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  • Publication . Part of book or chapter of book . 2022
    Open Access English
    Authors: 
    Richard Paul; Olivier Telle; Samuel Benkimoun;
    Publisher: HAL CCSD
    Country: France

    International audience; The SARS-CoV-2 pandemic has led to the implementation of unprecedented public health intervention measures, not least the lockdown of countries worldwide. In our hyperconnected world exemplified by social media, it is now possible to derive quantitative measures of human mobilities at useful spatial scales. In this chapter we discuss how the use of Facebook data enables us not only to capture the impact of lockdown on human mobility but also to assess how changes in mobility contribute to the spread of the virus. By performing a comparative analysis across four countries of differing levels of lockdown—Sweden, US, France and Colombia—we show that mobility contributes a substantial amount to the spread of the disease. This contribution is strongest when the local number of cases is low, but, importantly, is maintained even when the virus is widespread. Current epidemiological models do not take into account such mobility patterns and yet there exists a developed theoretical framework within which mobility can be included. Inclusion of mobility data would allow public health authorities to focus on highly connected hubs of infection and, because mobility patterns are relatively stable over time, would also enable forecasting of how the spread of this or another novel virus is going to occur. Anticipating epidemics and their spread is key for developing suitable but targeted intervention strategies and avoiding draconian lockdowns that are so harmful to the economy.

  • Open Access English
    Authors: 
    Quentin Pagneux; Alain Roussel; Hiba Saada; Christian Cambillau; Béatrice Amigues; Vincent Delauzun; Ilka Engelmann; Enagnon Kazali Alidjinou; Judith Ogiez; Anne Sophie Rolland; +6 more
    Publisher: HAL CCSD
    Country: France

    Abstract Background An ongoing need during the COVID-19 pandemic has been the requirement for accurate and efficient point-of-care testing platforms to distinguish infected from non-infected people, and to differentiate SARS-CoV-2 infections from other viruses. Electrochemical platforms can detect the virus via its envelope spike protein by recording changes in voltammetric signals between samples. However, this remains challenging due to the limited sensitivity of these sensing platforms. Methods Here, we report on a nanobody-functionalized electrochemical platform for the rapid detection of whole SARS-CoV-2 viral particles in complex media such as saliva and nasopharyngeal swab samples. The sensor relies on the functionalization of gold electrode surface with highly-oriented Llama nanobodies specific to the spike protein receptor binding domain (RBD). The device provides results in 10 min of exposure to 200 µL of unprocessed samples with high specificity to SARS-CoV-2 viral particles in human saliva and nasopharyngeal swab samples. Results The developed sensor could discriminate between different human coronavirus strains and other respiratory viruses, with 90% positive and 90% negative percentage agreement on 80 clinical samples, as compared to RT-qPCR. Conclusions We believe this diagnostic concept, also validated for RBD mutants and successfully tested on Delta variant samples, to be a powerful tool to detect patients’ infection status, easily extendable to other viruses and capable of overcoming sensing-related mutation effects.

  • Open Access English
    Authors: 
    Carrat, Fabrice; Saba Villarroel, Paola Mariela; Lapidus, Nathanaël; Fourié, Toscane; Blanché, Hélène; Dorival, Céline; Nicol, Jérôme; Deleuze, Jean-François; Robineau, Olivier; Touvier, Mathilde; +3 more
    Publisher: HAL CCSD
    Country: France

    AbstractAssessment of the intensity, dynamics and determinants of the antibody response after SARS-CoV-2 infection or vaccination in the general population is critical to guide vaccination policies. This study characterized the anti-spike IgG titers in 13,971 participants included in a French multicohort population-based serological survey on COVID-19 between April and October 2020 and followed-up with serological testing between May and October 2021. Eight follow-up profiles were defined depending on SARS-CoV-2 infection (0, 1 or 2) and COVID-19 vaccination (0, 1, 2 or 3). The anti-spike titer was lower in adults with no vaccination even in case of infection or reinfection, while it was higher in adults with infection followed by vaccination. The anti-spike titer was negatively correlated with age in vaccinated but uninfected adults, whereas it was positively correlated with age in unvaccinated but infected adults. In adults with 2 vaccine injections and no infection, the vaccine protocol, age, gender, and time since the last vaccine injection were independently associated with the anti-spike titer. The decrease in anti-spike titer was much more rapid in vaccinated than in infected subjects. These results highlight the strong heterogeneity of the antibody response against SARS-CoV-2 in the general population depending on previous infection and vaccination.

  • Open Access English
    Authors: 
    Valentin Sencio; Nicolas Benech; Cyril Robil; Lucie Deruyter; Séverine Heumel; Arnaud Machelart; Thierry Sulpice; Antonin Lamazière; Corinne Grangette; François Briand; +2 more
    Publisher: HAL CCSD
    Country: France

    International audience; Obese patientss with nonalcoholic steatohepatitis (NASH) are particularly prone to developing severe forms of coronavirus disease 19 (COVID-19). The gut-to-lung axis is critical during viral infections of the respiratory tract, and a change in the gut microbiota's composition might have a critical role in disease severity. Here, we investigated the consequences of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the gut microbiota in the context of obesity and NASH. To this end, we set up a nutritional model of obesity with dyslipidemia and NASH in the golden hamster, a relevant preclinical model of COVID-19. Relative to lean non-NASH controls, obese NASH hamsters develop severe inflammation of the lungs and liver. 16S rRNA gene profiling showed that depending on the diet, SARS-CoV-2 infection induced various changes in the gut microbiota's composition. Changes were more prominent and transient at day 4 post-infection in lean animals, alterations still persisted at day 10 in obese NASH animals. A targeted, quantitative metabolomic analysis revealed changes in the gut microbiota's metabolic output, some of which were diet-specific and regulated over time. Our results showed that specifically diet-associated taxa are correlated with disease parameters. Correlations between infection variables and diet-associated taxa highlighted a number of potentially protective or harmful bacteria in SARS-CoV-2-infected hamsters. In particular, some taxa in obese NASH hamsters (e.g. Blautia and Peptococcus) were associated with pro-inflammatory parameters in both the lungs and the liver. These taxon profiles and their association with specific disease markers suggest that microbial patterns might influence COVID-19 outcomes.

  • Open Access
    Authors: 
    Perotin, Jeanne-Marie; Gierski, Fabien; Bolko, Lois; Dury, Sandra; Barrière, Sarah; Launois, Claire; Dewolf, Maxime; Chouabe, Stéphane; Bongrain, Eric; Picard, Davy; +10 more
    Publisher: Springer Science and Business Media LLC
    Country: France

    Abstract Background The mid-term respiratory sequelae in survivors of severe COVID-19 appear highly heterogeneous. In addition, factors associated with respiratory sequelae are not known. In this monocentric prospective study, we performed a multidisciplinary assessment for respiratory and muscular impairment and psychological distress 3 months after severe COVID-19. We analysed factors associated with severe persistent respiratory impairment, amongst demographic, COVID-19 severity, and 3-month assessment. Methods Patients with severe SARS-CoV-2 pneumonia requiring ≥ 4L/min were included for a systematic 3-month visit, including respiratory assessment (symptoms, lung function, CT scan), muscular evaluation (body composition, physical function and activity, disability), psychopathological evaluation (anxiety, depression, post-traumatic stress disorder-PTSD) and quality of life. A cluster analysis was performed to identify subgroups of patients based on objective functional measurements: DLCO, total lung capacity and 6-min walking distance (6MWD). Results Sixty-two patients were analysed, 39% had dyspnea on exercise (mMRC ≥ 2), 72% had DLCO < 80%, 90% had CT-scan abnormalities; 40% had sarcopenia/pre-sarcopenia and 31% had symptoms of PTSD. Cluster analysis identified a group of patients (n = 18, 30.5%) with a severe persistent (SP) respiratory impairment (DLCO 48 ± 12%, 6MWD 299 ± 141 m). This SP cluster was characterized by older age, severe respiratory symptoms, but also sarcopenia/pre-sarcopenia, symptoms of PTSD and markedly impaired quality of life. It was not associated with initial COVID-19 severity or management. Conclusions and clinical implication We identified a phenotype of patients with severe persistent respiratory and muscular impairment and psychological distress 3 months after severe COVID-19. Our results highlight the need for multidisciplinary assessment and management after severe SARS-CoV-2 pneumonia. Trial registration The study was registered on ClinicalTrials.gov (May 6, 2020): NCT04376840

  • Open Access English
    Authors: 
    Hoang Thi Giang; Nguyen Quang Duc; Jean-Pierre Molès; Vu Hai Vinh; Nicolas Nagot; Nham Thi Tuyet Thanh; Duong Thi Huong; Khuat Thi Hai Oanh; Pham Minh Khue; Le Sao Mai; +9 more
    Publisher: HAL CCSD
    Country: France

    International audience; Background: After the emergence of COVID-19, a one-month strict lockdown was imposed in April 2020 in Vietnam, followed by lighter social distancing restrictions over the year. We investigated whether those measures affected people who inject drugs (PWID) in terms of risk behaviors for HIV and HCV and access to prevention and care in the city of Haiphong, a historic hotspot for HIV and drug use.Methodology: We carried out a ‘before-after’ study from 2019 to 2020 using respondent-driven sampling method to enroll PWID. They were interviewed on their socioeconomic situation, drug use and sexual behaviors, relations to care services and tested for drugs and methadone in the urine, for HIV, HCV, and HIV plasma viral load when HIV-positive. Changes following the restrictions were assessed by comparing ‘before’ to ‘after’ data.Results: 780 PWID were enrolled. Mean age was 44 years; 94% were male. All were actively injecting heroin ‘before’, versus 56% ‘after’. Among those, frequency of consumption decreased from 24 to 17 days per month. No changes were observed in the frequency and practices of methamphetamine smoking. The proportion of PWID on MMT increased from 68.7 to 75.3%, and that of PWID engaging in risky behaviors related to drug injection decreased from 6.0 to 1.5%. No HIV seroconversions were observed; HCV incidence was 2.6/100 person-years (95% CI [0.7-6.7]). 9% of PWID reported a monthly income of less than 130USD ‘before’ versus 53% ‘after’.Conclusion: The case of Hai Phong shows that it is possible, during times of COVID-19 pandemic, to maintain access to harm reduction and care and to prevent HIV and HCV transmission among PWID in a resource-limited setting where severe social distancing restrictions are implemented. Further research is needed to assess the consequences of long-term economic difficulties and the impact of actual spread of SARS-Cov2 that has since emerged in Haiphong.

  • Open Access English
    Authors: 
    Amandine Fillol; Esther McSween-Cadieux; Bruno Ventelou; Marie-Pier Larose; Ulrich Boris Nguemdjo Kanguem; Kadidiatou Kadio; Christian Dagenais; Valéry Ridde;
    Publisher: HAL CCSD
    Country: France

    International audience; Background: Epistemic injustices are increasingly decried in global health. This study aims to investigate whether the source of knowledge influences the perception of that knowledge and the willingness to use it in francophone African health policy-making context. Methods: The study followed a randomized experimental design in which participants were randomly assigned to one of seven policy briefs that were designed with the same scientific content but with different organizations presented as authors. Each organization was representative of financial, scientific or moral authority. For each type of authority, two organizations were proposed: one North American or European, and the other African. Results: The initial models showed that there was no significant association between the type of authority or the location of the authoring organization and the two outcomes (perceived quality and reported instrumental use). Stratified analyses highlighted that policy briefs signed by the African donor organization (financial authority) were perceived to be of higher quality than policy briefs signed by the North American/European donor organization. For both perceived quality and reported instrumental use, these analyses found that policy briefs signed by the African university (scientific authority) were associated with lower scores than policy briefs signed by the North American/European university. Conclusions: The results confirm the significant influence of sources on perceived global health knowledge and the intersectionality of sources of influence. This analysis allows us to learn more about organizations in global health leadership, and to reflect on the implications for knowledge translation practices.; Contexte : Les injustices épistémiques sont de plus en plus décriées dans le domaine de la santé mondiale. Cette étude vise à déterminer si la source des connaissances influence la perception de ces connaissances et la volonté de les utiliser. Méthodes : L’étude suit un devis expérimental randomisé dans lequel les participant·es ont été assigné·es au hasard à l'une des sept notes politiques conçues avec le même contenu scientifique, mais avec différentes organisations présentées comme autrices. Chaque organisation était représentative d'une autorité financière, scientifique ou morale. Pour chaque type d'autorité, deux organisations étaient proposées : l'une nord-américaine ou européenne, l'autre africaine. Résultats : Les résultats montrent que le type d’autorité et la localisation des organisations autrices ne sont pas significativement associés à la qualité perçue et à l’utilisation instrumentale déclarée. Toutefois, des interactions entre le type d’autorité et la localisation étaient significatives. Ainsi, les analyses stratifiées ont mis en évidence que pour la qualité perçue, les notes de politique signées par l'organisme bailleur (autorité financière) africain obtenaient de meilleurs scores que les notes de politique signées par l’organisme bailleur nord-américain / européen. Tant pour la qualité perçue que pour l'utilisation instrumentale déclarée, ces analyses stratifiées ont révélé que les notes de politique signées par l'université africaine (autorité scientifique) étaient associées à des scores plus faibles que les notes de politique signées par l'université nord-américaine/européenne. Interprétation : Les résultats confirment l'influence significative des sources sur la perception des connaissances en santé mondiale et rappellent l’intersectionnalité de l’influence des sources d’autorité. Cette analyse nous permet à la fois d'en apprendre davantage sur les organisations qui dominent la scène de la gouvernance mondiale en santé et de réfléchir aux implications pour les pratiques d'application des connaissances.

  • Open Access English
    Authors: 
    Leducq, Valentin; Jary, Aude; Bridier-Nahmias, Antoine; Daniel, Lena; Zafilaza, Karen; Damond, Florence; Goldstein, Valérie; Duval, Audrey; Blanquart, François; Calvez, Vincent; +3 more
    Publisher: Nature Portfolio
    Country: France

    AbstractFrance went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of the pandemic along 2020 from the outlook of two major Parisian hospitals earliest involved in the fight against COVID-19. Genome sequencing and phylogenetic analysis were performed on samples from patients and health care workers (HCWs) from Bichat (BCB) and Pitié-Salpêtrière (PSL) hospitals. A tree-based phylogenetic clustering method and epidemiological data were used to investigate suspected nosocomial transmission clusters. Clades 20A, 20B and 20C were prevalent during the spring wave and, following summer, clades 20A.EU2 and 20E.EU1 emerged and took over. Phylogenetic clustering identified 57 potential transmission clusters. Epidemiological connections between participants were found for 17 of these, with a higher proportion of HCWs. The joint presence of HCWs and patients suggest viral contaminations between these two groups. We provide an enhanced overview of SARS-CoV-2 phylogenetic changes over 2020 in the Paris area, one of the regions with highest incidence in France. Despite the low genetic diversity displayed by the SARS-CoV-2, we showed that phylogenetic analysis, along with comprehensive epidemiological data, helps to identify and investigate healthcare associated clusters.

  • Open Access
    Authors: 
    Adele de Hoffer; Shahram Vatani; Corentin Cot; Giacomo Cacciapaglia; Maria Luisa Chiusano; Andrea Cimarelli; Francesco Conventi; Antonio Giannini; Stefan Hohenegger; Francesco Sannino;
    Publisher: Springer Science and Business Media LLC
    Country: France

    AbstractNever before such a vast amount of data, including genome sequencing, has been collected for any viral pandemic than for the current case of COVID-19. This offers the possibility to trace the virus evolution and to assess the role mutations play in its spread within the population, in real time. To this end, we focused on the Spike protein for its central role in mediating viral outbreak and replication in host cells. Employing the Levenshtein distance on the Spike protein sequences, we designed a machine learning algorithm yielding a temporal clustering of the available dataset. From this, we were able to identify and define emerging persistent variants that are in agreement with known evidences. Our novel algorithm allowed us to define persistent variants as chains that remain stable over time and to highlight emerging variants of epidemiological interest as branching events that occur over time. Hence, we determined the relationship and temporal connection between variants of interest and the ensuing passage to dominance of the current variants of concern. Remarkably, the analysis and the relevant tools introduced in our work serve as an early warning for the emergence of new persistent variants once the associated cluster reaches 1% of the time-binned sequence data. We validated our approach and its effectiveness on the onset of the Alpha variant of concern. We further predict that the recently identified lineage AY.4.2 (‘Delta plus’) is causing a new emerging variant. Comparing our findings with the epidemiological data we demonstrated that each new wave is dominated by a new emerging variant, thus confirming the hypothesis of the existence of a strong correlation between the birth of variants and the pandemic multi-wave temporal pattern. The above allows us to introduce the epidemiology of variants that we described via the Mutation epidemiological Renormalisation Group framework.

  • Publication . Part of book or chapter of book . 2022
    Closed Access English
    Authors: 
    Slim Zidi; Nadia Hamani; Lyes Kermad;
    Publisher: HAL CCSD
    Country: France

    Nowadays, supply chain disruptions caused by COVID-19 pandemic, demand variation, raw material shortage, etc., made the supply chains unable to deal with emerging market problems. Responding to the new requirements has underscored the need to ensure a reconfigurable supply chain in order to survive in this uncertain economic environment. Indeed, the objective of this study is to identify the quantitative factors of each reconfigurability characteristic representing the reconfigurability assessment indicators (modularity, integrability, convertibility, diagnosability, scalability and customization). Based on the literature review, quantitative factors used to assess the degree of reconfigurability in supply chain are determined. These factors allow classifying reconfigurability characteristics according to the degree of their influence on the supply chain structure or supply chain functions. Through this research work, we try to facilitate the assessment of reconfigurability based on its characteristics in order to determine the ability of the supply chain to cope with new emerging disruptions.