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  • Open Access English
    Authors: 
    Moritz U. G. Kraemer; Chia-Hung Yang; Bernardo Gutierrez; Chieh-Hsi Wu; Brennan Klein; David M. Pigott; Louis du Plessis; Nuno R. Faria; Ruoran Li; William P. Hanage; +7 more
    Publisher: American Association for the Advancement of Science
    Countries: France, United Kingdom, United Kingdom, United Kingdom
    Project: NIH | MIDAS Center for Communic... (1U54GM088558-01)

    The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19. One sentence summary: The spread of COVID-19 in China was driven by human mobility early on and mitigated substantially by drastic control measures implemented since the end of January.

  • Publication . Preprint . Article . 2022 . Embargo End Date: 01 Jan 2022
    Open Access
    Authors: 
    Fort, Gersende; Pascal, Barbara; Abry, Patrice; Pustelnik, Nelly;
    Publisher: arXiv
    Country: France

    Monitoring the Covid19 pandemic constitutes a critical societal stake that received considerable research efforts. The intensity of the pandemic on a given territory is efficiently measured by the reproduction number, quantifying the rate of growth of daily new infections. Recently, estimates for the time evolution of the reproduction number were produced using an inverse problem formulation with a nonsmooth functional minimization. While it was designed to be robust to the limited quality of the Covid19 data (outliers, missing counts), the procedure lacks the ability to output credibility interval based estimates. This remains a severe limitation for practical use in actual pandemic monitoring by epidemiologists that the present work aims to overcome by use of Monte Carlo sampling. After interpretation of the nonsmooth functional into a Bayesian framework, several sampling schemes are tailored to adjust the nonsmooth nature of the resulting posterior distribution. The originality of the devised algorithms stems from combining a Langevin Monte Carlo sampling scheme with Proximal operators. Performance of the new algorithms in producing relevant credibility intervals for the reproduction number estimates and denoised counts are compared. Assessment is conducted on real daily new infection counts made available by the Johns Hopkins University. The interest of the devised monitoring tools are illustrated on Covid19 data from several different countries.

  • English
    Authors: 
    Ulloa-Suárez, Carolina;
    Publisher: HAL CCSD
    Country: France

    The effects of the COVID-19 pandemic led many governments to suspend their fiscal rules to gain additional fiscal space to mitigate the social and economic consequences of the health crisis. As a result, the return and subsequent compliance with fiscal rules have been compromised, and the opportunity to improve them and consider the new global macroeconomic conditions has emerged. Understanding what elements relate to increased compliance with the rules and what has worked and has not can shed light on upcoming reforms. This paper uses an empirical model to investigate Latin American countries' factors influencing numerical compliance with fiscal rules. We associate three groups of specific factors with a greater or lesser probability of compliance with the rule: the macroeconomic and political environment of the countries and the design features of the enforced rules. We find that only changes in the macroeconomic and political context are associated with higher levels of compliance. In contrast, the institutional design of the fiscal rules does not seem to play an essential role in the compliance outcome. This result suggests that adjustments in this direction are not decisive for rule compliance.

  • French
    Authors: 
    Hantem, Aziz;
    Publisher: HAL CCSD
    Country: France
  • Open Access
    Authors: 
    Anthony Levasseur; Jeremy Delerce; Aurelia Caputo; Ludivine Brechard; Philippe Colson; Jean-Christophe Lagier; Pierre-Edouard Fournier; Didier Raoult;
    Publisher: Cold Spring Harbor Laboratory

    ABSTRACTThe novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

  • Open Access English
    Authors: 
    Paul Brandily; Clément Brébion; Simon Briole; Laura Khoury;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | PGSE (ANR-17-EURE-0001)

    Mortality inequalities remain substantial in many countries, and large shocks such as pandemics could amplify them further. The unequal distribution of COVID-19 confirmed cases suggests that this is the case. Yet, evidence on the causal effect of the epidemic on mortality inequalities remains scarce. In this paper, we exploit exhaustive municipality-level data in France, one of the most severely hit country in the world, to identify a negative relationship between income and excess mortality within urban areas, that persists over COVID-19 waves. Over the year 2020, the poorest municipalities experienced a 30% higher increase in excess mortality. Our analyses can rule out an independent contribution of lockdown policies to this heterogeneous impact. Finally, we find evidence that both labour-market exposure and housing conditions are major determinants of the epidemic-induced effects of COVID-19 on mortality inequalities, but that their respective role depends on the state of the epidemic.

  • English
    Authors: 
    Abidi, Hani; Amami, Rim; Trabelsi, Chiraz;
    Publisher: HAL CCSD
    Country: France

    The model descibes the epidemic dynamics of Covid-19 in a population after vaccination. Using the maximum principale, our goal is to prove the existence of an optimal strategy such that it minimize the number of infected people after vaccination. Finally, some numerical results are provided.

  • Open Access
    Authors: 
    Yves Levy; Aurélie Wiedemann; Boris P. Hejblum; Mélany Durand; Cécile Lefebvre; Mathieu Surenaud; Christine Lacabaratz; Matthieu Perreau; Emile Foucat; Marie Dechenaud; +13 more
    Publisher: Cold Spring Harbor Laboratory

    AbstractCOVID-19 SARS-CoV-2 infection exhibits wide inter-individual clinical variability, from silent infection to severe disease and death. The identification of high-risk patients is a continuing challenge in routine care. We aimed to identify factors that influence clinical worsening. We analyzed 52 cell populations, 71 analytes, and RNA-seq gene expression in the blood of severe patients from the French COVID cohort upon hospitalization (n = 61). COVID-19 patients showed severe abnormalities of 27 cell populations relative to healthy donors (HDs). Forty-two cytokines, neutrophil chemo-attractants, and inflammatory components were elevated in COVID-19 patients. Supervised gene expression analyses showed differential expression of genes for neutrophil activation, interferon signaling, T- and B-cell receptors, EIF2 signaling, and ICOS-ICOSL pathways in COVID-19 patients. Unsupervised analysis confirmed the prominent role of neutrophil activation, with a high abundance of CD177, a specific neutrophil activation marker. CD177 was the most highly differentially-expressed gene contributing to the clustering of severe patients and its abundance correlated with CD177 protein serum levels. CD177 levels were higher in COVID-19 patients from both the French and “confirmatory” Swiss cohort (n = 203) than in HDs (P< 0.01) and in ICU than non-ICU patients (P< 0.001), correlating with the time to symptoms onset (P = 0.002). Longitudinal measurements showed sustained levels of serum CD177 to discriminate between patients with the worst prognosis, leading to death, and those who recovered (P = 0.01). These results highlight neutrophil activation as a hallmark of severe disease and CD177 assessment as a reliable prognostic marker for routine care.

  • Open Access French
    Authors: 
    Bourbié, Thierry; Roche, Max; Chochillon, Christian; Fernandez, Corinne; Lagadec, Patrick; Hontebeyrie, Patrick;
    Publisher: HAL CCSD
    Country: France
  • Publication . Article . Preprint . 2020
    Open Access English
    Authors: 
    Alberto Alemanno;
    Publisher: HAL CCSD
    Country: France

    The European response to COVID-19 has revealed an inconvenient truth. Despite having integrated public health concerns across all its policies – be it agriculture, consumer protection, or security –, the Union cannot directly act to save people’s lives. Only member states can do so. Yet when they adopted unilateral measures to counter the spread of the virus, those proved not only ineffective but also disruptive on vital supply chains, by ultimately preventing the flow of essential goods and people across the Union. These fragmented efforts in tackling cross-border health threats have almost immediately prompted political calls for the urgent creation of a European Health Union. Yet this call raises more questions than answers. With the aim to offer a rigorous and timely blueprint to decision-makers and the public at large, this Special Issue of the European Journal of Risk Regulation contextualizes such a new political project within the broader constitutional and institutional framework of EU public health law and policy. By introducing the Special, this paper argues that unless the envisaged Health Union will tackle the root causes of what prevented the Union from effectively responding to COVID-19 – the divergent health capacity across the Union –, it might fall short of its declared objective of strengthening the EU’resilience for cross-border health threats.

Advanced search in
Research products
arrow_drop_down
Searching FieldsTerms
Any field
arrow_drop_down
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arrow_drop_down
Include:
1,686 Research products, page 1 of 169
  • Open Access English
    Authors: 
    Moritz U. G. Kraemer; Chia-Hung Yang; Bernardo Gutierrez; Chieh-Hsi Wu; Brennan Klein; David M. Pigott; Louis du Plessis; Nuno R. Faria; Ruoran Li; William P. Hanage; +7 more
    Publisher: American Association for the Advancement of Science
    Countries: France, United Kingdom, United Kingdom, United Kingdom
    Project: NIH | MIDAS Center for Communic... (1U54GM088558-01)

    The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19. One sentence summary: The spread of COVID-19 in China was driven by human mobility early on and mitigated substantially by drastic control measures implemented since the end of January.

  • Publication . Preprint . Article . 2022 . Embargo End Date: 01 Jan 2022
    Open Access
    Authors: 
    Fort, Gersende; Pascal, Barbara; Abry, Patrice; Pustelnik, Nelly;
    Publisher: arXiv
    Country: France

    Monitoring the Covid19 pandemic constitutes a critical societal stake that received considerable research efforts. The intensity of the pandemic on a given territory is efficiently measured by the reproduction number, quantifying the rate of growth of daily new infections. Recently, estimates for the time evolution of the reproduction number were produced using an inverse problem formulation with a nonsmooth functional minimization. While it was designed to be robust to the limited quality of the Covid19 data (outliers, missing counts), the procedure lacks the ability to output credibility interval based estimates. This remains a severe limitation for practical use in actual pandemic monitoring by epidemiologists that the present work aims to overcome by use of Monte Carlo sampling. After interpretation of the nonsmooth functional into a Bayesian framework, several sampling schemes are tailored to adjust the nonsmooth nature of the resulting posterior distribution. The originality of the devised algorithms stems from combining a Langevin Monte Carlo sampling scheme with Proximal operators. Performance of the new algorithms in producing relevant credibility intervals for the reproduction number estimates and denoised counts are compared. Assessment is conducted on real daily new infection counts made available by the Johns Hopkins University. The interest of the devised monitoring tools are illustrated on Covid19 data from several different countries.

  • English
    Authors: 
    Ulloa-Suárez, Carolina;
    Publisher: HAL CCSD
    Country: France

    The effects of the COVID-19 pandemic led many governments to suspend their fiscal rules to gain additional fiscal space to mitigate the social and economic consequences of the health crisis. As a result, the return and subsequent compliance with fiscal rules have been compromised, and the opportunity to improve them and consider the new global macroeconomic conditions has emerged. Understanding what elements relate to increased compliance with the rules and what has worked and has not can shed light on upcoming reforms. This paper uses an empirical model to investigate Latin American countries' factors influencing numerical compliance with fiscal rules. We associate three groups of specific factors with a greater or lesser probability of compliance with the rule: the macroeconomic and political environment of the countries and the design features of the enforced rules. We find that only changes in the macroeconomic and political context are associated with higher levels of compliance. In contrast, the institutional design of the fiscal rules does not seem to play an essential role in the compliance outcome. This result suggests that adjustments in this direction are not decisive for rule compliance.

  • French
    Authors: 
    Hantem, Aziz;
    Publisher: HAL CCSD
    Country: France
  • Open Access
    Authors: 
    Anthony Levasseur; Jeremy Delerce; Aurelia Caputo; Ludivine Brechard; Philippe Colson; Jean-Christophe Lagier; Pierre-Edouard Fournier; Didier Raoult;
    Publisher: Cold Spring Harbor Laboratory

    ABSTRACTThe novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

  • Open Access English
    Authors: 
    Paul Brandily; Clément Brébion; Simon Briole; Laura Khoury;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | PGSE (ANR-17-EURE-0001)

    Mortality inequalities remain substantial in many countries, and large shocks such as pandemics could amplify them further. The unequal distribution of COVID-19 confirmed cases suggests that this is the case. Yet, evidence on the causal effect of the epidemic on mortality inequalities remains scarce. In this paper, we exploit exhaustive municipality-level data in France, one of the most severely hit country in the world, to identify a negative relationship between income and excess mortality within urban areas, that persists over COVID-19 waves. Over the year 2020, the poorest municipalities experienced a 30% higher increase in excess mortality. Our analyses can rule out an independent contribution of lockdown policies to this heterogeneous impact. Finally, we find evidence that both labour-market exposure and housing conditions are major determinants of the epidemic-induced effects of COVID-19 on mortality inequalities, but that their respective role depends on the state of the epidemic.

  • English
    Authors: 
    Abidi, Hani; Amami, Rim; Trabelsi, Chiraz;
    Publisher: HAL CCSD
    Country: France

    The model descibes the epidemic dynamics of Covid-19 in a population after vaccination. Using the maximum principale, our goal is to prove the existence of an optimal strategy such that it minimize the number of infected people after vaccination. Finally, some numerical results are provided.

  • Open Access
    Authors: 
    Yves Levy; Aurélie Wiedemann; Boris P. Hejblum; Mélany Durand; Cécile Lefebvre; Mathieu Surenaud; Christine Lacabaratz; Matthieu Perreau; Emile Foucat; Marie Dechenaud; +13 more
    Publisher: Cold Spring Harbor Laboratory

    AbstractCOVID-19 SARS-CoV-2 infection exhibits wide inter-individual clinical variability, from silent infection to severe disease and death. The identification of high-risk patients is a continuing challenge in routine care. We aimed to identify factors that influence clinical worsening. We analyzed 52 cell populations, 71 analytes, and RNA-seq gene expression in the blood of severe patients from the French COVID cohort upon hospitalization (n = 61). COVID-19 patients showed severe abnormalities of 27 cell populations relative to healthy donors (HDs). Forty-two cytokines, neutrophil chemo-attractants, and inflammatory components were elevated in COVID-19 patients. Supervised gene expression analyses showed differential expression of genes for neutrophil activation, interferon signaling, T- and B-cell receptors, EIF2 signaling, and ICOS-ICOSL pathways in COVID-19 patients. Unsupervised analysis confirmed the prominent role of neutrophil activation, with a high abundance of CD177, a specific neutrophil activation marker. CD177 was the most highly differentially-expressed gene contributing to the clustering of severe patients and its abundance correlated with CD177 protein serum levels. CD177 levels were higher in COVID-19 patients from both the French and “confirmatory” Swiss cohort (n = 203) than in HDs (P< 0.01) and in ICU than non-ICU patients (P< 0.001), correlating with the time to symptoms onset (P = 0.002). Longitudinal measurements showed sustained levels of serum CD177 to discriminate between patients with the worst prognosis, leading to death, and those who recovered (P = 0.01). These results highlight neutrophil activation as a hallmark of severe disease and CD177 assessment as a reliable prognostic marker for routine care.

  • Open Access French
    Authors: 
    Bourbié, Thierry; Roche, Max; Chochillon, Christian; Fernandez, Corinne; Lagadec, Patrick; Hontebeyrie, Patrick;
    Publisher: HAL CCSD
    Country: France
  • Publication . Article . Preprint . 2020
    Open Access English
    Authors: 
    Alberto Alemanno;
    Publisher: HAL CCSD
    Country: France

    The European response to COVID-19 has revealed an inconvenient truth. Despite having integrated public health concerns across all its policies – be it agriculture, consumer protection, or security –, the Union cannot directly act to save people’s lives. Only member states can do so. Yet when they adopted unilateral measures to counter the spread of the virus, those proved not only ineffective but also disruptive on vital supply chains, by ultimately preventing the flow of essential goods and people across the Union. These fragmented efforts in tackling cross-border health threats have almost immediately prompted political calls for the urgent creation of a European Health Union. Yet this call raises more questions than answers. With the aim to offer a rigorous and timely blueprint to decision-makers and the public at large, this Special Issue of the European Journal of Risk Regulation contextualizes such a new political project within the broader constitutional and institutional framework of EU public health law and policy. By introducing the Special, this paper argues that unless the envisaged Health Union will tackle the root causes of what prevented the Union from effectively responding to COVID-19 – the divergent health capacity across the Union –, it might fall short of its declared objective of strengthening the EU’resilience for cross-border health threats.

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