Author
Simon Dellicour
Other affiliations: Rega Institute for Medical Research, Free University of Brussels, Katholieke Universiteit Leuven ...read more
Bio: Simon Dellicour is an academic researcher from Université libre de Bruxelles. The author has contributed to research in topics: Population & Biological dispersal. The author has an hindex of 27, co-authored 113 publications receiving 2722 citations. Previous affiliations of Simon Dellicour include Rega Institute for Medical Research & Free University of Brussels.
Papers
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Fred Hutchinson Cancer Research Center1, University of Edinburgh2, University of Southampton3, Katholieke Universiteit Leuven4, University of Oxford5, Broad Institute6, United States Department of the Army7, University of Cambridge8, Technical University of Denmark9, Erasmus University Rotterdam10, Wellcome Trust Sanger Institute11, Bernhard Nocht Institute for Tropical Medicine12, Public Health England13, Pasteur Institute14, University of Sierra Leone15, Harvard University16, University of Liverpool17, University of Makeni18, University of Bristol19, University of Birmingham20, Princeton University21, Centre national de la recherche scientifique22, Louisiana State University23, Scripps Health24, Scripps Research Institute25, World Health Organization26, Chinese Center for Disease Control and Prevention27, University of Sydney28, Imperial College London29, National Institutes of Health30, Centers for Disease Control and Prevention31, University of California, Los Angeles32
TL;DR: It is revealed that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity, which will help to inform interventions in future epidemics.
Abstract: The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.
354 citations
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University of Oxford1, University of São Paulo2, Federal University of Rio de Janeiro3, Université libre de Bruxelles4, Katholieke Universiteit Leuven5, Imperial College London6, University of Auvergne7, State University of Campinas8, Fundação Getúlio Vargas9, University of Edinburgh10, University of London11, University of Birmingham12, Universidade Federal de Minas Gerais13, DaimlerChrysler Aerospace14, Federal University of Uberlandia15, Federal University of Roraima16, Royal Veterinary College17, Faculdade de Medicina de São José do Rio Preto18, University of Southampton19
TL;DR: New light is shed on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and evidence that current interventions remain insufficient to keep virus transmission under control in this country is provided.
Abstract: Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in Sao Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.
286 citations
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University of Oxford1, Boston Children's Hospital2, Harvard University3, Oswaldo Cruz Foundation4, Federal University of Rio de Janeiro5, Universidade Federal de Minas Gerais6, University of Birmingham7, Katholieke Universiteit Leuven8, University of London9, Pasteur Institute10, University of KwaZulu-Natal11, Instituto Adolfo Lutz12, University of São Paulo13, Federal University of São Paulo14, Public Health England15, Centre for the AIDS Programme of Research in South Africa16, University of California, Los Angeles17
TL;DR: It is shown that the age and sex distribution of human cases is characteristic of sylvatic transmission, which establishes a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFFV epidemics.
Abstract: The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
261 citations
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05 Aug 2020
TL;DR: New light is shed on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and evidence that current interventions remain insufficient to keep virus transmission under control in the country is provided.
Abstract: Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in Sao Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within-state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.
138 citations
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TL;DR: HIV reservoirs persist in all deep tissues, and blood is the main source of dispersal, which may explain why eliminating HIV susceptibility in circulating T cells via bone marrow transplants allowed some people with HIV to have therapy free remission, even though deeper tissue reservoirs were not targeted.
Abstract: BACKGROUNDUnderstanding HIV dynamics across the human body is important for cure efforts. This goal has been hampered by technical difficulties and the challenge of obtaining fresh tissues.METHODSThis observational study evaluated 6 individuals with HIV (n = 4 with viral suppression using antiretroviral [ART] therapy; n = 2 with rebound viremia after stopping ART), who provided serial blood samples before death and their bodies for rapid autopsy. HIV reservoirs were characterized by digital droplet PCR, single-genome amplification, and sequencing of full-length (FL) envelope HIV. Phylogeographic methods were used to reconstruct HIV spread, and generalized linear models were tested for viral factors associated with dispersal.RESULTSAcross participants, HIV DNA levels varied from approximately 0 to 659 copies/106 cells (IQR: 22.9-126.5). A total of 605 intact FL env sequences were recovered in antemortem blood cells and across 28 tissues (IQR: 5-9). Sequence analysis showed (a) the emergence of large, identical, intact HIV RNA populations in blood after cessation of therapy, which repopulated tissues throughout the body; (b) that multiple sites acted as hubs for HIV dissemination but that blood and lymphoid tissues were the main source; (c) that viral exchanges occurred within brain areas and across the blood-brain barrier; and (d) that migration was associated with low HIV divergence between sites and greater diversity at the recipient site.CONCLUSIONHIV reservoirs persisted in all deep tissues, and blood was the main source of dispersal. This may explain why eliminating HIV susceptibility in circulating T cells via bone marrow transplants allowed some individuals with HIV to experience therapy-free remission, even though deeper tissue reservoirs were not targeted.TRIAL REGISTRATIONNot applicable.FUNDINGNIH grants P01 AI31385, P30 AI036214, AI131971-01, AI120009AI036214, HD094646, AI027763, AI134295, and AI68636.
124 citations
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TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
14,171 citations
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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Boston Children's Hospital1, Harvard University2, University of Oxford3, Northeastern University4, Universidad San Francisco de Quito5, University of Southampton6, Institute for Health Metrics and Evaluation7, University of Paris8, Pasteur Institute9, Institute for Scientific Interchange10, Beijing Normal University11, Royal Veterinary College12
TL;DR: Real-time mobility data from Wuhan and detailed case data including travel history are used to elucidate the role of case importation in transmission in cities across China and to ascertain the impact of control measures.
Abstract: The ongoing coronavirus disease 2019 (COVID-19) outbreak expanded rapidly throughout China. Major behavioral, clinical, and state interventions were undertaken to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, affected COVID-19 spread in China. We used real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation in transmission in cities across China and to ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was explained well by human mobility data. After the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases were still indicative of local chains of transmission outside of Wuhan. This study shows that the drastic control measures implemented in China substantially mitigated the spread of COVID-19.
2,362 citations
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TL;DR: The BEAST software package unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration.
Abstract: The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
2,184 citations
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TL;DR: How tumor-promoting inflammation closely resembles inflammatory processes typically found during development, immunity, maintenance of tissue homeostasis, or tissue repair is discussed and the distinctions between tissue-protective and pro-tumorigenic inflammation are illuminated.
1,563 citations