006526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 06/14/2018] [Accepted: 05/14/2018] [Indexed: 11/29/2022] Open
Abstract
Model-based epidemiological assessment is useful to support decision-making at the beginning of an emerging Aedes-transmitted outbreak. However, early forecasts are generally unreliable as little information is available in the first few incidence data points. Here, we show how past Aedes-transmitted epidemics help improve these predictions. The approach was applied to the 2015-2017 Zika virus epidemics in three islands of the French West Indies, with historical data including other Aedes-transmitted diseases (chikungunya and Zika) in the same and other locations. Hierarchical models were used to build informative a priori distributions on the reproduction ratio and the reporting rates. The accuracy and sharpness of forecasts improved substantially when these a priori distributions were used in models for prediction. For example, early forecasts of final epidemic size obtained without historical information were 3.3 times too high on average (range: 0.2 to 5.8) with respect to the eventual size, but were far closer (1.1 times the real value on average, range: 0.4 to 1.5) using information on past CHIKV epidemics in the same places. Likewise, the 97.5% upper bound for maximal incidence was 15.3 times (range: 2.0 to 63.1) the actual peak incidence, and became much sharper at 2.4 times (range: 1.3 to 3.9) the actual peak incidence with informative a priori distributions. Improvements were more limited for the date of peak incidence and the total duration of the epidemic. The framework can adapt to all forecasting models at the early stages of emerging Aedes-transmitted outbreaks.
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Affiliation(s)
- Julien Riou
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP UMR-S1136, F-75012 Paris, France
- EHESP School of Public Health, Rennes, France
| | - Chiara Poletto
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP UMR-S1136, F-75012 Paris, France
| | - Pierre-Yves Boëlle
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique, IPLESP UMR-S1136, F-75012 Paris, France
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48
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Bautista LE, Herrera VM. An assessment of public health surveillance of Zika virus infection and potentially associated outcomes in Latin America. BMC Public Health 2018; 18:656. [PMID: 29793453 PMCID: PMC5968501 DOI: 10.1186/s12889-018-5566-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We evaluated whether outbreaks of Zika virus (ZIKV) infection, newborn microcephaly, and Guillain-Barré syndrome (GBS) in Latin America may be detected through current surveillance systems, and how cases detected through surveillance may increase health care burden. METHODS We estimated the sensitivity and specificity of surveillance case definitions using published data. We assumed a 10% ZIKV infection risk during a non-outbreak period and hypothetical increases in risk during an outbreak period. We used sensitivity and specificity estimates to correct for non-differential misclassification, and calculated a misclassification-corrected relative risk comparing both periods. To identify the smallest hypothetical increase in risk resulting in a detectable outbreak we compared the misclassification-corrected relative risk to the relative risk corresponding to the upper limit of the endemic channel (mean + 2 SD). We also estimated the proportion of false positive cases detected during the outbreak. We followed the same approach for microcephaly and GBS, but assumed the risk of ZIKV infection doubled during the outbreak, and ZIKV infection increased the risk of both diseases. RESULTS ZIKV infection outbreaks were not detectable through non-serological surveillance. Outbreaks were detectable through serologic surveillance if infection risk increased by at least 10%, but more than 50% of all cases were false positive. Outbreaks of severe microcephaly were detected if ZIKV infection increased prevalence of this condition by at least 24.0 times. When ZIKV infection did not increase the prevalence of severe microcephaly, 34.7 to 82.5% of all cases were false positive, depending on diagnostic accuracy. GBS outbreaks were detected if ZIKV infection increased the GBS risk by at least seven times. For optimal GBS diagnosis accuracy, the proportion of false positive cases ranged from 29 to 54% and from 45 to 56% depending on the incidence of GBS mimics. CONCLUSIONS Current surveillance systems have a low probability of detecting outbreaks of ZIKV infection, severe microcephaly, and GBS, and could result in significant increases in health care burden, due to the detection of large numbers of false positive cases. In view of these limitations, Latin American countries should consider alternative options for surveillance.
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Affiliation(s)
- Leonelo E Bautista
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin at Madison, 610 Walnut Street, WARF 703, Madison, WI, 53726-2397, USA.
| | - Víctor M Herrera
- Center for Biomedical Research, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
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Huber JH, Childs ML, Caldwell JM, Mordecai EA. Seasonal temperature variation influences climate suitability for dengue, chikungunya, and Zika transmission. PLoS Negl Trop Dis 2018; 12:e0006451. [PMID: 29746468 PMCID: PMC5963813 DOI: 10.1371/journal.pntd.0006451] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/22/2018] [Accepted: 04/14/2018] [Indexed: 11/25/2022] Open
Abstract
Dengue, chikungunya, and Zika virus epidemics transmitted by Aedes aegypti mosquitoes have recently (re)emerged and spread throughout the Americas, Southeast Asia, the Pacific Islands, and elsewhere. Understanding how environmental conditions affect epidemic dynamics is critical for predicting and responding to the geographic and seasonal spread of disease. Specifically, we lack a mechanistic understanding of how seasonal variation in temperature affects epidemic magnitude and duration. Here, we develop a dynamic disease transmission model for dengue virus and Aedes aegypti mosquitoes that integrates mechanistic, empirically parameterized, and independently validated mosquito and virus trait thermal responses under seasonally varying temperatures. We examine the influence of seasonal temperature mean, variation, and temperature at the start of the epidemic on disease dynamics. We find that at both constant and seasonally varying temperatures, warmer temperatures at the start of epidemics promote more rapid epidemics due to faster burnout of the susceptible population. By contrast, intermediate temperatures (24–25°C) at epidemic onset produced the largest epidemics in both constant and seasonally varying temperature regimes. When seasonal temperature variation was low, 25–35°C annual average temperatures produced the largest epidemics, but this range shifted to cooler temperatures as seasonal temperature variation increased (analogous to previous results for diurnal temperature variation). Tropical and sub-tropical cities such as Rio de Janeiro, Fortaleza, and Salvador, Brazil; Cali, Cartagena, and Barranquilla, Colombia; Delhi, India; Guangzhou, China; and Manila, Philippines have mean annual temperatures and seasonal temperature ranges that produced the largest epidemics. However, more temperate cities like Shanghai, China had high epidemic suitability because large seasonal variation offset moderate annual average temperatures. By accounting for seasonal variation in temperature, the model provides a baseline for mechanistically understanding environmental suitability for virus transmission by Aedes aegypti. Overlaying the impact of human activities and socioeconomic factors onto this mechanistic temperature-dependent framework is critical for understanding likelihood and magnitude of outbreaks. Mosquito-borne viruses like dengue, Zika, and chikungunya have recently caused large epidemics that are partly driven by temperature. Using a mathematical model built from laboratory experimental data for Aedes aegypti mosquitoes and dengue virus, we examine the impact of variation in seasonal temperature regimes on epidemic size and duration. At constant temperatures, both low and high temperatures (20°C and 35°C) produce small epidemics, while intermediate temperatures like 25°C and 30°C produce much larger epidemics. In seasonally varying temperature environments, epidemics peak more rapidly at higher starting temperatures, while intermediate starting temperatures produce the largest epidemics. Seasonal mean temperatures of 25–35°C are most suitable for large epidemics when seasonality is low, but in more variable seasonal environments epidemic suitability peaks at lower annual average temperatures. Tropical and sub-tropical cities have the highest temperature suitability for epidemics, but more temperate cities with high seasonal variation also have the potential for very large epidemics.
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Affiliation(s)
- John H Huber
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Marissa L Childs
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Stanford, California, United States of America
| | - Jamie M Caldwell
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Erin A Mordecai
- Department of Biology, Stanford University, Stanford, California, United States of America
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Durham DP, Fitzpatrick MC, Ndeffo-Mbah ML, Parpia AS, Michael NL, Galvani AP. Evaluating Vaccination Strategies for Zika Virus in the Americas. Ann Intern Med 2018; 168:621-630. [PMID: 29610863 PMCID: PMC5955609 DOI: 10.7326/m17-0641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background Mosquito-borne and sexually transmitted Zika virus has become widespread across Central and South America and the Caribbean. Many Zika vaccine candidates are under active development. Objective To quantify the effect of Zika vaccine prioritization of females aged 9 to 49 years, followed by males aged 9 to 49 years, on incidence of prenatal Zika infections. Design A compartmental model of Zika transmission between mosquitoes and humans was developed and calibrated to empirical estimates of country-specific mosquito density. Mosquitoes were stratified into susceptible, exposed, and infected groups; humans were stratified into susceptible, exposed, infected, recovered, and vaccinated groups. Age-specific fertility rates, Zika sexual transmission, and country-specific demographics were incorporated. Setting 34 countries and territories in the Americas with documented Zika outbreaks. Target Population Males and females aged 9 to 49 years. Intervention Age- and sex-targeted immunization using a Zika vaccine with 75% efficacy. Measurements Annual prenatal Zika infections. Results For a base-case vaccine efficacy of 75% and vaccination coverage of 90%, immunizing females aged 9 to 49 years (the World Health Organization target population) would reduce the incidence of prenatal infections by at least 94%, depending on the country-specific Zika attack rate. In regions where an outbreak is not expected for at least 10 years, vaccination of women aged 15 to 29 years is more efficient than that of women aged 30 years or older. Limitation Population-level modeling may not capture all local and neighborhood-level heterogeneity in mosquito abundance or Zika incidence. Conclusion A Zika vaccine of moderate to high efficacy may virtually eliminate prenatal infections through a combination of direct protection and transmission reduction. Efficiency of age-specific targeting of Zika vaccination depends on the timing of future outbreaks. Primary Funding Source National Institutes of Health.
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Affiliation(s)
- DP Durham
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, 135 College St, New Haven, CT 06510
| | - MC Fitzpatrick
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, 135 College St, New Haven, CT 06510
- Center for Vaccine Development, University of Maryland School of Medicine, 685 W Baltimore St, Baltimore, MD 21201
| | - ML Ndeffo-Mbah
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, 135 College St, New Haven, CT 06510
| | - AS Parpia
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, 135 College St, New Haven, CT 06510
| | - NL Michael
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, 6720A Rockledge Drive, Bethesda, MD 20817
| | - AP Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, 135 College St, New Haven, CT 06510
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