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Hollingsworth BD, Cho C, Vella M, Roh H, Sass J, Lloyd AL, Brown ZS. Economic optimization of Wolbachia-infected Aedes aegypti release to prevent dengue. PEST MANAGEMENT SCIENCE 2024; 80:3829-3838. [PMID: 38507220 DOI: 10.1002/ps.8086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Dengue virus, primarily transmitted by the Aedes aegypti mosquito, is a major public health concern affecting ≈3.83 billion people worldwide. Recent releases of Wolbachia-transinfected Ae. aegypti in several cities worldwide have shown that it can reduce dengue transmission. However, these releases are costly, and, to date, no framework has been proposed for determining economically optimal release strategies that account for both costs associated with disease risk and releases. RESULTS We present a flexible stochastic dynamic programming framework for determining optimal release schedules for Wolbachia-transinfected mosquitoes that balances the cost of dengue infection with the costs of rearing and releasing transinfected mosquitoes. Using an ordinary differential equation model of Wolbachia and dengue in a hypothetical city loosely describing areas at risk of new dengue epidemics, we determined that an all-or-nothing release strategy that quickly brings Wolbachia to fixation is often the optimal solution. Based on this, we examined the optimal facility size, finding that it was inelastic with respect to the mosquito population size, with a 100% increase in population size resulting in a 50-67% increase in optimal facility size. Furthermore, we found that these results are robust to mosquito life-history parameters and are mostly determined by the mosquito population size and the fitness costs associated with Wolbachia. CONCLUSIONS These results reinforce that Wolbachia-transinfected mosquitoes can reduce the cost of dengue epidemics. Furthermore, they emphasize the importance of determining the size of the target population and fitness costs associated with Wolbachia before releases occur. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, NY, USA
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Chanheung Cho
- Department of Agricultural and Resource Economics, North Carolina State University, Raleigh, NC, USA
| | - Michael Vella
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Hyeongyul Roh
- Department of Agricultural and Resource Economics, North Carolina State University, Raleigh, NC, USA
| | - Julian Sass
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Zachary S Brown
- Department of Agricultural and Resource Economics, North Carolina State University, Raleigh, NC, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, USA
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2
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Chen Y, Xu Y, Wang L, Liang Y, Li N, Lourenço J, Yang Y, Lin Q, Wang L, Zhao H, Cazelles B, Song H, Liu Z, Wang Z, Brady OJ, Cauchemez S, Tian H. Indian Ocean temperature anomalies predict long-term global dengue trends. Science 2024; 384:639-646. [PMID: 38723095 DOI: 10.1126/science.adj4427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/09/2024] [Indexed: 05/31/2024]
Abstract
Despite identifying El Niño events as a factor in dengue dynamics, predicting the oscillation of global dengue epidemics remains challenging. Here, we investigate climate indicators and worldwide dengue incidence from 1990 to 2019 using climate-driven mechanistic models. We identify a distinct indicator, the Indian Ocean basin-wide (IOBW) index, as representing the regional average of sea surface temperature anomalies in the tropical Indian Ocean. IOBW is closely associated with dengue epidemics for both the Northern and Southern hemispheres. The ability of IOBW to predict dengue incidence likely arises as a result of its effect on local temperature anomalies through teleconnections. These findings indicate that the IOBW index can potentially enhance the lead time for dengue forecasts, leading to better-planned and more impactful outbreak responses.
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Affiliation(s)
- Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Wuhan, China
| | - Yiting Xu
- School of National Safety and Emergency Management, Beijing Normal University, Zhuhai, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yilin Liang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
| | - Naizhe Li
- School of National Safety and Emergency Management, Beijing Normal University, Zhuhai, China
| | - José Lourenço
- Católica Biomedical Research Center, Católica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
| | - Yun Yang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
| | - Qiushi Lin
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
| | - Ligui Wang
- Center of Disease Control and Prevention, PLA, Beijing, China
| | - He Zhao
- CMA Earth System Modeling and Prediction Centre, China Meteorological Administration, Beijing, China
| | - Bernard Cazelles
- Institut de Biologie de l'École Normale Supérieure UMR 8197, Eco-Evolutionary Mathematics, École Normale Supérieure, Paris, France
- Unité Mixte Internationnale 209, Mathematical and Computational Modeling of Complex Systems, Sorbonne Université, Paris, France
| | - Hongbin Song
- Center of Disease Control and Prevention, PLA, Beijing, China
| | - Ziyan Liu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
| | - Oliver J Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology and Dynamics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Beijing Normal University, Beijing, China
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3
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Leandro AS, Chiba de Castro WA, Garey MV, Maciel-de-Freitas R. Spatial analysis of dengue transmission in an endemic city in Brazil reveals high spatial structuring on local dengue transmission dynamics. Sci Rep 2024; 14:8930. [PMID: 38637572 PMCID: PMC11026424 DOI: 10.1038/s41598-024-59537-y] [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: 07/10/2023] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
In the last decades, dengue has become one of the most widespread mosquito-borne arboviruses in the world, with an increasing incidence in tropical and temperate regions. The mosquito Aedes aegypti is the dengue primary vector and is more abundant in highly urbanized areas. Traditional vector control methods have showing limited efficacy in sustaining mosquito population at low levels to prevent dengue virus outbreaks. Considering disease transmission is not evenly distributed in the territory, one perspective to enhance vector control efficacy relies on identifying the areas that concentrate arbovirus transmission within an endemic city, i.e., the hotspots. Herein, we used a 13-month timescale during the SARS-Cov-2 pandemic and its forced reduction in human mobility and social isolation to investigate the spatiotemporal association between dengue transmission in children and entomological indexes based on adult Ae. aegypti trapping. Dengue cases and the indexes Trap Positive Index (TPI) and Adult Density Index (ADI) varied seasonally, as expected: more than 51% of cases were notified on the first 2 months of the study, and higher infestation was observed in warmer months. The Moran's Eigenvector Maps (MEM) and Generalized Linear Models (GLM) revealed a strong large-scale spatial structuring in the positive dengue cases, with an unexpected negative correlation between dengue transmission and ADI. Overall, the global model and the purely spatial model presented a better fit to data. Our results show high spatial structure and low correlation between entomological and epidemiological data in Foz do Iguaçu dengue transmission dynamics, suggesting the role of human mobility might be overestimated and that other factors not evaluated herein could be playing a significant role in governing dengue transmission.
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Affiliation(s)
- André S Leandro
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Centro de Controle de Zoonoses, Secretaria Municipal de Saúde de Foz do Iguaçu, Foz do Iguaçu, Brazil
| | | | | | - Rafael Maciel-de-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
- Department of Arbovirology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
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4
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Pinotti F, Giovanetti M, de Lima MM, de Cerqueira EM, Alcantara LCJ, Gupta S, Recker M, Lourenço J. Shifting patterns of dengue three years after Zika virus emergence in Brazil. Nat Commun 2024; 15:632. [PMID: 38245500 PMCID: PMC10799945 DOI: 10.1038/s41467-024-44799-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
In 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue virus (DENV), which resurged in 2018-2019. We examine age-specific incidence data to investigate changes in DENV epidemiology before and after the emergence of ZIKV. We observe that incidence of DENV was concentrated in younger individuals during resurgence compared to 2013-2015. This trend was more pronounced in Brazilian states that had experienced larger ZIKV outbreaks. Using a mathematical model, we show that ZIKV-induced cross-protection alone, often invoked to explain DENV decline across Latin America, cannot explain the observed age-shift without also assuming some form of disease enhancement. Our results suggest that a sudden accumulation of population-level immunity to ZIKV could suppress DENV and reduce the mean age of DENV incidence via both protective and disease-enhancing interactions.
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Affiliation(s)
- Francesco Pinotti
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | | | - Luiz C J Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Sunetra Gupta
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Mario Recker
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - José Lourenço
- Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
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5
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Hamins-Puértolas M, Buddhari D, Salje H, Cummings DAT, Fernandez S, Farmer A, Kaewhiran S, Khampaen D, Iamsirithaworn S, Srikiatkhachorn A, Waickman A, Thomas SJ, Rothman AL, Endy T, Rodriguez-Barraquer I, Anderson KB. Household immunity and individual risk of infection with dengue virus in a prospective, longitudinal cohort study. Nat Microbiol 2024; 9:274-283. [PMID: 38110699 PMCID: PMC10895643 DOI: 10.1038/s41564-023-01543-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/02/2023] [Indexed: 12/20/2023]
Abstract
Although it is known that household infections drive the transmission of dengue virus (DENV), it is unclear how household composition and the immune status of inhabitants affect the individual risk of infection. Most population-based studies to date have focused on paediatric cohorts because more severe forms of dengue mainly occur in children, and the role of adults in dengue transmission is understudied. Here we analysed data from a multigenerational cohort study of 470 households, comprising 2,860 individuals, in Kamphaeng Phet, Thailand, to evaluate risk factors for DENV infection. Using a gradient-boosted regression model trained on annual haemagglutination inhibition antibody titre inputs, we identified 1,049 infections, 90% of which were subclinical. By analysing imputed infections, we found that individual antibody titres, household composition and antibody titres of other members in the same household affect an individual's risk of DENV infection. Those individuals living in households with high average antibody titres, or households with more adults, had a reduced risk of infection. We propose that herd immunity to dengue acts at the household level and may provide insight into the drivers of the recent change in the shifting age distribution of dengue cases in Thailand.
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Affiliation(s)
| | - Darunee Buddhari
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Aaron Farmer
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | | | - Anon Srikiatkhachorn
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Adam Waickman
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephen J Thomas
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
- Institute for Global Health and Translational Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Alan L Rothman
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Timothy Endy
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
- Coalition for Epidemic Preparedness Innovations (CEPI), Washington DC, USA
| | | | - Kathryn B Anderson
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA.
- Institute for Global Health and Translational Sciences, SUNY Upstate Medical University, Syracuse, NY, USA.
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6
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Gibb R, Colón-González FJ, Lan PT, Huong PT, Nam VS, Duoc VT, Hung DT, Dong NT, Chien VC, Trang LTT, Kien Quoc D, Hoa TM, Tai NH, Hang TT, Tsarouchi G, Ainscoe E, Harpham Q, Hofmann B, Lumbroso D, Brady OJ, Lowe R. Interactions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam. Nat Commun 2023; 14:8179. [PMID: 38081831 PMCID: PMC10713571 DOI: 10.1038/s41467-023-43954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Dengue is expanding globally, but how dengue emergence is shaped locally by interactions between climatic and socio-environmental factors is not well understood. Here, we investigate the drivers of dengue incidence and emergence in Vietnam, through analysing 23 years of district-level case data spanning a period of significant socioeconomic change (1998-2020). We show that urban infrastructure factors (sanitation, water supply, long-term urban growth) predict local spatial patterns of dengue incidence, while human mobility is a more influential driver in subtropical northern regions than the endemic south. Temperature is the dominant factor shaping dengue's distribution and dynamics, and using long-term reanalysis temperature data we show that warming since 1950 has expanded transmission risk throughout Vietnam, and most strongly in current dengue emergence hotspots (e.g., southern central regions, Ha Noi). In contrast, effects of hydrometeorology are complex, multi-scalar and dependent on local context: risk increases under either short-term precipitation excess or long-term drought, but improvements in water supply mitigate drought-associated risks except under extreme conditions. Our findings challenge the assumption that dengue is an urban disease, instead suggesting that incidence peaks in transitional landscapes with intermediate infrastructure provision, and provide evidence that interactions between recent climate change and mobility are contributing to dengue's expansion throughout Vietnam.
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Affiliation(s)
- Rory Gibb
- Department of Infectious Disease Epidemiology & Dynamics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK.
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Felipe J Colón-González
- Department of Infectious Disease Epidemiology & Dynamics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Data for Science and Health, Wellcome Trust, London, UK
| | - Phan Trong Lan
- General Department of Preventative Medicine (GDPM), Ministry of Health, Hanoi, Vietnam
| | - Phan Thi Huong
- General Department of Preventative Medicine (GDPM), Ministry of Health, Hanoi, Vietnam
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology (NIHE), Hanoi, Vietnam
| | - Vu Trong Duoc
- National Institute of Hygiene and Epidemiology (NIHE), Hanoi, Vietnam
| | - Do Thai Hung
- Pasteur Institute Nha Trang, Nha Trang, Khanh Hoa Province, Vietnam
| | | | - Vien Chinh Chien
- Tay Nguyen Institute of Hygiene and Epidemiology (TIHE), Buon Ma Thuot, Dak Lak Province, Vietnam
| | - Ly Thi Thuy Trang
- Tay Nguyen Institute of Hygiene and Epidemiology (TIHE), Buon Ma Thuot, Dak Lak Province, Vietnam
| | - Do Kien Quoc
- Pasteur Institute Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tran Minh Hoa
- Center for Disease Control, Dong Nai Province, Vietnam
| | | | | | | | | | | | | | | | - Oliver J Brady
- Department of Infectious Disease Epidemiology & Dynamics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Rachel Lowe
- Department of Infectious Disease Epidemiology & Dynamics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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7
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Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics. PLoS Pathog 2023; 19:e1011588. [PMID: 37651317 PMCID: PMC10470969 DOI: 10.1371/journal.ppat.1011588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
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Affiliation(s)
- Brandon D Hollingsworth
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Nathan D Grubaugh
- Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale University, New Haven, Connecticut, United States of America
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
| | - Courtney C Murdock
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host Microbe Interaction and Disease, Cornell University, Ithaca, New York, United States of America
- Northeast Regional Center for Excellence in Vector-borne Diseases, Cornell University, Ithaca, New York, United States of America
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8
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Sandfort M, Monteiro W, Lacerda M, Nguitragool W, Sattabongkot J, Waltmann A, Salje H, Vantaux A, Witkowski B, Robinson LJ, Mueller I, White M. The spatial signature of Plasmodium vivax and Plasmodium falciparum infections: quantifying the clustering of infections in cross-sectional surveys and cohort studies. Malar J 2023; 22:75. [PMID: 36870976 PMCID: PMC9985228 DOI: 10.1186/s12936-023-04515-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Over the last decades, enormous successes have been achieved in reducing malaria burden globally. In Latin America, South East Asia, and the Western Pacific, many countries now pursue the goal of malaria elimination by 2030. It is widely acknowledged that Plasmodium spp. infections cluster spatially so that interventions need to be spatially informed, e.g. spatially targeted reactive case detection strategies. Here, the spatial signature method is introduced as a tool to quantify the distance around an index infection within which other infections significantly cluster. METHODS Data were considered from cross-sectional surveys from Brazil, Thailand, Cambodia, and Solomon Islands, conducted between 2012 and 2018. Household locations were recorded by GPS and finger-prick blood samples from participants were tested for Plasmodium infection by PCR. Cohort studies from Brazil and Thailand with monthly sampling over a year from 2013 until 2014 were also included. The prevalence of PCR-confirmed infections was calculated at increasing distance around index infections (and growing time intervals in the cohort studies). Statistical significance was defined as prevalence outside of a 95%-quantile interval of a bootstrap null distribution after random re-allocation of locations of infections. RESULTS Prevalence of Plasmodium vivax and Plasmodium falciparum infections was elevated in close proximity around index infections and decreased with distance in most study sites, e.g. from 21.3% at 0 km to the global study prevalence of 6.4% for P. vivax in the Cambodian survey. In the cohort studies, the clustering decreased with longer time windows. The distance from index infections to a 50% reduction of prevalence ranged from 25 m to 3175 m, tending to shorter distances at lower global study prevalence. CONCLUSIONS The spatial signatures of P. vivax and P. falciparum infections demonstrate spatial clustering across a diverse set of study sites, quantifying the distance within which the clustering occurs. The method offers a novel tool in malaria epidemiology, potentially informing reactive intervention strategies regarding radius choices of operations around detected infections and thus strengthening malaria elimination endeavours.
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Affiliation(s)
- Mirco Sandfort
- Unité Malaria : Parasites Et Hôtes, Département Parasites Et Insectes Vecteurs, Institut Pasteur, Paris, France.
- Sorbonne Université, Collège Doctoral, Paris, France.
| | - Wuelton Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Universidade do Estado do Amazonas, Manaus, Brazil
| | - Marcus Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Universidade do Estado do Amazonas, Manaus, Brazil
- Instituto de Pesquisas Leônidas e Maria Deane, Manaus, Brazil
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine & Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Andreea Waltmann
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Leanne J Robinson
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Burnet Institute, Melbourne, Australia
| | - Ivo Mueller
- Unité Malaria : Parasites Et Hôtes, Département Parasites Et Insectes Vecteurs, Institut Pasteur, Paris, France
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Michael White
- Unité Malaria : Parasites Et Hôtes, Département Parasites Et Insectes Vecteurs, Institut Pasteur, Paris, France
- G5 Épidémiologie et Analyse des Maladies Infectieuses, Département de Santé Globale, Institut Pasteur, Paris, France
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9
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Vazquez-Prokopec GM, Morrison AC, Paz-Soldan V, Stoddard ST, Koval W, Waller LA, Alex Perkins T, Lloyd AL, Astete H, Elder J, Scott TW, Kitron U. Inapparent infections shape the transmission heterogeneity of dengue. PNAS NEXUS 2023; 2:pgad024. [PMID: 36909820 PMCID: PMC10003742 DOI: 10.1093/pnasnexus/pgad024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
Transmission heterogeneity, whereby a disproportionate fraction of pathogen transmission events result from a small number of individuals or geographic locations, is an inherent property of many, if not most, infectious disease systems. For vector-borne diseases, transmission heterogeneity is inferred from the distribution of the number of vectors per host, which could lead to significant bias in situations where vector abundance and transmission risk at the household do not correlate, as is the case with dengue virus (DENV). We used data from a contact tracing study to quantify the distribution of DENV acute infections within human activity spaces (AS), the collection of residential locations an individual routinely visits, and quantified measures of virus transmission heterogeneity from two consecutive dengue outbreaks (DENV-4 and DENV-2) that occurred in the city of Iquitos, Peru. Negative-binomial distributions and Pareto fractions showed evidence of strong overdispersion in the number of DENV infections by AS and identified super-spreading units (SSUs): i.e. AS where most infections occurred. Approximately 8% of AS were identified as SSUs, contributing to more than 50% of DENV infections. SSU occurrence was associated more with DENV-2 infection than with DENV-4, a predominance of inapparent infections (74% of all infections), households with high Aedes aegypti mosquito abundance, and high host susceptibility to the circulating DENV serotype. Marked heterogeneity in dengue case distribution, and the role of inapparent infections in defining it, highlight major challenges faced by reactive interventions if those transmission units contributing the most to transmission are not identified, prioritized, and effectively treated.
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Affiliation(s)
| | - Amy C Morrison
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Valerie Paz-Soldan
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Steven T Stoddard
- Division of Health Promotion & Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - William Koval
- Department of Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lance A Waller
- Department of Biostatistics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - T Alex Perkins
- Department of Biology, University of Notre Dame, South Bend, IN 46556, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27607, USA
| | - Helvio Astete
- Virology Department, Naval Medical Research Unit-6, Iquitos 16003, Peru
| | - John Elder
- Division of Health Promotion & Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Thomas W Scott
- Department of Entomology and Nematology, University of California, Davis, CA 95616, USA
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, GA 30322, USA
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10
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Estimating Dengue Transmission Intensity in China Using Catalytic Models Based on Serological Data. Trop Med Infect Dis 2023; 8:tropicalmed8020116. [PMID: 36828532 PMCID: PMC9967418 DOI: 10.3390/tropicalmed8020116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
In recent decades, the global incidence of dengue has risen sharply, with more than 75% of infected people showing mild or no symptoms. Since the year 2000, dengue in China has spread quickly. At this stage, there is an urgent need to fully understand its transmission intensity and spread in China. Serological data provide reliable evidence for symptomatic and recessive infections. Through a literature search, we included 23 studies that collected age-specific serological dengue data released from 1980 to 2021 in China. Fitting four catalytic models to these data, we distinguished the transmission mechanisms by deviation information criterion and estimated force of infection and basic reproduction number (R0), important parameters for quantifying transmission intensity. We found that transmission intensity varies over age in most of the study populations, and attenuation of antibody protection is identified in some study populations; the R0 of dengue in China is between 1.04-2.33. Due to the scarceness of the data, the temporal trend cannot be identified, but data shows that transmission intensity weakened from coastal to inland areas and from southern to northern areas in China if assuming it remained temporally steady during the study period. The results should be useful for the effective control of dengue in China.
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11
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López L, Paul RE, Cao-Lormeau VM, Rodó X. Considering waning immunity to better explain dengue dynamics. Epidemics 2022; 41:100630. [PMID: 36272245 DOI: 10.1016/j.epidem.2022.100630] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/25/2022] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
Life-long serotype-specific immunity following dengue virus infection may not always occur, but the true extent of this effect is unknown. Analysis of more than 20 years of monotypic epidemics in the isolated French Polynesian islands revealed that whilst the risk of symptomatic dengue infection did conform to the classical paradigms of homotypic immunity and increased disease risk in heterotypic secondary infections, incorporation of waning immunity improved the ability of epidemiological models to capture the observed epidemic dynamics. Not only does this show how inclusion of waning immunity into classical models can reveal important facets of the immune response to natural dengue virus infection, it also has significant ramifications for vaccine development and implementation in dengue endemic areas.
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Affiliation(s)
- Leonardo López
- CLIMA (Climate and Health) Program, ISGlobal, c/Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Richard E Paul
- Institut Pasteur, Université de Paris, CNRS UMR2000, Ecology and Emergence of Arthropod-borne Pathogens Unit, F-75015 Paris, France
| | - Van-Mai Cao-Lormeau
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, 98713 Papeete, Tahiti, French Polynesia
| | - Xavier Rodó
- CLIMA (Climate and Health) Program, ISGlobal, c/Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain.
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12
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Ribeiro Dos Santos G, Durovni B, Saraceni V, Souza Riback TI, Pinto SB, Anders KL, Moreira LA, Salje H. Estimating the effect of the wMel release programme on the incidence of dengue and chikungunya in Rio de Janeiro, Brazil: a spatiotemporal modelling study. THE LANCET. INFECTIOUS DISEASES 2022; 22:1587-1595. [PMID: 36182679 PMCID: PMC9630156 DOI: 10.1016/s1473-3099(22)00436-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Introgression of genetic material from species of the insect bacteria Wolbachia into populations of Aedes aegypti mosquitoes has been shown in randomised and non-randomised trials to reduce the incidence of dengue; however, evidence for the real-world effectiveness of large-scale deployments of Wolbachia-infected mosquitoes for arboviral disease control in endemic settings is still scarce. A large Wolbachia (wMel strain) release programme was implemented in 2017 in Rio de Janeiro, Brazil. We aimed to assess the effect of this programme on the incidence of dengue and chikungunya in the city. METHODS 67 million wMel-infected mosquitoes were released across 28 489 locations over an area of 86·8 km2 in Rio de Janeiro between Aug 29, 2017 and Dec 27, 2019. Following releases, mosquitoes were trapped and the presence of wMel was recorded. In this spatiotemporal modelling study, we assessed the effect of the release programme on the incidence of dengue and chikungunya. We used spatiotemporally explicit mathematical models applied to geocoded dengue cases (N=283 270) from 2010 to 2019 and chikungunya cases (N=57 705) from 2016 to 2019. FINDINGS On average, 32% of mosquitoes collected from the release zones between 1 month and 29 months after the initial release tested positive for wMel. Reduced wMel introgression occurred in locations and seasonal periods in which cases of dengue and chikungunya were historically high, with a decrease to 25% of mosquitoes testing positive for wMel during months in which disease incidence was at its highest. Despite incomplete introgression, we found that the releases were associated with a 38% (95% CI 32-44) reduction in the incidence of dengue and a 10% (4-16) reduction in the incidence of chikungunya. INTERPRETATION Stable establishment of wMel in the geographically diverse, urban setting of Rio de Janeiro seems to be more complicated than has been observed elsewhere. However, even intermediate levels of wMel seem to reduce the incidence of disease caused by two arboviruses. These findings will help to guide future release programmes. FUNDING Bill & Melinda Gates Foundation and the European Research Council.
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Affiliation(s)
| | - Betina Durovni
- Centre for Strategic Studies, Fiocruz, Rio de Janeiro, Brazil; World Mosquito Program, Fiocruz, Rio de Janeiro, Brazil
| | | | | | - Sofia B Pinto
- World Mosquito Program, Fiocruz, Rio de Janeiro, Brazil
| | - Katherine L Anders
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Luciano A Moreira
- World Mosquito Program, Fiocruz, Rio de Janeiro, Brazil; Instituto Rene Rachou, Fiocruz, Belo Horizonte, Brazil
| | - Henrik Salje
- Pathogen Dynamics Group, Department of Genetics, University of Cambridge, Cambridge, UK.
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13
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Bridging landscape ecology and urban science to respond to the rising threat of mosquito-borne diseases. Nat Ecol Evol 2022; 6:1601-1616. [DOI: 10.1038/s41559-022-01876-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/03/2022] [Indexed: 11/09/2022]
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14
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Huang L, Xiao G, Chen H, Niu X, Fu X, Xu H, Xu G, Ma S, Ong J, Ng LC. Geographical clusters of dengue outbreak in Singapore during the Covid-19 nationwide lockdown of 2020. Sci Data 2022; 9:547. [PMID: 36071062 PMCID: PMC9451123 DOI: 10.1038/s41597-022-01666-y] [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: 03/09/2022] [Accepted: 08/26/2022] [Indexed: 11/14/2022] Open
Abstract
Dengue, a mosquito-transmitted viral disease, has posed a public health challenge to Singaporean residents over the years. In 2020, Singapore experienced an unprecedented dengue outbreak. We collected a dataset of geographical dengue clusters reported by the National Environment Agency (NEA) from 15 February to 9 July in 2020, covering the nationwide lockdown associated with Covid-19 during the period from 7 April to 1 June. NEA regularly updates the dengue clusters during which an infected person may be tagged to one cluster based on the most probable infection location (residential apartment or workplace address), which is further matched to fine-grained spatial units with an average coverage of about 1.35 km2. Such dengue cluster dataset helps not only reveal the dengue transmission patterns, but also reflect the effects of lockdown on dengue spreading dynamics. The resulting data records are released in simple formats for easy access to facilitate studies on dengue epidemics.
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Affiliation(s)
- Liping Huang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Gaoxi Xiao
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Hechang Chen
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Xuetong Niu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiuju Fu
- Institute of High Performance Computing, Singapore, Singapore
| | - Haiyan Xu
- Institute of High Performance Computing, Singapore, Singapore
| | - George Xu
- Institute of High Performance Computing, Singapore, Singapore
| | - Stefan Ma
- Ministry of Health, Singapore, Singapore
| | - Janet Ong
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore, Singapore
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15
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Gramajo AA, Laneri K, Laguna MF. Mosquito populations and human social behavior: A spatially explicit agent-based model. Phys Rev E 2022; 106:034405. [PMID: 36266790 DOI: 10.1103/physreve.106.034405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Some mosquitoes are vectors for disease transmission to human populations. Aedes aegypti, the main vector for dengue in Argentina, mainly breeds in artificial containers as it is strongly adapted to urban environments. This highlights the relevance of understanding human social behavior to design successful vector control campaigns. We developed a model of mosquito populations that considers their main biological and behavioral features and incorporates parameters that model human behavior in relation to water container disposal. We performed extensive numerical simulations to study the variability of adult and aquatic mosquito populations when various protocols are applied, changing the effectiveness and frequency of water bucket disposal and the delay in the availability of water containers for breeding. We found an effectiveness threshold value above which it is possible to significantly limit mosquito dispersal. Interestingly, a nonsynchronized discard frequency, more attainable by human populations, was more efficient than a synchronized one to reduce the aquatic mosquito population. Scenarios with random delays in the availability of water containers indicate that it is not decisive to have a fixed time delay for the entire population, which is more realistic as it mimics a wider range of human behaviors. This simple model could help design dengue prevention campaigns aiming at mosquito population control.
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Affiliation(s)
- Ana Alicia Gramajo
- Statistical and Interdisciplinary Physics Group, Centro Atómico Bariloche and CONICET, R8402AGP Bariloche, Argentina
| | - Karina Laneri
- Statistical and Interdisciplinary Physics Group, Centro Atómico Bariloche and CONICET, R8402AGP Bariloche, Argentina
| | - María Fabiana Laguna
- Statistical and Interdisciplinary Physics Group, Centro Atómico Bariloche and CONICET, R8402AGP Bariloche, Argentina
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16
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Lefebvre B, Karki R, Misslin R, Nakhapakorn K, Daudé E, Paul RE. Importance of Public Transport Networks for Reconciling the Spatial Distribution of Dengue and the Association of Socio-Economic Factors with Dengue Risk in Bangkok, Thailand. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10123. [PMID: 36011755 PMCID: PMC9408777 DOI: 10.3390/ijerph191610123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Dengue is the most widespread mosquito-borne viral disease of man and spreading at an alarming rate. Socio-economic inequality has long been thought to contribute to providing an environment for viral propagation. However, identifying socio-economic (SE) risk factors is confounded by intra-urban daily human mobility, with virus being ferried across cities. This study aimed to identify SE variables associated with dengue at a subdistrict level in Bangkok, analyse how they explain observed dengue hotspots and assess the impact of mobility networks on such associations. Using meteorological, dengue case, national statistics, and transport databases from the Bangkok authorities, we applied statistical association and spatial analyses to identify SE variables associated with dengue and spatial hotspots and the extent to which incorporating transport data impacts the observed associations. We identified three SE risk factors at the subdistrict level: lack of education, % of houses being cement/brick, and number of houses as being associated with increased risk of dengue. Spatial hotspots of dengue were found to occur consistently in the centre of the city, but which did not entirely have the socio-economic risk factor characteristics. Incorporation of the intra-urban transport network, however, much improved the overall statistical association of the socio-economic variables with dengue incidence and reconciled the incongruous difference between the spatial hotspots and the SE risk factors. Our study suggests that incorporating transport networks enables a more real-world analysis within urban areas and should enable improvements in the identification of risk factors.
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Affiliation(s)
- Bertrand Lefebvre
- French Institute of Pondicherry, UMIFRE 21 CNRS-MEAE, Pondicherry 605001, India
| | - Rojina Karki
- CNRS, ARENES—UMR 6051, EHESP, Université de Rennes, 35000 Rennes, France
| | | | - Kanchana Nakhapakorn
- Faculty of Environment and Resource Studies, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Eric Daudé
- CNRS, UMR 6266 IDEES, 7 rue Thomas Becket, 76821 Rouen, France
| | - Richard E. Paul
- Institut Pasteur, Université de Paris, CNRS, UMR 2000, Unité de Génétique Fonctionnelle des Maladies Infectieuses, 75015 Paris, France
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17
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Dufault SM, Tanamas SK, Indriani C, Utarini A, Ahmad RA, Jewell NP, Simmons CP, Anders KL. Disruption of spatiotemporal clustering in dengue cases by wMel Wolbachia in Yogyakarta, Indonesia. Sci Rep 2022; 12:9890. [PMID: 35701454 PMCID: PMC9198086 DOI: 10.1038/s41598-022-13749-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/27/2022] [Indexed: 10/25/2022] Open
Abstract
Dengue exhibits focal clustering in households and neighborhoods, driven by local mosquito population dynamics, human population immunity, and fine scale human and mosquito movement. We tested the hypothesis that spatiotemporal clustering of homotypic dengue cases is disrupted by introduction of the arbovirus-blocking bacterium Wolbachia (wMel-strain) into the Aedes aegypti mosquito population. We analysed 318 serotyped and geolocated dengue cases (and 5921 test-negative controls) from a randomized controlled trial in Yogyakarta, Indonesia of wMel deployments. We find evidence of spatial clustering up to 300 m among the 265 dengue cases (3083 controls) in the untreated trial arm. Participant pairs enrolled within 30 days and 50 m had a 4.7-fold increase (compared to 95% CI on permutation-based null distribution: 0.1, 1.2) in the odds of being homotypic (i.e. potentially transmission-related) as compared to pairs occurring at any distance. In contrast, we find no evidence of spatiotemporal clustering among the 53 dengue cases (2838 controls) resident in the wMel-treated arm. Introgression of wMel Wolbachia into Aedes aegypti mosquito populations interrupts focal dengue virus transmission leading to reduced case incidence; the true intervention effect may be greater than the 77% efficacy measured in the primary analysis of the Yogyakarta trial.
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Affiliation(s)
- Suzanne M Dufault
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, USA.
| | - Stephanie K Tanamas
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, 3800, Australia
| | - Citra Indriani
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Nicholas P Jewell
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, USA
- London School of Hygiene and Tropical Medicine, Bloomsbury, London, WC1E 7HT, UK
| | - Cameron P Simmons
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, 3800, Australia
| | - Katherine L Anders
- World Mosquito Program, Institute of Vector-borne Disease, Monash University, Clayton, 3800, Australia
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18
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Niang M, Sandfort M, Mbodj AF, Diouf B, Talla C, Faye J, Sane R, Thiam LG, Thiam A, Badiane A, Vigan-Womas I, Diagne N, Diene Sarr F, Mueller I, Sokhna C, White M, Toure-Balde A. Fine-scale Spatiotemporal Mapping of Asymptomatic and Clinical Plasmodium falciparum Infections: Epidemiological Evidence for Targeted Malaria Elimination Interventions. Clin Infect Dis 2021; 73:2175-2183. [PMID: 33677477 DOI: 10.1093/cid/ciab161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A detailed understanding of the contribution of the asymptomatic Plasmodium reservoir to the occurrence of clinical malaria at individual and community levels is needed to guide effective elimination interventions. This study investigated the relationship between asymptomatic Plasmodium falciparum carriage and subsequent clinical malaria episodes in the Dielmo and Ndiop villages in Senegal. METHODS The study used a total of 2792 venous and capillary blood samples obtained from asymptomatic individuals and clinical malaria datasets collected from 2013 to 2016. Mapping, spatial clustering of infections, and risk analysis were performed using georeferenced households. RESULTS High incidences of clinical malaria episodes were observed to occur predominantly in households of asymptomatic P falciparum carriers. A statistically significant association was found between asymptomatic carriage in a household and subsequent episode of clinical malaria occurring in that household for each individual year (P values were 0.0017, 6 × 10-5, 0.005, and 0.008 for the years 2013, 2014, 2015, and 2016 respectively) and the combined years (P = 8.5 × 10-8), which was not found at the individual level. In both villages, no significant patterns of spatial clustering of P falciparum clinical cases were found, but there was a higher risk of clinical episodes <25 m from asymptomatic individuals in Ndiop attributable to clustering within households. CONCLUSION The findings provide strong epidemiological evidence linking the asymptomatic P falciparum reservoir to clinical malaria episodes at household scale in Dielmo and Ndiop villagers. This argues for a likely success of a mass testing and treatment intervention to move towards the elimination of malaria in the villages of Dielmo and Ndiop.
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Affiliation(s)
- Makhtar Niang
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Mirco Sandfort
- Malaria: Parasites and Hosts Unit, Department of Parasites & Insect Vectors, Institut Pasteur, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Adja Fatou Mbodj
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Babacar Diouf
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Cheikh Talla
- Institut Pasteur Dakar, Pôle Epidémiologie, Recherche Clinique et Science des données, Dakar, Sénégal
| | - Joseph Faye
- Institut Pasteur Dakar, Pôle Epidémiologie, Recherche Clinique et Science des données, Dakar, Sénégal
| | - Rokhaya Sane
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Laty Gaye Thiam
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Alassane Thiam
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | - Abdoulaye Badiane
- Institut Pasteur Dakar, Pôle Epidémiologie, Recherche Clinique et Science des données, Dakar, Sénégal
| | - Ines Vigan-Womas
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
| | | | - Fatoumata Diene Sarr
- Institut Pasteur Dakar, Pôle Epidémiologie, Recherche Clinique et Science des données, Dakar, Sénégal
| | - Ivo Mueller
- Malaria: Parasites and Hosts Unit, Department of Parasites & Insect Vectors, Institut Pasteur, Paris, France
| | - Cheikh Sokhna
- VITROME, Campus international IRD-UCAD, Dakar, Sénégal
| | - Michael White
- Malaria: Parasites and Hosts Unit, Department of Parasites & Insect Vectors, Institut Pasteur, Paris, France
| | - Aissatou Toure-Balde
- Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal
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19
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Cunha MDCM, Ju Y, Morais MHF, Dronova I, Ribeiro SP, Bruhn FRP, Lima LL, Sales DM, Schultes OL, Rodriguez DA, Caiaffa WT. Disentangling associations between vegetation greenness and dengue in a Latin American city: Findings and challenges. LANDSCAPE AND URBAN PLANNING 2021; 216:None. [PMID: 34675450 PMCID: PMC8519391 DOI: 10.1016/j.landurbplan.2021.104255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 08/11/2021] [Accepted: 09/14/2021] [Indexed: 05/07/2023]
Abstract
Being a Re-Emerging Infectious Disease, dengue causes 390 million cases globally and is prevalent in many urban areas in South America. Understanding the fine-scale relationships between dengue incidence and environmental and socioeconomic factors can guide improved disease prevention strategies. This ecological study examines the association between dengue incidence and satellite-based vegetation greenness in 3826 census tracts nested in 474 neighborhoods in Belo Horizonte, Brazil, during the 2010 dengue epidemic. To reduce potential bias in the estimated dengue-greenness association, we adjusted for socioeconomic vulnerability, population density, building height and density, land cover composition, elevation, weather patterns, and neighborhood random effects. We found that vegetation greenness was negatively associated with dengue incidence in a univariate model, and this association attenuated after controlling for additional covariates. The dengue-greenness association was modified by socioeconomic vulnerability: while a positive association was observed in the least vulnerable census tracts, the association was negative in the most vulnerable areas. Using greenness as a proxy for vegetation quality, our results show the potential of vegetation management in reducing dengue incidence, particularly in socioeconomically vulnerable areas. We also discuss the role of water infrastructure, sanitation services, and tree cover in lowering dengue risk.
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Affiliation(s)
- Maria da Consolação Magalhães Cunha
- Observatory for Urban health in Belo Horizonte, School of Medicine, Federal University of Minas Gerais, Brazil
- Pontifical Catholic University of Minas Gerais, Brazil
| | - Yang Ju
- Institute of Urban and Regional Development, University of California, 316 Wurster Hall, University of California, Berkeley, Berkeley, CA 94720, USA
- Corresponding author.
| | | | - Iryna Dronova
- Department of Environmental Science, Policy, and Management, Department of Landscape Architecture and Environmental Planning, University of California, Berkeley, USA
| | - Sérvio Pontes Ribeiro
- Laboratory of Ecology of Diseases and Forests, Nucleous of Biology/NUPEB and Institute of Exact and Biological Sciences, Federal University of Ouro Preto, Brazil
| | | | - Larissa Lopes Lima
- Observatory for Urban health in Belo Horizonte, School of Medicine, Federal University of Minas Gerais, Brazil
- Federal Center for Technological Education of Minas Gerais, Brazil
| | - Denise Marques Sales
- Observatory for Urban health in Belo Horizonte, School of Medicine, Federal University of Minas Gerais, Brazil
| | - Olivia Lang Schultes
- Observatory for Urban health in Belo Horizonte, School of Medicine, Federal University of Minas Gerais, Brazil
| | - Daniel A. Rodriguez
- Department of City and Regional Planning and Institute of Transportation Studies, University of California, Berkeley, USA
| | - Waleska Teixeira Caiaffa
- Observatory for Urban health in Belo Horizonte, School of Medicine, Federal University of Minas Gerais, Brazil
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20
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Rohani P, Drake JM. Untangling the evolution of dengue viruses. Science 2021; 374:941-942. [PMID: 34793209 DOI: 10.1126/science.abm6812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Pejman Rohani
- Odum School of Ecology, Department of Infectious Diseases, College of Veterinary Medicine, the Center for the Ecology of Infectious Diseases and the Center for Influenza Disease and Emergence Research (CIDER), University of Georgia, Athens, GA, USA
| | - John M Drake
- Odum School of Ecology, the Center for the Ecology of Infectious Diseases and CIDER, University of Georgia, Athens, GA, USA
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21
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Katzelnick LC, Zambrana JV, Elizondo D, Collado D, Garcia N, Arguello S, Mercado JC, Miranda T, Ampie O, Mercado BL, Narvaez C, Gresh L, Binder RA, Ojeda S, Sanchez N, Plazaola M, Latta K, Schiller A, Coloma J, Carrillo FB, Narvaez F, Halloran ME, Gordon A, Kuan G, Balmaseda A, Harris E. Dengue and Zika virus infections in children elicit cross-reactive protective and enhancing antibodies that persist long term. Sci Transl Med 2021; 13:eabg9478. [PMID: 34613812 DOI: 10.1126/scitranslmed.abg9478] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Leah C Katzelnick
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA.,Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3203, USA
| | | | | | | | - Nadezna Garcia
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Sonia Arguello
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Juan Carlos Mercado
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua 16064, Nicaragua
| | | | | | | | - César Narvaez
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Raquel A Binder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA.,Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | | | - Krista Latta
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Amy Schiller
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Fausto Bustos Carrillo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | | | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA 98195-1617, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua 12014, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua 16064, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
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22
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Wohl S, Giles JR, Lessler J. Sample size calculation for phylogenetic case linkage. PLoS Comput Biol 2021; 17:e1009182. [PMID: 34228722 PMCID: PMC8284614 DOI: 10.1371/journal.pcbi.1009182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/16/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies. Sequencing the genetic material of viral and bacterial pathogens has become an important part of tracking and combating human infectious diseases. Specifically, comparing the pathogen DNA or RNA sequences collected from infected individuals can allow researchers and public health experts to determine who infected whom, or detect when a pathogen entered a specific country or geographic area. However, it is often impossible to collect samples from every single infected person, and these missing sequences can pose problems for this type of analysis, especially if there is some bias behind which samples were selected for sequencing. We have developed a mathematical framework that allows users to determine the probability their conclusions about pathogen transmission are correct given the number and proportion of samples from a pathogen outbreak they have sequenced. This framework is freely available, easy to use, and broadly generalizable to any pathogen, and we hope that it can be used to inform the design and sampling strategies behind future sequencing-based studies.
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Affiliation(s)
- Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - John R Giles
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
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23
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Neighborhood level chronic respiratory disease prevalence estimation using search query data. PLoS One 2021; 16:e0252383. [PMID: 34106982 PMCID: PMC8189491 DOI: 10.1371/journal.pone.0252383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/15/2021] [Indexed: 11/19/2022] Open
Abstract
Estimation of disease prevalence at sub-city neighborhood scale allows early and targeted interventions that can help save lives and reduce public health burdens. However, the cost-prohibitive nature of highly localized data collection and sparsity of representative signals, has made it challenging to identify neighborhood scale prevalence of disease. To overcome this challenge, we utilize alternative data sources, which are both less sparse and representative of localized disease prevalence: using query data from a large commercial search engine, we identify the prevalence of respiratory illness in the United States, localized to census tract geographic granularity. Focusing on asthma and Chronic Obstructive Pulmonary Disease (COPD), we construct a set of features based on searches for symptoms, medications, and disease-related information, and use these to identify illness rates in more than 23 thousand tracts in 500 cities across the United States. Out of sample model estimates from search data alone correlate with ground truth illness rate estimates from the CDC at 0.69 to 0.76, with simple additions to these models raising those correlations to as high as 0.84. We then show that in practice search query data can be added to other relevant data such as census or land cover data to boost results, with models that incorporate all data sources correlating with ground truth data at 0.91 for asthma and 0.88 for COPD.
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24
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Pollington TM, Tildesley MJ, Hollingsworth TD, Chapman LA. Developments in statistical inference when assessing spatiotemporal disease clustering with the tau statistic. SPATIAL STATISTICS 2021; 42:100438. [PMID: 33816096 PMCID: PMC7985614 DOI: 10.1016/j.spasta.2020.100438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 06/12/2023]
Abstract
The tau statistic τ uses geolocation and, usually, symptom onset time to assess global spatiotemporal clustering from epidemiological data. We test different methods that could bias the clustering range estimate based on the statistic or affect its apparent precision, by comparison with a baseline analysis of an open access measles dataset. From re-analysing this data we find evidence against no clustering and no inhibition, p -value ∈ [ 0 , 0 ⋅ 022 ] (global envelope test). We develop a tau-specific modification of the Loh & Stein spatial bootstrap sampling method, which gives bootstrap tau estimates with 24% lower sampling error and a 110% higher estimated clustering endpoint than previously published (61⋅0 m vs. 29 m) and an equivalent increase in the clustering area of elevated disease odds by 342%. These differences could have important consequences for control efforts. Correct practice of graphical hypothesis testing of no clustering and clustering range estimation of the tau statistic are illustrated in the online Graphical abstract. We advocate proper implementation of this useful statistic, ultimately to reduce inaccuracies in control policy decisions made during disease clustering analysis.
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Affiliation(s)
- Timothy M. Pollington
- MathSys CDT, University of Warwick, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
| | - Michael J. Tildesley
- Zeeman Institute (SBIDER), School of Life Sciences, and Mathematics Institute, University of Warwick, UK
| | - T. Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
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25
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Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nat Commun 2021; 12:1810. [PMID: 33753725 PMCID: PMC7985522 DOI: 10.1038/s41467-021-21888-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogenetic framework that addresses these limitations by considering individual transmission events, reconstructed across spatial scales. We apply it to geocoded dengue virus sequences from Thailand (N = 726 over 18 years). We find infected individuals spend 96% of their time in their home community compared to 76% for the susceptible population (mainly children) and 42% for adults. Dynamic pockets of local immunity make transmission more likely in places with high heterotypic immunity and less likely where high homotypic immunity exists. Age-dependent mixing of individuals and vector distributions are not important in determining spread. This approach provides previously unknown insights into one of the most complex disease systems known and will be applicable to other pathogens. Phylogeographic analyses can provide broad descriptions of the spread of pathogens between populations, but are limited by incomplete sampling. Here, the authors develop an inference framework that reconstructs sequential transmission events and use it to characterise dynamics of dengue in Thailand.
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26
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Thiruchelvam L, Dass SC, Asirvadam VS, Daud H, Gill BS. Determine neighboring region spatial effect on dengue cases using ensemble ARIMA models. Sci Rep 2021; 11:5873. [PMID: 33712664 PMCID: PMC7955078 DOI: 10.1038/s41598-021-84176-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/11/2021] [Indexed: 01/06/2023] Open
Abstract
The state of Selangor, in Malaysia consist of urban and peri-urban centres with good transportation system, and suitable temperature levels with high precipitations and humidity which make the state ideal for high number of dengue cases, annually. This study investigates if districts within the Selangor state do influence each other in determining pattern of dengue cases. Study compares two different models; the Autoregressive Integrated Moving Average (ARIMA) and Ensemble ARIMA models, using the Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) measurement to gauge their performance tools. ARIMA model is developed using the epidemiological data of dengue cases, whereas ensemble ARIMA incorporates the neighbouring regions' dengue models as the exogenous variable (X), into traditional ARIMA model. Ensemble ARIMA models have better model fit compared to the basic ARIMA models by incorporating neighbuoring effects of seven districts which made of state of Selangor. The AIC and BIC values of ensemble ARIMA models to be smaller compared to traditional ARIMA counterpart models. Thus, study concludes that pattern of dengue cases for a district is subject to spatial effects of its neighbouring districts and number of dengue cases in the surrounding areas.
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Affiliation(s)
- Loshini Thiruchelvam
- Insititute of Autonomous Systems, Universiti Teknologi PETRONAS, Seri Iskandar, Perak, Malaysia
| | - Sarat Chandra Dass
- School of Mathematical and Computer Sciences, Heriot-Watt University Malaysia, Putrajaya, Malaysia
| | - Vijanth Sagayan Asirvadam
- Department of Electric and Electronic Engineering, Universiti Teknologi PETRONAS, Seri Iskandar, Perak, Malaysia.
| | - Hanita Daud
- Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, Seri Iskandar, Perak, Malaysia
| | - Balvinder Singh Gill
- Institute for Medical Research (IMR), Ministry of Health, Kuala Lumpur, Malaysia
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27
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Telle O, Nikolay B, Kumar V, Benkimoun S, Pal R, Nagpal BN, Paul RE. Social and environmental risk factors for dengue in Delhi city: A retrospective study. PLoS Negl Trop Dis 2021; 15:e0009024. [PMID: 33571202 PMCID: PMC7877620 DOI: 10.1371/journal.pntd.0009024] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
Global urbanization is leading to an inexorable spread of several major diseases that need to be stemmed. Dengue is one of these major diseases spreading in cities today, with its principal mosquito vector superbly adapted to the urban environment. Current mosquito control strategies are proving inadequate, especially in the face of such urbanisation and novel, evidence-based targeted approaches are needed. Through combined epidemiological and entomological approaches, we aimed to identify a novel sanitation strategy to alleviate the burden of dengue through how the dengue virus spreads through the community. We combined surveillance case mapping, prospective serological studies, year-round mosquito surveys, socio-economic and Knowledge Attitudes and Practices surveys across Delhi. We identified lack of access to tap water (≤98%) as an important risk factor for dengue virus IgG sero-positivity (adjusted Odds Ratio 4.69, 95% C.I. 2.06–10.67) and not poverty per se. Wealthier districts had a higher dengue burden despite lower mosquito densities than the Intermediary income communities (adjusted Odds Ratio 2.92, 95% C.I. 1.26–6.72). This probably reflects dengue being introduced by people travelling from poorer areas to work in wealthier houses. These poorer, high density areas, where temperatures are also warmer, also had dengue cases during the winter. Control strategies based on improved access to a reliable supply of tap water plus focal intervention in intra-urban heat islands prior to the dengue season could not only lead to a reduction in mosquito abundance but also eliminate the reservoir of dengue virus clearly circulating at low levels in winter in socio-economically disadvantaged areas. Identifying disease hotspots and individual risk factors for dengue can enable targeted intervention strategies. We conducted combined serological, entomological and socio-economic surveys across 18 areas within Delhi, taken from the total 1280 colonies (i.e. the administrative units of reference in Delhi) for which we classified their socio-economic typology. We additionally performed a Knowledge, Attitudes, Practices survey at a household level within the most socially disadvantaged sub-districts. Finally, we mapped all the winter dengue cases to 250 m x 250 m units along with their winter mean temperatures. We found that access to tap water was an important risk factor for exposure to dengue virus (DENV) and this was confirmed even within the socially disadvantaged sub-districts. The Wealthy colonies had a high burden of DENV infection despite low mosquito densities, likely linked to their connectedness through daily human mobility. The winter burden of dengue occurred majoritarily in the socio-economically disadvantaged colonies, which also have higher mean temperatures and urban heat islands. Improved access to tap water could lead to a reduction in dengue, not only for those directly affected but for the general population. Targeted intervention through mosquito control in winter in the socially disadvantaged areas could offer a rational strategy for optimising control efforts.
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Affiliation(s)
- Olivier Telle
- Géographie-cités, Université Paris-1 Panthéon-Sorbonne, Paris, France
- Centre for Policy Research, Dharam Marg, Delhi, India
- * E-mail:
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases, Institut Pasteur, Centre National de la Recherche Scientifique, Paris, France
| | - Vikram Kumar
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, India
| | - Samuel Benkimoun
- Géographie-cités, Université Paris-1 Panthéon-Sorbonne, Paris, France
- Centre de Sciences Humaines, UMIFRE 20 CNRS-MAE,Delhi, India
| | - Rupali Pal
- Centre de Sciences Humaines, UMIFRE 20 CNRS-MAE,Delhi, India
| | - BN Nagpal
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, India
| | - Richard E. Paul
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, France
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28
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Kiang MV, Santillana M, Chen JT, Onnela JP, Krieger N, Engø-Monsen K, Ekapirat N, Areechokchai D, Prempree P, Maude RJ, Buckee CO. Incorporating human mobility data improves forecasts of Dengue fever in Thailand. Sci Rep 2021; 11:923. [PMID: 33441598 PMCID: PMC7806770 DOI: 10.1038/s41598-020-79438-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023] Open
Abstract
Over 390 million people worldwide are infected with dengue fever each year. In the absence of an effective vaccine for general use, national control programs must rely on hospital readiness and targeted vector control to prepare for epidemics, so accurate forecasting remains an important goal. Many dengue forecasting approaches have used environmental data linked to mosquito ecology to predict when epidemics will occur, but these have had mixed results. Conversely, human mobility, an important driver in the spatial spread of infection, is often ignored. Here we compare time-series forecasts of dengue fever in Thailand, integrating epidemiological data with mobility models generated from mobile phone data. We show that geographically-distant provinces strongly connected by human travel have more highly correlated dengue incidence than weakly connected provinces of the same distance, and that incorporating mobility data improves traditional time-series forecasting approaches. Notably, no single model or class of model always outperformed others. We propose an adaptive, mosaic forecasting approach for early warning systems.
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Affiliation(s)
- Mathew V Kiang
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Mauricio Santillana
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Jarvis T Chen
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Nattwut Ekapirat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Darin Areechokchai
- Bureau of Vector Borne Disease, Ministry of Public Health, Nonthaburi, Thailand
| | - Preecha Prempree
- Bureau of Vector Borne Disease, Ministry of Public Health, Nonthaburi, Thailand
| | - Richard J Maude
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 5th Floor, Boston, MA, 02115, USA
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 5th Floor, Boston, MA, 02115, USA.
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29
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Schultes OL, Morais MHF, Cunha MDCM, Sobral A, Caiaffa WT. Spatial analysis of dengue incidence and Aedes aegypti ovitrap surveillance in Belo Horizonte, Brazil. Trop Med Int Health 2020; 26:237-255. [PMID: 33159826 DOI: 10.1111/tmi.13521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Understanding the intra-urban spatial dynamics of Aedes aegypti and dengue transmission is important to effectively guide vector control. Ovitraps are a sensitive, cost-effective vector surveillance tool, yet few longitudinal studies have evaluated ovitrap indices and dengue occurrence. We aimed to assess the spatial patterns of dengue incidence and Ae. aegypti ovitrap positivity index (OPI) over time and to examine the spatial relationship between these two variables. METHODS This study used 12 years (2007-2018) of dengue case records and biweekly Ae. aegypti ovitrap data in Belo Horizonte, Brazil. We aggregated data by year and health centre catchment area (n = 152) and used both univariate and bivariate global Moran's I statistic and LISA to evaluate spatial clustering. RESULTS Annual dengue incidence ranged from 18 to 6262/100 000 residents and displayed spatial autocorrelation in 10/12 years, with shifting areas of high incidence. Annual OPI ranged from 35.7 to 47.6% and was clustered in all study years, but unlike dengue had consistent spatial patterns over time. Bivariate analysis found both positive (6/12 years) and negative (1/12 years) spatial associations between the two variables. CONCLUSIONS Low detected presence of Ae. aegypti was not a limiting factor in dengue transmission. However, stable spatial distribution of OPI suggests that certain areas may have persistent breeding sites. Future research should identify factors related to persistent Ae. aegypti hotspots to better guide vector management. Vector control efforts should be paired with additional data on population immunity, circulating serotypes and urban factors to better predict and control outbreaks.
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Affiliation(s)
- Olivia Lang Schultes
- Urban Health Observatory of Belo Horizonte, Federal University of Minas Gerais, Brazil
| | | | | | - Andréa Sobral
- National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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30
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Kazazian L, Lima Neto AS, Sousa GS, do Nascimento OJ, Castro MC. Spatiotemporal transmission dynamics of co-circulating dengue, Zika, and chikungunya viruses in Fortaleza, Brazil: 2011-2017. PLoS Negl Trop Dis 2020; 14:e0008760. [PMID: 33104708 PMCID: PMC7644107 DOI: 10.1371/journal.pntd.0008760] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/05/2020] [Accepted: 08/30/2020] [Indexed: 12/16/2022] Open
Abstract
The mosquito-borne viruses dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV), now co-endemic in the Americas, pose growing threats to health worldwide. However, it remains unclear whether there exist interactions between these viruses that could shape their epidemiology. This study advances knowledge by assessing the transmission dynamics of co-circulating DENV, ZIKV, and CHIKV in the city of Fortaleza, Brazil. Spatiotemporal transmission dynamics of DENV, ZIKV, and CHIKV were analyzed using georeferenced data on over 210,000 reported cases from 2011 to 2017 in Fortaleza, Brazil. Local spatial clustering tests and space-time scan statistics were used to compare transmission dynamics across all years. The transmission of co-circulating viruses in 2016 and 2017 was evaluated at fine spatial and temporal scales using a measure of spatiotemporal dependence, the τ-statistic. Results revealed differences in the diffusion of CHIKV compared to previous DENV epidemics and spatially distinct transmission of DENV/ZIKV and CHIKV during the period of their co-circulation. Significant spatial clustering of viruses of the same type was observed within 14-day time intervals at distances of up to 6.8 km (p<0.05). These results suggest that arbovirus risk is not uniformly distributed within cities during co-circulation. Findings may guide outbreak preparedness and response efforts by highlighting the clustered nature of transmission of co-circulating arboviruses at the neighborhood level. The potential for competitive interactions between the arboviruses should be further investigated.
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Affiliation(s)
- Lilit Kazazian
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Antonio S. Lima Neto
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Health Surveillance Department, Fortaleza Municipal Health Secretariat (SMS-Fortaleza), Joaquim Távora, Fortaleza, Ceará, Brazil
- Health Sciences Center, University of Fortaleza (UNIFOR), Edson Queiroz, Fortaleza, Ceará, Brazil
| | - Geziel S. Sousa
- Health Surveillance Department, Fortaleza Municipal Health Secretariat (SMS-Fortaleza), Joaquim Távora, Fortaleza, Ceará, Brazil
| | - Osmar José do Nascimento
- Health Surveillance Department, Fortaleza Municipal Health Secretariat (SMS-Fortaleza), Joaquim Távora, Fortaleza, Ceará, Brazil
| | - Marcia C. Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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31
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Korevaar H, Metcalf CJ, Grenfell BT. Structure, space and size: competing drivers of variation in urban and rural measles transmission. J R Soc Interface 2020; 17:20200010. [PMID: 32634366 PMCID: PMC7423418 DOI: 10.1098/rsif.2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A key concern in public health is whether disparities exist between urban and rural areas. One dimension of potential variation is the transmission of infectious diseases. In addition to potential differences between urban and rural local dynamics, the question of whether urban and rural areas participate equally in national dynamics remains unanswered. Specifically, urban and rural areas may diverge in local transmission as well as spatial connectivity, and thus risk for receiving imported cases. Finally, the potential confounding relationship of spatial proximity with size and urban/rural district type has not been addressed by previous research. It is rare to have sufficient data to explore these questions thoroughly. We use exhaustive weekly case reports of measles in 954 urban and 468 rural districts of the UK (1944–1965) to compare both local disease dynamics as well as regional transmission. We employ the time-series susceptible–infected–recovered model to estimate disease transmission, epidemic severity, seasonality and import dependence. Congruent with past results, we observe a clear dependence on population size for the majority of these measures. We use a matched-pair strategy to compare proximate urban and rural districts and control for possible spatial confounders. This analytical strategy reveals a modest difference between urban and rural areas. Rural areas tend to be characterized by more frequent, smaller outbreaks compared to urban counterparts. The magnitude of the difference is slight and the results primarily reinforce the importance of population size, both in terms of local and regional transmission. In sum, urban and rural areas demonstrate remarkable epidemiological similarity in this recent UK context.
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Affiliation(s)
- Hannah Korevaar
- Office of Population Research, Princeton University, Princeton, NJ, USA.,Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - C Jessica Metcalf
- Office of Population Research, Princeton University, Princeton, NJ, USA.,Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA.,Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bryan T Grenfell
- Office of Population Research, Princeton University, Princeton, NJ, USA.,Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA.,Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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32
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Diptyanusa A, Lazuardi L, Jatmiko RH. Implementation of geographical information systems for the study of diseases caused by vector-borne arboviruses in Southeast Asia: A review based on the publication record. GEOSPATIAL HEALTH 2020; 15. [PMID: 32575973 DOI: 10.4081/gh.2020.862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
The spread of mosquito-borne diseases in Southeast Asia has dramatically increased in the latest decades. These infections include dengue, chikungunya and Japanese Encephalitis (JE), high-burden viruses sharing overlapping disease manifestation and vector distribution. The use of Geographical Information Systems (GIS) to monitor the dynamics of disease and vector distribution can assist in disease epidemic prediction and public health interventions, particularly in Southeast Asia where sustained high temperatures drive the epidemic spread of these mosquito-borne viruses. Due to lack of accurate data, the spatial and temporal dynamics of these mosquito-borne viral disease transmission countries are poorly understood, which has limited disease control effort. By following studies carried out on these three viruses across the region in a specific time period revealing general patterns of research activities and characteristics, this review finds the need to improve decision-support by disease mapping and management. The results presented, based on a publication search with respect to diseases due to arboviruses, specifically dengue, chikungunya and Japanese encephalitis, should improve opportunities for future studies on the implementation of GIS in the control of mosquito-borne viral diseases in Southeast Asia.
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Affiliation(s)
- Ajib Diptyanusa
- Department of Parasitology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jalan Farmako, Sekip Utara.
| | - Lutfan Lazuardi
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Jalan Farmako, Sekip Utara.
| | - Retnadi Heru Jatmiko
- Centre for Remote Sensing and Geographical Information System (PUSPICS), Universitas Gadjah Mada, Sekip Utara, Yogyakarta.
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33
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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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Evaluation of the usefulness of Aedes aegypti rapid larval surveys to anticipate seasonal dengue transmission between 2012-2015 in Fortaleza, Brazil. Acta Trop 2020; 205:105391. [PMID: 32057775 DOI: 10.1016/j.actatropica.2020.105391] [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: 09/02/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
Abstract
Rapid larval surveys have been mandated in nearly every urban Brazilian municipality and promoted by the Pan American Health Organization. These surveys purport to classify arbovirus transmission risk as a basis to triage local surveillance and vector control operations, yet no previous analyses have determined relative risk associated with marginal changes in infestation at administrative and temporal scales relevant to vector control. We estimated associations between entomological indices from six larval surveys and daily incidence rates of confirmed dengue cases in Fortaleza, Brazil using models adjusted for rainfall, and indicators of spatial association. Poor correspondence between infestation and incidence indicates that these surveys may systematically mislead vector control activities and treatment strategies in Fortaleza and in similar cities throughout Latin America. The co-circulation of multiple arboviruses enhances the importance of determining the true informational value of these surveys, and of identifying complementary tools to discern local and inter-annual transmission risk.
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35
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A Mapping Review on Urban Landscape Factors of Dengue Retrieved from Earth Observation Data, GIS Techniques, and Survey Questionnaires. REMOTE SENSING 2020. [DOI: 10.3390/rs12060932] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To date, there is no effective treatment to cure dengue fever, a mosquito-borne disease which has a major impact on human populations in tropical and sub-tropical regions. Although the characteristics of dengue infection are well known, factors associated with landscape are highly scale dependent in time and space, and therefore difficult to monitor. We propose here a mapping review based on 78 articles that study the relationships between landscape factors and urban dengue cases considering household, neighborhood and administrative levels. Landscape factors were retrieved from survey questionnaires, Geographic Information Systems (GIS), and remote sensing (RS) techniques. We structured these into groups composed of land cover, land use, and housing type and characteristics, as well as subgroups referring to construction material, urban typology, and infrastructure level. We mapped the co-occurrence networks associated with these factors, and analyzed their relevance according to a three-valued interpretation (positive, negative, non significant). From a methodological perspective, coupling RS and GIS techniques with field surveys including entomological observations should be systematically considered, as none digital land use or land cover variables appears to be an univocal determinant of dengue occurrences. Remote sensing urban mapping is however of interest to provide a geographical frame to distribute human population and movement in relation to their activities in the city, and as spatialized input variables for epidemiological and entomological models.
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36
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Teissier Y, Paul R, Aubry M, Rodo X, Dommar C, Salje H, Sakuntabhai A, Cazelles B, Cao-Lormeau VM. Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014. PLoS Negl Trop Dis 2020; 14:e0008110. [PMID: 32142511 PMCID: PMC7080275 DOI: 10.1371/journal.pntd.0008110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/18/2020] [Accepted: 02/02/2020] [Indexed: 01/18/2023] Open
Abstract
Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 117 islands of which 72 are inhabited, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype. Competitive serotype replacement has been observed previously and seems to be characteristic of the South Pacific. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti. Dengue virus is the most significant arthropod-borne virus infecting man. Understanding how long dengue virus can persist in populations of varying size is key to understanding its epidemiology. This is, however, impossible to achieve in settings where dengue is endemic, because of continued human movement and is further complexified by the occurrence of several co-circulating serotypes. By contrast, French Polynesia, an isolated group of 72 inhabited islands in the South Pacific, has had intermittent majoritarily monotypic dengue epidemics since the 1940s and offers a unique opportunity to address questions of viral persistence, turnover and the importance of spatial sub-structure in determining dengue epidemiology. Collating and analyzing a database of laboratory-confirmed dengue cases from across French Polynesia over a 35 year period we were able to show that dengue virus die-out can occur with or without replacement by a new serotype, monotypic transmission of dengue viruses fails to be maintained within small island populations but can persist for years among isolated islands connected via air and sea links. This remarkable long-term persistence of dengue virus in French Polynesia could be maintained by asynchronous viral transmission among connected islands and/or by repeated seeding from a reservoir of sub-clinical infections in the most populated island, Tahiti.
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Affiliation(s)
- Yoann Teissier
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
- Université Paris Descartes, PSL University, Paris, France
| | - Richard Paul
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, UMR 2000 CNRS, Paris, France
- Pasteur Kyoto International Joint Research Unit for Integrative Vaccinomics, Kyoto, Japan
- * E-mail: (RP); (VMCL)
| | - Maite Aubry
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Xavier Rodo
- ICREA, Barcelona, Spain
- CLIMA (Climate and Health) Program, ISGlobal, Barcelona, Spain
| | - Carlos Dommar
- CLIMA (Climate and Health) Program, ISGlobal, Barcelona, Spain
| | - Henrik Salje
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit, UMR 2000, Centre National de la Recherche Scientifique, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, UMR 2000 CNRS, Paris, France
- Pasteur Kyoto International Joint Research Unit for Integrative Vaccinomics, Kyoto, Japan
| | - Bernard Cazelles
- International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209, Sorbonne Université - IRD, Bondy cedex, France
- iGLOBE, UMI CNRS 3157, University of Arizona, Tucson, Arizona, United States of America
- IBENS, UMR 8197 CNRS-ENS Ecole Normale Supérieure, Paris, France
| | - Van-Mai Cao-Lormeau
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
- * E-mail: (RP); (VMCL)
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37
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Blight J, Alves E, Reyes-Sandoval A. Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention. Vaccines (Basel) 2019; 7:E203. [PMID: 31816907 PMCID: PMC6963661 DOI: 10.3390/vaccines7040203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 01/18/2023] Open
Abstract
Over three billion are at risk of dengue infection with more than 100 million a year presenting with symptoms that can lead to deadly haemorrhagic disease. There are however no treatments available and the only licensed vaccine shows limited efficacy and is able to enhance the disease in some cases. These failures have mainly been due to the complex pathology and lack of understanding of the correlates of protection for dengue virus (DENV) infection. With increasing data suggesting both a protective and detrimental effect for antibodies and CD8 T-cells whilst having complex environmental dynamics. This review discusses the roles of genomic and immunological aspects of DENV infection, providing both a historical interpretation and fresh discussion on how this information can be used for the next generation of dengue interventions.
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Affiliation(s)
- Joshua Blight
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK; (J.B.); (E.A.)
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
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38
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Jakobsen F, Nguyen-Tien T, Pham- Thanh L, Bui VN, Nguyen-Viet H, Tran- Hai S, Lundkvist Å, Bui- Ngoc A, Lindahl JF. Urban livestock-keeping and dengue in urban and peri-urban Hanoi, Vietnam. PLoS Negl Trop Dis 2019; 13:e0007774. [PMID: 31770384 PMCID: PMC6879131 DOI: 10.1371/journal.pntd.0007774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Urban livestock provides an important source of food and income, but it may increase the risks for disease transmission. Vectors, such as mosquitoes, might increase and thereby cause an enhanced transmission of infectious diseases, such as dengue fever; considered the most important mosquito-borne viral disease globally. This cross-sectional study evaluated the awareness of dengue fever and investigated how the presence of dengue vectors is affected by the keeping of livestock in urban households in the city of Hanoi, Vietnam. From February to March 2018, during the season of lowest occurrence of dengue in Hanoi, 140 households were interviewed, of which 69 kept livestock. A general trend was observed; respondents living in the Dan Phuong district, a peri-urban district, had better knowledge and practice regarding dengue as compared to the urban Ha Dong district. In total, 3899 mosquitoes were collected and identified, of which 52 (1.33%) were Aedes species. A significant difference between the two districts was observed, with more households in Ha Dong having Aedes spp. mosquitoes (p = 0.02) and a higher incidence of dengue fever (p = 0.001). There was no significant association between livestock-rearing and the presence of Aedes spp. mosquitoes (p = 0.955), or between livestock-rearing and the incidence of dengue fever (p = 0.08). In conclusion, this study could not find any indication that households keeping livestock were at higher risk of dengue virus infections in Hanoi during the season of lowest occurrence of dengue, but clearly indicated the need of more information provided to urban inhabitants, particularly on personal protection.
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Affiliation(s)
- Frida Jakobsen
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
| | - Thang Nguyen-Tien
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- International Livestock Research Institute, Hanoi, Vietnam
| | - Long Pham- Thanh
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- International Livestock Research Institute, Hanoi, Vietnam
| | | | - Hung Nguyen-Viet
- International Livestock Research Institute, Hanoi, Vietnam
- Hanoi University of Public Health, Hanoi, Vietnam
| | - Son Tran- Hai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Åke Lundkvist
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
| | - Anh Bui- Ngoc
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - Johanna F. Lindahl
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden
- International Livestock Research Institute, Hanoi, Vietnam
- Swedish University of Agricultural Sciences, Department of Clinical Sciences, Uppsala, Sweden
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39
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Succo T, Noël H, Nikolay B, Maquart M, Cochet A, Leparc-Goffart I, Catelinois O, Salje H, Pelat C, de Crouy-Chanel P, de Valk H, Cauchemez S, Rousseau C. Dengue serosurvey after a 2-month long outbreak in Nîmes, France, 2015: was there more than met the eye? ACTA ACUST UNITED AC 2019; 23. [PMID: 29897042 PMCID: PMC6152166 DOI: 10.2807/1560-7917.es.2018.23.23.1700482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Clusters of dengue cases have recently become more frequent in areas of southern France colonised by the vector mosquito Aedes albopictus. In July 2015, a 2-month outbreak of dengue virus serotype 1 (DENV-1) was reported in Nîmes. Aim: We conducted a serosurvey in the affected area at the end of the vector activity period to determine the true extent of dengue transmission. Methods: We collected capillary blood from consenting household members, and information on their medical and travel histories, and exposure to mosquito bites. Recent infections were identified using IgM and IgG anti-DENV ELISA, followed, when positive, by plaque reduction neutralisation tests on serum against DENV 1–4 and West Nile virus. The prevalence estimator was calibrated on reference demographic data. We quantified the spatial clustering of dengue cases within the affected community and inferred the transmission tree. Results: The study participation rate was 39% (564/1,431). Three of 564 participants tested positive for DENV-1 infection (after marginal calibration, 0.41%; 95% confidence interval: 0.00–0.84). The spatial analysis showed that cases were clustered at the household level. Most participants perceived the presence of mosquitos as abundant (83%) and reported frequent mosquito bites (57%). We incidentally identified six past West Nile virus infections (0.9%; 95% CI: 0.2–1.6). Conclusion: This serosurvey confirms the potential for arboviral diseases to cause outbreaks − albeit limited for now − in France and Europe.
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Affiliation(s)
- Tiphanie Succo
- These authors contributed equally to the study and writing of the article.,The French Public Health Agency (Santé publique France), Regional unit (Cire) Occitanie, Saint-Maurice, France
| | - Harold Noël
- The French Public Health Agency (Santé publique France), Saint-Maurice, France.,These authors contributed equally to the study and writing of the article
| | - Birgit Nikolay
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France.,Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Marianne Maquart
- Institut de Recherche Biomédicale des Armées, National Reference Center for arboviruses, Marseille, France
| | - Amandine Cochet
- The French Public Health Agency (Santé publique France), Regional unit (Cire) Occitanie, Saint-Maurice, France
| | - Isabelle Leparc-Goffart
- Institut de Recherche Biomédicale des Armées, National Reference Center for arboviruses, Marseille, France
| | - Olivier Catelinois
- These authors contributed equally to the study and writing of the article
| | - Henrik Salje
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France.,Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Camille Pelat
- The French Public Health Agency (Santé publique France), Saint-Maurice, France
| | | | - Henriette de Valk
- The French Public Health Agency (Santé publique France), Saint-Maurice, France
| | - Simon Cauchemez
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France.,Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Cyril Rousseau
- The French Public Health Agency (Santé publique France), Regional unit (Cire) Occitanie, Saint-Maurice, France
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40
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Azman AS, Luquero FJ, Salje H, Mbaïbardoum NN, Adalbert N, Ali M, Bertuzzo E, Finger F, Toure B, Massing LA, Ramazani R, Saga B, Allan M, Olson D, Leglise J, Porten K, Lessler J. Micro-Hotspots of Risk in Urban Cholera Epidemics. J Infect Dis 2019; 218:1164-1168. [PMID: 29757428 PMCID: PMC6107744 DOI: 10.1093/infdis/jiy283] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/09/2018] [Indexed: 12/05/2022] Open
Abstract
Targeted interventions have been delivered to neighbors of cholera cases in major epidemic responses globally despite limited evidence for the impact of such targeting. Using data from urban epidemics in Chad and Democratic Republic of the Congo, we estimate the extent of spatiotemporal zones of increased cholera risk around cases. In both cities, we found zones of increased risk of at least 200 meters during the 5 days immediately after case presentation to a clinic. Risk was highest for those living closest to cases and diminished in time and space similarly across settings. These results provide a rational basis for rapidly delivering targeting interventions.
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Affiliation(s)
- Andrew S Azman
- Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Francisco J Luquero
- Departments of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Epicentre, Paris, France
| | | | - Nathan Naibei Mbaïbardoum
- Epicentre, Paris, France.,Communauté des Amis de l'Informatique pour le Développement, N'Djamena, Chad
| | | | - Mohammad Ali
- Departments of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Enrico Bertuzzo
- Department of Environmental Science, Informatics and Statistics, Università Ca' Foscari Venezia, Venice, Italy
| | - Flavio Finger
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, United Kingom
| | | | - Louis Albert Massing
- Médecins sans Frontières (France), Kinshasa, The Democratic Republic of the Congo
| | - Romain Ramazani
- Médecins sans Frontières (France), Kalemie, The Democratic Republic of the Congo
| | | | | | | | | | | | - Justin Lessler
- Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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41
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Indriani C, Ahmad RA, Wiratama BS, Arguni E, Supriyati E, Sasmono RT, Kisworini FY, Ryan PA, O'Neill SL, Simmons CP, Utarini A, Anders KL. Baseline Characterization of Dengue Epidemiology in Yogyakarta City, Indonesia, before a Randomized Controlled Trial of Wolbachia for Arboviral Disease Control. Am J Trop Med Hyg 2019; 99:1299-1307. [PMID: 30226138 PMCID: PMC6221224 DOI: 10.4269/ajtmh.18-0315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Dengue is endemic in Indonesia. Here, we describe the epidemiology of dengue in the city of Yogyakarta, Central Java, as a prelude to implementation of a cluster-randomized trial of Wolbachia for the biocontrol of arboviral transmission. Surveillance records from 2006 to 2016 demonstrate seasonal oscillations of dengue incidence with varying magnitude. Two lines of evidence demonstrate a high force of infection; the hospitalized case burden of patients diagnosed with dengue hemorrhagic fever or dengue shock syndrome over the last decade consisted predominantly of children/adolescents, and a serosurvey of 314 healthy children aged 1–10 years found 68% possessed dengue virus–neutralizing antibodies. Finally, a mobility survey indicated children aged 1–10 years, and particularly 1–5 year-olds, spent most of their daytime hours at home. These findings inform the design of clinical trials to measure the impact of novel vector control methods such as Wolbachia introgression into Aedes aegypti mosquitoes, by providing baseline data on disease incidence and identifying subpopulations for recruitment into prospective studies of dengue virus infection and disease. The mobility survey findings indicate that in cluster trials of interventions applied at the community level, young children can reasonably be expected to spend most of their exposure time, in epidemiological terms, within the treatment arm to which they were randomized.
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Affiliation(s)
- Citra Indriani
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riris A Ahmad
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bayu S Wiratama
- Department of Epidemiology, Biostatistics and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Pediatrics, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | | | - Peter A Ryan
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Scott L O'Neill
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Cameron P Simmons
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Institute of Vector Borne Disease, Monash University, Melbourne, Australia
| | - Adi Utarini
- Department of Health Policy and Management, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Katherine L Anders
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia
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42
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Velez ID, Santacruz E, Kutcher SC, Duque SL, Uribe A, Barajas J, Gonzalez S, Patino AC, Zuluaga L, Martínez L, Muñoz E, Mejia MC, Arbelaez MP, Pulido H, Jewell NP, Dufault SM, O'Neill SL, Simmons CP, Anders KL, Tanamas SK. The impact of city-wide deployment of Wolbachia-carrying mosquitoes on arboviral disease incidence in Medellín and Bello, Colombia: study protocol for an interrupted time-series analysis and a test-negative design study. F1000Res 2019; 8:1327. [PMID: 34900237 PMCID: PMC8637243 DOI: 10.12688/f1000research.19858.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Dengue, chikungunya and Zika are viral infections transmitted by Aedes aegypti mosquitoes, and present major public health challenges in tropical regions. Traditional vector control methods have been ineffective at halting disease transmission. The World Mosquito Program has developed a novel approach to arbovirus control using Ae. aegypti stably transfected with the Wolbachia bacterium, which have significantly reduced ability to transmit dengue, Zika and chikungunya in laboratory experiments. Field releases in eight countries have demonstrated Wolbachia establishment in local Ae. aegypti populations. Methods: We describe a pragmatic approach to measuring the epidemiological impact of city-wide Wolbachia deployments in Bello and Medellín, Colombia. First, an interrupted time-series analysis will compare the incidence of dengue, chikungunya and Zika case notifications before and after Wolbachia releases, across the two municipalities. Second, a prospective case-control study using a test-negative design will be conducted in one quadrant of Medellín. Three of the six contiguous release zones in the case-control area were allocated to receive the first Wolbachia deployments in the city and three to be treated last, approximating a parallel two-arm trial for the >12-month period during which Wolbachia exposure remains discordant. Allocation, although non-random, aimed to maximise balance between arms in historical dengue incidence and demographics. Arboviral disease cases and arbovirus-negative controls will be enrolled concurrently from febrile patients presenting to primary care, with case/control status classified retrospectively following laboratory diagnostic testing. Intervention effect is estimated from an aggregate odds ratio comparing Wolbachia-exposure odds among test-positive cases versus test-negative controls. Discussion: The study findings will add to an accumulating body of evidence from global field sites on the efficacy of the Wolbachia method in reducing arboviral disease incidence, and can inform decisions on wider public health implementation of this intervention in the Americas and beyond. Trial registration: ClinicalTrials.gov: NCT03631719. Registered on 15 August 2018.
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Affiliation(s)
- Ivan D. Velez
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Eduardo Santacruz
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Simon C. Kutcher
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Sandra L. Duque
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Alexander Uribe
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Jovany Barajas
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Sandra Gonzalez
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | | | - Lina Zuluaga
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Luis Martínez
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | - Estefanía Muñoz
- World Mosquito Program, Universidad de Antioquia, Medellin, Colombia
| | | | | | | | - Nicholas P. Jewell
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Centre for Statistical Methodology, London School of Hygiene & Tropical Medicine, London, UK
| | - Suzanne M Dufault
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Scott L. O'Neill
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Cameron P. Simmons
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Katherine L. Anders
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Stephanie K. Tanamas
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
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Bartlow AW, Manore C, Xu C, Kaufeld KA, Del Valle S, Ziemann A, Fairchild G, Fair JM. Forecasting Zoonotic Infectious Disease Response to Climate Change: Mosquito Vectors and a Changing Environment. Vet Sci 2019; 6:E40. [PMID: 31064099 PMCID: PMC6632117 DOI: 10.3390/vetsci6020040] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Infectious diseases are changing due to the environment and altered interactions among hosts, reservoirs, vectors, and pathogens. This is particularly true for zoonotic diseases that infect humans, agricultural animals, and wildlife. Within the subset of zoonoses, vector-borne pathogens are changing more rapidly with climate change, and have a complex epidemiology, which may allow them to take advantage of a changing environment. Most mosquito-borne infectious diseases are transmitted by mosquitoes in three genera: Aedes, Anopheles, and Culex, and the expansion of these genera is well documented. There is an urgent need to study vector-borne diseases in response to climate change and to produce a generalizable approach capable of generating risk maps and forecasting outbreaks. Here, we provide a strategy for coupling climate and epidemiological models for zoonotic infectious diseases. We discuss the complexity and challenges of data and model fusion, baseline requirements for data, and animal and human population movement. Disease forecasting needs significant investment to build the infrastructure necessary to collect data about the environment, vectors, and hosts at all spatial and temporal resolutions. These investments can contribute to building a modeling community around the globe to support public health officials so as to reduce disease burden through forecasts with quantified uncertainty.
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Affiliation(s)
- Andrew W Bartlow
- Los Alamos National Laboratory, Biosecurity and Public Health, Los Alamos, NM 87545, USA.
| | - Carrie Manore
- Los Alamos National Laboratory, Information Systems and Modeling, Los Alamos, NM 87545, USA.
| | - Chonggang Xu
- Los Alamos National Laboratory, Earth Systems Observations, Los Alamos, NM 87545, USA.
| | - Kimberly A Kaufeld
- Los Alamos National Laboratory, Statistical Sciences, Los Alamos, NM 87545, USA.
| | - Sara Del Valle
- Los Alamos National Laboratory, Information Systems and Modeling, Los Alamos, NM 87545, USA.
| | - Amanda Ziemann
- Los Alamos National Laboratory, Space Data Science and Systems, Los Alamos, NM 87545, USA.
| | - Geoffrey Fairchild
- Los Alamos National Laboratory, Information Systems and Modeling, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Los Alamos National Laboratory, Biosecurity and Public Health, Los Alamos, NM 87545, USA.
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Champagne C, Paul R, Ly S, Duong V, Leang R, Cazelles B. Dengue modeling in rural Cambodia: Statistical performance versus epidemiological relevance. Epidemics 2019; 26:43-57. [DOI: 10.1016/j.epidem.2018.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 07/19/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
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Ruchusatsawat K, Wongjaroen P, Posanacharoen A, Rodriguez-Barraquer I, Sangkitporn S, Cummings DAT, Salje H. Long-term circulation of Zika virus in Thailand: an observational study. THE LANCET. INFECTIOUS DISEASES 2019; 19:439-446. [PMID: 30826189 DOI: 10.1016/s1473-3099(18)30718-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/12/2018] [Accepted: 11/09/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Little is known about the historical and current risk of Zika virus infection in southeast Asia, where the mosquito vector is widespread and other arboviruses circulate endemically. Centralised Zika virus surveillance began in Thailand in January, 2016. We assessed the long-term circulation of Zika virus in Thailand. METHODS In this observational study, we analysed data from individuals with suspected Zika virus infection who presented at hospitals throughout the country and had biological samples (serum, plasma, or urine) tested for confirmation with PCR at the National Institute of Health laboratories in Bangkok. We analysed the spatial and age distribution of cases, and constructed time-resolved phylogenetic trees using genomes from Thailand and elsewhere to estimate when Zika virus was first introduced. FINDINGS Of the 3089 samples from 1717 symptomatic individuals tested between January, 2016, and December, 2017, 368 were confirmed to have Zika virus infection. Cases of Zika virus infection were reported throughout the year, and from 29 of the 76 Thai provinces. Individuals had 2·8 times (95% CI 2·3-3·6) the odds of testing positive for Zika virus infection if they came from the same district and were sick within the same year of a person with a confirmed infection relative to the odds of testing positive anywhere, consistent with focal transmission. The probability of cases being younger than 10 years was 0·99 times (0·72-1·30) the probability of being that age in the underlying population. This probability rose to 1·62 (1·33-1·92) among those aged 21-30 years and fell to 0·53 (0·40-0·66) for those older than 50 years. This age distribution is consistent with that observed in the Zika virus epidemic in Colombia. Phylogenetic reconstructions suggest persistent circulation within Thailand since at least 2002. INTERPRETATION Our evidence shows that Zika virus has circulated at a low but sustained level for at least 16 years, suggesting that Zika virus can adapt to persistent endemic transmission. Health systems need to adapt to cope with regular occurrences of the severe complications associated with infection. FUNDING European Research Council, National Science Foundation, and National Institutes of Health.
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Affiliation(s)
- Kriangsak Ruchusatsawat
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Pattara Wongjaroen
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Arisara Posanacharoen
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Henrik Salje
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Champagne C, Cazelles B. Comparison of stochastic and deterministic frameworks in dengue modelling. Math Biosci 2019; 310:1-12. [PMID: 30735695 DOI: 10.1016/j.mbs.2019.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 11/16/2022]
Abstract
We perform estimations of compartment models for dengue transmission in rural Cambodia with increasing complexity regarding both model structure and the account for stochasticity. On the one hand, we successively account for three embedded sources of stochasticity: observation noise, demographic variability and environmental hazard. On the other hand, complexity in the model structure is increased by introducing vector-borne transmission, explicit asymptomatic infections and interacting virus serotypes. Using two sources of case data from dengue epidemics in Kampong Cham (Cambodia), models are estimated in the bayesian framework, with Markov Chain Monte Carlo and Particle Markov Chain Monte Carlo. We highlight the advantages and drawbacks of the different formulations in a practical setting. Although in this case the deterministic models provide a good approximation of the mean trajectory for a low computational cost, the stochastic frameworks better reflect and account for parameter and simulation uncertainty.
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Affiliation(s)
- Clara Champagne
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197,46 rue d'Ulm, Paris 75005, France; CREST, ENSAE, Université Paris Saclay, 5, avenue Henry Le Chatelier, Palaiseau cedex 91764, France.
| | - Bernard Cazelles
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197,46 rue d'Ulm, Paris 75005, France; International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209 Sorbonne Université - IRD, Bondy cedex, France
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47
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Truelove SA, Graham M, Moss WJ, Metcalf CJE, Ferrari MJ, Lessler J. Characterizing the impact of spatial clustering of susceptibility for measles elimination. Vaccine 2019; 37:732-741. [PMID: 30579756 PMCID: PMC6348711 DOI: 10.1016/j.vaccine.2018.12.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 01/16/2023]
Abstract
Measles elimination efforts are primarily focused on achieving and maintaining national vaccination coverage goals, based on estimates of the critical vaccination threshold (Vc): the proportion of the population that must be immune to prevent sustained epidemics. Traditionally, Vc estimates assume evenly mixing populations, an invalid assumption. If susceptible individuals preferentially contact one another, communities may remain vulnerable to epidemics even when vaccination coverage targets are met at the national level. Here we present a simple method to estimate Vc and the effective reproductive number, R, while accounting for spatial clustering of susceptibility. For measles, assuming R0 = 15 and 95% population immunity, adjustment for high clustering of susceptibility increases R from 0.75 to 1.29, Vc from 93% to 96%, and outbreak probability after a single introduction from <1% to 23%. The impact of clustering remains minimal until vaccination coverage nears elimination levels. We illustrate our approach using Demographic and Health Survey data from Tanzania and show how non-vaccination clustering potentially contributed to continued endemic transmission of measles virus during the last two decades. Our approach demonstrates why high national vaccination coverage sometimes fails to achieve measles elimination, and that a shift from national to subnational focus is needed as countries approach elimination.
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Affiliation(s)
- Shaun A Truelove
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
| | - Matthew Graham
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; The Hospital for Tropical Diseases, Wellcome Trust Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - William J Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Office of Population Research, Woodrow Wilson School, Princeton University, Princeton, NJ, USA
| | - Matthew J Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA; Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Abstract
Spatial epidemiology is a rapidly advancing field, pushing our abilities to measure, monitor and map pathogens at increasingly finer spatiotemporal scales. However, these scales often do not align with the abilities of control programmes to act at them, building a disconnect between academia and implementation. Efforts are being made to feed innovations into government, build spatial data skills, and strengthen links between disease control programmes and universities, yet work remains to be done if goals for disease control, elimination and 'leaving no one behind' are to be met.
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Affiliation(s)
- Andrew J Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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49
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Kang JY, Aldstadt J. Using Multiple Scale Spatio-Temporal Patterns for Validating Spatially Explicit Agent-Based Models. INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE : IJGIS 2018; 33:193-213. [PMID: 31695574 PMCID: PMC6834355 DOI: 10.1080/13658816.2018.1535121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
Spatially explicit agent-based models (ABMs) have been widely utilized to simulate the dynamics of spatial processes that involve the interactions of individual agents. The assumptions embedded in the ABMs may be responsible for uncertainty in the model outcomes. To ensure the reliability of the outcomes in terms of their space-time patterns, model validation should be performed. In this paper, we propose the use of multiple scale spatio-temporal patterns for validating spatially explicit ABMs. We evaluated several specifications of vector-borne disease transmission models by comparing space-time patterns of model outcomes to observations at multiple scales via the sum of root mean square error (RMSE) measurement. The results indicate that specifications of the spatial configurations of residential area and immunity status of individual humans are of importance to reproduce observed patterns of dengue outbreaks at multiple space-time scales. Our approach to using multiple scale spatio-temporal patterns can help not only to understand the dynamic associations between model specifications and model outcomes, but also to validate spatially explicit ABMs.
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Affiliation(s)
- Jeon-Young Kang
- Department of Geography, University at Buffalo, The State University of New York, Buffalo, USA
| | - Jared Aldstadt
- Department of Geography, University at Buffalo, The State University of New York, Buffalo, USA
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Moore SM, Ten Bosch QA, Siraj AS, Soda KJ, España G, Campo A, Gómez S, Salas D, Raybaud B, Wenger E, Welkhoff P, Perkins TA. Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity. BMC Med 2018; 16:152. [PMID: 30157921 PMCID: PMC6116375 DOI: 10.1186/s12916-018-1127-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mathematical models of transmission dynamics are routinely fitted to epidemiological time series, which must inevitably be aggregated at some spatial scale. Weekly case reports of chikungunya have been made available nationally for numerous countries in the Western Hemisphere since late 2013, and numerous models have made use of this data set for forecasting and inferential purposes. Motivated by an abundance of literature suggesting that the transmission of this mosquito-borne pathogen is localized at scales much finer than nationally, we fitted models at three different spatial scales to weekly case reports from Colombia to explore limitations of analyses of nationally aggregated time series data. METHODS We adapted the recently developed Disease Transmission Kernel (DTK)-Dengue model for modeling chikungunya virus (CHIKV) transmission, given the numerous similarities of these viruses vectored by a common mosquito vector. We fitted versions of this model specified at different spatial scales to weekly case reports aggregated at different spatial scales: (1) single-patch national model fitted to national data; (2) single-patch departmental models fitted to departmental data; and (3) multi-patch departmental models fitted to departmental data, where the multiple patches refer to municipalities within a department. We compared the consistency of simulations from fitted models with empirical data. RESULTS We found that model consistency with epidemic dynamics improved with increasing spatial granularity of the model. Specifically, the sum of single-patch departmental model fits better captured national-level temporal patterns than did a single-patch national model. Likewise, multi-patch departmental model fits better captured department-level temporal patterns than did single-patch departmental model fits. Furthermore, inferences about municipal-level incidence based on multi-patch departmental models fitted to department-level data were positively correlated with municipal-level data that were withheld from model fitting. CONCLUSIONS Our model performed better when posed at finer spatial scales, due to better matching between human populations with locally relevant risk. Confronting spatially aggregated models with spatially aggregated data imposes a serious structural constraint on model behavior by averaging over epidemiologically meaningful spatial variation in drivers of transmission, impairing the ability of models to reproduce empirical patterns.
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Affiliation(s)
- Sean M Moore
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
| | - Quirine A Ten Bosch
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, 75015, Paris, France
- CNRS UMR2000: Génomique évolutive, modélisation et santé (GEMS), Institut Pasteur, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015, Paris, France
| | - Amir S Siraj
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - K James Soda
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Guido España
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Alfonso Campo
- Subdirección de Análisis de Riesgo y Respuesta Inmediata en Salud Pública, Instituto Nacional de Salud de Colombia, Bogotá, Colombia
| | - Sara Gómez
- Grupo de Enfermedades Transmisibles, Instituto Nacional de Salud de Colombia, Bogotá, Colombia
| | - Daniela Salas
- Grupo de Enfermedades Transmisibles, Instituto Nacional de Salud de Colombia, Bogotá, Colombia
| | | | | | | | - 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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