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38 Research products

  • COVID-19
  • 2019-2023
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  • French National Research Agency (ANR)
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  • Mémoires en Sciences de l'Information et de la Communication
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  • Hyper Article en Ligne - Sciences de l'Homme et de la Société

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  • Authors: Abry, Patrice; Chevallier, Juliette; Fort, Gersende; Pascal, Barbara;

    International audience; Pandemic intensity monitoring, from the earliest stages of the pandemic outbreak, constitutes a critical scientific challenge with major societal stakes. The task is significantly complicated by the low quality of reported infection counts, stemming from emergency and crisis contexts, and by the need for regular (daily) updates, while the pandemic is still active. The present work first proposes a parametric Hidden Markov Model (HMM) aiming to account jointly for epidemic propagation mechanisms and for low-quality data, while imposing epidemiccompliant constraints on the time-varying reproduction number, considered as a proxy for pandemic intensity quantification. Second, and to avoid the arbitrary or expert-based tuning of the parameters of the HMM, data-driven automated selection procedures are devised relying on tailoring a stochastic Expectation-Maximization algorithm. Credibility interval-based estimation of the time-varying reproduction number, modeled as a hidden variable, is then obtained from Monte Carlo sampling. The potential of the tools devised here is illustrated on real Covid19 daily new infection counts from Johns Hopkins University repository.

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    Authors: Boluda, Susana; Mokhtari, Karima; Mégarbane, Bruno; Annane, Djillali; +31 Authors

    In a neuropathological series of 20 COVID-19 cases, we analyzed six cases (three biopsies and three autopsies) with multiple foci predominantly affecting the white matter as shown by MRI. The cases presented with microhemorrhages evocative of small artery diseases. This COVID-19 associated cerebral microangiopathy (CCM) was characterized by perivascular changes: arterioles were surrounded by vacuolized tissue, clustered macrophages, large axonal swellings and a crown arrangement of aquaporin-4 immunoreactivity. There was evidence of blood-brain-barrier leakage. Fibrinoid necrosis, vascular occlusion, perivascular cuffing and demyelination were absent. While no viral particle or viral RNA was found in the brain, the SARS-CoV-2 spike protein was detected in the Golgi apparatus of brain endothelial cells where it closely associated with furin, a host protease known to play a key role in virus replication. Endothelial cells in culture were not permissive to SARS-CoV-2 replication. The distribution of the spike protein in brain endothelial cells differed from that observed in pneumocytes. In the latter, the diffuse cytoplasmic labeling suggested a complete replication cycle with viral release, notably through the lysosomal pathway. In contrast, in cerebral endothelial cells the excretion cycle was blocked in the Golgi apparatus. Interruption of the excretion cycle could explain the difficulty of SARS-CoV-2 to infect endothelial cells in vitro and to produce viral RNA in the brain. Specific metabolism of the virus in brain endothelial cells could weaken the cell walls and eventually lead to the characteristic lesions of COVID-19 associated cerebral microangiopathy. Furin as a modulator of vascular permeability could provide some clues for the control of late effects of microangiopathy. Free Neuropathology, Vol. 4 (2023)

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    Other literature type . 2023
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    Article . 2023
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  • Authors: Demont, Timothée; Horta Sáenz, Daniela; Raiber, Eva;

    Worrisome topics, such as climate change, economic crises, or the Covid-19 pandemic, are increasingly present and pervasive due to digital media and social networks. Do such worries affect cognitive performance? The effect of a distressing topic might be very different depending on whether people have the scope and means to cope with the consequences. It can also differ by how performance is rewarded, for instance, if is there a goal that people can focus on. In an online experiment during the Covid-19 pandemic, we test how the cognitive performance of university students responds to topics discussing (i) current mental health issues related to social restrictions or (ii) future labor market uncertainties linked to the economic contraction. Moreover, we study how the response is affected by a performance goal by conditioning payout on reaching a minimum level. We find that the labor market topic increases cognitive performance when performance is motivated by a goal. Conversely, there is no such effect after the mental health topic. We even find a weak negative effect among those mentally vulnerable when payout is not based on reaching a goal. The positive effect is driven by students with larger financial and social resources, pointing at an inequality-widening mechanism.

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    Authors: Carastan dos Santos, Danilo; Rzadca, Krzysztof; Sousa, Leonel; Trystram, Denis;

    Conferencing is one of the main pillars of Computer Science research activity regarding career and networking, with conference publications playing a more pronounced role compared to other disciplines. The COVID-19 pandemic forced us to switch to virtual conferencing, and many works have shown the benefits of virtual conferencing in terms of inclusivity and reduction of Green House Gas emissions. We are moving toward the usual conferencing format as it appears that the pandemic is increasingly under control. However, the changes imposed during the period of the pandemic brought many essential lessons regarding conferencing social and environmental effects. A crucial task is to gather these community experiences to give directions on how to keep the learned lessons post-COVID-19. We used the Euro-Par conference to synthesize these lessons in the Computer Science case. We show practical results that reinforce the marginal emissions of virtual conferencing compared to in-person conference travel. We also open the debate that rethinking the conference utility according to our objectives (scientific and ecologic) and being aware of social/geographical biases are essential factors in participating and organizing post-COVID-19 conferences.

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  • Authors: Layan, Maylis;

    Among the methods for the quantitative study of infectious diseases transmission in host populations, molecular epidemiology that reconstructs pathogen phylogenies by using pathogen genetic sequences and mathematical modelling of infectious diseases that fits mechanistic models of disease transmission to epidemiological data such as case counts are of particular interest to epidemiologists. These two approaches rely on different data sources whose availability depends on the setting. They also rely on different concepts and models leading to complementary pictures of disease transmission. The main objective of this thesis is to better understand how viral infectious diseases such as rabies and COVID-19 circulate in host populations using respectively geolocated and timestamped viral genetic sequences and detailed epidemiological data at the individual level. The first part of this thesis focuses on rabies, a neglected tropical zoonosis, that is estimated to cause 59,000 human deaths per year mostly among rural and poor populations in Africa and Asia. Its causing agent, rabies virus (RABV), mainly circulates in domestic dog populations. Despite being a vaccine-preventable disease in both humans and dogs, rabies remains poorly studied and its circulation in dogs poorly understood. First, we reviewed from the literature all mathematical models and molecular epidemiology studies on dog rabies circulation to synthesize the contribution of both approaches to the understanding of rabies dynamics in dogs. Then, we described RABV spread in Cambodia, one of the most affected countries worldwide, using RABV genomes isolated from dogs and Bayesian continuous phylogeography methods. We used Cambodia as a model of endemic circulation of RABV and exemplified how phylogeography can help characterize circulation in such context. We found that introductions from foreign countries are not necessary to sustain transmission in Cambodia. However, these results are conditional on the sampling of the RABV genomes. To further understand how sampling affects Bayesian phylogeography methods, we performed a simulation study where we evaluated the performances of three Bayesian discrete phylogeography algorithms under increasing levels of bias, and tested whether alternative sampling strategies, and integration of incidence data improve the performances of the algorithms under biased sampling conditions. The second part of this thesis concentrates on SARS-CoV-2 transmission at one of the smallest population scale, households. This setting is particularly suitable to detailed follow-up of household members after introduction of a case, and thus, enables to evaluate how susceptibility and infectivity vary between individuals. First, we estimated BNT162b2 vaccine effectiveness against infection and against transmission if infected during the Alpha wave in Israel using a mathematical model of SARS-CoV-2 transmission in partially vaccinated households. We further explored how model misspecification in a context of differing contact patterns between adults and children would impact estimates of relative infectivity and susceptibility of children compared to adults. Overall, this thesis explores how molecular epidemiology and modelling contribute to the understanding of infectious diseases transmission at the population level and highlights the need for data integration.; Parmi les méthodes pour l'étude quantitative de la transmission des maladies infectieuses dans les populations, les épidémiologistes ont récemment focalisé leur attention sur l'épidémiologie moléculaire qui vise à reconstruire la phylogénie des pathogènes en utilisant leurs séquences génétiques, et la modélisation mathématique des maladies infectieuses qui ajuste des modèles mécanistes de transmission des maladies à des données épidémiologiques telles que le nombre de cas. Ces deux approches se basent sur des données très différentes dont la disponibilité varie selon le contexte. Les concepts et les modèles qu'elles utilisent permettent d'explorer des facettes différentes de la transmission des maladies. L'objectif principal de cette thèse est de mieux comprendre comment les maladies virales comme la rage et la covid-19 circulent dans les populations hôtes en utilisant pour la première des séquences génétiques virales datées et géolocalisées, et pour la deuxième, des données épidémiologiques à l'échelle individuelle. La première partie de cette thèse s'intéresse à la rage, une zoonose tropicale négligée, responsable d'environ 59,000 morts chaque année principalement dans les populations pauvres et rurales d'Afrique et d'Asie. Son agent étiologique, le virus de la rage (RABV), circule principalement dans les populations canines domestiques dont les modes de transmission restent peu étudiés et mal compris malgré l'existence de vaccins efficaces chez l'homme et l'animal. Nous avons tout d'abord synthétisé dans une revue de la littérature l'apport relatif des modèles mathématiques et de l'épidémiologie moléculaire dans la compréhension des dynamiques de la rage chez le chien. Puis, nous avons décrit la circulation endémique de la rage au Cambodge, un des pays les plus affectés, à partir de génomes de la rage isolés chez le chien et analysés avec des méthodes de phylogéographie Bayésienne continue. Nous avons montré que les introductions depuis d'autres pays ne sont pas nécessaires au maintien de la circulation. Toutefois, ces résultats sont conditionnés par l'échantillonnage des génomes. Pour mieux comprendre leurs impacts sur les méthodes de phylogéographie Bayésienne, nous avons entrepris une étude de simulation dans laquelle nous avons comparé les performances de trois algorithmes de phylogéographie discrète face à un échantillonnage plus ou moins biaisé. Nous avons testé des stratégies d'échantillonnage alternatives et intégré des données épidémiologiques afin d'atténuer l'effet potentiel des biais d'échantillonnage sur la performance des trois algorithmes. La deuxième partie de la thèse se concentre sur la transmission du SARS-CoV-2 dans une des plus petites populations, les ménages. Cette configuration est particulièrement adaptée au suivi détaillé de l'ensemble des membres du foyer après l'introduction d'un cas et permet ainsi d'évaluer comment la susceptibilité et l'infectivité varient au niveau individuel. Dans un premier temps, nous avons estimé l'effectivité vaccinale contre l'infection et la transmission si infecté pendant la vague de variant Alpha en Israël grâce à un modèle de transmission dans des ménages partiellement vaccinés. Nous avons ensuite exploré comment l'hétérogénéité de contact dans les ménages, notamment entre les adultes et les enfants, impacte les estimations de l'infectivité et de la susceptibilité relatives des enfants par rapport aux adultes. En conclusion, cette thèse explore les contributions de l'épidémiologie moléculaire et de la modélisation pour la compréhension de la transmission des maladies infectieuses à différentes échelles de population et souligne la nécessité d'intégrer les données génétiques et épidémiologiques.

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  • Authors: Mathian, Alexis; Breillat, Paul; Dorgham, Karim; Bastard, Paul; +27 Authors

    International audience; Objectives: Type-I interferons (IFNs-I) have potent antiviral effects. IFNs-I are also overproduced in patients with systemic lupus erythematosus (SLE). Autoantibodies (AAbs) neutralising IFN-α, IFN-β and/or IFN-ω subtypes are strong determinants of hypoxemic COVID-19 pneumonia, but their impact on inflammation remains unknown.Methods: We retrospectively analysed a monocentric longitudinal cohort of 609 patients with SLE. Serum AAbs against IFN-α were quantified by ELISA and functionally assessed by abolishment of Madin-Darby bovine kidney cell protection by IFN-α2 against vesicular stomatitis virus challenge. Serum-neutralising activity against IFN-α2, IFN-β and IFN-ω was also determined with a reporter luciferase activity assay. SARS-CoV-2 antibody responses were measured against wild-type spike antigen, while serum-neutralising activity was assessed against the SARS-CoV-2 historical strain and variants of concerns.Results: Neutralising and non-neutralising anti-IFN-α antibodies are present at a frequency of 3.3% and 8.4%, respectively, in individuals with SLE. AAbs neutralising IFN-α, unlike non-neutralising AAbs, are associated with reduced IFN-α serum levels and a reduced likelihood to develop active disease. However, they predispose patients to an increased risk of herpes zoster and severe COVID-19 pneumonia. Severe COVID-19 pneumonia in patients with SLE is mostly associated with combined neutralisation of different IFNs-I. Finally, anti-IFN-α AAbs do not interfere with COVID-19 vaccine humoral immunogenicity.Conclusion: The production of non-neutralising and neutralising anti-IFN-I antibodies in SLE is likely to be a consequence of SLE-associated high IFN-I serum levels, with a beneficial effect on disease activity, yet a greater viral risk. This finding reinforces the recommendations for vaccination against SARS-CoV-2 in SLE.

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  • Authors: Borau, Sylvie; Couprie, Hélène; Hopfensitz, Astrid;

    Forthcoming in Journal of Economic Psychology; Single people are more likely to die from COVID-19. Here, we study whether this higher death rate could be partly explained by differences in compliance with protective health measures against COVID-19 between single and married people, and the drivers of this marital compliance gap. Data collected from 46,450 respondents in 67 countries reveal that married people are more likely to comply with protective measures than single people. This marital gap in compliance is higher for men (approximately 5%) than for women (approximately 2%). These results are robust across a large range of countries and independent of country level differences with respect to culture, values or infection rates. Prosocial characteristics linked to morality and social belonging explain more than 38% of the marital gap, while individual risk perceptions play a minor role. These findings help explain single people's and particularly single men's greater vulnerability to COVID-19, which in turn can be leveraged to improve the effectiveness of international public policy campaigns aimed at promoting protective health measures.

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  • Authors: Guillotreau, Patrice; Bistoquet, Kevin;

    International audience; Small Island Developing States (SIDS) are particularly vulnerable to climate change and ought to pay attention to their own contribution through the CO2 emissions resulting from the domestic production and consumption levels. Although poorly responsible of the worldwide carbon emissions by the modest level of their domestic demand, they can nonetheless contribute to the problem because of the global demand for their exported commodities. However, the carbon footprint is hardly assessed by SIDS because of a lack of data about greenhouse gas emissions or national account statistics. Taking the opportunity of the Covid-19 pandemic and the resulting economic shock, an environmentally-extended input-output model based on Eurostat data on air emissions is used to disentangle the CO2 emissions embodied in the domestic production and international trade, respectively, and to clearly identify the origin of emissions by industry. Not surprisingly, the consumption-based carbon footprint of Seychelles is deemed lower (6.79 tCO2 per capita) than the production-based inventory (9.55 tCO2 p.c.) for this small open economy relying to a large extent on exports of canned tuna and tourism services, hence a decrease of carbon dioxide emissions (-16%) in 2020 because of the Covid-19 pandemic. Could it be the right time to re-frame the international specialization of Seychelles?

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    Authors: Coquidé, Célestin; Lages, José; Ermann, Leonardo; Shepelyansky, Dima;

    Using the United Nations Comtrade database, we perform the Google matrix analysis of the multiproduct World Trade Network (WTN) for the years 2018-2020 comprising the emergence of the COVID-19 as a global pandemic. The applied algorithms -- the PageRank, the CheiRank and the reduced Google matrix -- take into account the multiplicity of the WTN links providing new insights on the international trade comparing to the usual import-export analysis. These algorithms establish new rankings and trade balances of countries and products considering every countries on equal grounds, independently of their wealth, and every products on the basis of their relative exchanged volumes. In comparison with the pre-COVID-19 period, significant changes in these metrics occur for the year 2020 highlighting a major rewiring of the international trade flows induced by the COVID-19 pandemic crisis. We define a new PageRank-CheiRank product trade balance, either export or import oriented, which is significantly perturbed by the pandemic. Comment: 22 pages, 2 tables, 13 figures, 2 appendices

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    Authors: Christakis, Theodore; Bannelier-Christakis, Karine; Castelluccia, Claude; Le Métayer, Daniel;

    Part 1 of our “MAPping the use of Facial Recognition in public spaces in Europe” (MAPFRE) project reports explained in detail what “facial recognition” means, addressed the issues surrounding definitions, presented the political landscape and set out the exact material and geographical scope of the study. Part 2 of our Reports presented, in the most accessible way possible, how facial recognition works and produced a “Classification Table” with illustrations, explanations and examples, detailing the uses of facial recognition/analysis in public spaces, in order to help avoid conflating the diverse ways in which facial recognition is used and to bring nuance and precision to the public debate. This 3rd Report focuses on what is, undoubtedly, the most widespread way in which Facial Recognition Technologies (FRT) are used in public (and private) spaces: Facial Recognitionfor authorisation purposes.Facial recognition is often used to authorise access to a space (e.g. access control) or to a service (e.g. to make a payment). Depending on the situation, both verification and identi fication functionalities (terms that are explained in our 2nd Report) can be used. Millions of people use FRT to unlock their phones every day. Private entities (such as banks) or public authorities (such as the French government in terms of the now abandoned ALICEM pro ject) increasingly envisage using FRT as a means of providing strong authentication in or der to control access to private or public online services, such as e-banking, or administra tive websites that concern income, health or other personal matters. FRT is increasingly being considered as a means of improving security when controlling and managing access to private areas (building entrances, goods warehouses, etc.). In public spaces, FRT is being used as an authentication tool for automated international border controls (for example at airports) or to manage access in places as diverse as airports, stadiums or schools. Pre Covid-19, there were a lot of projects to use in the future FRT in order to “accelerate people flows”, “improve the customer experience”, “speed up opera tions” and “reduce queuing time” for users of different services (e.g. passengers boarding a plane or shopping) but the advent of the Covid-19 pandemic has further boosted calls for investment in FRTs in order to provide contactless services and reduce the risk of contam ination. Supermarkets, such as Carrefour, which was involved in a pilot project in Romania, or transport utilities in “smart cities”, such as the EMT bus network in Madrid, which teamed with Mastercard to conduct a pilot project that enables users to pay on EMT buses using FRT, have implemented facial recognition payment systems that permit consumers to complete transactions by simply having their faces scanned. In Europe, similar pilot pro jects are currently being tested enabling the management of payments in restaurants, cafés and shops. Despite this widespread existing use or projected use of FRT for authorisation purposes we are not aware of any detailed study that is focusing on this specific issue. We hope that the present analytic study will help fill this gap by focusing on the specific issue of the use of FRT for authorisation purposes in public spaces in Europe. We have examined in detail seven “emblematic” cases of FRT being used for authorisation purposes in public spaces in Europe. We have reviewed the documents disseminated by data controllers concerning all of these cases (and several others). We have sought out the reactions of civil society and other actors. We have dived into EU and Member State laws. We have analysed a number of Data Protection Authority (DPA) opinions. We have iden tified Court decisions of relevance to this matter.

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  • Authors: Abry, Patrice; Chevallier, Juliette; Fort, Gersende; Pascal, Barbara;

    International audience; Pandemic intensity monitoring, from the earliest stages of the pandemic outbreak, constitutes a critical scientific challenge with major societal stakes. The task is significantly complicated by the low quality of reported infection counts, stemming from emergency and crisis contexts, and by the need for regular (daily) updates, while the pandemic is still active. The present work first proposes a parametric Hidden Markov Model (HMM) aiming to account jointly for epidemic propagation mechanisms and for low-quality data, while imposing epidemiccompliant constraints on the time-varying reproduction number, considered as a proxy for pandemic intensity quantification. Second, and to avoid the arbitrary or expert-based tuning of the parameters of the HMM, data-driven automated selection procedures are devised relying on tailoring a stochastic Expectation-Maximization algorithm. Credibility interval-based estimation of the time-varying reproduction number, modeled as a hidden variable, is then obtained from Monte Carlo sampling. The potential of the tools devised here is illustrated on real Covid19 daily new infection counts from Johns Hopkins University repository.

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    Authors: Boluda, Susana; Mokhtari, Karima; Mégarbane, Bruno; Annane, Djillali; +31 Authors

    In a neuropathological series of 20 COVID-19 cases, we analyzed six cases (three biopsies and three autopsies) with multiple foci predominantly affecting the white matter as shown by MRI. The cases presented with microhemorrhages evocative of small artery diseases. This COVID-19 associated cerebral microangiopathy (CCM) was characterized by perivascular changes: arterioles were surrounded by vacuolized tissue, clustered macrophages, large axonal swellings and a crown arrangement of aquaporin-4 immunoreactivity. There was evidence of blood-brain-barrier leakage. Fibrinoid necrosis, vascular occlusion, perivascular cuffing and demyelination were absent. While no viral particle or viral RNA was found in the brain, the SARS-CoV-2 spike protein was detected in the Golgi apparatus of brain endothelial cells where it closely associated with furin, a host protease known to play a key role in virus replication. Endothelial cells in culture were not permissive to SARS-CoV-2 replication. The distribution of the spike protein in brain endothelial cells differed from that observed in pneumocytes. In the latter, the diffuse cytoplasmic labeling suggested a complete replication cycle with viral release, notably through the lysosomal pathway. In contrast, in cerebral endothelial cells the excretion cycle was blocked in the Golgi apparatus. Interruption of the excretion cycle could explain the difficulty of SARS-CoV-2 to infect endothelial cells in vitro and to produce viral RNA in the brain. Specific metabolism of the virus in brain endothelial cells could weaken the cell walls and eventually lead to the characteristic lesions of COVID-19 associated cerebral microangiopathy. Furin as a modulator of vascular permeability could provide some clues for the control of late effects of microangiopathy. Free Neuropathology, Vol. 4 (2023)

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  • Authors: Demont, Timothée; Horta Sáenz, Daniela; Raiber, Eva;

    Worrisome topics, such as climate change, economic crises, or the Covid-19 pandemic, are increasingly present and pervasive due to digital media and social networks. Do such worries affect cognitive performance? The effect of a distressing topic might be very different depending on whether people have the scope and means to cope with the consequences. It can also differ by how performance is rewarded, for instance, if is there a goal that people can focus on. In an online experiment during the Covid-19 pandemic, we test how the cognitive performance of university students responds to topics discussing (i) current mental health issues related to social restrictions or (ii) future labor market uncertainties linked to the economic contraction. Moreover, we study how the response is affected by a performance goal by conditioning payout on reaching a minimum level. We find that the labor market topic increases cognitive performance when performance is motivated by a goal. Conversely, there is no such effect after the mental health topic. We even find a weak negative effect among those mentally vulnerable when payout is not based on reaching a goal. The positive effect is driven by students with larger financial and social resources, pointing at an inequality-widening mechanism.

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    Authors: Carastan dos Santos, Danilo; Rzadca, Krzysztof; Sousa, Leonel; Trystram, Denis;

    Conferencing is one of the main pillars of Computer Science research activity regarding career and networking, with conference publications playing a more pronounced role compared to other disciplines. The COVID-19 pandemic forced us to switch to virtual conferencing, and many works have shown the benefits of virtual conferencing in terms of inclusivity and reduction of Green House Gas emissions. We are moving toward the usual conferencing format as it appears that the pandemic is increasingly under control. However, the changes imposed during the period of the pandemic brought many essential lessons regarding conferencing social and environmental effects. A crucial task is to gather these community experiences to give directions on how to keep the learned lessons post-COVID-19. We used the Euro-Par conference to synthesize these lessons in the Computer Science case. We show practical results that reinforce the marginal emissions of virtual conferencing compared to in-person conference travel. We also open the debate that rethinking the conference utility according to our objectives (scientific and ecologic) and being aware of social/geographical biases are essential factors in participating and organizing post-COVID-19 conferences.

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  • Authors: Layan, Maylis;

    Among the methods for the quantitative study of infectious diseases transmission in host populations, molecular epidemiology that reconstructs pathogen phylogenies by using pathogen genetic sequences and mathematical modelling of infectious diseases that fits mechanistic models of disease transmission to epidemiological data such as case counts are of particular interest to epidemiologists. These two approaches rely on different data sources whose availability depends on the setting. They also rely on different concepts and models leading to complementary pictures of disease transmission. The main objective of this thesis is to better understand how viral infectious diseases such as rabies and COVID-19 circulate in host populations using respectively geolocated and timestamped viral genetic sequences and detailed epidemiological data at the individual level. The first part of this thesis focuses on rabies, a neglected tropical zoonosis, that is estimated to cause 59,000 human deaths per year mostly among rural and poor populations in Africa and Asia. Its causing agent, rabies virus (RABV), mainly circulates in domestic dog populations. Despite being a vaccine-preventable disease in both humans and dogs, rabies remains poorly studied and its circulation in dogs poorly understood. First, we reviewed from the literature all mathematical models and molecular epidemiology studies on dog rabies circulation to synthesize the contribution of both approaches to the understanding of rabies dynamics in dogs. Then, we described RABV spread in Cambodia, one of the most affected countries worldwide, using RABV genomes isolated from dogs and Bayesian continuous phylogeography methods. We used Cambodia as a model of endemic circulation of RABV and exemplified how phylogeography can help characterize circulation in such context. We found that introductions from foreign countries are not necessary to sustain transmission in Cambodia. However, these results are conditional on the sampling of the RABV genomes. To further understand how sampling affects Bayesian phylogeography methods, we performed a simulation study where we evaluated the performances of three Bayesian discrete phylogeography algorithms under increasing levels of bias, and tested whether alternative sampling strategies, and integration of incidence data improve the performances of the algorithms under biased sampling conditions. The second part of this thesis concentrates on SARS-CoV-2 transmission at one of the smallest population scale, households. This setting is particularly suitable to detailed follow-up of household members after introduction of a case, and thus, enables to evaluate how susceptibility and infectivity vary between individuals. First, we estimated BNT162b2 vaccine effectiveness against infection and against transmission if infected during the Alpha wave in Israel using a mathematical model of SARS-CoV-2 transmission in partially vaccinated households. We further explored how model misspecification in a context of differing contact patterns between adults and children would impact estimates of relative infectivity and susceptibility of children compared to adults. Overall, this thesis explores how molecular epidemiology and modelling contribute to the understanding of infectious diseases transmission at the population level and highlights the need for data integration.; Parmi les méthodes pour l'étude quantitative de la transmission des maladies infectieuses dans les populations, les épidémiologistes ont récemment focalisé leur attention sur l'épidémiologie moléculaire qui vise à reconstruire la phylogénie des pathogènes en utilisant leurs séquences génétiques, et la modélisation mathématique des maladies infectieuses qui ajuste des modèles mécanistes de transmission des maladies à des données épidémiologiques telles que le nombre de cas. Ces deux approches se basent sur des données très différentes dont la disponibilité varie selon le contexte. Les concepts et les modèles qu'elles utilisent permettent d'explorer des facettes différentes de la transmission des maladies. L'objectif principal de cette thèse est de mieux comprendre comment les maladies virales comme la rage et la covid-19 circulent dans les populations hôtes en utilisant pour la première des séquences génétiques virales datées et géolocalisées, et pour la deuxième, des données épidémiologiques à l'échelle individuelle. La première partie de cette thèse s'intéresse à la rage, une zoonose tropicale négligée, responsable d'environ 59,000 morts chaque année principalement dans les populations pauvres et rurales d'Afrique et d'Asie. Son agent étiologique, le virus de la rage (RABV), circule principalement dans les populations canines domestiques dont les modes de transmission restent peu étudiés et mal compris malgré l'existence de vaccins efficaces chez l'homme et l'animal. Nous avons tout d'abord synthétisé dans une revue de la littérature l'apport relatif des modèles mathématiques et de l'épidémiologie moléculaire dans la compréhension des dynamiques de la rage chez le chien. Puis, nous avons décrit la circulation endémique de la rage au Cambodge, un des pays les plus affectés, à partir de génomes de la rage isolés chez le chien et analysés avec des méthodes de phylogéographie Bayésienne continue. Nous avons montré que les introductions depuis d'autres pays ne sont pas nécessaires au maintien de la circulation. Toutefois, ces résultats sont conditionnés par l'échantillonnage des génomes. Pour mieux comprendre leurs impacts sur les méthodes de phylogéographie Bayésienne, nous avons entrepris une étude de simulation dans laquelle nous avons comparé les performances de trois algorithmes de phylogéographie discrète face à un échantillonnage plus ou moins biaisé. Nous avons testé des stratégies d'échantillonnage alternatives et intégré des données épidémiologiques afin d'atténuer l'effet potentiel des biais d'échantillonnage sur la performance des trois algorithmes. La deuxième partie de la thèse se concentre sur la transmission du SARS-CoV-2 dans une des plus petites populations, les ménages. Cette configuration est particulièrement adaptée au suivi détaillé de l'ensemble des membres du foyer après l'introduction d'un cas et permet ainsi d'évaluer comment la susceptibilité et l'infectivité varient au niveau individuel. Dans un premier temps, nous avons estimé l'effectivité vaccinale contre l'infection et la transmission si infecté pendant la vague de variant Alpha en Israël grâce à un modèle de transmission dans des ménages partiellement vaccinés. Nous avons ensuite exploré comment l'hétérogénéité de contact dans les ménages, notamment entre les adultes et les enfants, impacte les estimations de l'infectivité et de la susceptibilité relatives des enfants par rapport aux adultes. En conclusion, cette thèse explore les contributions de l'épidémiologie moléculaire et de la modélisation pour la compréhension de la transmission des maladies infectieuses à différentes échelles de population et souligne la nécessité d'intégrer les données génétiques et épidémiologiques.

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  • Authors: Mathian, Alexis; Breillat, Paul; Dorgham, Karim; Bastard, Paul; +27 Authors

    International audience; Objectives: Type-I interferons (IFNs-I) have potent antiviral effects. IFNs-I are also overproduced in patients with systemic lupus erythematosus (SLE). Autoantibodies (AAbs) neutralising IFN-α, IFN-β and/or IFN-ω subtypes are strong determinants of hypoxemic COVID-19 pneumonia, but their impact on inflammation remains unknown.Methods: We retrospectively analysed a monocentric longitudinal cohort of 609 patients with SLE. Serum AAbs against IFN-α were quantified by ELISA and functionally assessed by abolishment of Madin-Darby bovine kidney cell protection by IFN-α2 against vesicular stomatitis virus challenge. Serum-neutralising activity against IFN-α2, IFN-β and IFN-ω was also determined with a reporter luciferase activity assay. SARS-CoV-2 antibody responses were measured against wild-type spike antigen, while serum-neutralising activity was assessed against the SARS-CoV-2 historical strain and variants of concerns.Results: Neutralising and non-neutralising anti-IFN-α antibodies are present at a frequency of 3.3% and 8.4%, respectively, in individuals with SLE. AAbs neutralising IFN-α, unlike non-neutralising AAbs, are associated with reduced IFN-α serum levels and a reduced likelihood to develop active disease. However, they predispose patients to an increased risk of herpes zoster and severe COVID-19 pneumonia. Severe COVID-19 pneumonia in patients with SLE is mostly associated with combined neutralisation of different IFNs-I. Finally, anti-IFN-α AAbs do not interfere with COVID-19 vaccine humoral immunogenicity.Conclusion: The production of non-neutralising and neutralising anti-IFN-I antibodies in SLE is likely to be a consequence of SLE-associated high IFN-I serum levels, with a beneficial effect on disease activity, yet a greater viral risk. This finding reinforces the recommendations for vaccination against SARS-CoV-2 in SLE.

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  • Authors: Borau, Sylvie; Couprie, Hélène; Hopfensitz, Astrid;

    Forthcoming in Journal of Economic Psychology; Single people are more likely to die from COVID-19. Here, we study whether this higher death rate could be partly explained by differences in compliance with protective health measures against COVID-19 between single and married people, and the drivers of this marital compliance gap. Data collected from 46,450 respondents in 67 countries reveal that married people are more likely to comply with protective measures than single people. This marital gap in compliance is higher for men (approximately 5%) than for women (approximately 2%). These results are robust across a large range of countries and independent of country level differences with respect to culture, values or infection rates. Prosocial characteristics linked to morality and social belonging explain more than 38% of the marital gap, while individual risk perceptions play a minor role. These findings help explain single people's and particularly single men's greater vulnerability to COVID-19, which in turn can be leveraged to improve the effectiveness of international public policy campaigns aimed at promoting protective health measures.