MOnitoring Outbreak events for Disease surveillance in a data science context

Livrables

Blueprints for epidemiological data collection and management

This deliverable will provide the reference on how to collect, structure, and prepare the data to inputs the models and maps developed in WP4

Risk register

Register with all the risks noted by each WP, at project submission and updated during implementation of the project. It will also consist of a detailed description of the risks, their impact, and suitable preventive and response measures. This document will be updated at M24, M36 and M48.

Project management plan

Report with procedures for providing day-to-day administrative guidance, coordination & troubleshooting for the MOOD consortium partners

Preliminary report on impact and innovation pathway

This report will describe the innovation process and set up the methodology to monitor the impact of the MOOD project through the outcome assessment and the theory of change that is at work Some preliminary results about the KeyPerformance Indicators concerning the first outputs will be given

Scientific report on prototype pathogens and disease profiles

For each selected pathogen and disease, a detailed profile based on the state-of-the-art of the scientific knowledge and knowledge gaps will be produced.

Report on outreach of outcomes

The analysis of the outreach of the outcomes will be based on two crossed sources : a multicriteria evaluation method (OASIS-like survey) to compare end-user practices in the case countries at start and end of the project and a participatory assessment based on narratives of the change and participatory indicators.

Guidelines for consideration of local stakeholders' engagement

The guidelines will be built during and following the workshops with the local stakeholders of the study case in Corsica and Occitanie.

Report on users’ needs

The synthesis of operational needs will be based on the results of the crossed socio-technical analysis of individual interviews, and also the conclusions of the 2 first workshops about the operational problems to solve.

Report on learning loops fostering the utility of social and technical innovations

The lessons learnt from the collective learning of co-conception of tools and services (3 loops) will be summarised.

Standardized datasets (covariate, disease data sets, and pattern linking)

The dataset used within the project and processed according to DL3.1. These data will be stored in a traditional structured database system and made available through this database.

Integration chain (processing algorithms and protocols) for disease datasets

This deliverable will describe the data integration toolchain, including the data processing algorithms and the data exchange protocols that are focused on disease data, associated with Task 3.3 of WP3 and also with implications regarding other tasks (e.g., Tasks 3.1 and 3.4 of WP3). The envisioned toolchain will focus on data standardization and linking between disease and covariate data, according to spatial and temporal dimensions, and combining text-mining, spatial analysis, and semantic approaches. Specifically, the toolchain will ingest and standardize the different types of data, geo-reference the disease data in order for it to be linked to particular covariates, and make the results available for subsequent tasks. Deliverable 3.2 will specifically focus on the tools regarding data integration (e.g., the geo-referencing component), tailored for the processing of disease data.

Linking chain (processing algorithms and protocols) for disease and covariate datasets

The linking task is based on algorithms and processing that will be proposed, implemented and evaluated. These linking algorithms/process need specific features (and set of features) to extract in the disease and covariate data.

MOOD project website and social media

Project website (implemented via a Content Management System) and social media pages and channels including Twitter, , Linkedin, TIB (https://av.tib.eu/), Zenodo.org, and similar. Publication steps, house-style-sheet, and roles and responsibilities will be described in the project manual.

Online materials released in the open-source

Data processing tutorials, good practice documents and technical reports will be released via github (source code) with a copy on zenodo.org using the Github-zenodo webhooks (see e.g. https://doi.org/10.25815/3YZR-1564).

Data management plan

The DMP will detail what data MOOD will generate and how, how it will be curated and preserved, what datasets will be open, whether and how datasets will be exploited or made accessible for verification and re-use. First version delivered at month 6 and updated version at month 18 and 36.

Publications

Systematic Review on Crimean–Congo Hemorrhagic Fever Enzootic Cycle and Factors Favoring Virus Transmission: Special Focus on France, an Apparently Free-Disease Area in Europe

Auteurs: Célia Bernard, Philippe Holzmuller, Madiou Thierno Bah, Matthieu Bastien, Benoit Combes, Ferran Jori, Vladimir Grosbois and Laurence Vial
Publié dans: Frontiers in Veterinary Science, Numéro 22971769, 2022, ISSN 2297-1769
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fvets.2022.1007631

Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study

Auteurs: Juanjuan Zhang, Maria Litvinova, Wei Wang, Yan Wang, Xiaowei Deng, Xinghui Chen, Mei Li, Wen Zheng, Lan Yi, Xinhua Chen, Qianhui Wu, Yuxia Liang, Xiling Wang, Juan Yang, Kaiyuan Sun, Ira M Longini, M Elizabeth Halloran, Peng Wu, Benjamin J Cowling, Stefano Merler, Cecile Viboud, Alessandro Vespignani, Marco Ajelli, Hongjie Yu
Publié dans: The Lancet Infectious Diseases, Numéro 20/7, 2020, Page(s) 793-802, ISSN 1473-3099
Éditeur: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(20)30230-9

Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST

Auteurs: Simon Dellicour, Mandev S Gill, Nuno R Faria, Andrew Rambaut, Oliver G Pybus, Marc A Suchard, Philippe Lemey
Publié dans: Molecular Biology and Evolution, Numéro Volume 38, Numéro 8, August 2021, 2021, Page(s) 3486–3493, ISSN 1537-1719
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msab031

Epidemic intelligence in Europe: a user needs perspective to foster innovation in digital health surveillance

Auteurs: Fanny Bouyer, Oumy Thiongane, Alexandre Hobeika, Elena Arsevska, Aurélie Binot, Déborah Corrèges, Timothée Dub, Henna Mäkelä, Esther van Kleef, Ferran Jori, Renaud Lancelot, Alize Mercier, Francesca Fagandini, Sarah Valentin, Wim Van Bortel & Claire Ruault
Publié dans: BMC Public Health, Numéro 24, 973, 2024, ISSN 1471-2458
Éditeur: BioMed Central
DOI: 10.1186/s12889-024-18466-1

Ecological and environmental factors affecting the risk of tick-borne encephalitis in Europe, 2017 to 2021

Auteurs: Francesca Dagostin, Valentina Tagliapietra, Giovanni Marini, Claudia Cataldo, Maria Bellenghi, Scilla Pizzarelli, Rosaria Rosanna Cammarano, William Wint, Neil S Alexander, Markus Neteler, Julia Haas, Timothée Dub, Luca Busani, Annapaola Rizzoli
Publié dans: Eurosurveillance, Numéro Volume 28, Numéro 42, 2023, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2023.28.42.2300121

Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019

Auteurs: Van Borm S, Boseret G, Dellicour S, Steensels M, Roupie V, Vandenbussche F, Mathijs E, Vilain A, Driesen M, Dispas M, Delcloo AW, Lemey P, Mertens I, Gilbert M, Lambrecht B, van den Berg T
Publié dans: Emerging Infectious Diseases, Numéro 29(2), 2023, Page(s) 351-359, ISSN 1080-6059
Éditeur: Centers for Disease Control and Prevention
DOI: 10.3201/eid2902.220765

An Evaluation Framework for Comparing Epidemic Intelligence Systems

Auteurs: Nejat Arinik; Roberto Interdonato; Mathieu Roche; Maguelonne Teisseire
Publié dans: IEEE Access, Numéro 35, 2023, Page(s) 11 : 31880- 31901, ISSN 2169-3536
Éditeur: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2023.3262462

Increasing situational awareness through nowcasting of the reproduction number

Auteurs: Andrea Bizzotto, Giorgio Guzzetta, Valentina Marziano, Martina Del Manso, Alberto Mateo Urdiales, Daniele Petrone, Andrea Cannone, Chiara Sacco, Piero Poletti, Mattia Manica, Agnese Zardini, Filippo Trentini, Massimo Fabiani, Antonino Bella, Flavia Riccardo, Patrizio Pezzotti, Marco Ajelli, Stefano Merler
Publié dans: Frontiers in Public Health, Numéro 12, 2024, ISSN 2296-2565
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fpubh.2024.1430920

icumonitoring.ch: a platform for short-term forecasting of intensive care unit occupancy during the COVID-19 epidemic in Switzerland

Auteurs: Cheng Zhao, Burcu Tepekule, Nicola G. Criscuolo, Pedro D. Wendel Garcia, Matthias P. Hilty, RISC-19-ICU consortium Investigators in Switzerland, Thierry Fumeaux, Thomas Van Boeckel
Publié dans: Swiss Medical Weekly, Numéro 150, 2020, Page(s) w20277, ISSN 1424-3997
Éditeur: EMH Swiss Medical Publishers Ltd.
DOI: 10.4414/smw.2020.20277

Spatial and temporal dynamics of West Nile virus between Africa and Europe

Auteurs: Giulia Mencattelli, Marie Henriette Dior Ndione, Andrea Silverj, Moussa Moise Diagne, Valentina Curini, Liana Teodori, Marco Di Domenico, Rassoul Mbaye, Alessandra Leone, Maurilia Marcacci, Alioune Gaye, ElHadji Ndiaye, Diawo Diallo, Massimo Ancora, Barbara Secondini, Valeria Di Lollo, Iolanda Mangone, Andrea Bucciacchio, Andrea Polci, Giovanni Marini, Roberto Rosà, Nicola Segata, Gamou Fall, Ces
Publié dans: Nature Communications, Numéro 14, 6440, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-42185-7

Modelling the West Nile virus force of infection in the European human population

Auteurs: Giovanni Marini, Andrea Pugliese, William Wint, Neil S. Alexander, Annapaola Rizzoli, Roberto Rosà
Publié dans: One Health, Numéro Volume 15, 2022, Page(s) 100462, ISSN 2352-7714
Éditeur: Elsevier B.V.
DOI: 10.1016/j.onehlt.2022.100462

Projecting the COVID-19 epidemic risk in France for the summer 2021

Auteurs: Mattia Mazzoli, PhD, Eugenio Valdano, PhD, Vittoria Colizza
Publié dans: Journal of Travel Medicine, Numéro Volume 28, Numéro 7, 2021, Page(s) aab129, ISSN 1708-8305
Éditeur: International Society of Travel Medicine
DOI: 10.1093/jtm/taab129

Risk factors for tick attachment in companion animals in Great Britain: a spatiotemporal analysis covering 2014–2021

Auteurs: Elena Arsevska, Tomislav Hengl, David A. Singleton, Peter-John M. Noble, Cyril Caminade, Obiora Eneanya, Philip H. Jones, Kayleigh Hansford, Jolyon Medlock, Carmelo Bonannella, Alan D. Radford
Publié dans: Parasites Vectors, Numéro 17, 29, 2024, ISSN 1756-3305
Éditeur: BioMed Central
DOI: 10.1186/s13071-023-06094-4

Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden

Auteurs: Laura Di Domenico, Yair Goldberg, Vittoria Colizza
Publié dans: Infectious Disease Modelling, Numéro 10, 2024, Page(s) 150-162, ISSN 2468-0427
Éditeur: Elsevier B.V
DOI: 10.1016/j.idm.2024.09.002

Evaluating the effect of demographic factors, socioeconomic factors, and risk aversion on mobility during the COVID-19 epidemic in France under lockdown: a population-based study

Auteurs: Giulia Pullano, Eugenio Valdano, Nicola Scarpa, Stefania Rubrichi, Vittoria Colizza
Publié dans: The Lancet Digital Health, Numéro 2/12, 2020, Page(s) e638-e649, ISSN 2589-7500
Éditeur: Elsevier
DOI: 10.1016/s2589-7500(20)30243-0

Investigating COVID-19 Vaccine Impact on the Risk of Hospitalisation through the Analysis of National Surveillance Data Collected in Belgium

Auteurs: Diana Erazo, Maria F. Vincenti-Gonzalez, Joris A. F. van Loenhout, Pierre Hubin, Mathil Vandromme, Piet Maes, Maxime Taquet, Johan Van Weyenbergh, Lucy Catteau and Simon Dellicour
Publié dans: Viruses, Numéro 14(6), 2022, Page(s) 1315, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061315

Predictive Mapping of Antimicrobial Resistance for Escherichia coli, Salmonella, and Campylobacter in Food-Producing Animals, Europe, 2000–2021

Auteurs: Ranya Mulchandani, Cheng Zhao, Katie Tiseo, João Pires, Thomas Van Boeckel
Publié dans: Emerging Infectious Diseases, Numéro Volume 30, Number 1, 2024, ISSN 1080-6059
Éditeur: Center for Disease Control and Prevention
DOI: 10.3201/eid3001.221450

Global patterns and drivers of influenza decline during the COVID-19 pandemic

Auteurs: Francesco Bonacina, Pierre-Yves Boëlle, Vittoria Colizza, Olivier Lopez, Maud Thomas, Chiara Poletto
Publié dans: International Journal of Infectious Diseases, Numéro January 03, 2023, 2023, ISSN 1878-3511
Éditeur: Amsterdam Elsevier
DOI: 10.1016/j.ijid.2022.12.042

PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

Auteurs: Sarah Valentina, Elena Arsevska, Julien Rabatel, Sylvain Falala, Alizé Mercier, Renaud Lancelot, Mathieu Roche
Publié dans: One Health, Numéro Vol 13, Dec 2021, 2021, Page(s) 100357, ISSN 2352-7714
Éditeur: Elsevier
DOI: 10.1016/j.onehlt.2021.100357

Emergence of an early SARS-CoV-2 epidemic in the United States

Auteurs: Mark Zeller, Karthik Gangavarapu, Catelyn Anderson, Allison R. Smither, John A. Vanchiere, Rebecca Rose, Daniel J. Snyder, Gytis Dudas, Alexander Watts, Nathaniel L. Matteson, Refugio Robles-Sikisaka, Maximilian Marshall, Amy K. Feehan, Gilberto Sabino-Santos, Antoinette R. Bell-Kareem, Laura D. Hughes, Manar Alkuzweny, Patricia Snarski, Julia Garcia-Diaz, Rona S. Scott, Lilia I. Melnik, Raphaëll
Publié dans: Cell, Numéro Volume 184, Numéro 19, 2021, 2021, Page(s) 4939-4952.e15, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2021.07.030

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha

Auteurs: Benjamin Faucher, Chiara E. Sabbatini, Peter Czuppon, Moritz U. G. Kraemer, Philippe Lemey, Vittoria Colizza, François Blanquart, Pierre-Yves Boëlle & Chiara Poletto
Publié dans: Nature communications, Numéro 15, 2152, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-46345-1

A systematic review of environmental factors related to WNV circulation in European and Mediterranean countries

Auteurs: Christine Giesen, Zaida Herrador, Beatriz Fernandez-Martinez, Jordi Figuerola, Laura Gangoso, Ana Vazquez, Diana Gómez-Barroso
Publié dans: One Health, Numéro Volume 16, 2023, Page(s) 100478, ISSN 2352-7714
Éditeur: Elsevier BV
DOI: 10.1016/j.onehlt.2022.100478

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Auteurs: Nuno R. Faria, Thomas A. Mellan, Charles Whittaker, Ingra M. Claro, Darlan da S. Candido, Swapnil Mishra, Myuki A. E. Crispim, Flavia C. S. Sales, Iwona Hawryluk, John T. McCrone, Ruben J. G. Hulswit, Lucas A. M. Franco, Mariana S. Ramundo, Jaqueline G. de Jesus, Pamela S. Andrade, Thais M. Coletti, Giulia M. Ferreira, Camila A. M. Silva, Erika R. Manuli, Rafael H. M. Pereira, Pedro S. Peixoto, Mo
Publié dans: Science, Numéro 372/6544, 2021, Page(s) 815-821, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abh2644

GeospatRE: extraction and geocoding of spatial relation entities in textual documents

Auteurs: Mehtab Alam Syed, Elena Arsevska, Mathieu Roche & Maguelonne Teisseire
Publié dans: Cartography and Geographic Information Science, 2023, ISSN 1545-0465
Éditeur: TAYLOR & FRANCIS INC
DOI: 10.1080/15230406.2023.2264753

Modelling safe protocols for reopening schools during the COVID-19 pandemic in France

Auteurs: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
Publié dans: Nature Communications, Numéro 12/1, 2021, Page(s) 1073, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-21249-6

An annotated dataset for event-based surveillance of antimicrobial resistance

Auteurs: Nejat Arınık, Wim Van Bortel, Bahdja Boudoua, Luca Busani, Rémy Decoupes, Roberto Interdonato, Rodrique Kafando, Esther van Kleef, Mathieu Roche, Mehtab Alam Syed, Maguelonne Teisseire
Publié dans: Data in Brief, Numéro Volume 46, 2023, Page(s) 108870, ISSN 2352-3409
Éditeur: Elsevier BV
DOI: 10.1016/j.dib.2022.108870

A review of models applied to the geographic spread of Zika virus

Auteurs: Sabrina L Li, Jane P Messina, Oliver G Pybus, Moritz U G Kraemer, Lauren Gardner
Publié dans: Transactions of The Royal Society of Tropical Medicine and Hygiene, Numéro trab009, 2021, ISSN 0035-9203
Éditeur: Royal Society of Tropical Medicine and Hygiene
DOI: 10.1093/trstmh/trab009

Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France

Auteurs: Laura Di Domenico, Chiara E Sabbatini, Giulia Pullano, Daniel Lévy-Bruhl, Vittoria Colizza
Publié dans: Eurosurveillance, Numéro 26/15, 2021, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2021.26.15.2100272

Contribution of climate change to the spatial expansion of West Nile virus in Europe

Auteurs: Diana Erazo, Luke Grant, Guillaume Ghisbain, Giovanni Marini, Felipe J Colón-González, William Wint, Annapaola Rizzoli, Wim Van Bortel, Chantal B.F. Vogels, Nathan D. Grubaugh, Matthias Mengel, Katja Frieler, Wim Thiery, Simon Dellicour
Publié dans: Nature Communications, Numéro 15, Article number: 1196, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-45290-3

Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China

Auteurs: Aogui Hu, Jinfeng Wang, Hui Lin, Corrine W Ruktanonchai, Chengdong Xu, Bin Meng, Xin Zhang, Alessandra Carioli, Yuqing Feng, Qian Yin, Jessica R Floyd, Nick W Ruktanonchai, Zhongjie Li, Weizhong Yang, Andrew J Tatem, Shengjie Lai
Publié dans: Clinical Infectious Diseases, Numéro Volume 75, Numéro 1, 1 July 2022, 2022, Page(s) Pages e234–e240, ISSN 1058-4838
Éditeur: University of Chicago Press
DOI: 10.1093/cid/ciab836

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Auteurs: Vogels CBF, Brackney DE, Dupuis II AP, Robich RM, Fauver JR, Brito AF, Williams SC, Anderson JF, Lubelczyk CB, Lange RE, Prusinski MA, Kramer LD, Gangloff-Kaufmann JL, Goodman LB, Baele G, Smith RP, Armstrong PM, Ciota AT, Dellicour S, Grubaugh ND
Publié dans: PNAS, Numéro 120 (16) e2218012120, 2023, ISSN 1091-6490
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2218012120

Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030

Auteurs: Katie Tiseo, Laura Huber, Marius Gilbert, Timothy P. Robinson, Thomas P. Van Boeckel
Publié dans: Antibiotics, Numéro 9/12, 2020, Page(s) 918, ISSN 2079-6382
Éditeur: MDPI
DOI: 10.3390/antibiotics9120918

The impact of spatial connectivity on NPIs effectiveness

Auteurs: Chiara E. Sabbatini, Giulia Pullano, Laura Di Domenico, Stefania Rubrichi, Shweta Bansal, Vittoria Colizza
Publié dans: BMC Infectious Diseases, Numéro 24, Article number: 21, 2024, ISSN 1471-2334
Éditeur: BioMed Central
DOI: 10.1186/s12879-023-08900-x

High habitat richness reduces the risk of tick-borne encephalitis in Europe: a multi-scale study

Auteurs: Dagostin Francesca, Tagliapietra Valentina, Marini Giovanni, Ferrari Giulia, Cervellini Marco, Wint William, Alexander Niel S., Zuccali Maria Grazia, Molinaro Silvia, Fiorito Nahuel, Dub Timothée, Rocchini Duccio, Rizzoli Annapaola
Publié dans: One Health, Numéro Volume 18, June 2024, 100669, 2024, ISSN 2352-7714
Éditeur: Elsevier
DOI: 10.1016/j.onehlt.2023.100669

One Health challenges and actions: Integration of gender considerations to reduce risks at the human-animal-environmental interface

Auteurs: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
Publié dans: One Health, Numéro Volume 16, 2023, ISSN 2352-7714
Éditeur: Elsevier
DOI: 10.1016/j.onehlt.2023.100530

Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion.

Auteurs: Iris Claudel, Ronan Brouazin, Renaud Lancelot, Louis-Clément Gouagna, Marlène Dupraz, Thierry Baldet & Jérémy Bouyer
Publié dans: Nature Sciences Report, Numéro 20452322, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-24191-9

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

Auteurs: Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A Suchard, Guy Baele, and Philippe Lemey
Publié dans: Virus Evolution, Numéro 8(2), 2022, Page(s) veac088, ISSN 2057-1577
Éditeur: Oxford: Oxford University Press
DOI: 10.1093/ve/veac088

Estimating SARS‐CoV‐2 infections and associated changes in COVID‐19 severity and fatality

Auteurs: Valentina Marziano; Giorgio Guzzetta; Francesco Menegale; Chiara Sacco; Daniele Petrone; Alberto Mateo Urdiales; Martina Del Manso; Antonino Bella; Massimo Fabiani; Maria Fenicia Vescio; Flavia Riccardo; Piero Poletti; Mattia Manica; Agnese Zardini; Valeria d'Andrea; Filippo Trentini; Paola Stefanelli; Giovanni Rezza; Anna Teresa Palamara; Silvio Brusaferro; Marco Ajelli; Patrizio Pezzotti; Stefan
Publié dans: Influenza Other Respi Viruses, Numéro 2023;17:e13181, 2023, ISSN 1750-2659
Éditeur: Oxford Blackwell
DOI: 10.1111/irv.13181

SNEToolkit: Spatial named entities disambiguation toolkit

Auteurs: Rodrique Kafando; Rémy Decoupes; Mathieu Roche; Maguelonne Teisseire
Publié dans: SoftwareX, Numéro 61, 2023, Page(s) Volume 23, 101480, July 2023, ISSN 2352-7110
Éditeur: Elsevier
DOI: 10.1016/j.softx.2023.101480

Assessing the impact of coordinated COVID-19 exit strategies across Europe

Auteurs: N. W. Ruktanonchai, J. R. Floyd, S. Lai, C. W. Ruktanonchai, A. Sadilek, P. Rente-Lourenco, X. Ben, A. Carioli, J. Gwinn, J. E. Steele, O. Prosper, A. Schneider, A. Oplinger, P. Eastham, A. J. Tatem
Publié dans: Science, Numéro 369/6510, 2020, Page(s) 1465-1470, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abc5096

Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy

Auteurs: Mattia Manica, Giorgio Guzzetta, Flavia Riccardo, Antonio Valenti, Piero Poletti, Valentina Marziano, Filippo Trentini, Xanthi Andrianou, Alberto Mateo-Urdiales, Martina del Manso, Massimo Fabiani, Maria Fenicia Vescio, Matteo Spuri, Daniele Petrone, Antonino Bella, Sergio Iavicoli, Marco Ajelli, Silvio Brusaferro, Patrizio Pezzotti, Stefano Merler
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-24832-z

Screening and vaccination against COVID-19 to minimise school closure: a modelling study

Auteurs: Elisabetta Colosi, Giulia Bassignana, Diego Andrés Contreras, Canelle Poirier, Pierre-Yves Boëlle, Simon Cauchemez, Yazdan Yazdanpanah, Bruno Lina, Arnaud Fontanet, Alain Barrat, Vittoria Colizza
Publié dans: The Lancet Infectious Diseases, Numéro Volume 22, Numéro 7, 2022, Page(s) 977-989, ISSN 1473-3099
Éditeur: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(22)00138-4

Epidemic intelligence activities among national public and animal health agencies: a European cross-sectional study

Auteurs: Timothee Dub, Henna Mäkelä, Esther Van Kleef, Agnes Leblond, Alizé Mercier, Viviane Hénaux, Fanny Bouyer, Aurelie Binot, Oumy Thiongane, Renaud Lancelot, Valentina Delconte, Lea Zamuner, Wim Van Bortel & Elena Arsevska
Publié dans: BMC Public Health, Numéro 23, Article number: 1488, 2023, ISSN 1471-2458
Éditeur: BioMed Central
DOI: 10.1186/s12889-023-16396-y

Model-based evaluation of alternative reactive class closure strategies against COVID-19.

Auteurs: Quan-Hui Liu, Juanjuan Zhang, Cheng Peng, Maria Litvinova, Shudong Huang, Piero Poletti, Filippo Trentini, Giorgio Guzzetta, Valentina Marziano, Tao Zhou, Cecile Viboud, Ana I. Bento, Jiancheng Lv, Alessandro Vespignani, Stefano Merler, Hongjie Yu & Marco Ajelli
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-27939-5

Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy

Auteurs: Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini and West Nile Working Group
Publié dans: Viruses, Numéro 15(1), 35, 2023, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15010035

Epidemiology of West Nile virus in Africa: An underestimated threat

Auteurs: Giulia Mencattelli, Marie Henriette Dior Ndione, Roberto Rosà, Giovanni Marini, Cheikh Tidiane Diagne, Moussa Moise Diagne, Gamou Fall, Ousmane Faye, Mawlouth Diallo, Oumar Faye, Giovanni Savini, Annapaola Rizzoli
Publié dans: PLos Negl Trop Dis, Numéro 16(1), 2022, Page(s) e0010075, ISSN 1935-2735
Éditeur: PLOS
DOI: 10.1371/journal.pntd.0010075

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

Auteurs: Charles N Agoti; Lynette Isabella Ochola-Oyier; Simon Dellicour; Khadija Said Mohammed; Arnold W Lambisia; Zaydah R de Laurent; John M Morobe; Maureen W Mburu; Donwilliams O Omuoyo; Edidah M Ongera; Leonard Ndwiga; Eric Maitha; Benson Kitole; Thani Suleiman; Mohamed Mwakinangu; John K Nyambu; John Otieno; Barke Salim; Jennifer Musyoki; Nickson Murunga; Edward Otieno; John N Kiiru; Kadondi Kasera;
Publié dans: eLife, Numéro 11:e71703, 2022, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.71703

Correlation between airborne pollen data and the risk of tick-borne encephalitis in northern Italy

Auteurs: Giovanni Marini, Valentina Tagliapietra, Fabiana Cristofolini, Antonella Cristofori, Francesca Dagostin, Maria Grazia Zuccali, Silvia Molinaro, Elena Gottardini & Annapaola Rizzoli
Publié dans: Nature Scientific Reports, Numéro 13, 8262 (2023), 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-35478-w

Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy: a cross-sectional survey and modelling study

Auteurs: Giulia de Meijere, Eugenio Valdano, Claudio Castellano, Marion Debin, Charly Kengne-Kuetche, Clément Turbelin, Harold Noël, Joshua S. Weitz, Daniela Paolotti, Lisa Hermans, Niel Hens, Vittoria Colizza
Publié dans: The Lancet Regional Health - Europe, Numéro Volume 28, 2023, ISSN 0140-6736
Éditeur: The Lancet Publishing Group
DOI: 10.1016/j.lanepe.2023.100614

Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks

Auteurs: Cuypers L, Keyaerts E, Hong SL, Gorissen S, Soraya MM, Marick S, Van Elslande J, Weemaes M, Wawina-Bokalanga T, Marti-Carreras J, Vanmechelen B, Van Holm B, Bloemen M, Dogné JM, Dufrasne F, Durkin K, Ruelle J, De Mendonca R, Wollants E, Vermeersch P, COVID-19 Genomics Belgium Consortium, Boulouffe C, Djiena A, Broucke C, Catry B, Lagrou K, Van Ranst M, Neyts J, Baele G, Maes P*, André E, Dellico
Publié dans: Nature aging, Numéro 3, 2023, Page(s) 722–733, ISSN 2662-8465
Éditeur: Nature aging
DOI: 10.1038/s43587-023-00421-1

Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence—Belgium as a study case

Auteurs: Simon Dellicour, Catherine Linard, Nina Van Goethem, Daniele Da Re, Jean Artois, Jérémie Bihin, Pierre Schaus, François Massonnet, Herman Van Oyen, Sophie O. Vanwambeke, Niko Speybroeck & Marius Gilbert
Publié dans: International Journal of Health Geographics, Numéro 20, Article number: 29 (2021), 2021, ISSN 1476-072X
Éditeur: BioMed Central
DOI: 10.1186/s12942-021-00281-1

Impact of lockdown on COVID-19 epidemic in Île-de-France and possible exit strategies

Auteurs: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
Publié dans: BMC Medicine, Numéro 18/1, 2020, ISSN 1741-7015
Éditeur: BioMed Central
DOI: 10.1186/s12916-020-01698-4

Global trends in antimicrobial use in food-producing animals: 2020 to 2030

Auteurs: Ranya Mulchandani,Yu Wang,Marius Gilbert,Thomas P. Van Boeckel
Publié dans: PLOS Global Public Health, Numéro 3(2): e0001305, 2023, ISSN 2767-3375
Éditeur: San Francisco California: Public Library of Science
DOI: 10.1371/journal.pgph.0001305

Meteorological and climatic variables predict the phenology of Ixodes ricinus nymph activity in France, accounting for habitat heterogeneity.

Auteurs: Phrutsamon Wongnak, Séverine Bord, Maude Jacquot, Albert Agoulon, Frédéric Beugnet, Laure Bournez, Nicolas Cèbe, Adélie Chevalier, Jean-François Cosson, Naïma Dambrine, Thierry Hoch, Frédéric Huard, Nathalie Korboulewsky, Isabelle Lebert, Aurélien Madouasse, Anders Mårell, Sara Moutailler, Olivier Plantard, Thomas Pollet, Valérie Poux, Magalie René-Martellet, Muriel Vayssier-Taussat,
Publié dans: Scientific Reports, Numéro 20452322, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-11479-z

ITEXT-BIO: Intelligent Term EXTraction for BIOmedical analysis

Auteurs: Rodrique Kafando, Rémy Decoupes, Sarah Valentin, Lucile Sautot, Maguelonne Teisseire, Mathieu Roche
Publié dans: Health Information Science and Systems, Numéro 9/1, 2021, ISSN 2047-2501
Éditeur: Springer
DOI: 10.1007/s13755-021-00156-6

Effect of non-pharmaceutical interventions to contain COVID-19 in China

Auteurs: Shengjie Lai, Nick W. Ruktanonchai, Liangcai Zhou, Olivia Prosper, Wei Luo, Jessica R. Floyd, Amy Wesolowski, Mauricio Santillana, Chi Zhang, Xiangjun Du, Hongjie Yu, Andrew J. Tatem
Publié dans: Nature, Numéro 585/7825, 2020, Page(s) 410-413, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-020-2293-x

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Auteurs: Hugo G. Castelán-Sánchez; Luis Delaye; Rhys P. D. Inward; Simon Dellicour; Bernardo Gutierrez; Natalia Martinez de la Vina; Celia Boukadida; Oliver G Pybus; Guillermo de Anda Jáuregui; Plinio Guzmán; Marisol Garrido Flores; Óscar Fontanelli; Maribel Hernández Rosales; Amilcar Meneses; Gabriela Olmedo-Alvarez; Alfredo Herrera-Estrella; Alejandro Sanchez-Flores; José Esteban Muñoz-Medina; An
Publié dans: eLife, Numéro 12:e82069, 2023, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.82069

Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021

Auteurs: Paola Stefanelli, Filippo Trentini, Giorgio Guzzetta, Valentina Marziano, Alessia Mammone, Monica Sane Schepisi, Piero Poletti, Carla Molina Grané, Mattia Manica, Martina del Manso, Xanthi Andrianou, Marco Ajelli, Giovanni Rezza, Silvio Brusaferro, Stefano Merler, COVID-19 National Microbiology Surveillance Study Group
Publié dans: Eurosurveillance, Numéro Volume 27, Numéro 5, 2022, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2022.27.5.2100429

Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022

Auteurs: Stefanelli P; Trentini F; Petrone D; Mammone A; Ambrosio L; Manica M; Guzzetta G; d'Andrea V; Marziano V; Zardini A; Molina Grane' C; Ajelli M; Di Martino A; Riccardo F; Bella A; Sane Schepisi M; Maraglino F; Poletti P; Palamara AT; Brusaferro S; Rezza G; Pezzotti P; Merler S; Tramuto F
Publié dans: Eurosurveillance, Numéro vol 27, Numéro 45, 10/Nov/2022, 2022, Page(s) pii=2200125, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2022.27.45.2200125

Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy.

Auteurs: Andrea Piccioli; Maria Fenicia Vescio; Patrizio Pezzotti; Antonino Bella; Stefano Merler; Alberto Mateo Urdiales; Martina Del Manso; Stefano Boros; Giovanni Rezza; Giorgio Guzzetta; Valentina Marziano; Piero Poletti; Silvio Brusaferro; Filippo Trentini; Xanthi D. Andrianou; Stefania Bellino; Massimo Fabiani; Flavia Riccardo; Marco Ajelli
Publié dans: Emerging Infectious Diseases, Numéro 17(1), 2021, Page(s) 267-270, ISSN 1080-6059
Éditeur: CDC
DOI: 10.3201/eid2701.202114

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Auteurs: Darlan S. Candido, Ingra M. Claro, Jaqueline G. de Jesus, William M. Souza, Filipe R. R. Moreira, Simon Dellicour, Thomas A. Mellan, Louis du Plessis, Rafael H. M. Pereira, Flavia C. S. Sales, Erika R. Manuli, Julien Thézé, Luiz Almeida, Mariane T. Menezes, Carolina M. Voloch, Marcilio J. Fumagalli, Thaís M. Coletti, Camila A. M. da Silva, Mariana S. Ramundo, Mariene R. Amorim, Henrique H. Hoel
Publié dans: Science, Numéro 369/6508, 2020, Page(s) 1255-1260, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abd2161

Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China

Auteurs: Jin Zhao, Simon Dellicour https://orcid.org/0000-0001-9558-1052, Ziqing Yan, Michael Veit, Mandev S. Gill, Wan-Ting He, Xiaofeng Zhai, Xiang Ji, Marc A. Suchard, Philippe Lemey, Shuo Su
Publié dans: Journal of Virology, Numéro Vol. 97, No. 1, 2023, ISSN 1098-5514
Éditeur: American Society for Microbiology
DOI: 10.1128/jvi.01091-22

Underdetection of cases of COVID-19 in France threatens epidemic control

Auteurs: Giulia Pullano, Laura Di Domenico, Chiara E. Sabbatini, Eugenio Valdano, Clément Turbelin, Marion Debin, Caroline Guerrisi, Charly Kengne-Kuetche, Cécile Souty, Thomas Hanslik, Thierry Blanchon, Pierre-Yves Boëlle, Julie Figoni, Sophie Vaux, Christine Campèse, Sibylle Bernard-Stoecklin, Vittoria Colizza
Publié dans: Nature, Numéro 590/7844, 2021, Page(s) 134-139, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-020-03095-6

Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic

Auteurs: Laura Di Domenico; Chiara E. Sabbatini; Pierre-Yves Boëlle; Chiara Poletto; Pascal Crépey; Juliette Paireau; Simon Cauchemez; François Beck; Harold Noel; Daniel Lévy-Bruhl; Vittoria Colizza
Publié dans: Communications Medicine, Numéro 2730664X, 2021, ISSN 2730-664X
Éditeur: Nature Portfolio
DOI: 10.1038/s43856-021-00057-5

Reporting delays of chikungunya cases during the 2017 outbreak in Lazio region, Italy

Auteurs: Mattia Manica, Giovanni Marini, Angelo Solimini, Giorgio Guzzetta, Piero Poletti, Paola Scognamiglio, Chiara Virgillito, Alessandra della Torre, Stefano Merler, Roberto Rosà, Francesco Vairo, Beniamino Caputo
Publié dans: PLOS Neglected Tropical Diseases, 2023, ISSN 1935-2727
Éditeur: Public Library of Science
DOI: 10.1371/journal.pntd.0011610

Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection

Auteurs: Jesús A. Moreno López, Beatriz Arregui García, Piotr Bentkowski, Livio Bioglio, Francesco Pinotti, Pierre-Yves Boëlle, Alain Barrat, Vittoria Colizza, Chiara Poletto
Publié dans: Science Advances, Numéro 7/15, 2021, Page(s) eabd8750, ISSN 2375-2548
Éditeur: AAAS
DOI: 10.1126/sciadv.abd8750

Identifying associations between epidemiological entities in news data for animal disease surveillance

Auteurs: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publié dans: Artificial Intelligence in Agriculture, Numéro 5, 2021, Page(s) 163-174, ISSN 2589-7217
Éditeur: Elsevier
DOI: 10.1016/j.aiia.2021.07.003

Epidemic graph diagrams as analytics for epidemic control in the data-rich era.

Auteurs: Eugenio Valdano, Davide Colombi, Chiara Poletto, Vittoria Colizza
Publié dans: Nature communications, Numéro 14, 8472, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-43856-1

Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion

Auteurs: Ronan Brouazin, Iris Claudel, Renaud Lancelot, Guillaume Dupuy, Louis‑Clément Gouagna, Marlène Dupraz, Thierry Baldet & Jérémy Bouyer
Publié dans: Nature Scientific Reports, Numéro 20452322, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-23137-5

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Auteurs: Philippe Lemey, Samuel L. Hong, Verity Hill, Guy Baele, Chiara Poletto, Vittoria Colizza, Áine O’Toole, John T. McCrone, Kristian G. Andersen, Michael Worobey, Martha I. Nelson, Andrew Rambaut, Marc A. Suchard
Publié dans: Nature Communications, Numéro 11/1, 2020, Page(s) 5110, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-18877-9

Potential short-term outcome of an uncontrolled COVID-19 epidemic in Lombardy, Italy, February to March 2020

Auteurs: Giorgio Guzzetta, Piero Poletti, Marco Ajelli, Filippo Trentini, Valentina Marziano, Danilo Cereda, Marcello Tirani, Giulio Diurno, Annalisa Bodina, Antonio Barone, Lucia Crottogini, Maria Gramegna, Alessia Melegaro, Stefano Merler
Publié dans: Eurosurveillance, Numéro 25/12, 2020, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2020.25.12.2000293

Modelling COVID-19 in school settings to evaluate prevention and control protocols

Auteurs: Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Vittoria Colizza
Publié dans: Anaesthesia Critical Care & Pain Medicine, Numéro Volume 41, Numéro 2, 2022, ISSN 2352-5568
Éditeur: Science Direct
DOI: 10.1016/j.accpm.2022.101047

Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil

Auteurs: Sabrina L. Li, André L. Acosta, Sarah C. Hill, Oliver J. Brady, Marco A. B. de Almeida, Jader da C. Cardoso, Arran Hamlet, Luis F. Mucci, Juliana Telles de Deus, Felipe C. M. Iani, Neil S. Alexander, G. R. William Wint, Oliver G. Pybus, Moritz U. G. Kraemer, Nuno R. Faria, Jane P. Messina
Publié dans: PLOS Neglected Tropical Diseases, Numéro 16(1), 2022, Page(s) e0010019, ISSN 1935-2735
Éditeur: PLOS
DOI: 10.1371/journal.pntd.0010019

Understanding West Nile virus transmission: Mathematical modelling to quantify the most critical parameters to predict infection dynamics

Auteurs: Elisa Fesce , Giovanni Marini, Roberto Rosà, Davide Lelli, Monica Pierangela Cerioli, Mario Chiari, Marco Farioli, Nicola Ferrari
Publié dans: Plos Neglected Tropical Diseases, Numéro 17(5): e0010252, 2023, ISSN 1935-2735
Éditeur: San Francisco CA: Public Library of Science
DOI: 10.1371/journal.pntd.0010252

Polygon vector map distortion for increasing the readability ofone-to-many flow maps

Auteurs: Laëtitia Viau, Arnaud Sallaberry, Nancy Rodriguez, Jean-François Girres & Pascal Poncelet
Publié dans: International Journal of Geographical Information Science, Numéro Volume 37, Numéro 6, 2023, Page(s) 1288-1314, ISSN 1365-8824
Éditeur: Taylor & Francis online
DOI: 10.1080/13658816.2023.2190374

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Auteurs: Oscar A. MacLean, Spyros Lytras, Steven Weaver, Joshua B. Singer, Maciej F. Boni, Philippe Lemey, Sergei L. Kosakovsky Pond, David L. Robertson
Publié dans: PLOS Biology, Numéro 19/3, 2021, Page(s) e3001115, ISSN 1545-7885
Éditeur: PLOS Biology
DOI: 10.1371/journal.pbio.3001115

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

Auteurs: Raphaëlle Klitting, Liana E. Kafetzopoulou, Wim Thiery, Gytis Dudas, Sophie Gryseels, Anjali Kotamarthi, Bram Vrancken, Karthik Gangavarapu, Mambu Momoh, John Demby Sandi, Augustine Goba, Foday Alhasan, Donald S. Grant, Sylvanus Okogbenin, Ephraim Ogbaini-Emovo, Robert F. Garry, Allison R. Smither, Mark Zeller, Matthias G. Pauthner, Michelle McGraw, Laura D. Hughes, Sophie Duraffour, Stephan Gü
Publié dans: Nature Communications, Numéro 13, 5596, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-33112-3

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Auteurs: Viana, Raquel; Moyo, Sikhulile; Amoako, Daniel G.; Tegally, Houriiyah; Scheepers, Cathrine; Althaus, Christian L.; Anyaneji, Ugochukwu J.; Bester, Phillip A.; Boni, Maciej F.; Chand, Mohammed; Choga, Wonderful T.; Colquhoun, Rachel; Davids, Michaela; Deforche, Koen; Doolabh, Deelan; du Plessis, Louis; Engelbrecht, Susan; Everatt, Josie; Giandhari, Jennifer; Giovanetti, Marta; Hardie, Diana; et al.
Publié dans: Nature, 603 (7902), Numéro 5, 2022, Page(s) pages 679–686, ISSN 1476-4687
Éditeur: Nature
DOI: 10.3929/ethz-b-000525678

Considerable escape of SARS-CoV-2 Omicron to antibody neutralization

Auteurs: Delphine Planas; Nell Saunders; Piet Maes; Florence Guivel-Benhassine; Cyril Planchais; Julian Buchrieser; William-Henry Bolland; Françoise Porrot; Isabelle Staropoli; Frederic Lemoine; Hélène Péré; David Veyer; Julien Puech; Julien Rodary; Guy Baele; Simon Dellicour; Joren Raymenants; Sarah Gorissen; Caspar Geenen; Bert Vanmechelen; Tony Wawina-Bokalanga; Joan Martí-Carreras; Lize Cuypers;
Publié dans: Nature, Numéro 602, 2022, Page(s) 671–675, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/d41586-021-03827-2

West Nile Virus in Africa: current epidemiological situation and knowledge gaps

Auteurs: Mencattelli, G.; Ndione, M. H. D.; Rosa, R.; Giovanni Marini; Diagne, C. T.; Diagne, M. M.; Fall, G.; Faye, O.; Diallo, M.; Faye, O.; Savini, G.; Annapaola Rizzoli
Publié dans: International Journal of Infectious Diseases, Numéro Volume 116, Supplement, 2022, Page(s) 1201-9712, ISSN 1201-9712
Éditeur: Elsevier BV
DOI: 10.1016/j.ijid.2021.12.291

Accommodating sampling location uncertainty in continuous phylogeography

Auteurs: Simon Dellicour, Philippe Lemey, Marc A Suchard, Marius Gilbert, Guy Baele
Publié dans: Virus Evolution, Numéro Volume 8, Numéro 1, 2022, Page(s) veac041, ISSN 2057-1577
Éditeur: Oxford University press
DOI: 10.1093/ve/veac041

Epid data explorer: A visualization tool for exploring and comparing spatio-temporal epidemiological data

Auteurs: Laetitia Viau, Jérôme Azé, Fati Chen, Pierre Pompidor, Pascal Poncelet, Vincent Raveneau, Nancy Rodriguez, Arnaud Sallaberry
Publié dans: Health Informatics Journal, Numéro 30, 2024, ISSN 1460-4582
Éditeur: SAGE Publications
DOI: 10.1177/14604582241279720

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Auteurs: Louis du Plessis, John T. McCrone, Alexander E. Zarebski, Verity Hill, Christopher Ruis, Bernardo Gutierrez, Jayna Raghwani, Jordan Ashworth, Rachel Colquhoun, Thomas R. Connor, Nuno R. Faria, Ben Jackson, Nicholas J. Loman, Áine O’Toole, Samuel M. Nicholls, Kris V. Parag, Emily Scher, Tetyana I. Vasylyeva, Erik M. Volz, Alexander Watts, Isaac I. Bogoch, Kamran Khan, David M. Aanensen, Moritz U
Publié dans: Science, Numéro 371/6530, 2021, Page(s) 708-712, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abf2946

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Auteurs: Joseph L.-H. Tsui, John T. McCrone, Ben Lambert, Sumali Bajaj, Rhys P. D. Inward,Paolo Bosetti, Rosario Evans Pena, Houriiyah Tegally, Verity Hill, Alexander E. Zarebski, Thomas P. Peacock, Luyang Liu, Neo Wu, Megan Davis, Isaac I. Bogoch,Kamran Khan, Meaghan Kall, Nurin Iwani Binti Abdul Aziz, Rachel Colquhoun, Áine O’Toole, Ben Jackson, Abhishek Dasgupta, Eduan Wilkinson, Tulio de Oliveira, T
Publié dans: Science, Numéro 381, Numéro 6655, 2023, Page(s) 336-343, ISSN 1095-9203
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.adg6605

Highlighting socio-economic constraints on mobility reductions during COVID-19 restrictions in France can inform effective and equitable pandemic response

Auteurs: Eugenio Valdano, Jonggul Lee, Shweta Bansal, Stefania Rubrichi, Vittoria Colizza
Publié dans: Journal of Travel Medicine, Numéro 28/4, 2021, ISSN 1195-1982
Éditeur: B.C. Decker Inc.
DOI: 10.1093/jtm/taab045

H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic?

Auteurs: Rémy Decoupes, Rodrique Kafando, Mathieu Roche, Maguelonne Teisseire
Publié dans: AGILE: GIScience Series, Numéro 2, 2021, Page(s) 1-8, ISSN 2700-8150
Éditeur: Copernicus publications
DOI: 10.5194/agile-giss-2-2-2021

Assessing spread risk of COVID-19 in early 2020

Auteurs: Shengjie Lai; Isaac Bogoch; Nick Ruktanonchai; Alexander Watts; Xin Lu; Weizhong Yang; Hongjie Yu; Kamran Khan; Andrew J Tatem
Publié dans: Data Science and Management, Numéro Volume 5, Numéro 4, 2022, Page(s) 212-218, ISSN 2666-7649
Éditeur: Elsevier
DOI: 10.1016/j.dsm.2022.08.004

GeoNLPlify: A spatial data augmentation enhancing text classification for crisis monitoring

Auteurs: Rémy Decoupes; Mathieu Roche; Maguelonne Teisseire
Publié dans: "Intelligent Data Analysis, 2023, pp.1-25. ⟨10.3233/IDA-230040⟩", Numéro 25, 2023, Page(s) 1-25, ISSN 1088-467X
Éditeur: Elsevier Science
DOI: 10.3233/ida-230040

Association of Age With Likelihood of Developing Symptoms and Critical Disease Among Close Contacts Exposed to Patients With Confirmed SARS-CoV-2 Infection in Italy

Auteurs: Piero Poletti, Marcello Tirani, Danilo Cereda, Filippo Trentini, Giorgio Guzzetta, Giuliana Sabatino, Valentina Marziano, Ambra Castrofino, Francesca Grosso, Gabriele Del Castillo, Raffaella Piccarreta, Aida Andreassi, Alessia Melegaro, Maria Gramegna, Marco Ajelli, Stefano Merler
Publié dans: JAMA Network Open, Numéro 4/3, 2021, Page(s) e211085, ISSN 2574-3805
Éditeur: American Medical Association
DOI: 10.1001/jamanetworkopen.2021.1085

Elaboration of a new framework for fine-grained epidemiological annotation

Auteurs: Sarah Valentin; Elena Arsevska; Aline Vilain; Valérie De Waele; Renaud Lancelot; Mathieu Roche
Publié dans: Scientific Data, Numéro 1, 2022, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/s41597-022-01743-2

Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants

Auteurs: Lize Cuypers, Simon Dellicour, Samuel L. Hong, Barney I. Potter, Bruno Verhasselt, Nick Vereecke, Laurens Lambrechts, Keith Durkin, Vincent Bours, Sofieke Klamer, Guillaume Bayon-Vicente, Carl Vael, Kevin K. Ariën, Ricardo De Mendonca, Oriane Soetens, Charlotte Michel, Bertrand Bearzatto, Reinout Naesens, Jeremie Gras, Anne Vankeerberghen, Veerle Matheeussen, Geert Martens, Dagmar Obbels, Ann Lem
Publié dans: Viruses, Numéro 14(10), 2022, Page(s) 2301, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14102301

Evaluation of Waning of SARS-CoV-2 Vaccine–Induced Immunity. A Systematic Review and Meta-analysis

Auteurs: Francesco Menegale, Mattia Manica, Agnese Zardini, Giorgio Guzzetta, Valentina Marziano, Valeria d'Andrea, Filippo Trentini, Marco Ajelli, Piero Poletti, Stefano Merler
Publié dans: JAMA Network Open, Numéro 6(5):e2310650, 2023, ISSN 2574-3805
Éditeur: American Medical Association
DOI: 10.1001/jamanetworkopen.2023.10650

Is clinical primary care surveillance for tularaemia a useful addition to laboratory surveillance? An analysis of notification data for Finland, 2013 to 2019

Auteurs: Charlotte C Hammer, Timothee Dub, Oskari Luomala, Jussi Sane
Publié dans: Eurosurveillance, Numéro 2022;27(4), 2022, Page(s) pii=2100098, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2022.27.4.2100098

A population-based cohort approach to assess excess mortality due to the spread of COVID-19 in Italy, January-May 2020

Auteurs: Maria Dorrucci, Giada Minelli, Stefano Boros, Valerio Manno, Sabrina Prati, Marco Battaglini, Gianni Corsetti, Xanthi Andrianou, Flavia Riccardo, Massimo Fabiani, Maria Fenicia Vescio, Matteo Spuri, Alberto Mateo-Urdiales, Martina Del Manso, Patrizio Pezzotti, Antonino Bella and the Italian Integrated Surveillance COVID-19 Group
Publié dans: Annali dell'Istituto Superiore di Sanità, Numéro Vol. 58, No. 1, 2022, Page(s) 25-33, ISSN 2384-8553
Éditeur: Istituto Superiore di Sanità
DOI: 10.4415/ann_22_01_04

On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy

Auteurs: Luca Bianco, Mirko Moser, Andrea Silverj, Diego Micheletti, Giovanni Lorenzin, Lucia Collini, Mattia Barbareschi, Paolo Lanzafame, Nicola Segata, Massimo Pindo, Pietro Franceschi, Omar Rota-Stabelli, Annapaola Rizzoli, Paolo Fontana, and Claudio Donati
Publié dans: Viruses, Numéro 19994915, 2022, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14030580

An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients

Auteurs: Gonçalves, Bronner P.; Gómez Junyent, Joan; Olliaro Piero L.; ISARIC Clinical Characterisation Group
Publié dans: eLife, Numéro 11:e80556, 2022, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.80556

A social-ecological systems approach to tick bite and tick-borne disease risk management: Exploring collective action in the Occitanie region in southern France

Auteurs: Iyonna Zortman, Michel de Garine-Wichatitsky, Elena Arsevska, Timothée Dub, Wim Van Bortel, Estelle Lefrançois, Laurence Vial, Thomas Pollet, Aurélie Binot
Publié dans: One Health, Numéro Volume 17, 2023, 100630, 2023, ISSN 2352-7714
Éditeur: ScienceDirect.com
DOI: 10.1016/j.onehlt.2023.100630

Novel coronavirus (2019-nCoV) early-stage importation risk to Europe, January 2020

Auteurs: Giulia Pullano, Francesco Pinotti, Eugenio Valdano, Pierre-Yves Boëlle, Chiara Poletto, Vittoria Colizza
Publié dans: Eurosurveillance, Numéro 25/4, 2020, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2020.25.4.2000057

Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study

Auteurs: Marius Gilbert, Giulia Pullano, Francesco Pinotti, Eugenio Valdano, Chiara Poletto, Pierre-Yves Boëlle, Eric D'Ortenzio, Yazdan Yazdanpanah, Serge Paul Eholie, Mathias Altmann, Bernardo Gutierrez, Moritz U G Kraemer, Vittoria Colizza
Publié dans: The Lancet, Numéro 395/10227, 2020, Page(s) 871-877, ISSN 0140-6736
Éditeur: The Lancet Publishing Group
DOI: 10.1016/s0140-6736(20)30411-6

The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak

Auteurs: Matteo Chinazzi, Jessica T. Davis, Marco Ajelli, Corrado Gioannini, Maria Litvinova, Stefano Merler, Ana Pastore y Piontti, Kunpeng Mu, Luca Rossi, Kaiyuan Sun, Cécile Viboud, Xinyue Xiong, Hongjie Yu, M. Elizabeth Halloran, Ira M. Longini, Alessandro Vespignani
Publié dans: Science, 2020, Page(s) eaba9757, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aba9757

Labeled entities from social media data related to avian influenza disease

Auteurs: Camille Schaeffer; Roberto Interdonato; Renaud Lancelot; Mathieu Roche; Maguelonne Teisseire
Publié dans: Data in Brief, Numéro 23523409, 2022, ISSN 2352-3409
Éditeur: Elsevier BV
DOI: 10.1016/j.dib.2022.108317

The values and risks of an Intergovernmental Panel for One Health to strengthen pandemic prevention, preparedness, and response

Auteurs: Alexandre Hobeika, Maxime Henri Tibault Stauffer, Timothée Dub, Wim van Bortel, Martin Beniston, Salome Bukachi, Gian Luca Burci, Lisa Crump, Wanda Markotter, Ludovico Pasquale Sepe, Enrichetta Placella, Benjamin Roche, Oumy Thiongane, Zhanyun Wang, Frédérique Guérin, Esther van Kleef
Publié dans: The Lancet Global Health, Numéro Volume 11, ISSUE 8, 2023, Page(s) 1301-1307, ISSN 2214-109X
Éditeur: Elsevier BV
DOI: 10.1016/s2214-109x(23)00246-2

Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron

Auteurs: Dellicour S, Hong SL, Hill V, Dimartino D, Marier C, Zappile P, Harkins GW, Lemey P, Baele G, Duerr R, Heguy A
Publié dans: PLoS Pathogens, Numéro 19(4): e1011348, 2023, ISSN 1553-7366
Éditeur: Public Library of Science
DOI: 10.1371/journal.ppat.1011348

Influence of Temperature on the Life-Cycle Dynamics of Aedes albopictus Population Established at Temperate Latitudes: A Laboratory Experiment

Auteurs: Giovanni Marini, Mattia Manica, Daniele Arnoldi, Enrico Inama, Roberto Rosà, Annapaola Rizzoli
Publié dans: Insects, Numéro 11/11, 2020, Page(s) 808, ISSN 2075-4450
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/insects11110808

Dissemination of information in event-based surveillance, a case study of Avian Influenza

Auteurs: Sarah Valentin, Bahdja Boudoua, Kara Sewalk, Nejat Arınık, Mathieu Roche, Renaud Lancelot, Elena Arsevska
Publié dans: PLoS ONE, 2023, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0285341

COVID-19 and Media datasets: Period- and location-specific textual data mining

Auteurs: Mathieu Roche
Publié dans: Data in Brief, Numéro 33, 2020, Page(s) 106356, ISSN 2352-3409
Éditeur: Elsevier BV
DOI: 10.1016/j.dib.2020.106356

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Auteurs: Moritz U. G. Kraemer, Verity Hill, Christopher Ruis, Simon Dellicour, Sumali Bajaj, John T. McCrone, Guy Baele, Kris V. Parag, Anya Lindström Battle, Bernardo Gutierrez, Ben Jackson, Rachel Colquhoun, Áine O’Toole, Brennan Klein, Alessandro Vespignani, Erik Volz, Nuno R. Faria, David M. Aanensen, Nicholas J. Loman, Louis du Plessis, Simon Cauchemez, Andrew Rambaut, Samuel V. Scarpino, Oliver G
Publié dans: Science, Numéro 373/6557, 2021, Page(s) 889-895, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abj0113

The early phase of the COVID-19 epidemic in Lombardy, Italy

Auteurs: Danilo Cereda, Mattia Manica, MarcelloTirani, Francesca Rovida, Vittorio Demicheli, Marco Ajelli, Piero Poletti, FilippoTrentini, Giorgio Guzzetta, Valentina Marziano, Raffaella Piccarreta, Antonio Barone, Michele Magoni, Silvia Deandrea, Giulio Diurno, Massimo Lombardo, Marino Faccini, Angelo Pan,…Stefano Merler
Publié dans: Epidemics, Numéro Vol 37, 2021, Page(s) 100528, ISSN 1755-4365
Éditeur: Elsevier BV
DOI: 10.1016/j.epidem.2021.100528

Pressure on the Health-Care System and Intensive Care Utilization During the COVID-19 Outbreak in the Lombardy Region of Italy: A Retrospective Observational Study in 43,538 Hospitalized Patients

Auteurs: Filippo Trentini, Valentina Marziano, Giorgio Guzzetta, Marcello Tirani, Danilo Cereda, Piero Poletti, Raffaella Piccarreta, Antonio Barone, Giuseppe Preziosi, Fabio Arduini, Petra Giulia Della Valle, Alberto Zanella, Francesca Grosso, Gabriele del Castillo, Ambra Castrofino, Giacomo Grasselli, Alessia Melegaro, Alessandra Piatti, Aida Andreassi, Maria Gramegna, Marco Ajelli, Stefano Merler
Publié dans: American Journal of Epidemiology, 2021, ISSN 0002-9262
Éditeur: Oxford University Press
DOI: 10.1093/aje/kwab252

Socioeconomic patterns and COVID-19 outcomes before, during and after the lockdown in Italy (2020)

Auteurs: Alberto Mateo-Urdiales, Massimo Fabiani, Aldo Rosano, Maria Fenicia Vescio, Martina Del Manso, Antonino Bella, Flavia Riccardo, Patrizio Pezzotti, Enrique Regidor, Xanthi Andrianou
Publié dans: Health & Place, Numéro 71, 2021, Page(s) 102642, ISSN 1353-8292
Éditeur: Elsevier BV
DOI: 10.1016/j.healthplace.2021.102642

Crowding and the shape of COVID-19 epidemics

Auteurs: Benjamin Rader, Samuel V. Scarpino, Anjalika Nande, Alison L. Hill, Ben Adlam, Robert C. Reiner, David M. Pigott, Bernardo Gutierrez, Alexander E. Zarebski, Munik Shrestha, John S. Brownstein, Marcia C. Castro, Christopher Dye, Huaiyu Tian, Oliver G. Pybus, Moritz U. G. Kraemer
Publié dans: Nature Medicine, Numéro 26/12, 2020, Page(s) 1829-1834, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-020-1104-0

VectAbundance: a spatio-temporal database of Aedes mosquitoes observations

Auteurs: Daniele Da Re, Giovanni Marini, Carmelo Bonannella, Fabrizio Laurini, Mattia Manica, Nikoleta Anicic, Alessandro Albieri, Paola Angelini, Daniele Arnoldi, Marharyta Blaha, Federica Bertola, Beniamino Caputo, Claudio De Liberato, Alessandra della Torre, Eleonora Flacio, Alessandra Franceschini, Francesco Gradoni, Përparim Kadriaj, Valeria Lencioni, Irene Del Lesto, Francesco La Russa, Riccardo Pao
Publié dans: Scientific Data, Numéro 11, 636, 2024, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/s41597-024-03482-y

Monitoring key epidemiological parameters of SARS-CoV-2 transmission

Auteurs: Moritz U. G. Kraemer, Oliver G. Pybus, Christophe Fraser, Simon Cauchemez, Andrew Rambaut, Benjamin J. Cowling
Publié dans: Nature Medicine, 2021, ISSN 1078-8956
Éditeur: Nature Publishing Group
DOI: 10.1038/s41591-021-01545-w

Trade-offs between individual and ensemble forecasts of an emerging infectious disease

Auteurs: Oidtman, R.J., Omodei, E., Kraemer, M.U.G. et al.
Publié dans: Nature Communications, Numéro 20411723, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-25695-0

Untangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories

Auteurs: Yong Ge, Wen-Bin Zhang, Xilin Wu, Corrine W. Ruktanonchai, Haiyan Liu, Jianghao Wang, Yongze Song, Mengxiao Liu, Wei Yan, Juan Yang, Eimear Cleary, Sarchil H. Qader, Fatumah Atuhaire, Nick W. Ruktanonchai, Andrew J. Tatem & Shengjie Lai
Publié dans: Nature Communications, Numéro 13, 3106, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-30897-1

Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study

Auteurs: Francesco Pinotti, Laura Di Domenico, Ernesto Ortega, Marco Mancastroppa, Giulia Pullano, Eugenio Valdano, Pierre-Yves Boëlle, Chiara Poletto, Vittoria Colizza
Publié dans: PLOS Medicine, Numéro 17/7, 2020, Page(s) e1003193, ISSN 1549-1676
Éditeur: Public Library of science
DOI: 10.1371/journal.pmed.1003193

Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID‐19 emergence

Auteurs: Sarah Valentin, Alizé Mercier, Renaud Lancelot, Mathieu Roche, Elena Arsevska
Publié dans: Transboundary and Emerging Diseases, Numéro 2020 Aug 2 : 10.1111/tbed.13738, 2020, ISSN 1865-1674
Éditeur: Blackwell-Wiss.-Verl
DOI: 10.1111/tbed.13738

Minimising school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy, in January 2022

Auteurs: Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Bruno Lina, Philippe Vanhems, Julia Bielicki, Vittoria Colizza
Publié dans: Eurosurveillance, Numéro 28(5), 2022, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2023.28.5.2200192

Fusion of spatiotemporal and thematic features of textual data for animal disease surveillance

Auteurs: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publié dans: Information Processing in Agriculture, Numéro 22143173, 2022, ISSN 2214-3173
Éditeur: Elsevier B.V.
DOI: 10.1016/j.inpa.2022.03.004

Spring temperature shapes West Nile virus transmission in Europe

Auteurs: Giovanni Marini, Mattia Manica, Luca Delucchi, Andrea Pugliese, Roberto Rosà
Publié dans: Acta Tropica, Numéro 215, 2021, Page(s) 105796, ISSN 0001-706X
Éditeur: Elsevier BV
DOI: 10.1016/j.actatropica.2020.105796

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Auteurs: Darren P Martin, Steven Weaver, Houryiah Tegally, Emmanuel James San, Stephen D Shank, Eduan Wilkinson, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J Lessells, NGS-SA, COVID-19 Genomics UK (COG-UK), Ravindra K Gupta, Joel O Wertheim, Anton Nekturenko, Ben Murrell, Gordon W Harkins, Philippe Lemey, Oscar A MacLean, David L Robertson, Tulio de Oliveira, Sergei L Kosa
Publié dans: Cell, Numéro Volume 184, Numéro 20, 30 September 2021, 2021, Page(s) Pages 5189-5200.e7, ISSN 1097-4172
Éditeur: Elsevier
DOI: 10.1016/j.cell.2021.09.003

Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium

Auteurs: Darcis, Majdouline El Moussaoui; Nathalie Maes; Samuel L. Hong; Nicolas Lambert; Stéphanie Gofflot; Patricia Dellot; Yasmine Belhadj; Pascale Huynen; Marie-Pierre Hayette; Cécile Meex; Sébastien Bontems; Justine Defêche; Lode Godderis; Geert Molenberghs; Christelle Meuris; Maria Artesi; Keith Durkin; Souad Rahmouni; Céline Grégoire; Yves Beguin; Michel Moutschen; Simon Dellicour; Gilles
Publié dans: Viruses, Numéro 14(6), 1302, 2022, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061302

Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19

Auteurs: Benjamin Faucher; Rania Assab; Jonathan Roux; Daniel Levy-Bruhl; Cécile Tran Kiem; Simon Cauchemez; Laura Zanetti; Vittoria Colizza; Pierre-Yves Boëlle; Chiara Poletto
Publié dans: Nature Communications, Numéro 20411723, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-29015-y

The Spatial Distribution of Crimean–Congo Haemorrhagic Fever and Its Potential Vectors in Europe and Beyond

Auteurs: Jane Paula Messina and G. R. William Wint
Publié dans: Insects, Numéro 14(9), 2023, Page(s) 771, ISSN 2075-4450
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/insects14090771

Outdoor recreation, tick borne encephalitis incidence and seasonality in Finland, Norway and Sweden during the COVID-19 pandemic (2020/2021)

Auteurs: Solveig Jore, Hildegunn Viljugrein, Marika Hjertqvist, Timothée Dub, Henna Mäkelä
Publié dans: INFECTION ECOLOGY & EPIDEMIOLOGY, Numéro 2023, VOL. 13, 2281055, 2023, ISSN 2000-8686
Éditeur: Taylor and Francis Ltd.
DOI: 10.1080/20008686.2023.2281055

Risk of Symptomatic Infection During a Second Coronavirus Disease 2019 Wave in Severe Acute Respiratory Syndrome Coronavirus 2–Seropositive Individuals

Auteurs: Mattia Manica, Serena Pancheri, Piero Poletti, Giulia Giovanazzi, Giorgio Guzzetta, Filippo Trentini, Valentina Marziano, Marco Ajelli, Maria Grazia Zuccali, Pier Paolo Benetollo, Stefano Merler, Antonio Ferro
Publié dans: Clinical Infectious Diseases, Numéro Volume 74, Numéro 5, 1 March 2022, 2022, Page(s) Pages 893-896, ISSN 1058-4838
Éditeur: University of Chicago Press
DOI: 10.1093/cid/ciab556

Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities

Auteurs: Bo Huang, Jionghua Wang, Jixuan Cai, Shiqi Yao, Paul Kay Sheung Chan, Tony Hong-wing Tam, Ying-Yi Hong, Corrine W. Ruktanonchai, Alessandra Carioli, Jessica R. Floyd, Nick W. Ruktanonchai, Weizhong Yang, Zhongjie Li, Andrew J. Tatem, Shengjie Lai
Publié dans: Nature Human Behaviour, Numéro 5/6, 2021, Page(s) 695-705, ISSN 2397-3374
Éditeur: Springer Nature
DOI: 10.1038/s41562-021-01063-2

Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality

Auteurs: Van Bortel, W; Mariën, J; Jacobs, BKM; Sinzinkayo, D; Sinarinzi, P; Lampaert, E; D'hondt, R; Mafuko, J-M; De Weggheleire, A; Vogt, F; Alexander, N; Wint, W; Maes, P; Vanlerberghe, V; Leclair, C
Publié dans: BMJ Global Health, Numéro Vol 7, issue 12, 2022, Page(s) e009674, ISSN 2059-7908
Éditeur: BMJ Publishing Group Ltd
DOI: 10.1136/bmjgh-2022-009674

Animal disease surveillance: How to represent textual data for classifying epidemiological information

Auteurs: Sarah Valentin, Rémy Decoupes, Renaud Lancelot, Mathieu Roche
Publié dans: Preventive Veterinary Medicine, Numéro Volume 216, 2023, 105932, 2023, ISSN 0167-5877
Éditeur: Elsevier BV
DOI: 10.1016/j.prevetmed.2023.105932

Limited data on infectious disease distribution exposes ambiguity in epidemic modeling choices

Auteurs: Laura Di Domenico, Eugenio Valdano, Vittoria Colizza
Publié dans: Physical Review Research, Numéro 6, 2024, ISSN 2643-1564
Éditeur: American Physical Society
DOI: 10.1103/physrevresearch.6.023265

A quantitative assessment of epidemiological parameters to model COVID- 19 burden

Auteurs: Zardini, Agnese; Galli, Margherita; Tirani, Marcello; Cereda, Danilo; Manica, Mattia; Trentini, Filippo; Guzzetta, Giorgio; Marziano, Valentina; Piccarreta, Raffaella; Melegaro, Alessia; Ajelli, Marco; Poletti, Piero; Merler, Stefano
Publié dans: Epidemics, Numéro Vol 37, December 2021, 2021, Page(s) 100530, ISSN 2352-7714
Éditeur: Elsevier
DOI: 10.1016/j.epidem.2021.100530

Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China

Auteurs: Juanjuan Zhang, Maria Litvinova, Yuxia Liang, Yan Wang, Wei Wang, Shanlu Zhao, Qianhui Wu, Stefano Merler, Cécile Viboud, Alessandro Vespignani, Marco Ajelli, Hongjie Yu
Publié dans: Science, Numéro 368/6498, 2020, Page(s) 1481-1486, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abb8001

Phycova — a tool for exploring covariates of pathogen spread

Auteurs: Tim Blokker, Guy Baele, Philippe Lemey, Simon Dellicour
Publié dans: Virus Evolution, Numéro 20571577, 2022, ISSN 2057-1577
Éditeur: Oxford University Press
DOI: 10.1093/ve/veac015

The effect of COVID-19 vaccination in Italy and perspectives for living with the virus

Auteurs: Valentina Marziano, ProfileGiorgio Guzzetta, Alessia Mammone, ProfileFlavia Riccardo, Piero Poletti, Filippo Trentini, Mattia Manica, Andrea Siddu, Paola Stefanelli, Patrizio Pezzotti, Marco Ajelli, Silvio Brusaferro, Giovanni Rezza, Stefano Merler
Publié dans: Nature Communications, Numéro 12, 7272 (2021), 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-27532-w

Prior water availability modifies the effect of heavy rainfall on dengue transmission: a time series analysis of passive surveillance data from southern China

Auteurs: Cheng Q, Jing Q, Collender PA, Head JR, Li Q, Yu H, Li Z, Ju Y, Chen T, Wang P, Cleary E and Lai S
Publié dans: Front. Public Health, Numéro 11:1287678, 2023, ISSN 2296-2565
Éditeur: Lausanne Frontiers Media S.A.
DOI: 10.3389/fpubh.2023.1287678

Untangling introductions and persistence in COVID-19 resurgence in Europe

Auteurs: Philippe Lemey, Nick Ruktanonchai, Samuel L. Hong, Vittoria Colizza, Chiara Poletto, Frederik Van den Broeck, Mandev S. Gill, Xiang Ji, Anthony Levasseur, Bas B. Oude Munnink, Marion Koopmans, Adam Sadilek, Shengjie Lai, Andrew J. Tatem, Guy Baele, Marc A. Suchard, Simon Dellicour
Publié dans: Nature, 2021, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-021-03754-2

Drivers and epidemiological patterns of West Nile virus in Serbia

Auteurs: Giovanni Marini, Mitra B. Drakulovic, Verica Jovanovic, Francesca Dagostin, Willy Wint, Valentina Tagliapietra, Milena Vasic, Annapaola Rizzoli
Publié dans: Frontiers in Public Health, Numéro 12, 2024, ISSN 2296-2565
Éditeur: Frontiers Media S.A
DOI: 10.3389/fpubh.2024.1429583

One Health and sex and gender-related perspective in the ecosystem: Interactions among drivers involved in the risk of leptospirosis in Europe. A scoping review

Auteurs: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
Publié dans: One Health, Numéro Vol 19, 100841, 2024, ISSN 2352-7714
Éditeur: Elsevier B.V.
DOI: 10.1016/j.onehlt.2024.100841

Gender gap reduction and the one health benefits

Auteurs: Claudia Cataldo, Roberta Masella, Luca Busani
Publié dans: One Health, Numéro Volume 16, 2023, 100496, 2023, ISSN 2352-7714
Éditeur: Eslevier
DOI: 10.1016/j.onehlt.2023.100496

Retrospective analysis of the Italian exit strategy from COVID-19 lockdown

Auteurs: Valentina Marziano, Giorgio Guzzetta, Bruna Maria Rondinone, Fabio Boccuni, Flavia Riccardo, Antonino Bella, Piero Poletti, Filippo Trentini, Patrizio Pezzotti, Silvio Brusaferro, Giovanni Rezza, Sergio Iavicoli, Marco Ajelli, Stefano Merler
Publié dans: Proceedings of the National Academy of Sciences, Numéro 118/4, 2021, Page(s) e2019617118, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2019617118

Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020

Auteurs: Brecht Ingelbeen, Laurène Peckeu, Marie Laga, Ilona Hendrix, Inge Neven, Marianne AB van der Sande, Esther van Kleef
Publié dans: Eurosurveillance, Numéro 26/7, 2021, Page(s) pii=2100065, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2021.26.7.2100065

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Auteurs: Simon Dellicour, Sebastian Lequime, Bram Vrancken, Mandev S. Gill, Paul Bastide, Karthik Gangavarapu, Nathaniel L. Matteson, Yi Tan, Louis du Plessis, Alexander A. Fisher, Martha I. Nelson, Marius Gilbert, Marc A. Suchard, Kristian G. Andersen, Nathan D. Grubaugh, Oliver G. Pybus, Philippe Lemey
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-19122-z

Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates

Auteurs: Rhys P.D. Inward; Felix Jackson; Abhishek Dasgupta; Graham Lee; Anya Lindström Battle; Kris V. Parag; Moritz U.G. Kraemer
Publié dans: Epidemics, Numéro vol 41, 2022, Page(s) 100627, ISSN 1755-4365
Éditeur: Elsevier BV
DOI: 10.1016/j.epidem.2022.100627

Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021

Auteurs: Suvanto, Maija T and Uusitalo, Ruut and Otte im Kampe, Eveline and Vuorinen, Tytti and Kurkela, Satu and Vapalahti, Olli and Dub, Timothée and Huhtamo, Eili and Korhonen, Essi M
Publié dans: Eurosurveillance, Numéro 27, 2200580 (2022), 2022, ISSN 1560-7917
Éditeur: ECDC
DOI: 10.2807/1560-7917.es.2022.27.31.2200580

The emergence of SARS-CoV-2 in Europe and North America.

Auteurs: Martha I. Nelson; Brendan B. Larsen; Michael Worobey; Jonathan Pekar; Verity Hill; Philippe Lemey; Marc A. Suchard; Jeffrey B. Joy; Joel O. Wertheim; Andrew Rambaut
Publié dans: Science, Numéro Vol 370, Numéro 6516, 2020, Page(s) 564-570, ISSN 0000-0000
Éditeur: American Association for the Advancement of Science
DOI: 10.1101/2020.05.21.109322

Expected impact of exit strategies after the second lockdown-France, Nov 2020.

Auteurs: Giulia Pullano, Laura Di Domenico, Chiara E Sabbatini, Vittoria Colizza
Publié dans: Epicx-lab, report 23, Numéro 23, 2020
Éditeur: INSERM

Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data

Auteurs: Manica, Mattia; Litvinova, Maria; De Bellis, Alfredo; Guzzetta, Giorgio; Mancuso, Pamela; Vicentini, Massimo; Venturelli, Francesco; Bisaccia, Eufemia; Bento, Ana I.; Poletti, Piero; Marziano, Valentina; Zardini, Agnese; d'Andrea, Valeria; Trentini, Filippo; Bella, Antonino; Riccardo, Flavia; Pezzotti, Patrizio; Ajelli, Marco; Rossi, Paolo Giorgi; Merler, Stefano; Group, the Reggio Emilia COVID-19
Publié dans: arXiv, Numéro 2203.07063, 2022, ISSN 2331-8422
Éditeur: Cornell University
DOI: 10.48550/arxiv.2203.07063

Expected impact of school closure and telework to mitigate COVID-19 epidemic in France

Auteurs: Di Domenico L., Pullano G., Sabbatini C.E., Boëlle P-Y., Colizza V.
Publié dans: Epicx-lab, report 8, Numéro 8, 2020
Éditeur: INSERM

Early assessment of the Omicron variant’s presence and growth rate in regions of France

Auteurs: Mattia Mazzoli, Laura Di Domenico, EMERGEN Consortium, Vittoria Colizza
Publié dans: Epicx-lab, report 35, Numéro 35, 2021
Éditeur: Inserm

The spatial distribution of Crimean-Congo haemorrhagic fever in Europe and neighbouring areas

Auteurs: Jane Messina, William Wint
Publié dans: ECDC technical report, 2023, ISBN 978-92-9498-676-4
Éditeur: European Centre for Disease Prevention and Control
DOI: 10.2900/222576

Epidemic scenarios of Delta variant in France in the summer 2021

Auteurs: Laura Di Domenico, Vittoria Colizza
Publié dans: Epicx-lab, report 31, Numéro 31, 2021
Éditeur: INSERM

Telework and other measures reducing the presence at work to slow downCOVID-19pdmin France (Sept 2020)

Auteurs: Giulia Pullano, Laura Di Domenico, Vittoria Colizza
Publié dans: Epicx-lab, report 16, Numéro 16, 2020
Éditeur: INSERM

Mobility during the first week of the second lockdown in France.

Auteurs: Eugenio Valdano, Jonggul Lee, Stefania Rubrichi, Vittoria Colizza
Publié dans: Epicx-lab, report 22, Numéro 22, 2020
Éditeur: INSERM

Impact of contact data resolution on the evaluation of interventions in mathematical models of infectious diseases

Auteurs: Diego Andrés Contreras; Elisabetta Colosi; Giulia Bassignana; Vittoria Colizza; Alain Barrat
Publié dans: Journal of the Royal Society Interface, Numéro 20545703, 2022, ISSN 2054-5703
Éditeur: Royal Society open science
DOI: 10.1098/rsif.2022.0164

Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis

Auteurs: Giorgio Guzzetta, Francesco Vairo, Alessia Mammone, Simone Lanini, Piero Poletti, Mattia Manica, Roberto Rosa, Beniamino Caputo, Angelo Solimini, Alessandra Della Torre, Paola Scognamiglio, Alimuddin Zumla, Giuseppe Ippolito, Stefano Merler
Publié dans: BMC Medicine, Numéro 18/1, 2020, ISSN 1741-7015
Éditeur: BioMed Central
DOI: 10.1186/s12916-020-01674-y

Estimating rodent population abundance using early climatic predictors

Auteurs: Giovanni Marini, Daniele Arnoldi, Annapaola Rizzoli, Valentina Tagliepietra
Publié dans: European Journal of Wildlife Research, Numéro 69, 36, 2023, ISSN 1612-4642
Éditeur: Springer Verlag
DOI: 10.1007/s10344-023-01666-2

GeoXTag: Relative Spatial Information Extraction and Tagging

Auteurs: Mehtab Alam SYED, Elena ARSEVSKA, Mathieu ROCHE, Maguelonne TEISSEIRE
Publié dans: AGILE: GIScience Series, Numéro 27008150, 2022, ISSN 2700-8150
Éditeur: AGILE: GIScience Series
DOI: 10.5194/agile-giss-3-16-2022

Feature Selection for Sentiment Classification of COVID-19 Tweets: H-TFIDF Featuring BERT

Auteurs: Syed, M.; Arsevska, E.; Roche, M. and Teisseire, M.
Publié dans: Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies - HEALTHINF, 2022, Page(s) 648-656, ISSN 2184-4305
Éditeur: Setúbal: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0010887800003123

How Textual Datasets Enhance the PADI-Web Tool?

Auteurs: Mathieu Roche, Elena Arsevska, Sarah Valentin, Sylvain Falala, Julien Rabatel and Renaud Lancelot
Publié dans: Proceedings of the 18th International Conference on Web Information Systems and Technologies, Numéro Volume 1, 2022, Page(s) 327-331, ISBN 978-989-758-613-2
Éditeur: Science and Technology Publications
DOI: 10.5220/0011590400003318

Quantifying Valence and Arousal in Text with Multilingual Pre-trained Transformers

Auteurs: Mendes, Gonçalo Azevedo; Martins, Bruno
Publié dans: arXIV, Numéro 2302.14021, 2023, ISSN 2331-8422
Éditeur: Cornell University
DOI: 10.48550/arxiv.2302.14021

Enriching Epidemiological Thematic Features For Disease Surveillance Corpora Classification

Auteurs: Edmond Menya, Mathieu Roche, Roberto Interdonato, Dickson Owuor
Publié dans: Proceedings of the Thirteenth Language Resources and Evaluation Conference, Marseille, France, Numéro 2022.lrec-1.399, 2022, Page(s) 3741–3750, ISBN 979-10-95546-72-6
Éditeur: European Language Resources Association

Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases

Auteurs: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publié dans: Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing, 2020, Page(s) 33-36, ISBN 2-9517408-6-7
Éditeur: European Language Resources Association

A Data-Driven Score Model to Assess Online News Articles in Event-Based Surveillance System

Auteurs: Alam, S.M., Arsevska, E., Roche, M., Teisseire, M.
Publié dans: Computer and Information Science, Numéro CCIS,volume 1577, 2022, Page(s) 264–280, ISBN 978-3-031-04446-5
Éditeur: Springer
DOI: 10.1007/978-3-031-04447-2_18

A metadata approach to classify domain-specific documents for Event-based Surveillance Systems

Auteurs: M. A. Syed, E. Arsevska, M. Roche and M. Teissere
Publié dans: 2023 International Conference on Communication, Computing and Digital Systems (C-CODE), 2023, Page(s) 2023, pp. 1-5, ISBN 979-8-3503-3239-1
Éditeur: IEEE
DOI: 10.1109/c-code58145.2023.10139883

PADI-web: an event-based surveillance system for detecting, classifying and processing online news.

Auteurs: Sarah Valentin, Elena Arsevska, Alize Mercier, Sylvain Falala, Julien Rabatel, Renaud Lancelot, Mathieu Roche.
Publié dans: Human language technology. Challenges for computer science and linguistics., Numéro Language and Technology Conference. 8, Poznan, Pologne, 17 Novembre 2017/19 Novembre 2017, 2020, Page(s) 87-101, ISBN 978-3-030-66527-2
Éditeur: Springer
DOI: 10.1007/978-3-030-66527-2_7

Unsupervised Key-Phrase Extraction from Long Texts with Multilingual Sentence Transformers

Auteurs: Dias, H., Guimarães, A., Martins, B., Roche, M
Publié dans: Discovery Science 26th International Conference, DS 2023, Porto, Portugal, October 9–11, 2023, Numéro vol 14276, 2023, Page(s) 141-145, ISBN 978-3-031-45275-8
Éditeur: Springer, Cham
DOI: 10.1007/978-3-031-45275-8_10

A co-training approach for spatial data disaggregation

Auteurs: João Monteiro, Bruno Martins, Miguel Costa, João M. Pires
Publié dans: SIGSPATIAL '22: Proceedings of the 30th International Conference on Advances in Geographic Information SystemsNovember 2022 Article No.: 91Pages 1–10https://doi.org/10.1145/3557915.3561475, Numéro November 2022 Article No.: 91, 2022, Page(s) 1-10, ISSN 1552-5996
Éditeur: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries
DOI: 10.1145/3557915.3561475

Explainable epidemiological thematic features for event based disease surveillance

Auteurs: Edmond Menya, Roberto Interdonato, Dickson Owuor, Mathieu Roche
Publié dans: Expert Systems with Applications, Numéro Vol 250, 2024, Page(s) 123894, ISSN 0957-4174
Éditeur: Elsevier
DOI: 10.1016/j.eswa.2024.123894

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