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.
43.
Domenico, Laura Di; Pullano, Giulia; Sabbatini, Chiara E.; Bo""elle, Pierre-Yves; Colizza, Vittoria
Modelling safe protocols for reopening schools during the COVID-19 pandemic in France Journal Article
In: 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.
42.
Valentin, Sarah; Mercier, Alizé; Lancelot, Renaud; Roche, Mathieu; Arsevska, Elena
Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID-19 emergence Journal Article
In: Transboundary and emerging diseases, vol. 68, no. 3, pp. 981–986, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (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.
41.
MacLean, Oscar A; Lytras, Spyros; Weaver, Steven; Singer, Joshua B; Boni, Maciej F; Lemey, Philippe; Pond, Sergei L Kosakovsky; Robertson, David L
Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen Journal Article
In: PLoS biology, vol. 19, no. 3, pp. e3001115, 2021.
Abstract | BibTeX | Tags: Covid-19 (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.
40.
Kraemer, MUG; Hill, V; Ruis, C; Dellicour, S; Bajaj, S; McCrone, JT; Baele, G; Parag, KV; Battle, AL; Gutierrez, B; Jackson, B; Colquhoun, R; O'Toole, A; Klein, B; Vespignani, A; Consortium, COVID-19 Genomics UK (COG-UK); Volz, E; Faria, NR; Aanensen, DM; NJ, NJ Loman; du Plessis, L; Cauchemez, S; A, A Rambaut; SV, SV Scarpino; Pybus, OG
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence Journal Article
In: Science, vol. 373, no. 6557, pp. 889-895, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{doi:10.1126/science.abj0113,
title = {Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence},
author = {MUG Kraemer and V Hill and C Ruis and S Dellicour and S Bajaj and JT McCrone and G Baele and KV Parag and AL Battle and B Gutierrez and B Jackson and R Colquhoun and A O'Toole and B Klein and A Vespignani and COVID-19 Genomics UK (COG-UK) Consortium and E Volz and NR Faria and DM Aanensen and NJ Loman NJ and L du Plessis and S Cauchemez and A Rambaut A and SV Scarpino SV and OG Pybus },
url = {https://www.science.org/doi/abs/10.1126/science.abj0113},
doi = {10.1126/science.abj0113},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Science},
volume = {373},
number = {6557},
pages = {889-895},
abstract = {The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al. explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. Disentangling the factors that contribute to the rapid spread of virus variants is essential for understanding their epidemiological consequences. Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al. explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. Disentangling the factors that contribute to the rapid spread of virus variants is essential for understanding their epidemiological consequences. Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
39.
Trentini, Filippo; Marziano, Valentina; Guzzetta, Giorgio; Tirani, Marcello; Cereda, Danilo; Poletti, Piero; Piccarreta, Raffaella; Barone, Antonio; Preziosi, Giuseppe; Arduini, Fabio; Valle, Petra Giulia Della; Zanella, Alberto; Grosso, Francesca; Castillo, Gabriele; Castrofino, Ambra; Grasselli, Giacomo; Melegaro, Alessia; Piatti, Alessandra; Andreassi, Aida; Gramegna, Maria; Ajelli, Marco; Merler, Stefano
In: American Journal of Epidemiology, 2021, ISSN: 0002-9262, (kwab252).
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{10.1093/aje/kwab252,
title = {Pressure on the Health-Care System and Intensive Care Utilization During the COVID-19 Outbreak in the Lombardy Region of Italy: A Retrospective Observational Study in 43,538 Hospitalized Patients},
author = {Filippo Trentini and Valentina Marziano and Giorgio Guzzetta and Marcello Tirani and Danilo Cereda and Piero Poletti and Raffaella Piccarreta and Antonio Barone and Giuseppe Preziosi and Fabio Arduini and Petra Giulia Della Valle and Alberto Zanella and Francesca Grosso and Gabriele Castillo and Ambra Castrofino and Giacomo Grasselli and Alessia Melegaro and Alessandra Piatti and Aida Andreassi and Maria Gramegna and Marco Ajelli and Stefano Merler},
url = {https://doi.org/10.1093/aje/kwab252},
doi = {10.1093/aje/kwab252},
issn = {0002-9262},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {American Journal of Epidemiology},
abstract = {During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-March 13), the period of highest pressure on healthcare (March 14-April 25, when COVID-19 patients exceeded the ICU pre-pandemic bed capacity), and the declining phase (April 26-July 12).Compared to the early phase, patients above 70 years of age were admitted less often to an ICU during highest pressure on healthcare (odds ratio OR 0.47, 95%CI: 0.41-0.54) with longer delays (incidence rate ratio IRR 1.82, 95%CI: 1.52-2.18), and lower chances of death in ICU (OR 0.47, 95%CI: 0.34-0.64). Patients under 56 years of age reported more limited changes in the probability (OR 0.65, 95%CI: 0.56-0.76) and delay to ICU admission (IRR 1.16, 95%CI: 0.95-1.42) and an increased mortality (OR 1.43, 95%CI: 1.00-2.07). In the declining phase, all quantities decreased for all age groups.These patterns may suggest that limited healthcare resources during the peak epidemic phase in Lombardy forced a shift in ICU admission criteria to prioritize patients with higher chances of survival.},
note = {kwab252},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-March 13), the period of highest pressure on healthcare (March 14-April 25, when COVID-19 patients exceeded the ICU pre-pandemic bed capacity), and the declining phase (April 26-July 12).Compared to the early phase, patients above 70 years of age were admitted less often to an ICU during highest pressure on healthcare (odds ratio OR 0.47, 95%CI: 0.41-0.54) with longer delays (incidence rate ratio IRR 1.82, 95%CI: 1.52-2.18), and lower chances of death in ICU (OR 0.47, 95%CI: 0.34-0.64). Patients under 56 years of age reported more limited changes in the probability (OR 0.65, 95%CI: 0.56-0.76) and delay to ICU admission (IRR 1.16, 95%CI: 0.95-1.42) and an increased mortality (OR 1.43, 95%CI: 1.00-2.07). In the declining phase, all quantities decreased for all age groups.These patterns may suggest that limited healthcare resources during the peak epidemic phase in Lombardy forced a shift in ICU admission criteria to prioritize patients with higher chances of survival.
38.
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.
37.
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}
}
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.
Pullano, Giulia; Domenico, Laura Di; Sabbatini, Chiara E; Valdano, Eugenio; Turbelin, Clément; Debin, Marion; Guerrisi, Caroline; Kengne-Kuetche, Charly; Souty, Cécile; Hanslik, Thomas; others,
Underdetection of cases of COVID-19 in France threatens epidemic control Journal Article
In: Nature, vol. 590, no. 7844, pp. 134–139, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{pullano2021underdetection,
title = {Underdetection of cases of COVID-19 in France threatens epidemic control},
author = {Giulia Pullano and Laura Di Domenico and Chiara E Sabbatini and Eugenio Valdano and Clément Turbelin and Marion Debin and Caroline Guerrisi and Charly Kengne-Kuetche and Cécile Souty and Thomas Hanslik and others},
doi = { https://doi.org/10.1038/s41586-020-03095-6},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature},
volume = {590},
number = {7844},
pages = {134--139},
publisher = {Nature Publishing Group},
abstract = {As countries in Europe gradually relaxed lockdown restrictions after the first wave, test–trace–isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6–8%) to 38% (35–44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
As countries in Europe gradually relaxed lockdown restrictions after the first wave, test–trace–isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6–8%) to 38% (35–44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.
34.
Lemey, Philippe; Ruktanonchai, Nick; Hong, Samuel L; Colizza, Vittoria; Poletto, Chiara; den Broeck, Frederik Van; Gill, Mandev S; Ji, Xiang; Levasseur, Anthony; Munnink, Bas B Oude; others,
Untangling introductions and persistence in COVID-19 resurgence in Europe Journal Article
In: Nature, vol. 595, no. 7869, pp. 713–717, 2021.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{lemey2021untangling,
title = {Untangling introductions and persistence in COVID-19 resurgence in Europe},
author = {Philippe Lemey and Nick Ruktanonchai and Samuel L Hong and Vittoria Colizza and Chiara Poletto and Frederik Van den Broeck and Mandev S Gill and Xiang Ji and Anthony Levasseur and Bas B Oude Munnink and others},
doi = {https://doi.org/10.1038/s41586-021-03754-2},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature},
volume = {595},
number = {7869},
pages = {713--717},
publisher = {Nature Publishing Group},
abstract = {After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.
33.
Oidtman, Rachel J; Omodei, Elisa; Kraemer, Moritz UG; Casteneda-Orjuela, Carlos A; Cruz-Rivera, Erica; Misnaza-Castrillon, Sandra; Cifuentes, Myriam Patricia; Rincon, Luz Emilse; Canon, Viviana; Alarcon, Pedro; others,
Trade-offs between individual and ensemble forecasts of an emerging infectious disease Journal Article
In: Nature Communications, vol. 12, no. 5379 , 2021.
Abstract | Links | BibTeX | Tags: OpenDataSet, Zika
@article{oidtman2021trade,
title = {Trade-offs between individual and ensemble forecasts of an emerging infectious disease},
author = {Rachel J Oidtman and Elisa Omodei and Moritz UG Kraemer and Carlos A Casteneda-Orjuela and Erica Cruz-Rivera and Sandra Misnaza-Castrillon and Myriam Patricia Cifuentes and Luz Emilse Rincon and Viviana Canon and Pedro Alarcon and others},
url = {https://www.nature.com/articles/s41467-021-25695-0},
doi = {https://doi.org/10.1038/s41467-021-25695-0},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nature Communications},
volume = {12},
number = {5379 },
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about human mobility, spatiotemporal variation in transmission potential, and the number of virus introductions. We found that which model assumptions had the most ensemble weight changed through time. We additionally identified a trade-off whereby some individual models outperformed ensemble models early in the epidemic, but on average the ensembles outperformed all individual models. Our results suggest that multiple models spanning uncertainty across alternative assumptions are necessary to obtain robust forecasts for emerging infectious diseases.},
keywords = {OpenDataSet, Zika},
pubstate = {published},
tppubtype = {article}
}
Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about human mobility, spatiotemporal variation in transmission potential, and the number of virus introductions. We found that which model assumptions had the most ensemble weight changed through time. We additionally identified a trade-off whereby some individual models outperformed ensemble models early in the epidemic, but on average the ensembles outperformed all individual models. Our results suggest that multiple models spanning uncertainty across alternative assumptions are necessary to obtain robust forecasts for emerging infectious diseases.
32.
Mateo-Urdiales, Alberto; Fabiani, Massimo; Rosano, Aldo; Vescio, Maria Fenicia; Manso, Martina Del; Bella, Antonino; Riccardo, Flavia; Pezzotti, Patrizio; Regidor, Enrique; Andrianou, Xanthi
Socioeconomic patterns and COVID-19 outcomes before, during and after the lockdown in Italy (2020) Journal Article
In: Health & Place, vol. 71, pp. 102642, 2021, ISSN: 1353-8292.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{MATEOURDIALES2021102642,
title = {Socioeconomic patterns and COVID-19 outcomes before, during and after the lockdown in Italy (2020)},
author = {Alberto Mateo-Urdiales and Massimo Fabiani and Aldo Rosano and Maria Fenicia Vescio and Martina Del Manso and Antonino Bella and Flavia Riccardo and Patrizio Pezzotti and Enrique Regidor and Xanthi Andrianou},
url = {https://www.sciencedirect.com/science/article/pii/S1353829221001386},
doi = {https://doi.org/10.1016/j.healthplace.2021.102642},
issn = {1353-8292},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Health & Place},
volume = {71},
pages = {102642},
abstract = {The objective was to investigate the association between deprivation and COVID-19 outcomes in Italy during pre-lockdown, lockdown and post-lockdown periods using a retrospective cohort study with 38,534,169 citizens and 222,875 COVID-19 cases. Multilevel negative binomial regression models, adjusting for age, sex, population-density and region of residence were conducted to evaluate the association between area-level deprivation and COVID-19 incidence, case-hospitalisation rate and case-fatality. During lockdown and post-lockdown, but not during pre-lockdown, higher incidence of cases was observed in the most deprived municipalities compared with the least deprived ones. No differences in case-hospitalisation and case-fatality according to deprivation were observed in any period under study.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
The objective was to investigate the association between deprivation and COVID-19 outcomes in Italy during pre-lockdown, lockdown and post-lockdown periods using a retrospective cohort study with 38,534,169 citizens and 222,875 COVID-19 cases. Multilevel negative binomial regression models, adjusting for age, sex, population-density and region of residence were conducted to evaluate the association between area-level deprivation and COVID-19 incidence, case-hospitalisation rate and case-fatality. During lockdown and post-lockdown, but not during pre-lockdown, higher incidence of cases was observed in the most deprived municipalities compared with the least deprived ones. No differences in case-hospitalisation and case-fatality according to deprivation were observed in any period under study.
31.
Marziano, Valentina; Guzzetta, Giorgio; Rondinone, Bruna Maria; Boccuni, Fabio; Riccardo, Flavia; Bella, Antonino; Poletti, Piero; Trentini, Filippo; Pezzotti, Patrizio; Brusaferro, Silvio; Rezza, Giovanni; Iavicoli, Sergio; Ajelli, Marco; Merler, Stefano
Retrospective analysis of the Italian exit strategy from COVID-19 lockdown Proceedings Article
In: National Academy of Sciences, 2021, ISSN: 0027-8424.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@inproceedings{Marzianoe2019617118,
title = {Retrospective analysis of the Italian exit strategy from COVID-19 lockdown},
author = {Valentina Marziano and Giorgio Guzzetta and Bruna Maria Rondinone and Fabio Boccuni and Flavia Riccardo and Antonino Bella and Piero Poletti and Filippo Trentini and Patrizio Pezzotti and Silvio Brusaferro and Giovanni Rezza and Sergio Iavicoli and Marco Ajelli and Stefano Merler},
url = {https://www.pnas.org/content/118/4/e2019617118},
doi = {10.1073/pnas.2019617118},
issn = {0027-8424},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {118},
number = {4},
publisher = {National Academy of Sciences},
abstract = {We use a mathematical model to evaluate the Italian exit strategy after the lockdown imposed against the COVID-19 epidemics, comparing it to a number of alternative scenarios. We highlight that a successful reopening requires two critical conditions: a low value of the reproduction number and a low incidence of infection. The first is needed to allow some margin for expansion after the lifting of restrictions; the second is needed because the level of incidence will be maintained approximately constant after the reproduction number has grown to values close to one. Furthermore, we suggest that, even with significant reductions of transmission rates, resuming social contacts at prepandemic levels escalates quickly the COVID-19 burden.After the national lockdown imposed on March 11, 2020, the Italian government has gradually resumed the suspended economic and social activities since May 4, while maintaining the closure of schools until September 14. We use a model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission to estimate the health impact of different exit strategies. The strategy adopted in Italy kept the reproduction number Rt at values close to one until the end of September, with marginal regional differences. Based on the estimated postlockdown transmissibility, reopening of workplaces in selected industrial activities might have had a minor impact on the transmissibility. Reopening educational levels in May up to secondary schools might have influenced SARS-CoV-2 transmissibility only marginally; however, including high schools might have resulted in a marked increase of the disease burden. Earlier reopening would have resulted in disproportionately higher hospitalization incidence. Given community contacts in September, we project a large second wave associated with school reopening in the fall.Epidemic curves by date of symptom onset and hospital admission have been deposited in Zenodo (10.5281/zenodo.4300101).},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {inproceedings}
}
We use a mathematical model to evaluate the Italian exit strategy after the lockdown imposed against the COVID-19 epidemics, comparing it to a number of alternative scenarios. We highlight that a successful reopening requires two critical conditions: a low value of the reproduction number and a low incidence of infection. The first is needed to allow some margin for expansion after the lifting of restrictions; the second is needed because the level of incidence will be maintained approximately constant after the reproduction number has grown to values close to one. Furthermore, we suggest that, even with significant reductions of transmission rates, resuming social contacts at prepandemic levels escalates quickly the COVID-19 burden.After the national lockdown imposed on March 11, 2020, the Italian government has gradually resumed the suspended economic and social activities since May 4, while maintaining the closure of schools until September 14. We use a model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission to estimate the health impact of different exit strategies. The strategy adopted in Italy kept the reproduction number Rt at values close to one until the end of September, with marginal regional differences. Based on the estimated postlockdown transmissibility, reopening of workplaces in selected industrial activities might have had a minor impact on the transmissibility. Reopening educational levels in May up to secondary schools might have influenced SARS-CoV-2 transmissibility only marginally; however, including high schools might have resulted in a marked increase of the disease burden. Earlier reopening would have resulted in disproportionately higher hospitalization incidence. Given community contacts in September, we project a large second wave associated with school reopening in the fall.Epidemic curves by date of symptom onset and hospital admission have been deposited in Zenodo (10.5281/zenodo.4300101).
30.
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.
29.
Lemey, Philippe; Hong, Samuel L; Hill, Verity; Baele, Guy; Poletto, Chiara; Colizza, Vittoria; O’Toole, Áine; McCrone, John T.; Andersen, Kristian G.; Worobey, Michael; Nelson, Martha I.; Rambaut, Andrew; Suchard, Marc A.
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 Journal Article
In: Nature Communications, vol. 11, no. 5110, 2020.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2},
author = {Philippe Lemey and Samuel L Hong and Verity Hill and Guy Baele and Chiara Poletto and Vittoria Colizza and Áine O’Toole and John T. McCrone and Kristian G. Andersen and Michael Worobey and Martha I. Nelson and Andrew Rambaut and Marc A. Suchard },
doi = {https://doi.org/10.1038/s41467-020-18877-9},
year = {2020},
date = {2020-10-09},
urldate = {2020-10-09},
journal = {Nature Communications},
volume = {11},
number = {5110},
abstract = {Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.
28.
The emergence of SARS-CoV-2 in Europe and North America Journal Article
In: Science, vol. 370, no. 6516, pp. 564-570, 2020.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {The emergence of SARS-CoV-2 in Europe and North America},
url = {https://www.science.org/doi/10.1126/science.abc8169},
doi = {https://doi.org/10.1126/science.abc8169},
year = {2020},
date = {2020-09-10},
urldate = {2020-09-10},
journal = {Science},
volume = {370},
number = {6516},
pages = {564-570},
abstract = {Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks. Here we elucidate when, where, and how the earliest sustained severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission networks became established in Europe and North America. Our results suggest that rapid early interventions successfully prevented early introductions of the virus from taking hold in Germany and the United States. Other, later introductions of the virus from China to both Italy and Washington state, United States, founded the earliest sustained European and North America transmission networks. Our analyses demonstrate the effectiveness of public health measures in preventing onward transmission and show that intensive testing and contact tracing could have prevented SARS-CoV-2 outbreaks from becoming established in these regions.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks. Here we elucidate when, where, and how the earliest sustained severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission networks became established in Europe and North America. Our results suggest that rapid early interventions successfully prevented early introductions of the virus from taking hold in Germany and the United States. Other, later introductions of the virus from China to both Italy and Washington state, United States, founded the earliest sustained European and North America transmission networks. Our analyses demonstrate the effectiveness of public health measures in preventing onward transmission and show that intensive testing and contact tracing could have prevented SARS-CoV-2 outbreaks from becoming established in these regions.
27.
Domenico, Laura Di
Impact of lockdown on COVID-19 epidemic in Île-de-France and possible exit strategies Journal Article
In: 2020.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Impact of lockdown on COVID-19 epidemic in Île-de-France and possible exit strategies},
author = {Laura Di Domenico et al.},
url = {https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-020-01698-4#article-info},
doi = {10.1186/s12916-020-01698-4},
year = {2020},
date = {2020-07-30},
urldate = {2020-07-30},
abstract = {Background
More than half of the global population is under strict forms of social distancing. Estimating the expected impact of lockdown and exit strategies is critical to inform decision makers on the management of the COVID-19 health crisis.
Methods
We use a stochastic age-structured transmission model integrating data on age profile and social contacts in Île-de-France to (i) assess the epidemic in the region, (ii) evaluate the impact of lockdown, and (iii) propose possible exit strategies and estimate their effectiveness. The model is calibrated to hospital admission data before lockdown. Interventions are modeled by reconstructing the associated changes in the contact matrices and informed by mobility reductions during lockdown evaluated from mobile phone data. Different types and durations of social distancing are simulated, including progressive and targeted strategies, with large-scale testing.
Results
We estimate the reproductive number at 3.18 [3.09, 3.24] (95% confidence interval) prior to lockdown and at 0.68 [0.66, 0.69] during lockdown, thanks to an 81% reduction of the average number of contacts. Model predictions capture the disease dynamics during lockdown, showing the epidemic curve reaching ICU system capacity, largely strengthened during the emergency, and slowly decreasing. Results suggest that physical contacts outside households were largely avoided during lockdown. Lifting the lockdown with no exit strategy would lead to a second wave overwhelming the healthcare system, if conditions return to normal. Extensive case finding and isolation are required for social distancing strategies to gradually relax lockdown constraints.
Conclusions
As France experiences the first wave of COVID-19 pandemic in lockdown, intensive forms of social distancing are required in the upcoming months due to the currently low population immunity. Extensive case finding and isolation would allow the partial release of the socio-economic pressure caused by extreme measures, while avoiding healthcare demand exceeding capacity. Response planning needs to urgently prioritize the logistics and capacity for these interventions.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background
More than half of the global population is under strict forms of social distancing. Estimating the expected impact of lockdown and exit strategies is critical to inform decision makers on the management of the COVID-19 health crisis.
Methods
We use a stochastic age-structured transmission model integrating data on age profile and social contacts in Île-de-France to (i) assess the epidemic in the region, (ii) evaluate the impact of lockdown, and (iii) propose possible exit strategies and estimate their effectiveness. The model is calibrated to hospital admission data before lockdown. Interventions are modeled by reconstructing the associated changes in the contact matrices and informed by mobility reductions during lockdown evaluated from mobile phone data. Different types and durations of social distancing are simulated, including progressive and targeted strategies, with large-scale testing.
Results
We estimate the reproductive number at 3.18 [3.09, 3.24] (95% confidence interval) prior to lockdown and at 0.68 [0.66, 0.69] during lockdown, thanks to an 81% reduction of the average number of contacts. Model predictions capture the disease dynamics during lockdown, showing the epidemic curve reaching ICU system capacity, largely strengthened during the emergency, and slowly decreasing. Results suggest that physical contacts outside households were largely avoided during lockdown. Lifting the lockdown with no exit strategy would lead to a second wave overwhelming the healthcare system, if conditions return to normal. Extensive case finding and isolation are required for social distancing strategies to gradually relax lockdown constraints.
Conclusions
As France experiences the first wave of COVID-19 pandemic in lockdown, intensive forms of social distancing are required in the upcoming months due to the currently low population immunity. Extensive case finding and isolation would allow the partial release of the socio-economic pressure caused by extreme measures, while avoiding healthcare demand exceeding capacity. Response planning needs to urgently prioritize the logistics and capacity for these interventions.
More than half of the global population is under strict forms of social distancing. Estimating the expected impact of lockdown and exit strategies is critical to inform decision makers on the management of the COVID-19 health crisis.
Methods
We use a stochastic age-structured transmission model integrating data on age profile and social contacts in Île-de-France to (i) assess the epidemic in the region, (ii) evaluate the impact of lockdown, and (iii) propose possible exit strategies and estimate their effectiveness. The model is calibrated to hospital admission data before lockdown. Interventions are modeled by reconstructing the associated changes in the contact matrices and informed by mobility reductions during lockdown evaluated from mobile phone data. Different types and durations of social distancing are simulated, including progressive and targeted strategies, with large-scale testing.
Results
We estimate the reproductive number at 3.18 [3.09, 3.24] (95% confidence interval) prior to lockdown and at 0.68 [0.66, 0.69] during lockdown, thanks to an 81% reduction of the average number of contacts. Model predictions capture the disease dynamics during lockdown, showing the epidemic curve reaching ICU system capacity, largely strengthened during the emergency, and slowly decreasing. Results suggest that physical contacts outside households were largely avoided during lockdown. Lifting the lockdown with no exit strategy would lead to a second wave overwhelming the healthcare system, if conditions return to normal. Extensive case finding and isolation are required for social distancing strategies to gradually relax lockdown constraints.
Conclusions
As France experiences the first wave of COVID-19 pandemic in lockdown, intensive forms of social distancing are required in the upcoming months due to the currently low population immunity. Extensive case finding and isolation would allow the partial release of the socio-economic pressure caused by extreme measures, while avoiding healthcare demand exceeding capacity. Response planning needs to urgently prioritize the logistics and capacity for these interventions.
26.
Pinotti, Francesco; Domenico, Laura Di; Ortega, Ernesto; Mancastroppa, Marco; Pullano, Giulia; Valdano, Eugenio; Boëlle, Pierre-Yves; Poletto, Chiara; Colizza, Vittoria
Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study Journal Article
In: PLOS Medicine, vol. 17, no. 7, pp. 1-13, 2020.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study},
author = {Francesco Pinotti and Laura Di Domenico and Ernesto Ortega and Marco Mancastroppa and Giulia Pullano and Eugenio Valdano and Pierre-Yves Boëlle and Chiara Poletto and Vittoria Colizza },
doi = {https://doi.org/10.1371/journal.pmed.1003193},
year = {2020},
date = {2020-07-01},
urldate = {2020-07-01},
journal = {PLOS Medicine},
volume = {17},
number = {7},
pages = {1-13},
abstract = {Background In the early months of 2020, a novel coronavirus disease (COVID-19) spread rapidly from China across multiple countries worldwide. As of March 17, 2020, COVID-19 was officially declared a pandemic by the World Health Organization. We collected data on COVID-19 cases outside China during the early phase of the pandemic and used them to predict trends in importations and quantify the proportion of undetected imported cases. Methods and findings Two hundred and eighty-eight cases have been confirmed out of China from January 3 to February 13, 2020. We collected and synthesized all available information on these cases from official sources and media. We analyzed importations that were successfully isolated and those leading to onward transmission. We modeled their number over time, in relation to the origin of travel (Hubei province, other Chinese provinces, other countries) and interventions. We characterized the importation timeline to assess the rapidity of isolation and epidemiologically linked clusters to estimate the rate of detection. We found a rapid exponential growth of importations from Hubei, corresponding to a doubling time of 2.8 days, combined with a slower growth from the other areas. We predicted a rebound of importations from South East Asia in the successive weeks. Time from travel to detection has considerably decreased since first importation, from 14.5 ± 5.5 days on January 5, 2020, to 6 ± 3.5 days on February 1, 2020. However, we estimated 36% of detection of imported cases. This study is restricted to the early phase of the pandemic, when China was the only large epicenter and foreign countries had not discovered extensive local transmission yet. Missing information in case history was accounted for through modeling and imputation. Conclusions Our findings indicate that travel bans and containment strategies adopted in China were effective in reducing the exportation growth rate. However, the risk of importation was estimated to increase again from other sources in South East Asia. Surveillance and management of traveling cases represented a priority in the early phase of the epidemic. With the majority of imported cases going undetected (6 out of 10), countries experienced several undetected clusters of chains of local transmissions, fueling silent epidemics in the community. These findings become again critical to prevent second waves, now that countries have reduced their epidemic activity and progressively phase out lockdown},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background In the early months of 2020, a novel coronavirus disease (COVID-19) spread rapidly from China across multiple countries worldwide. As of March 17, 2020, COVID-19 was officially declared a pandemic by the World Health Organization. We collected data on COVID-19 cases outside China during the early phase of the pandemic and used them to predict trends in importations and quantify the proportion of undetected imported cases. Methods and findings Two hundred and eighty-eight cases have been confirmed out of China from January 3 to February 13, 2020. We collected and synthesized all available information on these cases from official sources and media. We analyzed importations that were successfully isolated and those leading to onward transmission. We modeled their number over time, in relation to the origin of travel (Hubei province, other Chinese provinces, other countries) and interventions. We characterized the importation timeline to assess the rapidity of isolation and epidemiologically linked clusters to estimate the rate of detection. We found a rapid exponential growth of importations from Hubei, corresponding to a doubling time of 2.8 days, combined with a slower growth from the other areas. We predicted a rebound of importations from South East Asia in the successive weeks. Time from travel to detection has considerably decreased since first importation, from 14.5 ± 5.5 days on January 5, 2020, to 6 ± 3.5 days on February 1, 2020. However, we estimated 36% of detection of imported cases. This study is restricted to the early phase of the pandemic, when China was the only large epicenter and foreign countries had not discovered extensive local transmission yet. Missing information in case history was accounted for through modeling and imputation. Conclusions Our findings indicate that travel bans and containment strategies adopted in China were effective in reducing the exportation growth rate. However, the risk of importation was estimated to increase again from other sources in South East Asia. Surveillance and management of traveling cases represented a priority in the early phase of the epidemic. With the majority of imported cases going undetected (6 out of 10), countries experienced several undetected clusters of chains of local transmissions, fueling silent epidemics in the community. These findings become again critical to prevent second waves, now that countries have reduced their epidemic activity and progressively phase out lockdown
25.
Valentin, Sarah; Lancelot, Renaud; Roche, Mathieu
Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases Proceedings Article
In: Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing (MultilingualBIO 2020), pp. 33–36, European Language Resources Association, Marseille, France, 2020, ISBN: 979-10-95546-65-8.
Abstract | Links | BibTeX | Tags: Text mining
@inproceedings{valentin-etal-2020-automated,
title = {Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases},
author = {Sarah Valentin and Renaud Lancelot and Mathieu Roche},
url = {https://aclanthology.org/2020.multilingualbio-1.6},
isbn = {979-10-95546-65-8},
year = {2020},
date = {2020-05-01},
urldate = {2020-05-01},
booktitle = {Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing (MultilingualBIO 2020)},
pages = {33--36},
publisher = {European Language Resources Association},
address = {Marseille, France},
abstract = {The Platform for Automated extraction of animal Disease Information from the web (PADI-web) is an automated system which monitors the web for monitoring and detecting emerging animal infectious diseases. The tool automatically collects news via customised multilingual queries, classifies them and extracts epidemiological information. We detail the processing of multilingual online sources by PADI-web and analyse the translated outputs in a case study},
keywords = {Text mining},
pubstate = {published},
tppubtype = {inproceedings}
}
The Platform for Automated extraction of animal Disease Information from the web (PADI-web) is an automated system which monitors the web for monitoring and detecting emerging animal infectious diseases. The tool automatically collects news via customised multilingual queries, classifies them and extracts epidemiological information. We detail the processing of multilingual online sources by PADI-web and analyse the translated outputs in a case study
24.
Domenico, Laura Di; Pullano, Giulia; Coletti, Pietro; Hens, Niel; Colizza, Vittoria
Expected impact of school closure and telework to mitigate COVID-19 epidemic in France Technical Report
2020.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@techreport{nokey,
title = {Expected impact of school closure and telework to mitigate COVID-19 epidemic in France },
author = {Laura Di Domenico and Giulia Pullano and Pietro Coletti and Niel Hens and Vittoria Colizza},
url = {https://www.epicx-lab.com/uploads/9/6/9/4/9694133/inserm_covid-19-school-closure-french-regions_20200313.pdf},
year = {2020},
date = {2020-03-14},
urldate = {2020-03-14},
abstract = {With COVID-19 now a global pandemic, several countries face sustained and extensive epidemic spread in their territories. Forty-nine countries have announced or implemented school closures to mitigate the epidemic, 30 of which are nationwide (including China, Republic of Korea, Japan, Italy, France). French authorities announced on March 12, 2020 that school closure will be implemented nationwide starting March 16. These measures have been evaluated for seasonal or pandemic influenza, but their effectiveness for COVID-19 remains unclear. Focusing on the 3 regions in France reporting more than 300 confirmed cases (as of March 13, 2020) and showing an increase in the influenza-like-illness incidence from sentinel surveillance (Île-de-France, Hauts-de-France, Grand Est), we evaluate the impact of school closure and telework through a stochastic age-structured data-driven epidemic model. The model is based on demographic and social contact data between children and adults for each region, and is parameterized to COVID-19 epidemic, accounting for current uncertainties in the relative susceptibility and transmissibility of children. Numerical results show that school closure alone would have limited benefit in reducing the peak incidence (less than 10% reduction with 8-week school closure for regions in the early phase of the epidemic). When coupled with 25% adults teleworking, 8-week school closure would be enough to delay the peak by almost 2 months with an approximately 40% reduction of the case incidence at the peak. This is critical to reduce the burden on the healthcare system in the weeks of highest demand. Moderate overall reduction of the final attack rate (15%) would also be achieved. Results across regions are qualitatively similar, with differences in predictions due to different age profiles, the current epidemic situation, and epidemic growth. Different hypotheses on children 2 epicx-lab.com susceptibility and infectivity relative to adults show similar epidemic and intervention outcomes. Explicit guidance on telework and interventions to facilitate its application to all professional categories who can adopt it should be urgently provided. These findings help informing countries to prepare for effective COVID-19 epidemic mitigation. },
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {techreport}
}
With COVID-19 now a global pandemic, several countries face sustained and extensive epidemic spread in their territories. Forty-nine countries have announced or implemented school closures to mitigate the epidemic, 30 of which are nationwide (including China, Republic of Korea, Japan, Italy, France). French authorities announced on March 12, 2020 that school closure will be implemented nationwide starting March 16. These measures have been evaluated for seasonal or pandemic influenza, but their effectiveness for COVID-19 remains unclear. Focusing on the 3 regions in France reporting more than 300 confirmed cases (as of March 13, 2020) and showing an increase in the influenza-like-illness incidence from sentinel surveillance (Île-de-France, Hauts-de-France, Grand Est), we evaluate the impact of school closure and telework through a stochastic age-structured data-driven epidemic model. The model is based on demographic and social contact data between children and adults for each region, and is parameterized to COVID-19 epidemic, accounting for current uncertainties in the relative susceptibility and transmissibility of children. Numerical results show that school closure alone would have limited benefit in reducing the peak incidence (less than 10% reduction with 8-week school closure for regions in the early phase of the epidemic). When coupled with 25% adults teleworking, 8-week school closure would be enough to delay the peak by almost 2 months with an approximately 40% reduction of the case incidence at the peak. This is critical to reduce the burden on the healthcare system in the weeks of highest demand. Moderate overall reduction of the final attack rate (15%) would also be achieved. Results across regions are qualitatively similar, with differences in predictions due to different age profiles, the current epidemic situation, and epidemic growth. Different hypotheses on children 2 epicx-lab.com susceptibility and infectivity relative to adults show similar epidemic and intervention outcomes. Explicit guidance on telework and interventions to facilitate its application to all professional categories who can adopt it should be urgently provided. These findings help informing countries to prepare for effective COVID-19 epidemic mitigation.