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Jato-Espino D, Mayor-Vitoria F, Moscardó V, Capra-Ribeiro F, Bartolomé del Pino LE. Toward One Health: a spatial indicator system to model the facilitation of the spread of zoonotic diseases. Front Public Health 2023; 11:1215574. [PMID: 37457260 PMCID: PMC10340543 DOI: 10.3389/fpubh.2023.1215574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Recurrent outbreaks of zoonotic infectious diseases highlight the importance of considering the interconnections between human, animal, and environmental health in disease prevention and control. This has given rise to the concept of One Health, which recognizes the interconnectedness of between human and animal health within their ecosystems. As a contribution to the One Health approach, this study aims to develop an indicator system to model the facilitation of the spread of zoonotic diseases. Initially, a literature review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement to identify relevant indicators related to One Health. The selected indicators focused on demographics, socioeconomic aspects, interactions between animal and human populations and water bodies, as well as environmental conditions related to air quality and climate. These indicators were characterized using values obtained from the literature or calculated through distance analysis, geoprocessing tasks, and other methods. Subsequently, Multi-Criteria Decision-Making (MCDM) techniques, specifically the Entropy and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) methods, were utilized to combine the indicators and create a composite metric for assessing the spread of zoonotic diseases. The final indicators selected were then tested against recorded zoonoses in the Valencian Community (Spain) for 2021, and a strong positive correlation was identified. Therefore, the proposed indicator system can be valuable in guiding the development of planning strategies that align with the One Health principles. Based on the results achieved, such strategies may prioritize the preservation of natural landscape features to mitigate habitat encroachment, protect land and water resources, and attenuate extreme atmospheric conditions.
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Affiliation(s)
- Daniel Jato-Espino
- GREENIUS Research Group, Universidad Internacional de Valencia—VIU, Calle Pintor Sorolla, Valencia, Spain
| | - Fernando Mayor-Vitoria
- GREENIUS Research Group, Universidad Internacional de Valencia—VIU, Calle Pintor Sorolla, Valencia, Spain
| | - Vanessa Moscardó
- GREENIUS Research Group, Universidad Internacional de Valencia—VIU, Calle Pintor Sorolla, Valencia, Spain
| | - Fabio Capra-Ribeiro
- GREENIUS Research Group, Universidad Internacional de Valencia—VIU, Calle Pintor Sorolla, Valencia, Spain
- School of Architecture, College of Art and Design, Louisiana State University, Baton Rouge, LA, United States
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Bustos Carrillo FA, Mercado BL, Monterrey JC, Collado D, Saborio S, Miranda T, Barilla C, Ojeda S, Sanchez N, Plazaola M, Laguna HS, Elizondo D, Arguello S, Gajewski AM, Maier HE, Latta K, Carlson B, Coloma J, Katzelnick L, Sturrock H, Balmaseda A, Kuan G, Gordon A, Harris E. Epidemics of chikungunya, Zika, and COVID-19 reveal bias in case-based mapping. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.07.23.21261038. [PMID: 34341804 PMCID: PMC8328077 DOI: 10.1101/2021.07.23.21261038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Accurate tracing of epidemic spread over space enables effective control measures. We examined three metrics of infection and disease in a pediatric cohort (N≈3,000) over two chikungunya and one Zika epidemic, and in a household cohort (N=1,793) over one COVID-19 epidemic in Managua, Nicaragua. We compared spatial incidence rates (cases/total population), infection risks (infections/total population), and disease risks (cases/infected population). We used generalized additive and mixed-effects models, Kulldorf's spatial scan statistic, and intracluster correlation coefficients. Across different analyses and all epidemics, incidence rates considerably underestimated infection and disease risks, producing large and spatially non-uniform biases distinct from biases due to incomplete case ascertainment. Infection and disease risks exhibited distinct spatial patterns, and incidence clusters inconsistently identified areas of either risk. While incidence rates are commonly used to infer infection and disease risk in a population, we find that this can induce substantial biases and adversely impact policies to control epidemics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sergio Ojeda
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua, Nicaragua
| | | | | | | | | | | | | | - Krista Latta
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - Josefina Coloma
- University of California, Berkeley, Berkeley, California, USA
| | - Leah Katzelnick
- University of California, Berkeley, Berkeley, California, USA
| | - Hugh Sturrock
- University of California, San Francisco, San Francisco, California, USA
- Locational, Poole, UK
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Ministry of Health, Managua, Nicaragua
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Ministry of Health, Managua, Nicaragua
| | | | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
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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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Lee-Cruz L, Lenormand M, Cappelle J, Caron A, De Nys H, Peeters M, Bourgarel M, Roger F, Tran A. Mapping of Ebola virus spillover: Suitability and seasonal variability at the landscape scale. PLoS Negl Trop Dis 2021; 15:e0009683. [PMID: 34424896 PMCID: PMC8425568 DOI: 10.1371/journal.pntd.0009683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 09/08/2021] [Accepted: 07/26/2021] [Indexed: 01/06/2023] Open
Abstract
The unexpected Ebola virus outbreak in West Africa in 2014 involving the Zaire ebolavirus made clear that other regions outside Central Africa, its previously documented niche, were at risk of future epidemics. The complex transmission cycle and a lack of epidemiological data make mapping areas at risk of the disease challenging. We used a Geographic Information System-based multicriteria evaluation (GIS-MCE), a knowledge-based approach, to identify areas suitable for Ebola virus spillover to humans in regions of Guinea, Congo and Gabon where Ebola viruses already emerged. We identified environmental, climatic and anthropogenic risk factors and potential hosts from a literature review. Geographical data layers, representing risk factors, were combined to produce suitability maps of Ebola virus spillover at the landscape scale. Our maps show high spatial and temporal variability in the suitability for Ebola virus spillover at a fine regional scale. Reported spillover events fell in areas of intermediate to high suitability in our maps, and a sensitivity analysis showed that the maps produced were robust. There are still important gaps in our knowledge about what factors are associated with the risk of Ebola virus spillover. As more information becomes available, maps produced using the GIS-MCE approach can be easily updated to improve surveillance and the prevention of future outbreaks. Ebola virus disease is a highly pathogenic disease transmitted from wildlife to humans. It was first described in 1976 and its distribution remained restricted to Central Africa until 2014, when an outbreak in West Africa, causing more than 28,000 cases and more than 11,000 deaths, took place. Anthropogenic factors, such as bushmeat hunting, trade and consumption, and environmental and climatic factors, may promote the contact between humans and infected animals, such as bats, primates and duikers, increasing the risk of virus transmission to the human population. In this study, we used the spatial multicriteria evaluation framework to gather all available information on risk factors and animal species susceptible to infection, and produce maps of areas suitable for Ebola virus spillover in regions in Guinea, Congo and Gabon. The resulting maps highlighted high spatial and temporal variability in the suitability for Ebola virus spillover. Data from reported cases of Ebola virus transmission from wild animals to humans were used to validate the maps. The approach developed is capable of integrating a wide diversity of risk factors, and provides a flexible and simple tool for surveillance, which can be updated as more data and knowledge on risk factors become available.
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Affiliation(s)
- Larisa Lee-Cruz
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR TETIS, Montpellier, France
- TETIS, Univ Montpellier, AgroParisTech, CIRAD, CNRS, INRAE, Montpellier, France
| | - Maxime Lenormand
- TETIS, Univ Montpellier, AgroParisTech, CIRAD, CNRS, INRAE, Montpellier, France
| | - Julien Cappelle
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Alexandre Caron
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- Faculdade Veterinaria, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Hélène De Nys
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ASTRE, Harare, Zimbabwe
| | - Martine Peeters
- TransVIHMI, IRD, INSERM, Univ Montpellier, Montpellier, France
| | - Mathieu Bourgarel
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ASTRE, Harare, Zimbabwe
| | - François Roger
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Annelise Tran
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR TETIS, Montpellier, France
- TETIS, Univ Montpellier, AgroParisTech, CIRAD, CNRS, INRAE, Montpellier, France
- * E-mail:
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Lee SA, Jarvis CI, Edmunds WJ, Economou T, Lowe R. Spatial connectivity in mosquito-borne disease models: a systematic review of methods and assumptions. J R Soc Interface 2021; 18:20210096. [PMID: 34034534 PMCID: PMC8150046 DOI: 10.1098/rsif.2021.0096] [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: 02/02/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Spatial connectivity plays an important role in mosquito-borne disease transmission. Connectivity can arise for many reasons, including shared environments, vector ecology and human movement. This systematic review synthesizes the spatial methods used to model mosquito-borne diseases, their spatial connectivity assumptions and the data used to inform spatial model components. We identified 248 papers eligible for inclusion. Most used statistical models (84.2%), although mechanistic are increasingly used. We identified 17 spatial models which used one of four methods (spatial covariates, local regression, random effects/fields and movement matrices). Over 80% of studies assumed that connectivity was distance-based despite this approach ignoring distant connections and potentially oversimplifying the process of transmission. Studies were more likely to assume connectivity was driven by human movement if the disease was transmitted by an Aedes mosquito. Connectivity arising from human movement was more commonly assumed in studies using a mechanistic model, likely influenced by a lack of statistical models able to account for these connections. Although models have been increasing in complexity, it is important to select the most appropriate, parsimonious model available based on the research question, disease transmission process, the spatial scale and availability of data, and the way spatial connectivity is assumed to occur.
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Affiliation(s)
- Sophie A. Lee
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Christopher I. Jarvis
- 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
| | - 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
| | | | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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Mahmud AS, Kabir MI, Engø-Monsen K, Tahmina S, Riaz BK, Hossain MA, Khanom F, Rahman MM, Rahman MK, Sharmin M, Hossain DM, Yasmin S, Ahmed MM, Lusha MAF, Buckee CO. Megacities as drivers of national outbreaks: The 2017 chikungunya outbreak in Dhaka, Bangladesh. PLoS Negl Trop Dis 2021; 15:e0009106. [PMID: 33529229 PMCID: PMC7880496 DOI: 10.1371/journal.pntd.0009106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 02/12/2021] [Accepted: 01/04/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Several large outbreaks of chikungunya have been reported in the Indian Ocean region in the last decade. In 2017, an outbreak occurred in Dhaka, Bangladesh, one of the largest and densest megacities in the world. Population mobility and fluctuations in population density are important drivers of epidemics. Measuring population mobility during outbreaks is challenging but is a particularly important goal in the context of rapidly growing and highly connected cities in low- and middle-income countries, which can act to amplify and spread local epidemics nationally and internationally. METHODS We first describe the epidemiology of the 2017 chikungunya outbreak in Dhaka and estimate incidence using a mechanistic model of chikungunya transmission parametrized with epidemiological data from a household survey. We combine the modeled dynamics of chikungunya in Dhaka, with mobility estimates derived from mobile phone data for over 4 million subscribers, to understand the role of population mobility on the spatial spread of chikungunya within and outside Dhaka during the 2017 outbreak. RESULTS We estimate a much higher incidence of chikungunya in Dhaka than suggested by official case counts. Vector abundance, local demographics, and population mobility were associated with spatial heterogeneities in incidence in Dhaka. The peak of the outbreak in Dhaka coincided with the annual Eid holidays, during which large numbers of people traveled from Dhaka to other parts of the country. We show that travel during Eid likely resulted in the spread of the infection to the rest of the country. CONCLUSIONS Our results highlight the impact of large-scale population movements, for example during holidays, on the spread of infectious diseases. These dynamics are difficult to capture using traditional approaches, and we compare our results to a standard diffusion model, to highlight the value of real-time data from mobile phones for outbreak analysis, forecasting, and surveillance.
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Affiliation(s)
- Ayesha S. Mahmud
- Department of Demography, University of California, Berkeley, Berkeley, California, United States of America
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Md. Iqbal Kabir
- National Institute of Preventive and Social Medicine, Dhaka, Bangladesh
- Directorate General of Health Services, Dhaka, Bangladesh
| | | | - Sania Tahmina
- Directorate General of Health Services, Dhaka, Bangladesh
| | | | - Md. Akram Hossain
- National Institute of Preventive and Social Medicine, Dhaka, Bangladesh
| | - Fahmida Khanom
- National Institute of Preventive and Social Medicine, Dhaka, Bangladesh
| | | | | | | | | | | | | | | | - Caroline O. Buckee
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Lim JK, Carabali M, Camacho E, Velez DC, Trujillo A, Egurrola J, Lee KS, Velez ID, Osorio JE. Epidemiology and genetic diversity of circulating dengue viruses in Medellin, Colombia: a fever surveillance study. BMC Infect Dis 2020; 20:466. [PMID: 32615988 PMCID: PMC7331258 DOI: 10.1186/s12879-020-05172-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
Background Dengue fever is a major public health problem in Colombia. A fever surveillance study was conducted for evaluation of the clinical, epidemiological, and molecular patterns of dengue, prior to Chikungunya and Zika epidemics. Methods In November 2011–February 2014, a passive facility-based surveillance was implemented in Santa Cruz Hospital, Medellin, and enrolled eligible febrile patients between 1 and 65 years-of-age. Acute and convalescent blood samples were collected 10–21 days apart and tested for dengue using IgM/IgG ELISA. RNA was extracted for serotyping using RT-PCR on acute samples and genotyping was performed by sequencing. Results Among 537 febrile patients enrolled during the study period, 29% (n = 155) were identified to be dengue-positive. Only 7% of dengue cases were hospitalized, but dengue-positive patients were 2.6 times more likely to be hospitalized, compared to non-dengue cases, based on a logistic regression. From those tested with RT-PCR (n = 173), 17 were dengue-confirmed based on PCR and/or virus isolation showing mostly DENV-3 (n = 9) and DENV-4 (n = 7) with 1 DENV-1. Genotyping results showed that: DENV-1 isolate belongs to the genotype V or American/African genotype; DENV-3 isolates belong to genotype III; and DENV-4 isolates belong to the II genotype and specifically to the IIb sub-genotype or linage. Conclusions Our surveillance documented considerable dengue burden in Santa Cruz comuna during non-epidemic years, and genetic diversity of circulating DENV isolates, captured prior to Chikungunya epidemic in 2014 and Zika epidemic in 2015. Our study findings underscore the need for continued surveillance and monitoring of dengue and other arboviruses and serve as epidemiological and molecular evidence base for future studies to assess changes in DENV transmission in Medellin, given emerging and re-emerging arboviral diseases in the region.
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Affiliation(s)
- Jacqueline Kyungah Lim
- Dengue Vaccine Initiative, International Vaccine Institute, SNU Research Park, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Mabel Carabali
- Dengue Vaccine Initiative, International Vaccine Institute, SNU Research Park, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 845 Sherbrooke St., W, Montreal, Quebec, H3A 0G4, Canada
| | - Erwin Camacho
- Investigaciones Biomedicas, Universidad de Sucre, Cra 28 # 5-267, Barrio Puerta Roja, Sincelejo, Sucre, Colombia
| | - Diana Carolina Velez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, calle 67 No. 53, 108, Medellín, Antioquia, Colombia
| | - Andrea Trujillo
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, calle 67 No. 53, 108, Medellín, Antioquia, Colombia
| | - Jorge Egurrola
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, calle 67 No. 53, 108, Medellín, Antioquia, Colombia
| | - Kang-Sung Lee
- Dengue Vaccine Initiative, International Vaccine Institute, SNU Research Park, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ivan Dario Velez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, calle 67 No. 53, 108, Medellín, Antioquia, Colombia
| | - Jorge E Osorio
- Department of Pathobiological Sciences, University of Wisconsin, 500 Lincoln Dr, Madison, WI, 53706, USA
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Perkins TA, Rodriguez-Barraquer I, Manore C, Siraj AS, España G, Barker CM, Johansson MA, Reiner RC. Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data. Epidemics 2019; 29:100357. [PMID: 31607654 DOI: 10.1016/j.epidem.2019.100357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 06/25/2019] [Accepted: 07/19/2019] [Indexed: 11/25/2022] Open
Abstract
Time series data provide a crucial window into infectious disease dynamics, yet their utility is often limited by the spatially aggregated form in which they are presented. When working with time series data, violating the implicit assumption of homogeneous dynamics below the scale of spatial aggregation could bias inferences about underlying processes. We tested this assumption in the context of the 2015-2016 Zika epidemic in Colombia, where time series of weekly case reports were available at national, departmental, and municipal scales. First, we performed a descriptive analysis, which showed that the timing of departmental-level epidemic peaks varied by three months and that departmental-level estimates of the time-varying reproduction number, R(t), showed patterns that were distinct from a national-level estimate. Second, we applied a classification algorithm to six features of proportional cumulative incidence curves, which showed that variability in epidemic duration, the length of the epidemic tail, and consistency with a cumulative normal density curve made the greatest contributions to distinguishing groups. Third, we applied this classification algorithm to data simulated with a stochastic transmission model, which showed that group assignments were consistent with simulated differences in the basic reproduction number, R0. This result, along with associations between spatial drivers of transmission and group assignments based on observed data, suggests that the classification algorithm is capable of detecting differences in temporal patterns that are associated with differences in underlying drivers of incidence patterns. Overall, this diversity of temporal patterns at local scales underscores the value of spatially disaggregated time series data.
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Affiliation(s)
- T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, United States.
| | | | - Carrie Manore
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, United States.
| | - Amir S Siraj
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, United States.
| | - Guido España
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, United States.
| | - Christopher M Barker
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, United States.
| | - Michael A Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, United States; Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, United States.
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, United States.
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Kerr CC. Is epidemiology ready for Big Software? Pathog Dis 2019; 77:5304613. [PMID: 30715264 DOI: 10.1093/femspd/ftz006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/29/2019] [Indexed: 01/18/2023] Open
Abstract
Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over 'single-use' models designed by individual research teams, including comprehensive documentation, automated testing and extensive support. In addition, as an individual-based model, it allows much greater complexity and flexibility than the compartmental models that are most commonly used in epidemiology. Adopting modern software development practices, as embodied by EMOD, is essential for ensuring that the best models are available to the greatest number of people.
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Affiliation(s)
- Cliff C Kerr
- A28 Physics Rd, Camperdown, Complex Systems Group, School of Physics, University of Sydney, NSW 2006, Australia
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Abstract
Infectious diseases continue to pose a significant public health burden despite the great progress achieved in their prevention and control over the last few decades. Our ability to disentangle the factors and mechanisms driving their propagation in space and time has dramatically advanced in recent years. The current era is rich in mathematical and computational tools and detailed geospatial information, including sociodemographic, geographic, and environmental data, which are essential to elucidate key drivers of infectious disease transmission from epidemiological and genetic data. Indeed, this paradigm shift was driven by dramatic advances in complex systems approaches along with substantial improvements in data availability and computational power. The burgeoning output of infectious disease spatial modeling suggests that we are close to a fully integrated approach for early epidemic detection and intervention. This special collection in BMC Medicine aims to bring together a broad range of quantitative investigations that improve our understanding of the spatiotemporal transmission dynamics of infectious diseases in order to mitigate their impact on the human population.
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Affiliation(s)
- G Chowell
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA.
| | - R Rothenberg
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
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