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Xu J, Wang Z, Moghadas SM. Modelling the effect of travel-related policies on disease control in a meta-population structure. J Math Biol 2023; 87:55. [PMID: 37688625 DOI: 10.1007/s00285-023-01990-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/15/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023]
Abstract
Travel restrictions, while delaying the spread of an emerging disease from the source, could inflict substantial socioeconomic burden. Travel-related policies, such as quarantine and testing of travelers, may be considered as alternative strategies to mitigate the negative impact of travel bans. We developed a meta-population, delay-differential model to evaluate a strategy that combines testing of travelers prior to departure from the source of infection with quarantine and testing at exit from quarantine in the destination population. Our results, based on early parameter estimates of SARS-CoV-2 infection, indicate that testing travelers at exit from quarantine is more effective in delaying case importation than testing them before departure or upon arrival. We show that a 1-day quarantine with an exit test could outperform a longer, 3-day quarantine without testing in delaying the outbreak peak. Rapid, large-scale testing capacities with short turnaround times provide important means of detecting infectious cases and reducing case importation, while shortening quarantine duration for travelers at destination.
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Affiliation(s)
- Jingjing Xu
- Agent-Based Modelling Laboratory, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Zhen Wang
- Agent-Based Modelling Laboratory, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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Ren J, Liu M, Liu Y, Liu J. TransCode: Uncovering COVID-19 transmission patterns via deep learning. Infect Dis Poverty 2023; 12:14. [PMID: 36855184 PMCID: PMC9971690 DOI: 10.1186/s40249-023-01052-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND The heterogeneity of COVID-19 spread dynamics is determined by complex spatiotemporal transmission patterns at a fine scale, especially in densely populated regions. In this study, we aim to discover such fine-scale transmission patterns via deep learning. METHODS We introduce the notion of TransCode to characterize fine-scale spatiotemporal transmission patterns of COVID-19 caused by metapopulation mobility and contact behaviors. First, in Hong Kong, China, we construct the mobility trajectories of confirmed cases using their visiting records. Then we estimate the transmissibility of individual cases in different locations based on their temporal infectiousness distribution. Integrating the spatial and temporal information, we represent the TransCode via spatiotemporal transmission networks. Further, we propose a deep transfer learning model to adapt the TransCode of Hong Kong, China to achieve fine-scale transmission characterization and risk prediction in six densely populated metropolises: New York City, San Francisco, Toronto, London, Berlin, and Tokyo, where fine-scale data are limited. All the data used in this study are publicly available. RESULTS The TransCode of Hong Kong, China derived from the spatial transmission information and temporal infectiousness distribution of individual cases reveals the transmission patterns (e.g., the imported and exported transmission intensities) at the district and constituency levels during different COVID-19 outbreaks waves. By adapting the TransCode of Hong Kong, China to other data-limited densely populated metropolises, the proposed method outperforms other representative methods by more than 10% in terms of the prediction accuracy of the disease dynamics (i.e., the trend of case numbers), and the fine-scale spatiotemporal transmission patterns in these metropolises could also be well captured due to some shared intrinsically common patterns of human mobility and contact behaviors at the metapopulation level. CONCLUSIONS The fine-scale transmission patterns due to the metapopulation level mobility (e.g., travel across different districts) and contact behaviors (e.g., gathering in social-economic centers) are one of the main contributors to the rapid spread of the virus. Characterization of the fine-scale transmission patterns using the TransCode will facilitate the development of tailor-made intervention strategies to effectively contain disease transmission in the targeted regions.
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Affiliation(s)
- Jinfu Ren
- grid.221309.b0000 0004 1764 5980Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China
| | - Mutong Liu
- grid.221309.b0000 0004 1764 5980Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yang Liu
- grid.221309.b0000 0004 1764 5980Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China.
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Cui J, Wu Y, Guo S. Effect of Non-homogeneous Mixing and Asymptomatic Individuals on Final Epidemic Size and Basic Reproduction Number in a Meta-Population Model. Bull Math Biol 2022; 84:38. [PMID: 35132526 PMCID: PMC8821870 DOI: 10.1007/s11538-022-00996-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 01/18/2022] [Indexed: 11/29/2022]
Abstract
To uncover the effective interventions during the pandemic period, a novel mathematical model, which incorporates separate compartments for incubation and asymptomatic individuals, has been developed in this paper. On the basis of a general mixing, final size relation and next-generation matrix are derived for a meta-population model by introducing the matrix blocking. The final size (\documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {F}}$$\end{document}F) and the basic reproduction number (\documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {R}}_{0}$$\end{document}R0) are no longer a simple monotonous relationship. The analytical results of heterogeneity illustrate that activity is more sensitive than the others. And the proportion of asymptomatic individuals is a key factor for final epidemic size compared to the regulatory factor. Furthermore, the impact of preferential contact level on \documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {F}}$$\end{document}F and \documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {R}}_{0}$$\end{document}R0 is comparatively complex. The isolation can effectively reduce the final size, which further verifies its effectiveness. When vaccination is considered, the mixing methods maybe influence the doses of vaccination used and its effective. Moreover, using the present predictive model, we can provide the valuable reference about identifying the ideal strategies to curb the pandemic disease.
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Affiliation(s)
- Jingan Cui
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, 102616, People's Republic of China.
| | - Yucui Wu
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, 102616, People's Republic of China
| | - Songbai Guo
- School of Science, Beijing University of Civil Engineering and Architecture, Beijing, 102616, People's Republic of China
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Aini NK, Wardiatno Y, Effendi H, Mashar A, Madduppa H. High genetic diversity and mixing of coastal horseshoe crabs ( Tachypleus gigas) across major habitats in Sundaland, Indonesia. PeerJ 2021; 9:e11739. [PMID: 34414023 PMCID: PMC8340900 DOI: 10.7717/peerj.11739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (F ST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p < 0.05). Additionally, the 34 analysis of molecular variance (AMOVA) showed the most variation within populations (95.23%) compared to less among populations (4.77%). The haplotype network showed evidence of shared haplotypes between populations. Tajima's D and Fu's F S test values indicated a population expansion. Our results showed a low level of differentiation, suggesting a single stock and high connectivity. Therefore, a regionally-based conservation strategy is recommended for the coastal horseshoe crab in Indonesia.
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Affiliation(s)
- Naila Khuril Aini
- Study Program of Aquatic Resources, Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Graduate School, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia
| | - Yusli Wardiatno
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Environmental Research Center, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hefni Effendi
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Environmental Research Center, Institut Pertanian Bogor, Bogor, Indonesia
| | - Ali Mashar
- Department of Aquatic Resources Management, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty of Fisheries and Marine Sciences, Institut Pertanian Bogor, Bogor, Jawa Barat, Indonesia.,Oceanogen Environmental Biotechnology Laboklinikum, Bogor, Indonesia
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Moualeu DP, Bowong S, Tsanou B, Temgoua A. A patchy model for the transmission dynamics of tuberculosis in sub-Saharan Africa. Int J Dyn Control 2017; 6:122-139. [PMID: 32288982 PMCID: PMC7133616 DOI: 10.1007/s40435-017-0310-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) spreads through contact between a susceptible person and smear positive pulmonary TB case (TPM+). The spread of TB is highly dependent on people migration between cities or regions that may have different contact rates and different environmental parameters, leading to different disease spread speed in the population. In this work, a metapopulation model, i.e., networks of populations connected by migratory flows, which overcomes the assumption of homogeneous mixing between different regions was constructed. The TB model was combined to a simple demographic structure for the population living in a multi-patch environment (cities, towns, regions or countries). The model consist of a system of differential equations coupling TB epidemic at different strength and mobility between the patches. Constant recruitment rate, slow and fast progression to the disease, effective chemoprophylaxis, diagnostic and treatment are taken into account to make the model including the reality of people in the sub-Saharan African countries. The basic reproduction number ( R 0 ) was computed and it was demonstrated that the disease-free equilibrium is globally asymptotically stable ifR 0 < 1 . WhenR 0 > 1 , the disease-free equilibrium is unstable and there exists one endemic equilibrium. Moreover, the impact of increasing migration rate between patches on the TB spread was quantified using numerical implementation of the model. Using an example on 15 inter-connected patches on the same road, we demonstrated that most people was most likely to get infected if the disease starts in a patch in the middle than in border patches.
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Affiliation(s)
- D. P. Moualeu
- Institute for Horticultural Production Systems, Vegetable Systems Modelling Section, Faculty of Natural Sciences, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - S. Bowong
- Department of Mathematics and Computer Science, Faculty of Science, University of Douala, PO Box 24157, Douala, Cameroon
- UMI 209 IRD/UPMC UMMISCO, Bondy-France and GRIMCAPE-Cameroon, The African Center of Excellence in Information and Communication Technologies (CETIC), University of Yaounde 1, Yaounde, Cameroon
| | - B. Tsanou
- Department of Mathematics and Computer Science, Faculty of Science, University of Dschang, PO Box 47, Dschang, Cameroon
| | - A. Temgoua
- Department of Mathematics and Computer Science, Faculty of Science, University of Douala, PO Box 24157, Douala, Cameroon
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Crook DA, Lowe WH, Allendorf FW, Erős T, Finn DS, Gillanders BM, Hadwen WL, Harrod C, Hermoso V, Jennings S, Kilada RW, Nagelkerken I, Hansen MM, Page TJ, Riginos C, Fry B, Hughes JM. Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation. Sci Total Environ 2015; 534:52-64. [PMID: 25917446 DOI: 10.1016/j.scitotenv.2015.04.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/30/2015] [Accepted: 04/10/2015] [Indexed: 06/04/2023]
Abstract
Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.
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Affiliation(s)
- David A Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory 0909, Australia.
| | - Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Tibor Erős
- Balaton Limnological Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Klebelsberg, K.u. 3., H-8237, Hungary
| | - Debra S Finn
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; Departamento de Recursos Hídricos y Ciencias Ambientales, Universidad de Cuenca, Cuenca, Ecuador
| | - Bronwyn M Gillanders
- Southern Seas Ecology Laboratories, School of Biological Sciences and The Environment Institute, DX 650 418, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Wade L Hadwen
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Avenida Angamos, 601 Antofagasta, Chile
| | - Virgilio Hermoso
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Simon Jennings
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft Laboratory, Lowestoft NR33 0HT, UK; School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Raouf W Kilada
- Biology Department, University of New Brunswick (Saint John), Canada
| | - Ivan Nagelkerken
- Southern Seas Ecology Laboratories, School of Biological Sciences and The Environment Institute, DX 650 418, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade, Bldg. 1540, DK-8000 Aarhus C, Denmark
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Brian Fry
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, QLD 4111, Australia
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Chaine AS, Legendre S, Clobert J. The co-evolution of multiply-informed dispersal: information transfer across landscapes from neighbors and immigrants. PeerJ 2013; 1:e44. [PMID: 23638381 PMCID: PMC3628985 DOI: 10.7717/peerj.44] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/08/2013] [Indexed: 11/20/2022] Open
Abstract
Dispersal plays a key role in natural systems by shaping spatial population and evolutionary dynamics. Dispersal has been largely treated as a population process with little attention to individual decisions and the influence of information use on the fitness benefits of dispersal despite clear empirical evidence that dispersal behavior varies among individuals. While information on local density is common, more controversial is the notion that indirect information use can easily evolve. We used an individual-based model to ask under what conditions indirect information use in dispersal will evolve. We modeled indirect information provided by immigrant arrival into a population which should be linked to overall metapopulation density. We also modeled direct information use of density which directly impacts fitness. We show that immigrant-dependent dispersal evolves and does so even when density dependent information is available. Use of two sources of information also provides benefits at the metapopulation level by reducing extinction risk and prolonging the persistence of populations. Our results suggest that use of indirect information in dispersal can evolve under conservative conditions and thus could be widespread.
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Affiliation(s)
- Alexis S Chaine
- Station d'Ecologie Expérimentale du CNRS à Moulis , Moulis , France
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