scispace - formally typeset
Search or ask a question
Author

Simon Dellicour

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
More filters
Journal ArticleDOI
Gytis Dudas1, Gytis Dudas2, Luiz Max Carvalho2, Trevor Bedford1, Andrew J. Tatem3, Guy Baele4, Nuno R. Faria5, Daniel J. Park6, Jason T. Ladner7, Armando Arias8, Armando Arias9, Danny Asogun, Filip Bielejec4, Sarah L Caddy8, Matthew Cotten10, Matthew Cotten11, Jonathan D'ambrozio7, Simon Dellicour4, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour12, Michael J. Elmore13, Lawrence Fakoli, Ousmane Faye14, Merle L. Gilbert7, Sahr M. Gevao15, Stephen K. Gire16, Stephen K. Gire6, Adrianne Gladden-Young6, Andreas Gnirke6, Augustine Goba, Donald S. Grant, Bart L. Haagmans10, Julian A. Hiscox17, Umaru Jah18, Jeffrey R. Kugelman7, Di Liu, Jia Lu8, Christine M. Malboeuf6, Suzanne Mate7, David A. Matthews19, Christian B. Matranga6, Luke W. Meredith8, Luke W. Meredith18, James Qu6, Joshua Quick20, Susan D. Pas10, My V. T. Phan11, My V. T. Phan10, Georgios Pollakis17, Chantal B.E.M. Reusken10, Mariano Sanchez-Lockhart7, Stephen F. Schaffner6, John S. Schieffelin, Rachel Sealfon6, Rachel Sealfon21, Etienne Simon-Loriere22, Etienne Simon-Loriere14, Saskia L. Smits10, Kilian Stoecker, Lucy Thorne8, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson11, Kendra West6, Shannon L.M. Whitmer, Michael R. Wiley7, Sarah M. Winnicki23, Sarah M. Winnicki6, Shirlee Wohl16, Shirlee Wohl6, Roman Wölfel, Nathan L. Yozwiak6, Nathan L. Yozwiak16, Kristian G. Andersen24, Kristian G. Andersen25, Sylvia O. Blyden, Fatorma K. Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo26, Pierre Formenty26, Christophe Fraser5, George F. Gao27, Robert F. Garry, Ian Goodfellow8, Ian Goodfellow18, Stephan Günther12, Christian T. Happi, Edward C. Holmes28, Brima Kargbo, Sakoba Keita, Paul Kellam29, Paul Kellam11, Marion Koopmans10, Jens H. Kuhn30, Nicholas J. Loman20, N’Faly Magassouba, Dhamari Naidoo26, Stuart T. Nichol31, Tolbert Nyenswah, Gustavo Palacios7, Oliver G. Pybus5, Pardis C. Sabeti6, Pardis C. Sabeti16, Amadou A. Sall14, Ute Ströher31, Isatta Wurie15, Marc A. Suchard32, Philippe Lemey4, Andrew Rambaut2 
20 Apr 2017-Nature
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

Journal ArticleDOI
Darlan da Silva Candido1, Darlan da Silva Candido2, Ingra Morales Claro2, Jaqueline Goes de Jesus2, William Marciel de Souza, Filipe R. R. Moreira3, Simon Dellicour4, Simon Dellicour5, Thomas A. Mellan6, Louis du Plessis1, Rafael Henrique Moraes Pereira, Flavia C. S. Sales2, Erika R. Manuli2, Julien Thézé7, Luiz Carlos de Almeida, Mariane Talon de Menezes3, Carolina M. Voloch3, Marcílio Jorge Fumagalli, Thais M. Coletti2, Camila A. M. Silva2, Mariana S. Ramundo2, Mariene R. Amorim8, Henrique Hoeltgebaum6, Swapnil Mishra6, Mandev S. Gill5, Luiz Max Carvalho9, Lewis F Buss2, Carlos A. Prete2, Jordan Ashworth10, Helder I. Nakaya2, Pedro S. Peixoto2, Oliver J. Brady11, Samuel M. Nicholls12, Amilcar Tanuri3, Átila Duque Rossi3, Carlos Kaue Vieira Braga, Alexandra L. Gerber, Ana Paula de C Guimarães, Nelson Gaburo, Cecila Salete Alencar2, Alessandro C. S. Ferreira, Cristiano Xavier Lima13, José Eduardo Levi14, Celso Francisco Hernandes Granato, Giulia M. Ferreira15, Ronaldo da Silva Francisco, Fabiana Granja8, Fabiana Granja16, Márcia Teixeira Garcia8, Maria Luiza Moretti8, Mauricio W. Perroud8, Terezinha M. P. P. Castineiras3, Carolina S. Lazari2, Sarah C. Hill1, Sarah C. Hill17, Andreza Aruska de Souza Santos1, Camila L. Simeoni8, Julia Forato8, Andrei C. Sposito8, Angelica Zaninelli Schreiber8, Magnun N. N. Santos8, Camila Zolini de Sá13, Renan P. Souza13, Luciana C. Resende-Moreira13, Mauro M. Teixeira13, Josy Hubner13, Patricia Asfora Falabella Leme8, Rennan G. Moreira13, Maurício Lacerda Nogueira18, Neil M. Ferguson2, Silvia Figueiredo Costa8, José Luiz Proença-Módena, Ana Tereza Ribeiro de Vasconcelos6, Samir Bhatt5, Philippe Lemey19, Chieh-Hsi Wu10, Andrew Rambaut12, Nicholas J. Loman13, Renato Santana Aguiar1, Oliver G. Pybus2, Ester Cerdeira Sabino6, Ester Cerdeira Sabino1, Ester Cerdeira Sabino2, Nuno R. Faria1, Nuno R. Faria2, Nuno R. Faria6 
23 Jul 2020-Science
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

Journal ArticleDOI
Nuno R. Faria1, Moritz U. G. Kraemer2, Moritz U. G. Kraemer3, Moritz U. G. Kraemer1, Sarah C. Hill1, Jaqueline Goes de Jesus4, Renato S. Aguiar5, Felipe Campos de Melo Iani6, Joilson Xavier4, Joshua Quick7, L. du Plessis1, Simon Dellicour8, Julien Thézé1, Rodrigo Dias de Oliveira Carvalho6, Guy Baele8, Chieh-Hsi Wu1, Paola P. Silveira5, Monica B. Arruda5, Maira Alves Pereira, Gavin Pereira, José Lourenço1, Uri Obolski1, Leandro Abade1, Tetyana I. Vasylyeva1, Marta Giovanetti6, Marta Giovanetti4, D. Yi3, Daniel J. Weiss1, William Wint1, Freya M Shearer1, Sebastian Funk9, Birgit Nikolay10, Vagner Fonseca11, Vagner Fonseca6, Talita Émile Ribeiro Adelino, Marluce Aparecida Assunção Oliveira, Marcos Vieira Silva, Lívia Sacchetto6, Poliana de Oliveira Figueiredo6, Izabela Maurício de Rezende6, Érica Munhoz de Mello6, Rodrigo Fabiano do Carmo Said, Deise Aparecida dos Santos, Marcela Lencine Ferraz, Mariana Gontijo de Brito, Ludmila Ferraz de Santana, Mariane Talon de Menezes5, Rodrigo Brindeiro5, Amilcar Tanuri5, Fabiana Cristina Pereira dos Santos12, Mariana Sequetin Cunha12, Juliana Silva Nogueira12, Iray Maria Rocco12, A. C. da Costa13, Shirley Vasconcelos Komninakis14, Vasco Azevedo6, Alexandre Otavio Chieppe, Eliane Saraiva Machado de Araújo4, Marcos Cesar Lima de Mendonça4, Carolina Cardoso dos Santos4, Cintia Damasceno dos Santos Rodrigues4, Maria Angelica Mares Guia4, Rita Maria Ribeiro Nogueira4, Patrícia Carvalho de Sequeira4, Ricardo Gadelha de Abreu, Marcio Henrique de Oliveira Garcia, André Luis de Abreu, Osnei Okumoto, Erna Geessien Kroon6, Carlos Frederico Campelo de Albuquerque, Kuiama Lewandowski15, Steven T. Pullan15, Miles W. Carroll15, T. de Oliveira4, T. de Oliveira11, T. de Oliveira16, Ester Cerdeira Sabino13, Renato Pereira de Souza12, Marc A. Suchard17, Philippe Lemey8, Giliane de Souza Trindade6, Betânia Paiva Drumond6, Ana Maria Bispo de Filippis4, Nicholas J. Loman7, Simon Cauchemez10, Luiz Carlos Junior Alcantara4, Luiz Carlos Junior Alcantara6, Oliver G. Pybus1 
31 Aug 2018-Science
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

DOI
Darlan da Silva Candido, Ingra Morales Claro, Jaqueline Goes de Jesus, William Marciel de Souza, Filipe R. R. Moreira, Simon Dellicour, Thomas A. Mellan, Louis du Plessis, Rafael Henrique Moraes Pereira, Flavia C. S. Sales, Erika R. Manuli, Julien Thézé, Luiz Carlos de Almeida, Mariane Talon de Menezes, Carolina M. Voloch, Marcílio Jorge Fumagalli, Thais M. Coletti, Camila A. M. Silva, Mariana S. Ramundo, Mariene R. Amorim, Henrique Hoeltgebaum, Swapnil Mishra, Mandev S. Gill, Luiz Max Carvalho, Lewis F Buss, Carlos A. Prete, Jordan Ashworth, Helder I. Nakaya, Pedro S. Peixoto, Oliver J. Brady, Samuel M. Nicholls, Amilcar Tanuri, Átila Duque Rossi, Carlos Kaue Vieira Braga, Alexandra L. Gerber, Ana Paula de C Guimarães, Nelson Gaburo, Cecila Salete Alencar, Alessandro C. S. Ferreira, Cristiano Xavier Lima, José Eduardo Levi, Celso Francisco Hernandes Granato, Giulia M. Ferreira, Ronaldo da Silva Francisco, Fabiana Granja, Márcia Teixeira Garcia, Maria Luiza Moretti, Mauricio W. Perroud, Terezinha M. P. P. Castineiras, Carolina S. Lazari, Sarah C. Hill, Andreza Aruska de Souza Santos, Camila L. Simeoni, Julia Forato, Andrei C. Sposito, Angelica Zaninelli Schreiber, Magnun N. N. Santos, Camila Zolini de Sá, Renan P. Souza, Luciana C. Resende-Moreira, Mauro M. Teixeira, Josy Hubner, Patricia Asfora Falabella Leme, Rennan G. Moreira, Maurício Lacerda Nogueira, Neil M. Ferguson, Silvia Figueiredo Costa, José Luiz Proença-Módena, Ana Tereza Ribeiro de Vasconcelos, Samir Bhatt, Philippe Lemey, Chieh-Hsi Wu, Andrew Rambaut, Nicholas J. Loman, Renato Santana Aguiar, Oliver G. Pybus, Ester Cerdeira Sabino, Nuno R. Faria 
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

Journal ArticleDOI
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


Cited by
More filters
Journal ArticleDOI
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

Journal ArticleDOI
01 May 2020-Science
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

Journal ArticleDOI
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

Journal ArticleDOI
16 Jul 2019-Immunity
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