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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.

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.

SummaryDuring the current COVID-19 pandemic, governments must make decisions based on a variety of information including estimations of infection spread, health care capacity, economic and psychosocial considerations. The disparate validity of current short-term forecasts of these factors is a major challenge to governments. By causally linking an established epidemiological spread model with dynamically evolving psychosocial variables, using Bayesian inference we estimate the strength and direction of these interactions for German and Danish data of disease spread, human mobility, and psychosocial factors based on the serial cross-sectional COVID-19 Snapshot Monitoring (COSMO;N= 16,981). We demonstrate that the strength of cumulative influence of psychosocial variables on infection rates is of a similar magnitude as the influence of physical distancing. We further show that the efficacy of political interventions to contain the disease strongly depends on societal diversity, in particular group-specific sensitivity to affective risk perception. As a consequence, the model may assist in quantifying the effect and timing of interventions, forecasting future scenarios, and differentiating the impact on diverse groups as a function of their societal organization. Importantly, the careful handling of societal factors, including support to the more vulnerable groups, adds another direct instrument to the battery of political interventions fighting epidemic spread.

When the threat of COVID-19 became widely acknowledged, many hoped that this epidemic would squash "the anti-vaccine movement". However, when vaccines started arriving in rich countries at the end of 2020, it appeared that vaccine hesitancy might be an issue even in the context of this major epidemic. Does it mean that the mobilization of vaccine-critical activists on social media is one of the main causes of this reticence to vaccinate against COVID-19? In this paper, we wish to contribute to current work on vaccine hesitancy during the COVID-19 epidemic by looking at one of the many mechanisms which can cause reticence towards vaccines: the capacity of vaccine-critical activists to influence a wider public on social media. We analyze the evolution of debates over the COVID-19 vaccine on the French Twittosphere, during two first years of the pandemic, with a particular attention to the spreading capacity of vaccine-critical websites. We address two main questions: 1) Did vaccine-critical contents gain ground during this period? 2) Who were the central actors in the diffusion of these contents? While debates over vaccines experienced a tremendous surge during this period, the share of vaccine-critical contents in these debates remains stable except for a limited number of short periods associated with specific events. Secondly, analyzing the community structure of the re-tweets hyper-graph, we reconstruct the mesoscale structure of the information flows, identifying and characterizing the major communities of users. We analyze their role in the information ecosystem: the largest right-wing community has a typical echo-chamber behavior collecting all the vaccine-critical tweets from outside and recirculating it inside the community. The smaller left-wing community is less permeable to vaccine-critical contents but, has a large capacity to spread it once adopted. 18 pages, 7 figures and 2 tables

AbstractWe report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.

ABSTRACTTo identify novel cellular modulators of HIV-1 infection in IFN-stimulated myeloid cells, we have carried out a screen that combines functional and evolutionary analyses in THP-1-PMA cells that led us to the Tripartite Motif Protein 69 (Trim69), a poorly studied member of the Trim family of innate immunity regulators. Trim69 inhibits HIV-1, primate lentiviruses and the negative and positive-strand RNA viruses VSV and SARS-CoV2, overall indicating it is a broad-spectrum antiviral factor. Trim69 binds directly to microtubules and its antiviral activity is intimately linked to its ability to promote the accumulation of stable MTs, a specialized subset of microtubules. By analyzing the behavior of primary blood cells, we provide evidence that a program of MT stabilization is commonly observed in response to IFN-I in cells of the myeloid lineage and Trim69 is the key factor behind this program.Overall, our study identifies Trim69 as the first antiviral innate defense factor that regulates the properties of microtubules to limit viral spread, highlighting the possibility that the cytoskeleton may be a novel unappreciated fighting ground in the host-pathogen interactions that underlie viral infections.