MOOD project is at the forefront of European research of infectious disease surveillance and modelling from a data science perspective, investigating the impact of global warming on disease outbreaks, and proposing innovations for building of One Health systems across Europe and the world.
In the table below are listed all MOOD publications. Use the filter to select the most relevant articles.
51.
Huang, Bo; Wang, Jionghua; Cai, Jixuan; Yao, Shiqi; Chan, Paul Kay Sheung; Tam, Tony Hong-wing; Hong, Ying-Yi; Ruktanonchai, Corrine W.; Carioli, Alessandra; Floyd, Jessica R.; Ruktanonchai, Nick W.; Yang, Weizhong; Li, Zhongjie; Tatem, Andrew J.; Lai, Shengjie
Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities Journal Article
In: Nature Human Behaviour, vol. 5, pp. 695–705, 2021.
Abstract | Links | BibTeX | Tags: China, COVID-19, epidemiology, vaccine
@article{nokey,
title = {Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities},
author = {Bo Huang and Jionghua Wang and Jixuan Cai and Shiqi Yao and Paul Kay Sheung Chan and Tony Hong-wing Tam and Ying-Yi Hong and Corrine W. Ruktanonchai and Alessandra Carioli and Jessica R. Floyd and Nick W. Ruktanonchai and Weizhong Yang and Zhongjie Li and Andrew J. Tatem and Shengjie Lai },
doi = {https://doi.org/10.1038/s41562-021-01063-2},
year = {2021},
date = {2021-02-18},
journal = {Nature Human Behaviour},
volume = {5},
pages = {695–705},
abstract = {The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city’s population density and social contact patterns.},
keywords = {China, COVID-19, epidemiology, vaccine},
pubstate = {published},
tppubtype = {article}
}
The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city’s population density and social contact patterns.
50.
Marini, Giovanni; Manica, Mattia; Delucchi, Luca; Pugliese, Andrea; Ros`a, Roberto
Spring temperature shapes West Nile virus transmission in Europe Journal Article
In: Acta Tropica, vol. 215, pp. 105796, 2021.
Abstract | Links | BibTeX | Tags: Animal disease surveillance, Climate, Environmental change, Italy, West Nile Virus
@article{marini2021spring,
title = {Spring temperature shapes West Nile virus transmission in Europe},
author = {Giovanni Marini and Mattia Manica and Luca Delucchi and Andrea Pugliese and Roberto Ros`a},
doi = {https://doi.org/10.1016/j.actatropica.2020.105796},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Acta Tropica},
volume = {215},
pages = {105796},
publisher = {Elsevier},
abstract = {West Nile Virus (WNV) is now endemic in many European countries, causing hundreds of human cases every year, with a high spatial and temporal heterogeneity. Previous studies have suggested that spring temperature might play a key role at shaping WNV transmission. Specifically, warmer temperatures in April-May might amplify WNV circulation, thus increasing the risk for human transmission later in the year. To test this hypothesis, we collated publicly available data on the number of human infections recorded in Europe between 2011 and 2019. We then applied generalized linear models to quantify the relationship between human cases and spring temperature, considering both average conditions (over years 2003-2010) and deviations from the average for subsequent years (2011-2019). We found a significant positive association both spatial (average conditions) and temporal (deviations). The former indicates that WNV circulation is higher in usually warmer regions while the latter implies a predictive value of spring conditions over the coming season. We also found a positive association with WNV detection during the previous year, which can be interpreted as an indication of the reliability of the surveillance system but also of WNV overwintering capacity. Weather anomalies at the beginning of the mosquito breeding season might act as an early warning signal for public health authorities, enabling them to strengthen in advance ongoing surveillance and prevention strategies.},
keywords = {Animal disease surveillance, Climate, Environmental change, Italy, West Nile Virus},
pubstate = {published},
tppubtype = {article}
}
West Nile Virus (WNV) is now endemic in many European countries, causing hundreds of human cases every year, with a high spatial and temporal heterogeneity. Previous studies have suggested that spring temperature might play a key role at shaping WNV transmission. Specifically, warmer temperatures in April-May might amplify WNV circulation, thus increasing the risk for human transmission later in the year. To test this hypothesis, we collated publicly available data on the number of human infections recorded in Europe between 2011 and 2019. We then applied generalized linear models to quantify the relationship between human cases and spring temperature, considering both average conditions (over years 2003-2010) and deviations from the average for subsequent years (2011-2019). We found a significant positive association both spatial (average conditions) and temporal (deviations). The former indicates that WNV circulation is higher in usually warmer regions while the latter implies a predictive value of spring conditions over the coming season. We also found a positive association with WNV detection during the previous year, which can be interpreted as an indication of the reliability of the surveillance system but also of WNV overwintering capacity. Weather anomalies at the beginning of the mosquito breeding season might act as an early warning signal for public health authorities, enabling them to strengthen in advance ongoing surveillance and prevention strategies.
49.
Ingelbeen, Brecht; Peckeu, Laur`ene; Laga, Marie; Hendrix, Ilona; Neven, Inge; Sande, Marianne AB; Kleef, Esther
Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020 Journal Article
In: Eurosurveillance, vol. 26, no. 7, pp. 2100065, 2021.
Abstract | Links | BibTeX | Tags: Belgium, COVID-19, epidemiology, Model, school, transmission
@article{ingelbeen2021reducing,
title = {Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020},
author = {Brecht Ingelbeen and Laur`ene Peckeu and Marie Laga and Ilona Hendrix and Inge Neven and Marianne AB Sande and Esther Kleef},
doi = {https://doi.org/10.1371/journal.pbio.3001115},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Eurosurveillance},
volume = {26},
number = {7},
pages = {2100065},
publisher = {European Centre for Disease Prevention and Control},
abstract = {To evaluate the effect of physical distancing and school reopening in Brussels between August and November 2020, we monitored changes in the number of reported contacts per SARS-CoV-2 case and associated SARS-CoV-2 transmission. The second COVID-19 pandemic wave in Brussels was the result of increased social contact across all ages following school reopening. Physical distancing measures including closure of bars and restaurants, and limiting close contacts, while primary and secondary schools remained open, reduced social mixing and controlled SARS-CoV-2 transmission.},
keywords = {Belgium, COVID-19, epidemiology, Model, school, transmission},
pubstate = {published},
tppubtype = {article}
}
To evaluate the effect of physical distancing and school reopening in Brussels between August and November 2020, we monitored changes in the number of reported contacts per SARS-CoV-2 case and associated SARS-CoV-2 transmission. The second COVID-19 pandemic wave in Brussels was the result of increased social contact across all ages following school reopening. Physical distancing measures including closure of bars and restaurants, and limiting close contacts, while primary and secondary schools remained open, reduced social mixing and controlled SARS-CoV-2 transmission.
48.
Valentin, Sarah; Lancelot, Renaud; Roche, Mathieu
Identifying associations between epidemiological entities in news data for animal disease surveillance Journal Article
In: Artificial Intelligence in Agriculture, vol. 5, pp. 163-174, 2021, ISSN: 2589-7217.
Abstract | Links | BibTeX | Tags: Animal disease surveillance, Event extraction, Text mining
@article{VALENTIN2021163,
title = {Identifying associations between epidemiological entities in news data for animal disease surveillance},
author = {Sarah Valentin and Renaud Lancelot and Mathieu Roche},
url = {https://www.sciencedirect.com/science/article/pii/S2589721721000246},
doi = {https://doi.org/10.1016/j.aiia.2021.07.003},
issn = {2589-7217},
year = {2021},
date = {2021-01-01},
journal = {Artificial Intelligence in Agriculture},
volume = {5},
pages = {163-174},
abstract = {Event-based surveillance systems are at the crossroads of human and animal (and plant and ecosystem) health, epidemiology, statistics, and informatics. Thus, their deployment faces many challenges specific to each domain and their intersections, such as relations among automation, artificial intelligence, and expertise. In this context, our work pertins to the extraction of epidemiological events in textual data (i.e. news) by unsupervised methods. We define the event extraction task as detecting pairs of epidemiological entities (e.g. a disease name and location). The quality of the ranked lists of pairs was evaluated using specific ranking evaluation metrics. We used a publicly available annotated corpus of 438 documents (i.e. news articles) related to animal disease events. The statistical approach was able to detect event-related pairs of epidemiological features with a good trade-off between precision and recall. Our results showed that using a window of words outperformed document-based and sentence-based approaches, while reducing the probability of detecting false pairs. Our results indicated that Mutual Information was less adapted than the Dice coefficient for ranking pairs of features in the event extraction framework. We believe that Mutual Information would be more relevant for rare pair detection (i.e. weak signals), but requires higher manual curation to avoid false positive extraction pairs. Moreover, generalising the country-level spatial features enabled better discrimination (i.e. ranking) of relevant disease-location pairs for event extraction.},
keywords = {Animal disease surveillance, Event extraction, Text mining},
pubstate = {published},
tppubtype = {article}
}
Event-based surveillance systems are at the crossroads of human and animal (and plant and ecosystem) health, epidemiology, statistics, and informatics. Thus, their deployment faces many challenges specific to each domain and their intersections, such as relations among automation, artificial intelligence, and expertise. In this context, our work pertins to the extraction of epidemiological events in textual data (i.e. news) by unsupervised methods. We define the event extraction task as detecting pairs of epidemiological entities (e.g. a disease name and location). The quality of the ranked lists of pairs was evaluated using specific ranking evaluation metrics. We used a publicly available annotated corpus of 438 documents (i.e. news articles) related to animal disease events. The statistical approach was able to detect event-related pairs of epidemiological features with a good trade-off between precision and recall. Our results showed that using a window of words outperformed document-based and sentence-based approaches, while reducing the probability of detecting false pairs. Our results indicated that Mutual Information was less adapted than the Dice coefficient for ranking pairs of features in the event extraction framework. We believe that Mutual Information would be more relevant for rare pair detection (i.e. weak signals), but requires higher manual curation to avoid false positive extraction pairs. Moreover, generalising the country-level spatial features enabled better discrimination (i.e. ranking) of relevant disease-location pairs for event extraction.
47.
Li, Sabrina L; Messina, Jane P; Pybus, Oliver G; Kraemer, Moritz U G; Gardner, Lauren
A review of models applied to the geographic spread of Zika virus Journal Article
In: Transactions of The Royal Society of Tropical Medicine and Hygiene, vol. 115, no. 9, pp. 956-964, 2021, ISSN: 0035-9203.
Abstract | Links | BibTeX | Tags: Animal disease surveillance, Event extraction, Text mining, Zika
@article{10.1093/trstmh/trab009,
title = {A review of models applied to the geographic spread of Zika virus},
author = {Sabrina L Li and Jane P Messina and Oliver G Pybus and Moritz U G Kraemer and Lauren Gardner},
url = {https://doi.org/10.1093/trstmh/trab009},
doi = {10.1093/trstmh/trab009},
issn = {0035-9203},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Transactions of The Royal Society of Tropical Medicine and Hygiene},
volume = {115},
number = {9},
pages = {956-964},
abstract = {In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.},
keywords = {Animal disease surveillance, Event extraction, Text mining, Zika},
pubstate = {published},
tppubtype = {article}
}
In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.
46.
Rodrique, Kafando; Decoupes, Rémy; Valentin, Sarah; Sautot, Lucile; Teisseire, Maguelonne; Roche, Mathieu
ITEXT-BIO: Intelligent Term EXTraction for BIOmedical analysis Journal Article
In: Health Information Science and Systems, vol. 9, 2021.
Abstract | Links | BibTeX | Tags: Biomedical terminology, Intelligent analysis, Terminology extraction
@article{article,
title = {ITEXT-BIO: Intelligent Term EXTraction for BIOmedical analysis},
author = {Kafando Rodrique and Rémy Decoupes and Sarah Valentin and Lucile Sautot and Maguelonne Teisseire and Mathieu Roche},
doi = {10.1007/s13755-021-00156-6},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Health Information Science and Systems},
volume = {9},
abstract = {Here, we introduce ITEXT-BIO, an intelligent process for biomedical domain terminology extraction from textual documents and subsequent analysis. The proposed methodology consists of two complementary approaches, including free and driven term extraction. The first is based on term extraction with statistical measures, while the second considers morphosyntactic variation rules to extract term variants from the corpus. The combination of two term extraction and analysis strategies is the keystone of ITEXT-BIO. These include combined intra-corpus strategies that enable term extraction and analysis either from a single corpus (intra), or from corpora (inter). We assessed the two approaches, the corpus or corpora to be analysed and the type of statistical measures used. Our experimental findings revealed that the proposed methodology could be used: (1) to efficiently extract representative, discriminant and new terms from a given corpus or corpora, and (2) to provide quantitative and qualitative analyses on these terms regarding the study domain.},
keywords = {Biomedical terminology, Intelligent analysis, Terminology extraction},
pubstate = {published},
tppubtype = {article}
}
Here, we introduce ITEXT-BIO, an intelligent process for biomedical domain terminology extraction from textual documents and subsequent analysis. The proposed methodology consists of two complementary approaches, including free and driven term extraction. The first is based on term extraction with statistical measures, while the second considers morphosyntactic variation rules to extract term variants from the corpus. The combination of two term extraction and analysis strategies is the keystone of ITEXT-BIO. These include combined intra-corpus strategies that enable term extraction and analysis either from a single corpus (intra), or from corpora (inter). We assessed the two approaches, the corpus or corpora to be analysed and the type of statistical measures used. Our experimental findings revealed that the proposed methodology could be used: (1) to efficiently extract representative, discriminant and new terms from a given corpus or corpora, and (2) to provide quantitative and qualitative analyses on these terms regarding the study domain.
45.
Poletti, Piero; Tirani, Marcello; Cereda, Danilo; Trentini, Filippo; Guzzetta, Giorgio; Sabatino, Giuliana; Marziano, Valentina; Castrofino, Ambra; Grosso, Francesca; Castillo, Gabriele Del; others,
In: JAMA network open, vol. 4, no. 3, pp. e211085–e211085, 2021.
Links | BibTeX | Tags: Contact tracing, COVID-19, Italy
@article{poletti2021association,
title = {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},
author = {Piero Poletti and Marcello Tirani and Danilo Cereda and Filippo Trentini and Giorgio Guzzetta and Giuliana Sabatino and Valentina Marziano and Ambra Castrofino and Francesca Grosso and Gabriele Del Castillo and others},
doi = {doi:10.1001/jamanetworkopen.2021.1085},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {JAMA network open},
volume = {4},
number = {3},
pages = {e211085--e211085},
publisher = {American Medical Association},
keywords = {Contact tracing, COVID-19, Italy},
pubstate = {published},
tppubtype = {article}
}
44.
Plessis, Louis; McCrone, John T.; Zarebski, Alexander E.; Hill, Verity; Ruis, Christopher; Gutierrez, Bernardo; Raghwani, Jayna; Ashworth, Jordan; Colquhoun, Rachel; Connor, Thomas R.; Faria, Nuno R.; Jackson, Ben; Loman, Nicholas J.; O’Toole, Ãine; Nicholls, Samuel M.; Parag, Kris V.; Scher, Emily; Vasylyeva, Tetyana I.; Volz, Erik M.; Watts, Alexander; Bogoch, Isaac I.; Khan, Kamran; null,; Aanensen, David M.; Kraemer, Moritz U. G.; Rambaut, Andrew; Pybus, Oliver G.
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK Journal Article
In: Science, vol. 371, no. 6530, pp. 708-712, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, epidemiology, genome, phylogenetic, travel, United Kingdom
@article{doi:10.1126/science.abf2946,
title = {Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK},
author = {Louis Plessis and John T. McCrone and Alexander E. Zarebski and Verity Hill and Christopher Ruis and Bernardo Gutierrez and Jayna Raghwani and Jordan Ashworth and Rachel Colquhoun and Thomas R. Connor and Nuno R. Faria and Ben Jackson and Nicholas J. Loman and Ãine O’Toole and Samuel M. Nicholls and Kris V. Parag and Emily Scher and Tetyana I. Vasylyeva and Erik M. Volz and Alexander Watts and Isaac I. Bogoch and Kamran Khan and null and David M. Aanensen and Moritz U. G. Kraemer and Andrew Rambaut and Oliver G. Pybus},
doi = {10.1126/science.abf2946 URL = https://www.science.org/doi/abs/10.1126/science.abf2946},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Science},
volume = {371},
number = {6530},
pages = {708-712},
abstract = {The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful. Science, this issue p. 708; see also p. 680 Large-scale virus genome sequencing reveals the genetic structure and importation dynamics of a national COVID-19 epidemic. The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in 1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.},
keywords = {COVID-19, epidemiology, genome, phylogenetic, travel, United Kingdom},
pubstate = {published},
tppubtype = {article}
}
The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful. Science, this issue p. 708; see also p. 680 Large-scale virus genome sequencing reveals the genetic structure and importation dynamics of a national COVID-19 epidemic. The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in 1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
43.
Domenico, Laura Di; Pullano, Giulia; Sabbatini, Chiara E.; Bo""elle, Pierre-Yves; Colizza, Vittoria
Modelling safe protocols for reopening schools during the COVID-19 pandemic in France Journal Article
In: medRxiv, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, France, Model, school
@article{DiDomenico2020.05.08.20095521,
title = {Modelling safe protocols for reopening schools during the COVID-19 pandemic in France},
author = {Laura Di Domenico and Giulia Pullano and Chiara E. Sabbatini and Pierre-Yves Bo""elle and Vittoria Colizza},
url = {https://www.medrxiv.org/content/early/2021/01/14/2020.05.08.20095521},
doi = {10.1101/2020.05.08.20095521},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {As countries in Europe implement strategies to control COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Ile-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on children role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist that maintain the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale tests and trace are required to maintain the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown.},
keywords = {COVID-19, France, Model, school},
pubstate = {published},
tppubtype = {article}
}
As countries in Europe implement strategies to control COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Ile-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on children role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist that maintain the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale tests and trace are required to maintain the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown.
42.
Valentin, Sarah; Mercier, Alizé; Lancelot, Renaud; Roche, Mathieu; Arsevska, Elena
Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID-19 emergence Journal Article
In: Transboundary and emerging diseases, vol. 68, no. 3, pp. 981–986, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, data mining, EBS, Event extraction, media extraction, monitoring, ProMed
@article{valentin2021monitoring,
title = {Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID-19 emergence},
author = {Sarah Valentin and Alizé Mercier and Renaud Lancelot and Mathieu Roche and Elena Arsevska},
doi = {https://doi.org/10.1111/tbed.13738},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Transboundary and emerging diseases},
volume = {68},
number = {3},
pages = {981--986},
publisher = {Wiley Online Library},
abstract = {Event-based surveillance (EBS) systems monitor a broad range of information sources to detect early signals of disease emergence, including new and unknown diseases. In December 2019, a newly identified coronavirus emerged in Wuhan (China), causing a global coronavirus disease (COVID-19) pandemic. A retrospective study was conducted to evaluate the capacity of three event-based surveillance (EBS) systems (ProMED, HealthMap and PADI-web) to detect early COVID-19 emergence signals. We focused on changes in online news vocabulary over the period before/after the identification of COVID-19, while also assessing its contagiousness and pandemic potential. ProMED was the timeliest EBS, detecting signals one day before the official notification. At this early stage, the specific vocabulary used was related to ‘pneumonia symptoms’ and ‘mystery illness’. Once COVID-19 was identified, the vocabulary changed to virus family and specific COVID-19 acronyms. Our results suggest that the three EBS systems are complementary regarding data sources, and all require timeliness improvements. EBS methods should be adapted to the different stages of disease emergence to enhance early detection of future unknown disease outbreaks.},
keywords = {COVID-19, data mining, EBS, Event extraction, media extraction, monitoring, ProMed},
pubstate = {published},
tppubtype = {article}
}
Event-based surveillance (EBS) systems monitor a broad range of information sources to detect early signals of disease emergence, including new and unknown diseases. In December 2019, a newly identified coronavirus emerged in Wuhan (China), causing a global coronavirus disease (COVID-19) pandemic. A retrospective study was conducted to evaluate the capacity of three event-based surveillance (EBS) systems (ProMED, HealthMap and PADI-web) to detect early COVID-19 emergence signals. We focused on changes in online news vocabulary over the period before/after the identification of COVID-19, while also assessing its contagiousness and pandemic potential. ProMED was the timeliest EBS, detecting signals one day before the official notification. At this early stage, the specific vocabulary used was related to ‘pneumonia symptoms’ and ‘mystery illness’. Once COVID-19 was identified, the vocabulary changed to virus family and specific COVID-19 acronyms. Our results suggest that the three EBS systems are complementary regarding data sources, and all require timeliness improvements. EBS methods should be adapted to the different stages of disease emergence to enhance early detection of future unknown disease outbreaks.
41.
MacLean, Oscar A; Lytras, Spyros; Weaver, Steven; Singer, Joshua B; Boni, Maciej F; Lemey, Philippe; Pond, Sergei L Kosakovsky; Robertson, David L
Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen Journal Article
In: PLoS biology, vol. 19, no. 3, pp. e3001115, 2021.
Abstract | BibTeX | Tags: COVID-19, genome
@article{maclean2021natural,
title = {Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen},
author = {Oscar A MacLean and Spyros Lytras and Steven Weaver and Joshua B Singer and Maciej F Boni and Philippe Lemey and Sergei L Kosakovsky Pond and David L Robertson},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {PLoS biology},
volume = {19},
number = {3},
pages = {e3001115},
publisher = {Public Library of Science San Francisco, CA USA},
abstract = {Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.},
keywords = {COVID-19, genome},
pubstate = {published},
tppubtype = {article}
}
Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.
40.
Kraemer, MUG; Hill, V; Ruis, C; Dellicour, S; Bajaj, S; McCrone, JT; Baele, G; Parag, KV; Battle, AL; Gutierrez, B; Jackson, B; Colquhoun, R; O'Toole, A; Klein, B; Vespignani, A; Consortium, COVID-19 Genomics UK (COG-UK); Volz, E; Faria, NR; Aanensen, DM; NJ, NJ Loman; du Plessis, L; Cauchemez, S; A, A Rambaut; SV, SV Scarpino; Pybus, OG
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence Journal Article
In: Science, vol. 373, no. 6557, pp. 889-895, 2021.
Abstract | Links | BibTeX | Tags: big data, COVID-19, genome, mobility, phylogenetic, United Kingdom, variants
@article{doi:10.1126/science.abj0113,
title = {Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence},
author = {MUG Kraemer and V Hill and C Ruis and S Dellicour and S Bajaj and JT McCrone and G Baele and KV Parag and AL Battle and B Gutierrez and B Jackson and R Colquhoun and A O'Toole and B Klein and A Vespignani and COVID-19 Genomics UK (COG-UK) Consortium and E Volz and NR Faria and DM Aanensen and NJ Loman NJ and L du Plessis and S Cauchemez and A Rambaut A and SV Scarpino SV and OG Pybus },
url = {https://www.science.org/doi/abs/10.1126/science.abj0113},
doi = {10.1126/science.abj0113},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Science},
volume = {373},
number = {6557},
pages = {889-895},
abstract = {The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al. explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. Disentangling the factors that contribute to the rapid spread of virus variants is essential for understanding their epidemiological consequences. Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.},
keywords = {big data, COVID-19, genome, mobility, phylogenetic, United Kingdom, variants},
pubstate = {published},
tppubtype = {article}
}
The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al. explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. Disentangling the factors that contribute to the rapid spread of virus variants is essential for understanding their epidemiological consequences. Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
39.
Hu, Maogui; Wang, Jinfeng; Lin, Hui; Ruktanonchai, Corrine W; Xu, Chengdong; Meng, Bin; Zhang, Xin; Carioli, Alessandra; Feng, Yuqing; Yin, Qian; Floyd, Jessica R; Ruktanonchai, Nick W; Li, Zhongjie; Yang, Weizhong; Tatem, Andrew J; Lai, Shengjie
Risk of SARS-CoV-2 Transmission among Air Passengers in China Journal Article
In: Clinical Infectious Diseases, 2021, ISSN: 1058-4838, (ciab836).
Abstract | Links | BibTeX | Tags: airplanes, COVID-19, mobility, transmission
@article{10.1093/cid/ciab836,
title = {Risk of SARS-CoV-2 Transmission among Air Passengers in China},
author = {Maogui Hu and Jinfeng Wang and Hui Lin and Corrine W Ruktanonchai and Chengdong Xu and Bin Meng and Xin Zhang and Alessandra Carioli and Yuqing Feng and Qian Yin and Jessica R Floyd and Nick W Ruktanonchai and Zhongjie Li and Weizhong Yang and Andrew J Tatem and Shengjie Lai},
url = {https://doi.org/10.1093/cid/ciab836},
doi = {10.1093/cid/ciab836},
issn = {1058-4838},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Clinical Infectious Diseases},
abstract = {Modern transportation plays a key role in the spread of SARS-CoV-2 and new variants. However, little is known about the exact transmission risk of the virus on airplanes.Using the itinerary and epidemiological data of COVID-19 cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on January 23, 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travellers.175 index cases were identified among 5797 passengers on 177 airplanes. The upper and lower attack rates (ARs) of a seat were 0.60% (34/5622, 95%CI 0.43%-0.84%) and 0.33% (18/5400, 95%CI 0.21%-0.53%), respectively. In the upper- and lower-bound risk estimates, each index case infected 0.19 (SD 0.45) and 0.10 (SD 0.32) cases respectively. The seats immediately adjacent to the index cases had an AR of 9.2% (95%CI 5.7%-14.4%), with a relative risk 27.8 (95%CI 14.4-53.7) compared to other seats in the upper limit estimation. The middle seat had the highest AR (0.7%, 95%CI 0.4%-1.2%). The upper-bound AR increased from 0.7% (95%CI 0.5%-1.0%) to 1.2% (95%CI 0.4%-3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travellers varied by seat distance from the index case and joint travel time, but the variation was not significant between the types of aircraft. The overall risk of SARS-CoV-2 transmission during domestic travel on planes was relatively low. These findings can improve our understanding of COVID-19 spread during travel and inform response efforts in the pandemic.},
note = {ciab836},
keywords = {airplanes, COVID-19, mobility, transmission},
pubstate = {published},
tppubtype = {article}
}
Modern transportation plays a key role in the spread of SARS-CoV-2 and new variants. However, little is known about the exact transmission risk of the virus on airplanes.Using the itinerary and epidemiological data of COVID-19 cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on January 23, 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travellers.175 index cases were identified among 5797 passengers on 177 airplanes. The upper and lower attack rates (ARs) of a seat were 0.60% (34/5622, 95%CI 0.43%-0.84%) and 0.33% (18/5400, 95%CI 0.21%-0.53%), respectively. In the upper- and lower-bound risk estimates, each index case infected 0.19 (SD 0.45) and 0.10 (SD 0.32) cases respectively. The seats immediately adjacent to the index cases had an AR of 9.2% (95%CI 5.7%-14.4%), with a relative risk 27.8 (95%CI 14.4-53.7) compared to other seats in the upper limit estimation. The middle seat had the highest AR (0.7%, 95%CI 0.4%-1.2%). The upper-bound AR increased from 0.7% (95%CI 0.5%-1.0%) to 1.2% (95%CI 0.4%-3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travellers varied by seat distance from the index case and joint travel time, but the variation was not significant between the types of aircraft. The overall risk of SARS-CoV-2 transmission during domestic travel on planes was relatively low. These findings can improve our understanding of COVID-19 spread during travel and inform response efforts in the pandemic.
38.
Trentini, Filippo; Marziano, Valentina; Guzzetta, Giorgio; Tirani, Marcello; Cereda, Danilo; Poletti, Piero; Piccarreta, Raffaella; Barone, Antonio; Preziosi, Giuseppe; Arduini, Fabio; Valle, Petra Giulia Della; Zanella, Alberto; Grosso, Francesca; Castillo, Gabriele; Castrofino, Ambra; Grasselli, Giacomo; Melegaro, Alessia; Piatti, Alessandra; Andreassi, Aida; Gramegna, Maria; Ajelli, Marco; Merler, Stefano
In: American Journal of Epidemiology, 2021, ISSN: 0002-9262, (kwab252).
Abstract | Links | BibTeX | Tags: big data, COVID-19, epidemiology, ICU, Italy, Public Health
@article{10.1093/aje/kwab252,
title = {The pressure on healthcare system and intensive care utilization during the COVID-19 outbreak in the Lombardy region: a retrospective observational study on 43,538 hospitalized patients},
author = {Filippo Trentini and Valentina Marziano and Giorgio Guzzetta and Marcello Tirani and Danilo Cereda and Piero Poletti and Raffaella Piccarreta and Antonio Barone and Giuseppe Preziosi and Fabio Arduini and Petra Giulia Della Valle and Alberto Zanella and Francesca Grosso and Gabriele Castillo and Ambra Castrofino and Giacomo Grasselli and Alessia Melegaro and Alessandra Piatti and Aida Andreassi and Maria Gramegna and Marco Ajelli and Stefano Merler},
url = {https://doi.org/10.1093/aje/kwab252},
doi = {10.1093/aje/kwab252},
issn = {0002-9262},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {American Journal of Epidemiology},
abstract = {During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-March 13), the period of highest pressure on healthcare (March 14-April 25, when COVID-19 patients exceeded the ICU pre-pandemic bed capacity), and the declining phase (April 26-July 12).Compared to the early phase, patients above 70 years of age were admitted less often to an ICU during highest pressure on healthcare (odds ratio OR 0.47, 95%CI: 0.41-0.54) with longer delays (incidence rate ratio IRR 1.82, 95%CI: 1.52-2.18), and lower chances of death in ICU (OR 0.47, 95%CI: 0.34-0.64). Patients under 56 years of age reported more limited changes in the probability (OR 0.65, 95%CI: 0.56-0.76) and delay to ICU admission (IRR 1.16, 95%CI: 0.95-1.42) and an increased mortality (OR 1.43, 95%CI: 1.00-2.07). In the declining phase, all quantities decreased for all age groups.These patterns may suggest that limited healthcare resources during the peak epidemic phase in Lombardy forced a shift in ICU admission criteria to prioritize patients with higher chances of survival.},
note = {kwab252},
keywords = {big data, COVID-19, epidemiology, ICU, Italy, Public Health},
pubstate = {published},
tppubtype = {article}
}
During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-March 13), the period of highest pressure on healthcare (March 14-April 25, when COVID-19 patients exceeded the ICU pre-pandemic bed capacity), and the declining phase (April 26-July 12).Compared to the early phase, patients above 70 years of age were admitted less often to an ICU during highest pressure on healthcare (odds ratio OR 0.47, 95%CI: 0.41-0.54) with longer delays (incidence rate ratio IRR 1.82, 95%CI: 1.52-2.18), and lower chances of death in ICU (OR 0.47, 95%CI: 0.34-0.64). Patients under 56 years of age reported more limited changes in the probability (OR 0.65, 95%CI: 0.56-0.76) and delay to ICU admission (IRR 1.16, 95%CI: 0.95-1.42) and an increased mortality (OR 1.43, 95%CI: 1.00-2.07). In the declining phase, all quantities decreased for all age groups.These patterns may suggest that limited healthcare resources during the peak epidemic phase in Lombardy forced a shift in ICU admission criteria to prioritize patients with higher chances of survival.
37.
Manica, Mattia; Guzzetta, Giorgio; Riccardo, Flavia; Valenti, Antonio; Poletti, Piero; Marziano, Valentina; Trentini, Filippo; Andrianou, Xanthi; Urdiales, Alberto Mateo; Manso, Martina; Fabiani, Massimo; Vescio, Maria Fenicia; Spuri, Matteo; Petrone, Daniele; Bella, Antonino; Iavicoli, Sergio; Ajelli, Marco; Brusaferro, Silvio; Pezzotti, Patrizio; Merler, Stefano
Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy Journal Article
In: medRxiv, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, Italy, measures, Public Health, surveillance
@article{Manica2021.01.10.21249532,
title = {Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy},
author = {Mattia Manica and Giorgio Guzzetta and Flavia Riccardo and Antonio Valenti and Piero Poletti and Valentina Marziano and Filippo Trentini and Xanthi Andrianou and Alberto Mateo Urdiales and Martina Manso and Massimo Fabiani and Maria Fenicia Vescio and Matteo Spuri and Daniele Petrone and Antonino Bella and Sergio Iavicoli and Marco Ajelli and Silvio Brusaferro and Patrizio Pezzotti and Stefano Merler},
url = {https://www.medrxiv.org/content/early/2021/02/24/2021.01.10.21249532},
doi = {10.1101/2021.01.10.21249532},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {To counter the second COVID-19 wave in autumn 2020, the Italian government introduced a system of physical distancing measures organized in progressively restrictive tiers (coded as yellow, orange, and red) and imposed on a regional basis according to epidemiological risk assessments. The individualstextquoteright attendance to locations outside the residential settings was progressively reduced with tiers, but less than during the national lockdown against the first COVID-19 wave in the spring. The reproduction number Rt decreased below the epidemic threshold in 85 out of 107 provinces after the introduction of the tier system, reaching average values of about 0.99, 0.89 and 0.77 in the yellow, orange and red tier, respectively. We estimate that the reduced transmissibility resulted in averting about 37% of the hospitalizations between November 5 and November 25, 2020. These results are instrumental to inform public health efforts aimed at preventing future resurgence of cases. Competing Interest Statement: M.A. has received research funding from Seqirus. The funding is not related to COVID-19. All other authors declare no competing interest. Funding StatementM.M., G.G., V.M., P. Poletti, F.T., and S.M. acknowledge funding from EU Grant 874850 MOOD (cataloged as MOOD 000). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the funderAuthor DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below: No IRB was required for this analysis. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData are available from the corresponding author upon reasonable request.},
keywords = {COVID-19, Italy, measures, Public Health, surveillance},
pubstate = {published},
tppubtype = {article}
}
To counter the second COVID-19 wave in autumn 2020, the Italian government introduced a system of physical distancing measures organized in progressively restrictive tiers (coded as yellow, orange, and red) and imposed on a regional basis according to epidemiological risk assessments. The individualstextquoteright attendance to locations outside the residential settings was progressively reduced with tiers, but less than during the national lockdown against the first COVID-19 wave in the spring. The reproduction number Rt decreased below the epidemic threshold in 85 out of 107 provinces after the introduction of the tier system, reaching average values of about 0.99, 0.89 and 0.77 in the yellow, orange and red tier, respectively. We estimate that the reduced transmissibility resulted in averting about 37% of the hospitalizations between November 5 and November 25, 2020. These results are instrumental to inform public health efforts aimed at preventing future resurgence of cases. Competing Interest Statement: M.A. has received research funding from Seqirus. The funding is not related to COVID-19. All other authors declare no competing interest. Funding StatementM.M., G.G., V.M., P. Poletti, F.T., and S.M. acknowledge funding from EU Grant 874850 MOOD (cataloged as MOOD 000). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the funderAuthor DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below: No IRB was required for this analysis. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData are available from the corresponding author upon reasonable request.
36.
Manica, Mattia; Guzzetta, Giorgio; Riccardo, Flavia; Valenti, Antonio; Poletti, Piero; Marziano, Valentina; Trentini, Filippo; Andrianou, Xanthi; Urdiales, Alberto Mateo; Manso, Martina Del; others,
Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy Journal Article
In: medRxiv, 2021.
BibTeX | Tags:
@article{manica2021impact,
title = {Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy},
author = {Mattia Manica and Giorgio Guzzetta and Flavia Riccardo and Antonio Valenti and Piero Poletti and Valentina Marziano and Filippo Trentini and Xanthi Andrianou and Alberto Mateo Urdiales and Martina Del Manso and others},
year = {2021},
date = {2021-01-01},
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
35.
Valdano, Eugenio; Lee, Jonggul; Bansal, Shweta; Rubrichi, Stefania; Colizza, Vittoria
In: Journal of Travel Medicine, vol. 28, no. 4, 2021, ISSN: 1708-8305, (taab045).
Links | BibTeX | Tags: COVID-19, France, mobility, social science
@article{10.1093/jtm/taab045,
title = {Highlighting socio-economic constraints on mobility reductions during COVID-19 restrictions in France can inform effective and equitable pandemic response},
author = {Eugenio Valdano and Jonggul Lee and Shweta Bansal and Stefania Rubrichi and Vittoria Colizza},
url = {https://doi.org/10.1093/jtm/taab045},
doi = {10.1093/jtm/taab045},
issn = {1708-8305},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Journal of Travel Medicine},
volume = {28},
number = {4},
note = {taab045},
keywords = {COVID-19, France, mobility, social science},
pubstate = {published},
tppubtype = {article}
}
34.
López, Jesús A. Moreno; García, Beatriz Arregui; Bentkowski, Piotr; Bioglio, Livio; Pinotti, Francesco; Boëlle, Pierre-Yves; Barrat, Alain; Colizza, Vittoria; Poletto, Chiara
Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection Journal Article
In: Science Advances, vol. 7, no. 15, pp. eabd8750, 2021.
Abstract | Links | BibTeX | Tags: Contact tracing, COVID-19, Human health, surveillance
@article{doi:10.1126/sciadv.abd8750,
title = {Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection},
author = {Jesús A. Moreno López and Beatriz Arregui García and Piotr Bentkowski and Livio Bioglio and Francesco Pinotti and Pierre-Yves Boëlle and Alain Barrat and Vittoria Colizza and Chiara Poletto},
doi = {10.1126/sciadv.abd8750 URL = https://www.science.org/doi/abs/10.1126/sciadv.abd8750},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Science Advances},
volume = {7},
number = {15},
pages = {eabd8750},
abstract = {Digital contact tracing apps could slow down COVID-19 transmission at moderate adoption: A model-based study. The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.},
keywords = {Contact tracing, COVID-19, Human health, surveillance},
pubstate = {published},
tppubtype = {article}
}
Digital contact tracing apps could slow down COVID-19 transmission at moderate adoption: A model-based study. The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
33.
Pullano, Giulia; Domenico, Laura Di; Sabbatini, Chiara E; Valdano, Eugenio; Turbelin, Clément; Debin, Marion; Guerrisi, Caroline; Kengne-Kuetche, Charly; Souty, Cécile; Hanslik, Thomas; others,
Underdetection of cases of COVID-19 in France threatens epidemic control Journal Article
In: Nature, vol. 590, no. 7844, pp. 134–139, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, epidemiology, France, surveillance
@article{pullano2021underdetection,
title = {Underdetection of cases of COVID-19 in France threatens epidemic control},
author = {Giulia Pullano and Laura Di Domenico and Chiara E Sabbatini and Eugenio Valdano and Clément Turbelin and Marion Debin and Caroline Guerrisi and Charly Kengne-Kuetche and Cécile Souty and Thomas Hanslik and others},
doi = { https://doi.org/10.1038/s41586-020-03095-6},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature},
volume = {590},
number = {7844},
pages = {134--139},
publisher = {Nature Publishing Group},
abstract = {As countries in Europe gradually relaxed lockdown restrictions after the first wave, test–trace–isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6–8%) to 38% (35–44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.},
keywords = {COVID-19, epidemiology, France, surveillance},
pubstate = {published},
tppubtype = {article}
}
As countries in Europe gradually relaxed lockdown restrictions after the first wave, test–trace–isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6–8%) to 38% (35–44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.
32.
Lemey, Philippe; Ruktanonchai, Nick; Hong, Samuel L; Colizza, Vittoria; Poletto, Chiara; den Broeck, Frederik Van; Gill, Mandev S; Ji, Xiang; Levasseur, Anthony; Munnink, Bas B Oude; others,
Untangling introductions and persistence in COVID-19 resurgence in Europe Journal Article
In: Nature, vol. 595, no. 7869, pp. 713–717, 2021.
Abstract | Links | BibTeX | Tags: big data, COVID-19, epidemiology, Europe, measures, mobility
@article{lemey2021untangling,
title = {Untangling introductions and persistence in COVID-19 resurgence in Europe},
author = {Philippe Lemey and Nick Ruktanonchai and Samuel L Hong and Vittoria Colizza and Chiara Poletto and Frederik Van den Broeck and Mandev S Gill and Xiang Ji and Anthony Levasseur and Bas B Oude Munnink and others},
doi = {https://doi.org/10.1038/s41586-021-03754-2},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature},
volume = {595},
number = {7869},
pages = {713--717},
publisher = {Nature Publishing Group},
abstract = {After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.},
keywords = {big data, COVID-19, epidemiology, Europe, measures, mobility},
pubstate = {published},
tppubtype = {article}
}
After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.