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Because SARS-CoV-2 constantly mutates to escape from the immune response, there is a reduction of neutralizing capacity of antibodies initially targeting the historical strain against emerging Variants of Concerns (VoC)s. That is why the measure of the protection conferred by vaccination cannot solely rely on the antibody levels, but also requires to measure their neutralization capacity. Here we used a mathematical model to follow the humoral response in 26 individuals that received up to three vaccination doses of Bnt162b2 vaccine, and for whom both anti-S IgG and neutralisation capacity was measured longitudinally against all main VoCs. Our model could identify two independent mechanisms that led to a marked increase in humoral response over the successive vaccination doses. In addition to the already known increase in IgG levels after each dose, we identified that the neutralization capacity was significantly increased after the third vaccine administration against all VoCs, despite large inter-individual variability. Consequently, the model projects that the mean duration of detectable neutralizing capacity against non-Omicron VoC is between 366 days (Beta variant, 95% Prediction Intervals PI [323; 366]) and 606 days (Alpha variant, 95% PI [555; 638]). Despite a very low protection after three doses, the mean duration of detectable neutralizing capacity against Omicron variants varies between 184 days (BA.5 variant, 95% PI [155; 215]) and 268 days (BA.1 variant, 95% PI [238; 302]). Our model shows the benefit of incorporating the neutralization capacity in the follow-up of patients to better inform on their level of protection against the different SARS-CoV-2 variants as well as their optimal timing of vaccine administration.

La crise de la Covid-19 a impacté le sport professionnel et amateur français avec la suspension des compétitions à partir du 12 mars 2020 puis l’arrêt prématuré et définitif de la saison 2019/20. C’est le cas du rugby professionnel masculin français pour lequel les championnats professionnels du TOP 14 (1re division) et de la PRO D2 (2e division) ont été suspendus puis clôturés définitivement. Le 1er mars 2020, la Ligue Nationale de Rugby (LNR) votait pour une saison sans vainqueur de championnat ni équipes promues et reléguées avec un classement arrê-té à la 17ème journée pour le TOP 14 et à la 23ème journée pour la PRO D2. En s’appuyant sur les travaux académiques menés sur le football amateur (Carin & Andreff, 2020), sur le basket professionnel (Carin, Desquennes, Jaworski et Andreff, 2021), cette recherche s’intéresse aux modèles économiques des clubs français professionnels masculins de rugby, à son évolution sur la période de 2008/09 à 2018/19 et aux effets économiques de la Covid-19 sur les finances des clubs.L’accès aux données financières des clubs professionnels des deux premières divisions et des échanges avec la Direction Nationale d’Aide au Contrôle de Gestion (DNACG) permettent de mieux cerner la répartition des revenus, des charges et la performance financière d’avant la crise Covid et d’apprécier les effets économiques à court terme de cette crise sur les saisons 2019/20 et 2020/21. Outre les effets économiques sur les deux premières saisons de la Covid, cette étude contribue à mettre en évidence la gestion de crise des organisations sportives de rugby profes-sionnel français. The Covid-19 crisis has had an impact on French professional and amateur sport with the suspension of competitions from 12 March 2020 and the premature and definitive closure of the 2019/20 season. This is the case for French men's professional rugby, for which the TOP 14 (1st division) and PRO D2 (2nd division) professional championships have been suspended and then definitively closed. On 1 March 2020, the French National Rugby League (LNR) voted for a season without a championship winner or promoted and relegated teams, with the rankings stopped at day 17 for the TOP 14 and day 23 for the PRO D2. Based on academic work carried out on amateur football (Carin & Andreff, 2020) and professional basketball (Carin, Desquennes, Jaworski and Andreff, 2021), this research focuses on the economic models of French professional men's rugby clubs, its evolution over the period from 2008/09 to 2018/19 and the economic effects of Covid-19 on club finances. Access to the financial data of professional clubs in the first two divisions and exchanges with the Direction Nationale d'Aide au Contrôle de Gestion (DNACG) allow us to better understand the distribution of revenues, expenses and financial performance before the Covid crisis and to assess the short-term economic effects of this crisis on the 2019/20 and 2020/21 seasons. In addition to the economic effects on the first two seasons of the Covid, this study helps to highlight the crisis management of French professional rugby sports organisations.

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.

Online ahead of print.; International audience; We analysed the influenza epidemic that occurred in Australia during the 2022 winter using an age-structured dynamic transmission model, which accounts for past epidemics to estimate the population susceptibility to an influenza infection. We applied the same model to five European countries. Our analysis suggests Europe might experience an early and moderately large influenza epidemic. Also, differences may arise between countries, with Germany and Spain experiencing larger epidemics, than France, Italy and the United Kingdom, especially in children.

AbstractInvestigating the role of host genetic factors in COVID-19 severity and susceptibility can inform our understanding of the underlying biological mechanisms that influence adverse outcomes and drug development1,2. Here we present a second updated genome-wide association study (GWAS) on COVID-19 severity and infection susceptibility to SARS-CoV-2 from the COVID-19 Host Genetic Initiative (data release 7). We performed a meta-analysis of up to 219,692 cases and over 3 million controls, identifying 51 distinct genome-wide significant loci—adding 28 loci from the previous data release2. The increased number of candidate genes at the identified loci helped to map three major biological pathways involved in susceptibility and severity: viral entry, airway defense in mucus, and type I interferon.

By considering the recently introduced SIRU model, in this paper we study the dynamic of COVID-19 pandemic under the temporally varying public intervention in the Chilean context. More precisely, we propose a method to forecast cumulative daily reported cases $CR(t)$, and a systematic way to identify the unreported daily cases given $CR(t)$ data. We firstly base on the recently introduced epidemic model SIRU (Susceptible, asymptomatic Infected, Reported infected, Unreported infected), and focus on the transmission rate parameter $\tau$. To understand the dynamic of the data, we extend the scalar $\tau$ to an unknown function $\tau(t)$ in the SIRU system, which is then inferred directly from the historical $CR(t)$ data, based on nonparametric estimation. The estimation of $\tau(t)$ leads to the estimation of other unobserved functions in the system, including the daily unreported cases. Furthermore, the estimation of $\tau(t)$ allows us to build links between the pandemic evolution and the public intervention, which is modeled by logistic regression. We then employ polynomial approximation to construct a predicted curve which evolves with the latest trend of $CR(t)$. In addition, we regularize the evolution of the forecast in such a way that it corresponds to the future intervention plan based on the previously obtained link knowledge. We test the proposed predictor on different time windows. The promising results show the effectiveness of the proposed methods.

ABSTRACTIn response to the COVID-19 epidemic, Egypt established a unique care model based on quarantine hospitals where only externally-referred confirmed COVID-19 patients were admitted, and healthcare workers resided continuously over 1-to 2-week working shifts. While the COVID-19 risk for HCWs has been widely reported in standard healthcare settings, it has not been evaluated yet in quarantine hospitals.Here, we relied on longitudinal data, including results of routine RT-PCR tests, collected within three quarantine hospitals located in Cairo and Fayoum, Egypt. Using a model-based approach that accounts for the time-since-exposure variation in false-negative rates of RT-PCR tests, we computed the incidence of SARS-CoV-2 infection among HCWs. Over a total follow-up of 6,064 person-days (PD), we estimated an incidence rate (per 100 PD) of 1.05 (95% CrI: 0.58–1.65) at Hospital 1, 1.92 (95% CrI: 0.93–3.28) at Hospital 2 and 7.62 (95% CrI: 3.47–13.70) at Hospital 3. The probability for an HCW to be infected at the end of a shift was 13.7% (95% CrI: 7.8%–20.8%) and 23.8% (95% CrI: 12.2%–37.3%) for a 2-week shift at Hospital 1 and Hospital 2, respectively, which lies within the range of risk levels previously documented in standard healthcare settings, whereas it was >3-fold higher for a 7-day shift at Hospital 2 (42.6%, 95%CrI: 21.9%–64.4%). Our model-based estimates unveil a proportion of undiagnosed infections among HCWs of 46.4% (95% CrI: 18.8%–66.7%), 45.0% (95% CrI: 5.6%–70.8%) and 59.2% (95% CrI: 34.8%–78.8%), for Hospitals 1 to 3, respectively.The large variation in SARS-CoV-2 incidence we document here suggests that HCWs from quarantine hospitals may face a high occupational risk of infection, but that, with sufficient anticipation and infection control measures, this risk can be brought down to levels similar to those observed in standard healthcare settings.WHAT THIS PAPER ADDSWhat is already known on this topicPrevious studies conducted in standard care settings have documented that frontline healthcare workers (HCWs) face high risk of COVID-19. Whether risk levels differ in alternative care models, such as COVID-19 quarantine hospitals in Egypt where HCWs resided in the hospital days and nights for various durations, is unknown.What this study addsCOVID-19 risk for HCWs in quarantine hospitals varies substantially between facilities, from risk levels that are in the range of those documented in standard healthcare settings to levels that were approximatively 3 times higher.How this study might affect research, practice or policyWith sufficient anticipation and infection control measures, occupational COVID-19 risk for HCWs working in quarantine hospitals can be brought down to levels similar to those observed in standard healthcare settings.

BackgroundMost of the studies on cystic fibrosis (CF) focused on SARS-CoV-2 prevalence and suggested a low incidence of infection in this population. We aimed to assess the impact of the pandemic and related lockdown measures implemented in May 2020 in response to the first wave of SARS-CoV-2 infection on healthcare access, health, and behavior in CF patients.MethodsA national questionnaire opened online from May 15th, 2020 to June 11th, 2020 was completed by 751 CF-patients, aged 14 years and over. It comprised questions about access to healthcare, anxiety and depression, smoking, alcohol, drug and psychotropic drug consumption, adherence to CF treatment, and constraints. A semi-structured comprehensive interview was performed no later than 1 month after the end of the lockdown in 16 CF-patients.ResultsThe mean age of the population was 28.0 [interquartile range (IQR) 20.0–37.0] years old. More than 75% of in-person consultations scheduled during the lockdown were canceled. Alternatively, 27% were postponed, and telehealth consultations were proposed and accepted in almost 40% of cases. More than 75% of the scheduled physiotherapy sessions were canceled and replaced mainly by self-drainage. Annual follow-up clinic visits were consistently postponed whereas required hospitalizations at CF centers for exacerbation were maintained in most cases. While 43.2% CF-patients had signs of anxiety, 51.0% presented symptoms of depression, both associated with increased use of psychotic medications and inversely correlated to COVID-19 prevalence. Among the lower and lower middle classes, very little medical information was obtained or requested by the patient, participation to sports or other activities was low, while excessive home confinement and isolation were more frequent. In contrast, in the upper middle and upper classes, individuals solicitated help to their CF centre, had more physical activities, and maintained contact with friends or families.ConclusionThe first lockdown in France had only minimal impact on the management care of CF-patients but was associated with increased symptoms of anxiety and depression, together with behavioral changes that varied with social class.Trial registrationNCT04463628.

Abstract Background SARS-CoV-2 is a rapidly spreading disease affecting human life and the economy on a global scale. The disease has caused so far more then 5.5 million deaths. The omicron outbreak that emerged in Botswana in the south of Africa spread around the globe at further increased rates, and caused unprecedented SARS-CoV-2 infection incidences in several countries. At the start of December 2021 the first omicron cases were reported in France. Methods In this paper we investigate the spreading potential of this novel variant relatively to the delta variant that was also in circulation in France at that time. Using a dynamic multi-variant model accounting for cross-immunity through a status-based approach, we analyze screening data reported by Santé Publique France over 13 metropolitan French regions between 1st of December 2021 and the 30th of January 2022. During the investigated period, the delta variant was replaced by omicron in all metropolitan regions in approximately three weeks. The analysis conducted retrospectively allows us to consider the whole replacement time window and compare regions with different times of omicron introduction and baseline levels of variants’ transmission potential. As large uncertainties regarding cross-immunity among variants persist, uncertainty analyses were carried out to assess its impact on our estimations. Results Assuming that 80% of the population was immunized against delta, a cross delta/omicron cross-immunity of 25% and an omicron generation time of 3.5 days, the relative strength of omicron to delta, expressed as the ratio of their respective reproduction rates, $$\frac{\hat{R}_{\textrm{omicron}}}{\hat{R}_{\textrm{delta}}}$$ R ^ omicron R ^ delta , was found to range between 1.51 and 1.86 across regions. Uncertainty analysis on epidemiological parameters led to $$\frac{\hat{R}_{\textrm{omicron}}}{\hat{R}_{\textrm{delta}}}$$ R ^ omicron R ^ delta ranging from 1.57 to 2.34 on average over the metropolitan French regions, weighted by population size. Conclusions Upon introduction, omicron spread rapidly through the French territory and showed a high fitness relative to delta. We documented considerable geographical heterogeneities on the spreading dynamics. The historical reconstruction of variant emergence dynamics provide valuable ground knowledge to face future variant emergence events.

Cette enquête a été réalisée au temps du premier confinement auprès d’un groupe de travailleuses et travailleurs du sexe (TDS) de Marseille et vise à comprendre comment iels se sont réorganisé.e.s face à la diminution ou à l’arrêt du travail imposés par le confinement. Parmi les populations les plus vulnérable, les TDS ont été particulièrement affecté.e.s par la pandémie, cependant le confinement n’a pas entrainé la même situation de détresse pour toutes les personnes que nous avons interviewé.e.s. Le confinement a fonctionné plutôt comme un révélateur : il a dévoilé et creusé les inégalités propres à la population des TDS, qui sont liées à la nationalité, au statut de migrant.e, au type d’activité exercée et à l’origine sociale, sans pour autant en être la cause. Les stratégies de réponse des TDS, face à cette crise, sont des stratégies de maximisation qui puisent dans des « bassins de ressources » complémentaires : elles mélangent le recours à la solidarité informelle, celle des réseaux d’entraide entre pairs, au recours à la solidarité formelle, celle des associations. Le manque d’engagement militant collectif, que nous avons observé auprès de la population d’enquête, n’implique pas l’absence d’une dimension collective dans la réponse à la crise. A l’époque du premier confinement, au contraire, la dimension collective a été centrale, mais elle a été mobilisée sous la forme de réseaux communautaires, toujours de manière informelle et invisible à un regard extérieur. This paper builds on a research we carried out in Marseille at the time of the first lockdown among a group of sex workers and aims to understand how they reacted to the reduction or of work imposed by the lockdown. Among the most vulnerable populations, sex workers were particularly affected by the pandemic; however, the lockdown did not engender the same distress for all the people we interviewed. It acted more as a revealing factor: it revealed and deepened the inequalities specific to the sex workers’ population, which are linked to nationality, migratory status, type of activity and social origin, without being the cause of them. Sex workers’ coping strategies drew on complementary "resource pools": they mixed recourse to informal solidarity, that of peer networks, with recourse to formal solidarity, that of associations. The lack of a joint militant response, which we observed, does not imply the absence of a collective dimension in the response to the crisis. On the contrary, at the time of the first lockdown, the collective dimension was central, but it was mobilized in the form of community networks, always in an informal way and invisible to outsiders.