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.
44.
Faucher, Benjamin; Assab, Rania; Roux, Jonathan; Levy-Bruhl, Daniel; Kiem, Cécile Tran; Cauchemez, Simon; Zanetti, Laura; Colizza, Vittoria; Boëlle, Pierre-Yves; Poletto, Chiara
Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19 Journal Article
In: Nature Communications, vol. 13, no. 1414, 2022.
Abstract | Links | BibTeX | Tags: COVID-19
@article{nokey,
title = {Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19},
author = {Benjamin Faucher and Rania Assab and Jonathan Roux and Daniel Levy-Bruhl and Cécile Tran Kiem and Simon Cauchemez and Laura Zanetti and Vittoria Colizza and Pierre-Yves Boëlle and Chiara Poletto},
url = {https://www.nature.com/articles/s41467-022-29015-y#Abs1},
doi = {10.1038/s41467-022-29015-y},
year = {2022},
date = {2022-03-17},
urldate = {2022-03-17},
journal = {Nature Communications},
volume = {13},
number = {1414},
abstract = {With vaccination against COVID-19 stalled in some countries, increasing vaccine accessibility and distribution could help keep transmission under control. Here, we study the impact of reactive vaccination targeting schools and workplaces where cases are detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, demographics, behavioural changes and social distancing. In most scenarios, reactive vaccination leads to a higher reduction in cases compared with non-reactive strategies using the same number of doses. The reactive strategy could however be less effective than a moderate/high pace mass vaccination program if initial vaccination coverage is high or disease incidence is low, because few people would be vaccinated around each case. In case of flare-ups, reactive vaccination could better mitigate spread if it is implemented quickly, is supported by enhanced test-trace-isolate and triggers an increased vaccine uptake. These results provide key information to plan an adaptive vaccination rollout.},
keywords = {COVID-19},
pubstate = {published},
tppubtype = {article}
}
With vaccination against COVID-19 stalled in some countries, increasing vaccine accessibility and distribution could help keep transmission under control. Here, we study the impact of reactive vaccination targeting schools and workplaces where cases are detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, demographics, behavioural changes and social distancing. In most scenarios, reactive vaccination leads to a higher reduction in cases compared with non-reactive strategies using the same number of doses. The reactive strategy could however be less effective than a moderate/high pace mass vaccination program if initial vaccination coverage is high or disease incidence is low, because few people would be vaccinated around each case. In case of flare-ups, reactive vaccination could better mitigate spread if it is implemented quickly, is supported by enhanced test-trace-isolate and triggers an increased vaccine uptake. These results provide key information to plan an adaptive vaccination rollout.
43.
Valdano, Eugenio; Lee, Jonggul; Rubrichi, Stefania; Colizza, Vittoria
Mobility during the first week of the second lockdown in France Technical Report
2021.
Abstract | Links | BibTeX | Tags: COVID-19, France, lock-down, surveillance
@techreport{nokey,
title = {Mobility during the first week of the second lockdown in France},
author = {Eugenio Valdano and Jonggul Lee and Stefania Rubrichi and Vittoria Colizza},
url = {http://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-lockdown2-mobility_20201112.pdf},
year = {2021},
date = {2021-12-11},
abstract = {France is on a second lockdown to stop the second wave of COVID-19. Closures and restrictions are
impacting mobility at different spatial and temporal scales. We use mobile phone data to analyze mobility
patterns during the first full working week of the current lockdown (Nov 2-6, 2020). We break down our
analysis by space (country-level, regional, local mobility), by time (weekly, daily, hourly), and by age class
(young, adults, seniors). We compare mobility patterns with the ones registered during the first full
working week of the first lockdown (Mar 23-27, 2020). Current mobility is down 33% below prepandemic levels, achieving a much smaller reduction than the 1st lockdown (67% below pre-pandemic
levels). Daytime mobility reductions follow daily averages, but modest reductions are observed during
morning rush hours – a key feature of the current lockdown, not shared by the previous one, and likely
due to keeping school opens and larger number of productive sectors open. An analysis of regional
mobility highlightsa split between most regions reaching below-average mobility reductions, and Île-deFrance reaching a markedly above-average reduction. Regional variations in this 2ndlockdown are
correlated with what measured in the 1st, but more pronounced. Analysis at a finer spatial scale shows
that higher-than-average reductions are concentrated in the Paris area, and close to the mountains. We
also measure a strong association between mobility reduction and socioeconomic indicators, indicating
that mobility restrictions are most effective among wealthier population strata, confirming results
already found during the 1st lockdown. Finally, we measure trafficamong France’s largest cities, and find
it to be consistently higher than during the 1st lockdown, when it all but stopped. Our analysis provides a
first quantitative assessment of the ongoing lockdown on population mobility patterns, comparing them
to the 1st lockdown. It helps evaluate the performance of current policies, and inform future possible
adjustments.},
keywords = {COVID-19, France, lock-down, surveillance},
pubstate = {published},
tppubtype = {techreport}
}
France is on a second lockdown to stop the second wave of COVID-19. Closures and restrictions are
impacting mobility at different spatial and temporal scales. We use mobile phone data to analyze mobility
patterns during the first full working week of the current lockdown (Nov 2-6, 2020). We break down our
analysis by space (country-level, regional, local mobility), by time (weekly, daily, hourly), and by age class
(young, adults, seniors). We compare mobility patterns with the ones registered during the first full
working week of the first lockdown (Mar 23-27, 2020). Current mobility is down 33% below prepandemic levels, achieving a much smaller reduction than the 1st lockdown (67% below pre-pandemic
levels). Daytime mobility reductions follow daily averages, but modest reductions are observed during
morning rush hours – a key feature of the current lockdown, not shared by the previous one, and likely
due to keeping school opens and larger number of productive sectors open. An analysis of regional
mobility highlightsa split between most regions reaching below-average mobility reductions, and Île-deFrance reaching a markedly above-average reduction. Regional variations in this 2ndlockdown are
correlated with what measured in the 1st, but more pronounced. Analysis at a finer spatial scale shows
that higher-than-average reductions are concentrated in the Paris area, and close to the mountains. We
also measure a strong association between mobility reduction and socioeconomic indicators, indicating
that mobility restrictions are most effective among wealthier population strata, confirming results
already found during the 1st lockdown. Finally, we measure trafficamong France’s largest cities, and find
it to be consistently higher than during the 1st lockdown, when it all but stopped. Our analysis provides a
first quantitative assessment of the ongoing lockdown on population mobility patterns, comparing them
to the 1st lockdown. It helps evaluate the performance of current policies, and inform future possible
adjustments.
impacting mobility at different spatial and temporal scales. We use mobile phone data to analyze mobility
patterns during the first full working week of the current lockdown (Nov 2-6, 2020). We break down our
analysis by space (country-level, regional, local mobility), by time (weekly, daily, hourly), and by age class
(young, adults, seniors). We compare mobility patterns with the ones registered during the first full
working week of the first lockdown (Mar 23-27, 2020). Current mobility is down 33% below prepandemic levels, achieving a much smaller reduction than the 1st lockdown (67% below pre-pandemic
levels). Daytime mobility reductions follow daily averages, but modest reductions are observed during
morning rush hours – a key feature of the current lockdown, not shared by the previous one, and likely
due to keeping school opens and larger number of productive sectors open. An analysis of regional
mobility highlightsa split between most regions reaching below-average mobility reductions, and Île-deFrance reaching a markedly above-average reduction. Regional variations in this 2ndlockdown are
correlated with what measured in the 1st, but more pronounced. Analysis at a finer spatial scale shows
that higher-than-average reductions are concentrated in the Paris area, and close to the mountains. We
also measure a strong association between mobility reduction and socioeconomic indicators, indicating
that mobility restrictions are most effective among wealthier population strata, confirming results
already found during the 1st lockdown. Finally, we measure trafficamong France’s largest cities, and find
it to be consistently higher than during the 1st lockdown, when it all but stopped. Our analysis provides a
first quantitative assessment of the ongoing lockdown on population mobility patterns, comparing them
to the 1st lockdown. It helps evaluate the performance of current policies, and inform future possible
adjustments.
42.
Pullano, Giulia; Domenico, Laura Di; Colizza, Vittoria
Telework and other measures reducing the presence at work to slow down COVID-19pdm in France (Sept 2020) Technical Report
2021.
Abstract | Links | BibTeX | Tags: COVID-19, epidemiology, France, measures
@techreport{nokey,
title = {Telework and other measures reducing the presence at work to slow down COVID-19pdm in France (Sept 2020)},
author = {Giulia Pullano and Laura Di Domenico and Vittoria Colizza},
url = {http://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-telework.pdf},
year = {2021},
date = {2021-11-28},
abstract = {COVID-19 pandemic shows a clear and substantial increase of activity in France since summer 2020.
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today},
keywords = {COVID-19, epidemiology, France, measures},
pubstate = {published},
tppubtype = {techreport}
}
COVID-19 pandemic shows a clear and substantial increase of activity in France since summer 2020.
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today
Certain regions are in highly vulnerable situations, with large number of hospitalizations per day,
important fraction of ICU beds occupied, and short doubling times (<2 weeks). At the same time,
activities are increasing since the beginning of September, with the reopening of schools and the return
to work after summer holidays (not yet reaching pre-pandemic levels), leaving further opportunities for
the virus to spread. Using mathematical models calibrated to the observed epidemic trajectory in each
region, this report analyzes possible scenarios of telework and other means to reduce the presence at
work, and assesses their impact on the epidemic trajectory in the following weeks. Numerical results
confirm that telework and other measures reducing the presence at work under realistic assumptions
may decelerate the epidemic curve gaining few weeks of time, but would not be enough to revert the
increasing tendency of the curve, unless coupled with other contact reduction measures. The situation is
particularly critical in IDF. In these conditions, if nothing changes, the level of hospitalizations of the peak
of the first wave is expected to be reached in IDF in about a month from now (earlier, if return to work
increases in the following weeks as suggested by the trend in the data and if not contrasted by telework).
Explicit guidance on telework and interventions to facilitate its application to all professional categories
who can adopt it should be urgently provided. This standard should be kept as a routine measure of
epidemic control for several months. More restrictive measures involving the closure of certain activities
to reduce avoidable contacts are urgently needed to slow down the epidemic increase to levels that are
manageable by the healthcare system. This analysis cannot account for the effect of the measures
implemented today
41.
Pullano, Giulia; Domenico, Laura Di; Sabbatini, Chiara E.; Colizza, Vittoria
Expected impact of exit strategies after the second lockdown - France, Nov 2020 Technical Report
2021.
Abstract | Links | BibTeX | Tags: COVID-19, France, lock-down, measures
@techreport{nokey,
title = {Expected impact of exit strategies after the second lockdown - France, Nov 2020},
author = {Giulia Pullano and Laura Di Domenico and Chiara E. Sabbatini and Vittoria Colizza},
url = {https://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-lockdown_schools_open-20201117.pdf},
year = {2021},
date = {2021-11-17},
abstract = {This report is an update of previous reports (Report #19, Report #21) on the expected impact of the
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow. },
keywords = {COVID-19, France, lock-down, measures},
pubstate = {published},
tppubtype = {techreport}
}
This report is an update of previous reports (Report #19, Report #21) on the expected impact of the
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow.
second lockdown implemented in France on Friday, October 30 to suppress the second wave of COVID-19
epidemic. We provide updated projections simulating a mild lockdown with schools open informed on the
estimates on mobility reduction recorded during the first week of lockdown from mobile phone data
(Report #22), and explore different exit strategies. The current report focuses on Île-de-France; analyses
for other regions will follow.
40.
Kraemer, Moritz U. G.; Fraser, Oliver G. Pybusand; Cauchemez, Christophe; Rambaut, Simon; Cowling, Andrew; Benjamin, J.
Monitoring key epidemiological parameters of SARS-CoV-2 transmission Journal Article
In: Nature Medicine, vol. 27, no. 1854–1855 , pp. 1–2, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, epidemiology, transmission
@article{kraemer2021monitoring,
title = {Monitoring key epidemiological parameters of SARS-CoV-2 transmission},
author = {Moritz U.G. Kraemer and Oliver G. Pybusand Fraser and Christophe Cauchemez and Simon Rambaut and Andrew Cowling and J. Benjamin},
doi = {https://doi.org/10.1038/s41591-021-01545-w},
year = {2021},
date = {2021-11-08},
urldate = {2021-11-08},
journal = {Nature Medicine},
volume = {27},
number = {1854–1855 },
pages = {1--2},
abstract = {Control of the SARS-CoV-2 pandemic requires targeted interventions, which in turn require precise estimates of quantities that describe transmission. Per-capita transmission rates are influenced by four quantities: (1) the latent period (time from infection to becoming infectious); (2) individual variability in infectiousness (defined by variation in intrinsic transmissibility and contact rate); (3) the incubation period (time from infection to symptom onset); and (4) the serial interval (time between symptom onset of an infector and an infected) (Fig. 1).},
keywords = {COVID-19, epidemiology, transmission},
pubstate = {published},
tppubtype = {article}
}
Control of the SARS-CoV-2 pandemic requires targeted interventions, which in turn require precise estimates of quantities that describe transmission. Per-capita transmission rates are influenced by four quantities: (1) the latent period (time from infection to becoming infectious); (2) individual variability in infectiousness (defined by variation in intrinsic transmissibility and contact rate); (3) the incubation period (time from infection to symptom onset); and (4) the serial interval (time between symptom onset of an infector and an infected) (Fig. 1).
39.
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: Brazil, COVID-19, epidemiology, phylogenetic
@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},
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 = {Brazil, COVID-19, epidemiology, phylogenetic},
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.
38.
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, disease x, EBS, infectious diseases, media extraction, monitoring
@article{nokey,
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},
url = {https://onlinelibrary.wiley.com/doi/10.1111/tbed.13738},
doi = {https://doi.org/10.1111/tbed.13738},
year = {2021},
date = {2021-07-19},
journal = {Transboundary and Emerging Diseases},
volume = {68},
number = {3},
pages = {981-986},
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, disease x, EBS, infectious diseases, media extraction, monitoring},
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.
37.
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, EBS, media extraction, Model, population dynamics, Public Health, Twitter
@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 = {2020-01-01},
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, EBS, media extraction, Model, population dynamics, Public Health, Twitter},
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.
36.
Domenico, Laura Di; Sabbatini, Chiara E.; Pullano, Giulia; Lévy-Bruhl, Daniel; Colizza, Vittoria
Impact of lockdown on COVID-19 epidemic in Ile-de-France and possible exit strategies Journal Article
In: medRxiv, no. 2, 2021.
Abstract | Links | BibTeX | Tags: COVID-19, epidemiology, Europe, Public Health
@article{,
title = {Impact of lockdown on COVID-19 epidemic in Ile-de-France and possible exit strategies},
author = {Laura Di Domenico and Chiara E. Sabbatini and Giulia Pullano and Daniel Lévy-Bruhl and Vittoria Colizza},
url = {https://www.medrxiv.org/content/10.1101/2021.02.14.21251708v2},
doi = { 10.2807/1560-7917.ES.2021.26.15.2100272},
year = {2021},
date = {2021-03-10},
urldate = {2021-03-10},
journal = {medRxiv},
number = {2},
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, epidemiology, Europe, Public Health},
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.
35.
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.
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.
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.
32.
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}
}
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: 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.
30.
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}
}
29.
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.
28.
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.
27.
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.
26.
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.
25.
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.