MOnitoring Outbreak events for Disease surveillance in a data science context

Resultado final

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

MOOD System Architecture

A report on the system architecture of the MOOD platform It will describe the conceptual design of all the platforms components and its subcomponents

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.

Publicaciones

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

Autores: Célia Bernard, Philippe Holzmuller, Madiou Thierno Bah, Matthieu Bastien, Benoit Combes, Ferran Jori, Vladimir Grosbois and Laurence Vial
Publicado en: Frontiers in Veterinary Science, Edición 22971769, 2022, ISSN 2297-1769
Editor: 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

Autores: 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
Publicado en: The Lancet Infectious Diseases, Edición 20/7, 2020, Página(s) 793-802, ISSN 1473-3099
Editor: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(20)30230-9

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

Autores: Simon Dellicour, Mandev S Gill, Nuno R Faria, Andrew Rambaut, Oliver G Pybus, Marc A Suchard, Philippe Lemey
Publicado en: Molecular Biology and Evolution, Edición Volume 38, Edición 8, August 2021, 2021, Página(s) 3486–3493, ISSN 1537-1719
Editor: Oxford University Press
DOI: 10.1093/molbev/msab031

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

Autores: 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
Publicado en: BMC Public Health, Edición 24, 973, 2024, ISSN 1471-2458
Editor: 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

Autores: 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
Publicado en: Eurosurveillance, Edición Volume 28, Edición 42, 2023, ISSN 1560-7917
Editor: 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

Autores: 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
Publicado en: Emerging Infectious Diseases, Edición 29(2), 2023, Página(s) 351-359, ISSN 1080-6059
Editor: Centers for Disease Control and Prevention
DOI: 10.3201/eid2902.220765

An Evaluation Framework for Comparing Epidemic Intelligence Systems

Autores: Nejat Arinik; Roberto Interdonato; Mathieu Roche; Maguelonne Teisseire
Publicado en: IEEE Access, Edición 35, 2023, Página(s) 11 : 31880- 31901, ISSN 2169-3536
Editor: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2023.3262462

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

Autores: 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
Publicado en: Swiss Medical Weekly, Edición 150, 2020, Página(s) w20277, ISSN 1424-3997
Editor: EMH Swiss Medical Publishers Ltd.
DOI: 10.4414/smw.2020.20277

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

Autores: 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
Publicado en: Nature Communications, Edición 14, 6440, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-42185-7

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

Autores: Giovanni Marini, Andrea Pugliese, William Wint, Neil S. Alexander, Annapaola Rizzoli, Roberto Rosà
Publicado en: One Health, Edición Volume 15, 2022, Página(s) 100462, ISSN 2352-7714
Editor: Elsevier B.V.
DOI: 10.1016/j.onehlt.2022.100462

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

Autores: Mattia Mazzoli, PhD, Eugenio Valdano, PhD, Vittoria Colizza
Publicado en: Journal of Travel Medicine, Edición Volume 28, Edición 7, 2021, Página(s) aab129, ISSN 1708-8305
Editor: 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

Autores: 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
Publicado en: Parasites Vectors, Edición 17, 29, 2024, ISSN 1756-3305
Editor: BioMed Central
DOI: 10.1186/s13071-023-06094-4

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

Autores: Giulia Pullano, Eugenio Valdano, Nicola Scarpa, Stefania Rubrichi, Vittoria Colizza
Publicado en: The Lancet Digital Health, Edición 2/12, 2020, Página(s) e638-e649, ISSN 2589-7500
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 14(6), 2022, Página(s) 1315, ISSN 1999-4915
Editor: 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

Autores: Ranya Mulchandani, Cheng Zhao, Katie Tiseo, João Pires, Thomas Van Boeckel
Publicado en: Emerging Infectious Diseases, Edición Volume 30, Number 1, 2024, ISSN 1080-6059
Editor: Center for Disease Control and Prevention
DOI: 10.3201/eid3001.221450

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

Autores: Francesco Bonacina, Pierre-Yves Boëlle, Vittoria Colizza, Olivier Lopez, Maud Thomas, Chiara Poletto
Publicado en: International Journal of Infectious Diseases, Edición January 03, 2023, 2023, ISSN 1878-3511
Editor: 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

Autores: Sarah Valentina, Elena Arsevska, Julien Rabatel, Sylvain Falala, Alizé Mercier, Renaud Lancelot, Mathieu Roche
Publicado en: One Health, Edición Vol 13, Dec 2021, 2021, Página(s) 100357, ISSN 2352-7714
Editor: Elsevier
DOI: 10.1016/j.onehlt.2021.100357

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

Autores: 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
Publicado en: Cell, Edición Volume 184, Edición 19, 2021, 2021, Página(s) 4939-4952.e15, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2021.07.030

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

Autores: Benjamin Faucher, Chiara E. Sabbatini, Peter Czuppon, Moritz U. G. Kraemer, Philippe Lemey, Vittoria Colizza, François Blanquart, Pierre-Yves Boëlle & Chiara Poletto
Publicado en: Nature communications, Edición 15, 2152, 2024, ISSN 2041-1723
Editor: 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

Autores: Christine Giesen, Zaida Herrador, Beatriz Fernandez-Martinez, Jordi Figuerola, Laura Gangoso, Ana Vazquez, Diana Gómez-Barroso
Publicado en: One Health, Edición Volume 16, 2023, Página(s) 100478, ISSN 2352-7714
Editor: Elsevier BV
DOI: 10.1016/j.onehlt.2022.100478

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

Autores: 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
Publicado en: Science, Edición 372/6544, 2021, Página(s) 815-821, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abh2644

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

Autores: Mehtab Alam Syed, Elena Arsevska, Mathieu Roche & Maguelonne Teisseire
Publicado en: Cartography and Geographic Information Science, 2023, ISSN 1545-0465
Editor: TAYLOR & FRANCIS INC
DOI: 10.1080/15230406.2023.2264753

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

Autores: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
Publicado en: Nature Communications, Edición 12/1, 2021, Página(s) 1073, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-21249-6

An annotated dataset for event-based surveillance of antimicrobial resistance

Autores: 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
Publicado en: Data in Brief, Edición Volume 46, 2023, Página(s) 108870, ISSN 2352-3409
Editor: Elsevier BV
DOI: 10.1016/j.dib.2022.108870

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

Autores: Sabrina L Li, Jane P Messina, Oliver G Pybus, Moritz U G Kraemer, Lauren Gardner
Publicado en: Transactions of The Royal Society of Tropical Medicine and Hygiene, Edición trab009, 2021, ISSN 0035-9203
Editor: 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

Autores: Laura Di Domenico, Chiara E Sabbatini, Giulia Pullano, Daniel Lévy-Bruhl, Vittoria Colizza
Publicado en: Eurosurveillance, Edición 26/15, 2021, ISSN 1560-7917
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 15, Article number: 1196, 2024, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Clinical Infectious Diseases, Edición Volume 75, Edición 1, 1 July 2022, 2022, Página(s) Pages e234–e240, ISSN 1058-4838
Editor: University of Chicago Press
DOI: 10.1093/cid/ciab836

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

Autores: 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
Publicado en: PNAS, Edición 120 (16) e2218012120, 2023, ISSN 1091-6490
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2218012120

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

Autores: Katie Tiseo, Laura Huber, Marius Gilbert, Timothy P. Robinson, Thomas P. Van Boeckel
Publicado en: Antibiotics, Edición 9/12, 2020, Página(s) 918, ISSN 2079-6382
Editor: MDPI
DOI: 10.3390/antibiotics9120918

The impact of spatial connectivity on NPIs effectiveness

Autores: Chiara E. Sabbatini, Giulia Pullano, Laura Di Domenico, Stefania Rubrichi, Shweta Bansal, Vittoria Colizza
Publicado en: BMC Infectious Diseases, Edición 24, Article number: 21, 2024, ISSN 1471-2334
Editor: 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

Autores: 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
Publicado en: One Health, Edición Volume 18, June 2024, 100669, 2024, ISSN 2352-7714
Editor: 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

Autores: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
Publicado en: One Health, Edición Volume 16, 2023, ISSN 2352-7714
Editor: 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.

Autores: Iris Claudel, Ronan Brouazin, Renaud Lancelot, Louis-Clément Gouagna, Marlène Dupraz, Thierry Baldet & Jérémy Bouyer
Publicado en: Nature Sciences Report, Edición 20452322, 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-022-24191-9

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

Autores: Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A Suchard, Guy Baele, and Philippe Lemey
Publicado en: Virus Evolution, Edición 8(2), 2022, Página(s) veac088, ISSN 2057-1577
Editor: Oxford: Oxford University Press
DOI: 10.1093/ve/veac088

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

Autores: 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
Publicado en: Influenza Other Respi Viruses, Edición 2023;17:e13181, 2023, ISSN 1750-2659
Editor: Oxford Blackwell
DOI: 10.1111/irv.13181

SNEToolkit: Spatial named entities disambiguation toolkit

Autores: Rodrique Kafando; Rémy Decoupes; Mathieu Roche; Maguelonne Teisseire
Publicado en: SoftwareX, Edición 61, 2023, Página(s) Volume 23, 101480, July 2023, ISSN 2352-7110
Editor: Elsevier
DOI: 10.1016/j.softx.2023.101480

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

Autores: 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
Publicado en: Science, Edición 369/6510, 2020, Página(s) 1465-1470, ISSN 0036-8075
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-24832-z

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

Autores: Elisabetta Colosi, Giulia Bassignana, Diego Andrés Contreras, Canelle Poirier, Pierre-Yves Boëlle, Simon Cauchemez, Yazdan Yazdanpanah, Bruno Lina, Arnaud Fontanet, Alain Barrat, Vittoria Colizza
Publicado en: The Lancet Infectious Diseases, Edición Volume 22, Edición 7, 2022, Página(s) 977-989, ISSN 1473-3099
Editor: 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

Autores: 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
Publicado en: BMC Public Health, Edición 23, Article number: 1488, 2023, ISSN 1471-2458
Editor: BioMed Central
DOI: 10.1186/s12889-023-16396-y

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

Autores: 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
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27939-5

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

Autores: 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
Publicado en: Viruses, Edición 15(1), 35, 2023, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15010035

Epidemiology of West Nile virus in Africa: An underestimated threat

Autores: 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
Publicado en: PLos Negl Trop Dis, Edición 16(1), 2022, Página(s) e0010075, ISSN 1935-2735
Editor: 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

Autores: 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;
Publicado en: eLife, Edición 11:e71703, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.71703

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

Autores: Giovanni Marini, Valentina Tagliapietra, Fabiana Cristofolini, Antonella Cristofori, Francesca Dagostin, Maria Grazia Zuccali, Silvia Molinaro, Elena Gottardini & Annapaola Rizzoli
Publicado en: Nature Scientific Reports, Edición 13, 8262 (2023), 2023, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: The Lancet Regional Health - Europe, Edición Volume 28, 2023, ISSN 0140-6736
Editor: 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

Autores: 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
Publicado en: Nature aging, Edición 3, 2023, Página(s) 722–733, ISSN 2662-8465
Editor: 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

Autores: 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
Publicado en: International Journal of Health Geographics, Edición 20, Article number: 29 (2021), 2021, ISSN 1476-072X
Editor: BioMed Central
DOI: 10.1186/s12942-021-00281-1

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

Autores: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
Publicado en: BMC Medicine, Edición 18/1, 2020, ISSN 1741-7015
Editor: BioMed Central
DOI: 10.1186/s12916-020-01698-4

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

Autores: Ranya Mulchandani,Yu Wang,Marius Gilbert,Thomas P. Van Boeckel
Publicado en: PLOS Global Public Health, Edición 3(2): e0001305, 2023, ISSN 2767-3375
Editor: 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.

Autores: 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,
Publicado en: Scientific Reports, Edición 20452322, 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-022-11479-z

ITEXT-BIO: Intelligent Term EXTraction for BIOmedical analysis

Autores: Rodrique Kafando, Rémy Decoupes, Sarah Valentin, Lucile Sautot, Maguelonne Teisseire, Mathieu Roche
Publicado en: Health Information Science and Systems, Edición 9/1, 2021, ISSN 2047-2501
Editor: Springer
DOI: 10.1007/s13755-021-00156-6

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

Autores: 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
Publicado en: Nature, Edición 585/7825, 2020, Página(s) 410-413, ISSN 0028-0836
Editor: 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

Autores: 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
Publicado en: eLife, Edición 12:e82069, 2023, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.82069

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

Autores: 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
Publicado en: Eurosurveillance, Edición Volume 27, Edición 5, 2022, ISSN 1560-7917
Editor: 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

Autores: 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
Publicado en: Eurosurveillance, Edición vol 27, Edición 45, 10/Nov/2022, 2022, Página(s) pii=2200125, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2022.27.45.2200125

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

Autores: 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
Publicado en: Emerging Infectious Diseases, Edición 17(1), 2021, Página(s) 267-270, ISSN 1080-6059
Editor: CDC
DOI: 10.3201/eid2701.202114

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

Autores: 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
Publicado en: Science, Edición 369/6508, 2020, Página(s) 1255-1260, ISSN 0036-8075
Editor: 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

Autores: 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
Publicado en: Journal of Virology, Edición Vol. 97, No. 1, 2023, ISSN 1098-5514
Editor: American Society for Microbiology
DOI: 10.1128/jvi.01091-22

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

Autores: 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
Publicado en: Nature, Edición 590/7844, 2021, Página(s) 134-139, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-020-03095-6

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

Autores: 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
Publicado en: Communications Medicine, Edición 2730664X, 2021, ISSN 2730-664X
Editor: Nature Portfolio
DOI: 10.1038/s43856-021-00057-5

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

Autores: 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
Publicado en: PLOS Neglected Tropical Diseases, 2023, ISSN 1935-2727
Editor: Public Library of Science
DOI: 10.1371/journal.pntd.0011610

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

Autores: Jesús A. Moreno López, Beatriz Arregui García, Piotr Bentkowski, Livio Bioglio, Francesco Pinotti, Pierre-Yves Boëlle, Alain Barrat, Vittoria Colizza, Chiara Poletto
Publicado en: Science Advances, Edición 7/15, 2021, Página(s) eabd8750, ISSN 2375-2548
Editor: AAAS
DOI: 10.1126/sciadv.abd8750

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

Autores: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publicado en: Artificial Intelligence in Agriculture, Edición 5, 2021, Página(s) 163-174, ISSN 2589-7217
Editor: Elsevier
DOI: 10.1016/j.aiia.2021.07.003

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

Autores: Eugenio Valdano, Davide Colombi, Chiara Poletto, Vittoria Colizza
Publicado en: Nature communications, Edición 14, 8472, 2023, ISSN 2041-1723
Editor: 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

Autores: Ronan Brouazin, Iris Claudel, Renaud Lancelot, Guillaume Dupuy, Louis‑Clément Gouagna, Marlène Dupraz, Thierry Baldet & Jérémy Bouyer
Publicado en: Nature Scientific Reports, Edición 20452322, 2022, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, Página(s) 5110, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Eurosurveillance, Edición 25/12, 2020, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2020.25.12.2000293

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

Autores: Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Vittoria Colizza
Publicado en: Anaesthesia Critical Care & Pain Medicine, Edición Volume 41, Edición 2, 2022, ISSN 2352-5568
Editor: 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

Autores: 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
Publicado en: PLOS Neglected Tropical Diseases, Edición 16(1), 2022, Página(s) e0010019, ISSN 1935-2735
Editor: PLOS
DOI: 10.1371/journal.pntd.0010019

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

Autores: Elisa Fesce , Giovanni Marini, Roberto Rosà, Davide Lelli, Monica Pierangela Cerioli, Mario Chiari, Marco Farioli, Nicola Ferrari
Publicado en: Plos Neglected Tropical Diseases, Edición 17(5): e0010252, 2023, ISSN 1935-2735
Editor: 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

Autores: Laëtitia Viau, Arnaud Sallaberry, Nancy Rodriguez, Jean-François Girres & Pascal Poncelet
Publicado en: International Journal of Geographical Information Science, Edición Volume 37, Edición 6, 2023, Página(s) 1288-1314, ISSN 1365-8824
Editor: 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

Autores: Oscar A. MacLean, Spyros Lytras, Steven Weaver, Joshua B. Singer, Maciej F. Boni, Philippe Lemey, Sergei L. Kosakovsky Pond, David L. Robertson
Publicado en: PLOS Biology, Edición 19/3, 2021, Página(s) e3001115, ISSN 1545-7885
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 13, 5596, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-33112-3

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

Autores: 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.
Publicado en: Nature, 603 (7902), Edición 5, 2022, Página(s) pages 679–686, ISSN 1476-4687
Editor: Nature
DOI: 10.3929/ethz-b-000525678

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

Autores: 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;
Publicado en: Nature, Edición 602, 2022, Página(s) 671–675, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/d41586-021-03827-2

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

Autores: 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
Publicado en: International Journal of Infectious Diseases, Edición Volume 116, Supplement, 2022, Página(s) 1201-9712, ISSN 1201-9712
Editor: Elsevier BV
DOI: 10.1016/j.ijid.2021.12.291

Accommodating sampling location uncertainty in continuous phylogeography

Autores: Simon Dellicour, Philippe Lemey, Marc A Suchard, Marius Gilbert, Guy Baele
Publicado en: Virus Evolution, Edición Volume 8, Edición 1, 2022, Página(s) veac041, ISSN 2057-1577
Editor: Oxford University press
DOI: 10.1093/ve/veac041

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

Autores: 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
Publicado en: Science, Edición 371/6530, 2021, Página(s) 708-712, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abf2946

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

Autores: 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
Publicado en: Science, Edición 381, Edición 6655, 2023, Página(s) 336-343, ISSN 1095-9203
Editor: 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

Autores: Eugenio Valdano, Jonggul Lee, Shweta Bansal, Stefania Rubrichi, Vittoria Colizza
Publicado en: Journal of Travel Medicine, Edición 28/4, 2021, ISSN 1195-1982
Editor: 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?

Autores: Rémy Decoupes, Rodrique Kafando, Mathieu Roche, Maguelonne Teisseire
Publicado en: AGILE: GIScience Series, Edición 2, 2021, Página(s) 1-8, ISSN 2700-8150
Editor: Copernicus publications
DOI: 10.5194/agile-giss-2-2-2021

Assessing spread risk of COVID-19 in early 2020

Autores: Shengjie Lai; Isaac Bogoch; Nick Ruktanonchai; Alexander Watts; Xin Lu; Weizhong Yang; Hongjie Yu; Kamran Khan; Andrew J Tatem
Publicado en: Data Science and Management, Edición Volume 5, Edición 4, 2022, Página(s) 212-218, ISSN 2666-7649
Editor: Elsevier
DOI: 10.1016/j.dsm.2022.08.004

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

Autores: Rémy Decoupes; Mathieu Roche; Maguelonne Teisseire
Publicado en: "Intelligent Data Analysis, 2023, pp.1-25. ⟨10.3233/IDA-230040⟩", Edición 25, 2023, Página(s) 1-25, ISSN 1088-467X
Editor: 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

Autores: 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
Publicado en: JAMA Network Open, Edición 4/3, 2021, Página(s) e211085, ISSN 2574-3805
Editor: American Medical Association
DOI: 10.1001/jamanetworkopen.2021.1085

Elaboration of a new framework for fine-grained epidemiological annotation

Autores: Sarah Valentin; Elena Arsevska; Aline Vilain; Valérie De Waele; Renaud Lancelot; Mathieu Roche
Publicado en: Scientific Data, Edición 1, 2022, ISSN 2052-4463
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 14(10), 2022, Página(s) 2301, ISSN 1999-4915
Editor: 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

Autores: Francesco Menegale, Mattia Manica, Agnese Zardini, Giorgio Guzzetta, Valentina Marziano, Valeria d'Andrea, Filippo Trentini, Marco Ajelli, Piero Poletti, Stefano Merler
Publicado en: JAMA Network Open, Edición 6(5):e2310650, 2023, ISSN 2574-3805
Editor: 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

Autores: Charlotte C Hammer, Timothee Dub, Oskari Luomala, Jussi Sane
Publicado en: Eurosurveillance, Edición 2022;27(4), 2022, Página(s) pii=2100098, ISSN 1560-7917
Editor: 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

Autores: 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
Publicado en: Annali dell'Istituto Superiore di Sanità, Edición Vol. 58, No. 1, 2022, Página(s) 25-33, ISSN 2384-8553
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 19994915, 2022, ISSN 1999-4915
Editor: 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

Autores: Gonçalves, Bronner P.; Gómez Junyent, Joan; Olliaro Piero L.; ISARIC Clinical Characterisation Group
Publicado en: eLife, Edición 11:e80556, 2022, ISSN 2050-084X
Editor: 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

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

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

Autores: Giulia Pullano, Francesco Pinotti, Eugenio Valdano, Pierre-Yves Boëlle, Chiara Poletto, Vittoria Colizza
Publicado en: Eurosurveillance, Edición 25/4, 2020, ISSN 1560-7917
Editor: 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

Autores: 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
Publicado en: The Lancet, Edición 395/10227, 2020, Página(s) 871-877, ISSN 0140-6736
Editor: 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

Autores: 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
Publicado en: Science, 2020, Página(s) eaba9757, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aba9757

Labeled entities from social media data related to avian influenza disease

Autores: Camille Schaeffer; Roberto Interdonato; Renaud Lancelot; Mathieu Roche; Maguelonne Teisseire
Publicado en: Data in Brief, Edición 23523409, 2022, ISSN 2352-3409
Editor: 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

Autores: 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
Publicado en: The Lancet Global Health, Edición Volume 11, ISSUE 8, 2023, Página(s) 1301-1307, ISSN 2214-109X
Editor: 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

Autores: Dellicour S, Hong SL, Hill V, Dimartino D, Marier C, Zappile P, Harkins GW, Lemey P, Baele G, Duerr R, Heguy A
Publicado en: PLoS Pathogens, Edición 19(4): e1011348, 2023, ISSN 1553-7366
Editor: 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

Autores: Giovanni Marini, Mattia Manica, Daniele Arnoldi, Enrico Inama, Roberto Rosà, Annapaola Rizzoli
Publicado en: Insects, Edición 11/11, 2020, Página(s) 808, ISSN 2075-4450
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/insects11110808

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

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

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

Autores: Mathieu Roche
Publicado en: Data in Brief, Edición 33, 2020, Página(s) 106356, ISSN 2352-3409
Editor: Elsevier BV
DOI: 10.1016/j.dib.2020.106356

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

Autores: 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
Publicado en: Science, Edición 373/6557, 2021, Página(s) 889-895, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abj0113

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

Autores: 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
Publicado en: Epidemics, Edición Vol 37, 2021, Página(s) 100528, ISSN 1755-4365
Editor: 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

Autores: 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
Publicado en: American Journal of Epidemiology, 2021, ISSN 0002-9262
Editor: Oxford University Press
DOI: 10.1093/aje/kwab252

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

Autores: Alberto Mateo-Urdiales, Massimo Fabiani, Aldo Rosano, Maria Fenicia Vescio, Martina Del Manso, Antonino Bella, Flavia Riccardo, Patrizio Pezzotti, Enrique Regidor, Xanthi Andrianou
Publicado en: Health & Place, Edición 71, 2021, Página(s) 102642, ISSN 1353-8292
Editor: Elsevier BV
DOI: 10.1016/j.healthplace.2021.102642

Crowding and the shape of COVID-19 epidemics

Autores: 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
Publicado en: Nature Medicine, Edición 26/12, 2020, Página(s) 1829-1834, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/s41591-020-1104-0

VectAbundance: a spatio-temporal database of Aedes mosquitoes observations

Autores: 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
Publicado en: Scientific Data, Edición 11, 636, 2024, ISSN 2052-4463
Editor: Springer Nature
DOI: 10.1038/s41597-024-03482-y

Monitoring key epidemiological parameters of SARS-CoV-2 transmission

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

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

Autores: Oidtman, R.J., Omodei, E., Kraemer, M.U.G. et al.
Publicado en: Nature Communications, Edición 20411723, 2021, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 13, 3106, 2022, ISSN 2041-1723
Editor: 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

Autores: Francesco Pinotti, Laura Di Domenico, Ernesto Ortega, Marco Mancastroppa, Giulia Pullano, Eugenio Valdano, Pierre-Yves Boëlle, Chiara Poletto, Vittoria Colizza
Publicado en: PLOS Medicine, Edición 17/7, 2020, Página(s) e1003193, ISSN 1549-1676
Editor: 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

Autores: Sarah Valentin, Alizé Mercier, Renaud Lancelot, Mathieu Roche, Elena Arsevska
Publicado en: Transboundary and Emerging Diseases, Edición 2020 Aug 2 : 10.1111/tbed.13738, 2020, ISSN 1865-1674
Editor: 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

Autores: Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Bruno Lina, Philippe Vanhems, Julia Bielicki, Vittoria Colizza
Publicado en: Eurosurveillance, Edición 28(5), 2022, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2023.28.5.2200192

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

Autores: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publicado en: Information Processing in Agriculture, Edición 22143173, 2022, ISSN 2214-3173
Editor: Elsevier B.V.
DOI: 10.1016/j.inpa.2022.03.004

Spring temperature shapes West Nile virus transmission in Europe

Autores: Giovanni Marini, Mattia Manica, Luca Delucchi, Andrea Pugliese, Roberto Rosà
Publicado en: Acta Tropica, Edición 215, 2021, Página(s) 105796, ISSN 0001-706X
Editor: Elsevier BV
DOI: 10.1016/j.actatropica.2020.105796

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

Autores: 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
Publicado en: Cell, Edición Volume 184, Edición 20, 30 September 2021, 2021, Página(s) Pages 5189-5200.e7, ISSN 1097-4172
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 14(6), 1302, 2022, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061302

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

Autores: Benjamin Faucher; Rania Assab; Jonathan Roux; Daniel Levy-Bruhl; Cécile Tran Kiem; Simon Cauchemez; Laura Zanetti; Vittoria Colizza; Pierre-Yves Boëlle; Chiara Poletto
Publicado en: Nature Communications, Edición 20411723, 2022, ISSN 2041-1723
Editor: 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

Autores: Jane Paula Messina and G. R. William Wint
Publicado en: Insects, Edición 14(9), 2023, Página(s) 771, ISSN 2075-4450
Editor: 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)

Autores: Solveig Jore, Hildegunn Viljugrein, Marika Hjertqvist, Timothée Dub, Henna Mäkelä
Publicado en: INFECTION ECOLOGY & EPIDEMIOLOGY, Edición 2023, VOL. 13, 2281055, 2023, ISSN 2000-8686
Editor: 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

Autores: 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
Publicado en: Clinical Infectious Diseases, Edición Volume 74, Edición 5, 1 March 2022, 2022, Página(s) Pages 893-896, ISSN 1058-4838
Editor: University of Chicago Press
DOI: 10.1093/cid/ciab556

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

Autores: 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
Publicado en: Nature Human Behaviour, Edición 5/6, 2021, Página(s) 695-705, ISSN 2397-3374
Editor: 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

Autores: 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
Publicado en: BMJ Global Health, Edición Vol 7, issue 12, 2022, Página(s) e009674, ISSN 2059-7908
Editor: BMJ Publishing Group Ltd
DOI: 10.1136/bmjgh-2022-009674

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

Autores: Sarah Valentin, Rémy Decoupes, Renaud Lancelot, Mathieu Roche
Publicado en: Preventive Veterinary Medicine, Edición Volume 216, 2023, 105932, 2023, ISSN 0167-5877
Editor: Elsevier BV
DOI: 10.1016/j.prevetmed.2023.105932

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

Autores: 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
Publicado en: Epidemics, Edición Vol 37, December 2021, 2021, Página(s) 100530, ISSN 2352-7714
Editor: Elsevier
DOI: 10.1016/j.epidem.2021.100530

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

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

Phycova — a tool for exploring covariates of pathogen spread

Autores: Tim Blokker, Guy Baele, Philippe Lemey, Simon Dellicour
Publicado en: Virus Evolution, Edición 20571577, 2022, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/veac015

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

Autores: 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
Publicado en: Nature Communications, Edición 12, 7272 (2021), 2021, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Front. Public Health, Edición 11:1287678, 2023, ISSN 2296-2565
Editor: Lausanne Frontiers Media S.A.
DOI: 10.3389/fpubh.2023.1287678

Untangling introductions and persistence in COVID-19 resurgence in Europe

Autores: 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
Publicado en: Nature, 2021, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-021-03754-2

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

Autores: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
Publicado en: One Health, Edición Vol 19, 100841, 2024, ISSN 2352-7714
Editor: Elsevier B.V.
DOI: 10.1016/j.onehlt.2024.100841

Gender gap reduction and the one health benefits

Autores: Claudia Cataldo, Roberta Masella, Luca Busani
Publicado en: One Health, Edición Volume 16, 2023, 100496, 2023, ISSN 2352-7714
Editor: Eslevier
DOI: 10.1016/j.onehlt.2023.100496

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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/4, 2021, Página(s) e2019617118, ISSN 0027-8424
Editor: 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

Autores: Brecht Ingelbeen, Laurène Peckeu, Marie Laga, Ilona Hendrix, Inge Neven, Marianne AB van der Sande, Esther van Kleef
Publicado en: Eurosurveillance, Edición 26/7, 2021, Página(s) pii=2100065, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2021.26.7.2100065

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

Autores: Rhys P.D. Inward; Felix Jackson; Abhishek Dasgupta; Graham Lee; Anya Lindström Battle; Kris V. Parag; Moritz U.G. Kraemer
Publicado en: Epidemics, Edición vol 41, 2022, Página(s) 100627, ISSN 1755-4365
Editor: Elsevier BV
DOI: 10.1016/j.epidem.2022.100627

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

Autores: 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
Publicado en: Eurosurveillance, Edición 27, 2200580 (2022), 2022, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2022.27.31.2200580

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

Autores: 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
Publicado en: Science, Edición Vol 370, Edición 6516, 2020, Página(s) 564-570, ISSN 0000-0000
Editor: 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.

Autores: Giulia Pullano, Laura Di Domenico, Chiara E Sabbatini, Vittoria Colizza
Publicado en: Epicx-lab, report 23, Edición 23, 2020
Editor: INSERM

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

Autores: 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
Publicado en: arXiv, Edición 2203.07063, 2022, ISSN 2331-8422
Editor: Cornell University
DOI: 10.48550/arxiv.2203.07063

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

Autores: Di Domenico L., Pullano G., Sabbatini C.E., Boëlle P-Y., Colizza V.
Publicado en: Epicx-lab, report 8, Edición 8, 2020
Editor: INSERM

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

Autores: Mattia Mazzoli, Laura Di Domenico, EMERGEN Consortium, Vittoria Colizza
Publicado en: Epicx-lab, report 35, Edición 35, 2021
Editor: Inserm

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

Autores: Jane Messina, William Wint
Publicado en: ECDC technical report, 2023, ISBN 978-92-9498-676-4
Editor: European Centre for Disease Prevention and Control
DOI: 10.2900/222576

Epidemic scenarios of Delta variant in France in the summer 2021

Autores: Laura Di Domenico, Vittoria Colizza
Publicado en: Epicx-lab, report 31, Edición 31, 2021
Editor: INSERM

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

Autores: Giulia Pullano, Laura Di Domenico, Vittoria Colizza
Publicado en: Epicx-lab, report 16, Edición 16, 2020
Editor: INSERM

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

Autores: Eugenio Valdano, Jonggul Lee, Stefania Rubrichi, Vittoria Colizza
Publicado en: Epicx-lab, report 22, Edición 22, 2020
Editor: INSERM

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

Autores: Diego Andrés Contreras; Elisabetta Colosi; Giulia Bassignana; Vittoria Colizza; Alain Barrat
Publicado en: Journal of the Royal Society Interface, Edición 20545703, 2022, ISSN 2054-5703
Editor: 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

Autores: 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
Publicado en: BMC Medicine, Edición 18/1, 2020, ISSN 1741-7015
Editor: BioMed Central
DOI: 10.1186/s12916-020-01674-y

Estimating rodent population abundance using early climatic predictors

Autores: Giovanni Marini, Daniele Arnoldi, Annapaola Rizzoli, Valentina Tagliepietra
Publicado en: European Journal of Wildlife Research, Edición 69, 36, 2023, ISSN 1612-4642
Editor: Springer Verlag
DOI: 10.1007/s10344-023-01666-2

GeoXTag: Relative Spatial Information Extraction and Tagging

Autores: Mehtab Alam SYED, Elena ARSEVSKA, Mathieu ROCHE, Maguelonne TEISSEIRE
Publicado en: AGILE: GIScience Series, Edición 27008150, 2022, ISSN 2700-8150
Editor: AGILE: GIScience Series
DOI: 10.5194/agile-giss-3-16-2022

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

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

How Textual Datasets Enhance the PADI-Web Tool?

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

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

Autores: Mendes, Gonçalo Azevedo; Martins, Bruno
Publicado en: arXIV, Edición 2302.14021, 2023, ISSN 2331-8422
Editor: Cornell University
DOI: 10.48550/arxiv.2302.14021

Enriching Epidemiological Thematic Features For Disease Surveillance Corpora Classification

Autores: Edmond Menya, Mathieu Roche, Roberto Interdonato, Dickson Owuor
Publicado en: Proceedings of the Thirteenth Language Resources and Evaluation Conference, Marseille, France, Edición 2022.lrec-1.399, 2022, Página(s) 3741–3750, ISBN 979-10-95546-72-6
Editor: European Language Resources Association

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

Autores: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Publicado en: Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing, 2020, Página(s) 33-36, ISBN 2-9517408-6-7
Editor: European Language Resources Association

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

Autores: Alam, S.M., Arsevska, E., Roche, M., Teisseire, M.
Publicado en: Computer and Information Science, Edición CCIS,volume 1577, 2022, Página(s) 264–280, ISBN 978-3-031-04446-5
Editor: Springer
DOI: 10.1007/978-3-031-04447-2_18

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

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

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

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

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

Autores: Dias, H., Guimarães, A., Martins, B., Roche, M
Publicado en: Discovery Science 26th International Conference, DS 2023, Porto, Portugal, October 9–11, 2023, Edición vol 14276, 2023, Página(s) 141-145, ISBN 978-3-031-45275-8
Editor: Springer, Cham
DOI: 10.1007/978-3-031-45275-8_10

A co-training approach for spatial data disaggregation

Autores: João Monteiro, Bruno Martins, Miguel Costa, João M. Pires
Publicado en: 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, Edición November 2022 Article No.: 91, 2022, Página(s) 1-10, ISSN 1552-5996
Editor: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries
DOI: 10.1145/3557915.3561475

Explainable epidemiological thematic features for event based disease surveillance

Autores: Edmond Menya, Roberto Interdonato, Dickson Owuor, Mathieu Roche
Publicado en: Expert Systems with Applications, Edición Vol 250, 2024, Página(s) 123894, ISSN 0957-4174
Editor: Elsevier
DOI: 10.1016/j.eswa.2024.123894

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