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 all publications to which the MOOD project contributed are listed. Use the filter to select the most relevant articles.
48.
Syed, Mehtab Alam; Decoupes, Remy; Arsevska, Elena; Roche, Mathieu; Teisseire, Maguelonne
Spatial opinion mining from COVID-19 twitter data Journal Article
In: International Journal of Infectious Diseases, vol. 116, iss. 549, pp. 527, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), Text mining
@article{nokey,
title = {Spatial opinion mining from COVID-19 twitter data},
author = {Mehtab Alam Syed and Remy Decoupes and Elena Arsevska and Mathieu Roche and Maguelonne Teisseire},
url = {https://www.ijidonline.com/article/S1201-9712(21)00957-7/pdf},
doi = {https://doi.org/10.1016/j.ijid.2021.12.065},
year = {2021},
date = {2021-11-06},
urldate = {2021-11-06},
journal = {International Journal of Infectious Diseases},
volume = {116},
issue = {549},
pages = {527},
abstract = {: In the first quarter of 2020, World Health Organization (WHO) declared COVID-19 as a public health emergency around the globe. Therefore, different users from all over the world shared their thoughts about COVID-19 on social media platforms i.e., Twitter, Facebook etc. So, it is important to analyze public opinions about COVID-19 from different regions over different period of time. To fulfill the spatial analysis issue, a previous work called H-TF-IDF (Hierarchy-based measure for tweet analysis) for term extraction from tweet data has been proposed. In this work, we focus on the sentiment analysis performed on terms selected by H-TFIDF for spatial tweets groups to know local situations during the ongoing epidemic COVID-19 over different time frames.},
keywords = {Covid-19 (Coronavirus), Text mining},
pubstate = {published},
tppubtype = {article}
}
: In the first quarter of 2020, World Health Organization (WHO) declared COVID-19 as a public health emergency around the globe. Therefore, different users from all over the world shared their thoughts about COVID-19 on social media platforms i.e., Twitter, Facebook etc. So, it is important to analyze public opinions about COVID-19 from different regions over different period of time. To fulfill the spatial analysis issue, a previous work called H-TF-IDF (Hierarchy-based measure for tweet analysis) for term extraction from tweet data has been proposed. In this work, we focus on the sentiment analysis performed on terms selected by H-TFIDF for spatial tweets groups to know local situations during the ongoing epidemic COVID-19 over different time frames.
47.
Faria, Nuno R.; Mellan, Thomas A.; Whittaker, Charles; Claro, Ingra M.; da S. Candido, Darlan; Mishra, Swapnil; Crispim, Myuki A. E.
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil Journal Article
In: Science, vol. 372, no. 6544, pp. 815-821, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil},
author = {Nuno R. Faria and Thomas A. Mellan and Charles Whittaker and Ingra M. Claro and Darlan da S. Candido and Swapnil Mishra and Myuki A. E. Crispim},
url = {https://www.science.org/doi/abs/10.1126/science.abh2644},
doi = {10.1126/science.abh2644},
year = {2021},
date = {2021-11-01},
urldate = {2021-11-01},
journal = {Science},
volume = {372},
number = {6544},
pages = {815-821},
abstract = {Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
46.
Hu, Maogui
Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China Journal Article
In: Clinical Infectious Diseases, vol. 75, iss. 1, pp. e234–e240, 2021, ISSN: 1058-4838.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{10.1093/cid/ciab836,,
title = {Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China },
author = {Maogui Hu et al.},
url = {https://academic.oup.com/cid/article/75/1/e234/6373518},
doi = {https://doi.org/10.1093/cid/ciab836},
issn = {1058-4838},
year = {2021},
date = {2021-09-21},
urldate = {2021-09-21},
journal = {Clinical Infectious Diseases},
volume = {75},
issue = {1},
pages = {e234–e240},
abstract = {Modern transportation plays a key role in the spread of severe acute respiratory syndrome coronavirus 2 (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 coronavirus disease 2019 (COVID-19) cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on 23 January 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travelers.In total, 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% confidence interval [CI] .43–.84%) and 0.33% (18/5400, 95% CI .21–.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 .4%–1.2%). The upper-bound AR increased from 0.7% (95% CI 0.5%–1.0%) to 1.2% (95% CI .4–3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travelers 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.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Modern transportation plays a key role in the spread of severe acute respiratory syndrome coronavirus 2 (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 coronavirus disease 2019 (COVID-19) cases and close contacts on domestic airplanes departing from Wuhan city in China before the lockdown on 23 January 2020, we estimated the upper and lower bounds of overall transmission risk of COVID-19 among travelers.In total, 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% confidence interval [CI] .43–.84%) and 0.33% (18/5400, 95% CI .21–.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 .4%–1.2%). The upper-bound AR increased from 0.7% (95% CI 0.5%–1.0%) to 1.2% (95% CI .4–3.3%) when the co-travel time increased from 2.0 hours to 3.3 hours.The ARs among travelers 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.
45.
Martin, Darren P; Weaver, Steven; Tegally, Houryiah; San, Emmanuel James; Shank, Stephen D; Wilkinson, Eduan; Giandhari, Jennifer; Naidoo, Sureshnee; Pillay, Yeshnee; Singh, Lavanya; Lessells, Richard J; NGS-SA,; (COG-UK), COVID-19 Genomics UK; Gupta, Ravindra K; Wertheim, Joel O; Nekturenko, Anton; Murrell, Ben; Harkins, Gordon W; Lemey, Philippe; MacLean, Oscar A; Robertson, David L; de Oliveira, Tulio; Pond, Sergei L Kosakovsky
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages Bachelor Thesis
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@bachelorthesis{nokey,
title = {The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages},
author = {Darren P Martin and Steven Weaver and Houryiah Tegally and Emmanuel James San and Stephen D Shank and Eduan Wilkinson and Jennifer Giandhari and Sureshnee Naidoo and Yeshnee Pillay and Lavanya Singh and Richard J Lessells and NGS-SA and COVID-19 Genomics UK (COG-UK) and Ravindra K Gupta and Joel O Wertheim and Anton Nekturenko and Ben Murrell and Gordon W Harkins and Philippe Lemey and Oscar A MacLean and David L Robertson and Tulio de Oliveira and Sergei L Kosakovsky Pond},
url = {https://doi.org/10.1016/j.cell.2021.09.003},
doi = {10.1016/j.cell.2021.09.003},
year = {2021},
date = {2021-09-06},
urldate = {2021-09-06},
journal = {Cell},
volume = {184},
issue = {20},
abstract = {The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {bachelorthesis}
}
The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.
44.
Mazzoli, Mattia; Valdano, Eugenio; Colizza, Vittoria
Projecting the COVID-19 epidemic risk in France for the summer 2021 Journal Article
In: Journal of Travel Medicine, vol. 28, no. 7, 2021, ISSN: 1708-8305.
Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{10.1093/jtm/taab129,
title = {Projecting the COVID-19 epidemic risk in France for the summer 2021},
author = {Mattia Mazzoli and Eugenio Valdano and Vittoria Colizza},
url = {https://academic.oup.com/jtm/article-pdf/28/7/taab129/41784325/taab129.pdf},
doi = {https://doi.org/10.1093/jtm/taab129},
issn = {1708-8305},
year = {2021},
date = {2021-08-19},
urldate = {2021-08-19},
journal = {Journal of Travel Medicine},
volume = {28},
number = {7},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
43.
Domenico, Laura Di; Colizza, Vittoria
Epidemic scenarios of Delta variant in France in the summer 2021 Technical Report
2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@techreport{nokey,
title = {Epidemic scenarios of Delta variant in France in the summer 2021},
author = {Laura Di Domenico and Vittoria Colizza},
url = {https://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm-covid-19-delta_projections_summer-20210710.pdf},
year = {2021},
date = {2021-07-10},
urldate = {2021-07-10},
abstract = {As the Delta variant rapidly progresses in France, with an estimated 43.2% of detected cases attributed to the L452R mutation in the week 26, concerns arise on the upcoming summer epidemic situation, also given the reported slowdown of vaccinations. This short report aims at presenting a range of possible epidemic scenarios, according to different hypotheses on vaccine administration rollout in the summer, conditions of mixing, seasonality and preventive measures, and considering different estimates for the transmissibility advantages of the circulating variants of concern. },
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {techreport}
}
As the Delta variant rapidly progresses in France, with an estimated 43.2% of detected cases attributed to the L452R mutation in the week 26, concerns arise on the upcoming summer epidemic situation, also given the reported slowdown of vaccinations. This short report aims at presenting a range of possible epidemic scenarios, according to different hypotheses on vaccine administration rollout in the summer, conditions of mixing, seasonality and preventive measures, and considering different estimates for the transmissibility advantages of the circulating variants of concern.
42.
Manica, Mattia; Pancheri, Serena; Poletti, Piero; Giovanazzi, Giulia; Guzzetta, Giorgio; Trentini, Filippo; Marziano, Valentina; Ajelli, Marco; Zuccali, Maria Grazia; Benetollo, Pier Paolo; Merler, Stefano; Ferro, Antonio
In: Clinical Infectious Diseases, vol. 74, no. 5, pp. 893-896, 2021, ISSN: 1058-4838.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Risk of Symptomatic Infection During a Second Coronavirus Disease 2019 Wave in Severe Acute Respiratory Syndrome Coronavirus 2–Seropositive Individuals },
author = {Mattia Manica and Serena Pancheri and Piero Poletti and Giulia Giovanazzi and Giorgio Guzzetta and Filippo Trentini and Valentina Marziano and Marco Ajelli and Maria Grazia Zuccali and Pier Paolo Benetollo and Stefano Merler and Antonio Ferro},
url = {https://academic.oup.com/cid/article/74/5/893/6301134},
doi = {10.1093/cid/ciab556},
issn = {1058-4838},
year = {2021},
date = {2021-06-16},
urldate = {2021-06-16},
journal = {Clinical Infectious Diseases},
volume = {74},
number = {5},
pages = {893-896},
abstract = {We analyzed 221 coronavirus disease 2019 cases identified between June 2020 and January 2021 in 6074 individuals screened for immunoglobulin G antibodies in May 2020, representing 77% of residents of 5 Italian municipalities. The relative risk of developing symptomatic infection in seropositive participants was 0.055 (95% confidence interval, .014–.220)},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
We analyzed 221 coronavirus disease 2019 cases identified between June 2020 and January 2021 in 6074 individuals screened for immunoglobulin G antibodies in May 2020, representing 77% of residents of 5 Italian municipalities. The relative risk of developing symptomatic infection in seropositive participants was 0.055 (95% confidence interval, .014–.220)
41.
Dellicour, Simon; Linard, Catherine; Goethem, Nina Van; Re, Daniele Da; Artois, Jean; Bihin, Jérémie; Schaus, Pierre; Massonnet, François; Oyen, Herman Van; Vanwambeke, Sophie O.; Speybroeck, Niko; Gilbert, Marius
Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence—Belgium as a study case Journal Article
In: International Journal of Health Geographics, iss. 20, no. 29, 2021, ISSN: 1476-072X.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence—Belgium as a study case},
author = {Simon Dellicour and Catherine Linard and Nina Van Goethem and Daniele Da Re and Jean Artois and Jérémie Bihin and Pierre Schaus and François Massonnet and Herman Van Oyen and Sophie O. Vanwambeke and Niko Speybroeck and Marius Gilbert },
url = {https://ij-healthgeographics.biomedcentral.com/articles/10.1186/s12942-021-00281-1},
doi = {https://doi.org/10.1186/s12942-021-00281-1},
issn = {1476-072X},
year = {2021},
date = {2021-06-14},
urldate = {2021-06-14},
journal = {International Journal of Health Geographics},
number = {29},
issue = {20},
abstract = {Background
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection.
Methods
To overcome these limitations, we propose an analytical framework to investigate potential drivers of the spatio–temporal heterogeneity in COVID-19 hospitalisation incidence when data are only available at the hospital level. Specifically, the approach is based on the delimitation of hospital catchment areas, which allows analysing associations between hospitalisation incidence and spatial or temporal covariates. We illustrate and apply our analytical framework to Belgium, a country heavily impacted by two COVID-19 epidemic waves in 2020, both in terms of mortality and hospitalisation incidence.
Results
Our spatial analyses reveal an association between the hospitalisation incidence and the local density of nursing home residents, which confirms the important impact of COVID-19 in elderly communities of Belgium. Our temporal analyses further indicate a pronounced seasonality in hospitalisation incidence associated with the seasonality of weather variables. Taking advantage of these associations, we discuss the feasibility of predictive models based on machine learning to predict future hospitalisation incidence.
Conclusion
Our reproducible analytical workflow allows performing spatially-explicit analyses of data aggregated at the hospital level and can be used to explore potential drivers and dynamic of COVID-19 hospitalisation incidence at regional or national scales.
40.
Decoupes, Rémy; Rodrique, Kafando; Roche, Mathieu; Teisseire, Maguelonne
H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic? Journal Article
In: AGILE: GIScience Series, vol. 2, no. 4, pp. 1-8, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{,
title = {H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic?},
author = {Rémy Decoupes and Kafando Rodrique and Mathieu Roche and Maguelonne Teisseire },
doi = {10.5194/agile-giss-2-2-2021},
year = {2021},
date = {2021-06-01},
urldate = {2021-06-01},
journal = {AGILE: GIScience Series},
volume = {2},
number = {4},
pages = {1-8},
publisher = {European Centre for Disease Prevention and Control},
abstract = {Data produced by social networks may contain weak signals of possible epidemic outbreaks. In this paper, we focus on Twitter data during the waiting period before the appearance of COVID-19 first cases outside China. Among the huge flow of tweets that reflects a global growing concern in all countries, we propose to analyze such data with an adaptation of the TF-IDF measure. It allows the users to extract the discriminant vocabularies used across time and space. The results are then discussed to show how the specific spatio-temporal anchoring of the extracted terms make it possible to follow the crisis dynamics on different scales of time and space.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Data produced by social networks may contain weak signals of possible epidemic outbreaks. In this paper, we focus on Twitter data during the waiting period before the appearance of COVID-19 first cases outside China. Among the huge flow of tweets that reflects a global growing concern in all countries, we propose to analyze such data with an adaptation of the TF-IDF measure. It allows the users to extract the discriminant vocabularies used across time and space. The results are then discussed to show how the specific spatio-temporal anchoring of the extracted terms make it possible to follow the crisis dynamics on different scales of time and space.
39.
Domenico, Laura Di; Sabbatini, Chiara E.; Pullano, Giulia; Lévy-Bruhl, Daniel; Colizza, Vittoria
Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France Journal Article
In: Eurosurveillance, vol. 26, iss. 15, no. 2, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{,
title = {Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France},
author = {Laura Di Domenico and Chiara E. Sabbatini and Giulia Pullano and Daniel Lévy-Bruhl and Vittoria Colizza},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.15.2100272},
doi = { 10.2807/1560-7917.ES.2021.26.15.2100272},
year = {2021},
date = {2021-04-15},
urldate = {2021-04-15},
journal = {Eurosurveillance},
volume = {26},
number = {2},
issue = {15},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.
38.
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: Covid-19 (Coronavirus), OpenDataSet
@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},
urldate = {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 = {Covid-19 (Coronavirus), OpenDataSet},
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.
37.
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 (Coronavirus), OpenDataSet
@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 (Coronavirus), OpenDataSet},
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.
36.
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: Covid-19 (Coronavirus)
@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 = {Covid-19 (Coronavirus)},
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.
35.
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: Covid-19 (Coronavirus), OpenDataSet
@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 = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
34.
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 (Coronavirus), OpenDataSet
@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 (Coronavirus), OpenDataSet},
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.
33.
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 (Coronavirus), OpenDataSet
@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 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
32.
Guzzetta, Giorgio; Riccardo, Flavia; Marziano, Valentina; Poletti, Piero; Trentini, Filippo; Bella, Antonino; Andrianou, Xanthi; Manso, Martina Del; Fabiani, Massimo; Bellino, Stefania; Boros, Stefano; Urdiales, Alberto Mateo; Vescio, Maria Fenicia; Piccioli, Andrea; Brusaferro, Silvio; Rezza, Giovanni; Pezzotti, Patrizio; Ajelli, Marco; Merler, Stefano; Group, COVID-19 Working
Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy Journal Article
In: Emerging Infectious Diseases, vol. 27, no. 1, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy},
author = {Giorgio Guzzetta and Flavia Riccardo and Valentina Marziano and Piero Poletti and Filippo Trentini and Antonino Bella and Xanthi Andrianou and Martina Del Manso and Massimo Fabiani and Stefania Bellino and Stefano Boros and Alberto Mateo Urdiales and Maria Fenicia Vescio and Andrea Piccioli and Silvio Brusaferro and Giovanni Rezza and Patrizio Pezzotti and Marco Ajelli and Stefano Merler and COVID-19 Working Group},
doi = {10.3201/eid2701.202114},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Emerging Infectious Diseases},
volume = {27},
number = {1},
abstract = {On March 11, 2020, Italy imposed a national lockdown to curtail the spread of severe acute respiratory syndrome coronavirus 2. We estimate that, 14 days after lockdown, the net reproduction number had dropped below 1 and remained stable at »0.76 (95% CI 0.67–0.85) in all regions for >3 of the following weeks.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
On March 11, 2020, Italy imposed a national lockdown to curtail the spread of severe acute respiratory syndrome coronavirus 2. We estimate that, 14 days after lockdown, the net reproduction number had dropped below 1 and remained stable at »0.76 (95% CI 0.67–0.85) in all regions for >3 of the following weeks.
31.
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: Nature Communications, vol. 12, no. 4570, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@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 = {Nature Communications},
volume = {12},
number = {4570},
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 (Coronavirus), OpenDataSet},
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.
30.
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: Nature Communications , vol. 12, no. 1073, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@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 = {10.1038/s41467-021-21249-6},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature Communications },
volume = {12},
number = {1073},
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 (Coronavirus), OpenDataSet},
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.
29.
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 (Coronavirus), OpenDataSet
@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 (Coronavirus), OpenDataSet},
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.