Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalisation and serological data: a modelling study.

BACKGROUND: Regional monitoring of the proportion of the population who have been infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys. We aimed to estimate in near real time the proportion of adults who have been infected by SARS-CoV-2. METHODS: In this modelling study, we developed a method to reconstruct the proportion of adults who have been infected by SARS-CoV-2 and the proportion of infections being detected, using the joint analysis of age-stratified seroprevalence, hospitalisation, and case data, with deconvolution methods. We developed our method on a dataset consisting of seroprevalence estimates from 9782 participants (aged ≥20 years) in the two worst affected regions of France in May, 2020, and applied our approach to the 13 French metropolitan regions over the period March, 2020, to January, 2021. We validated our method externally using data from a national seroprevalence study done between May and June, 2020. FINDINGS: We estimate that 5·7% (95% CI 5·1-6·4) of adults in metropolitan France had been infected with SARS-CoV-2 by May 11, 2020. This proportion remained stable until August, 2020, and increased to 14·9% (13·2-16·9) by Jan 15, 2021. With 26·5% (23·4-29·8) of adult residents having been infected in Île-de-France (Paris region) compared with 5·1% (4·5-5·8) in Brittany by January, 2021, regional variations remained large (coefficient of variation [CV] 0·50) although less so than in May, 2020 (CV 0·74). The proportion infected was twice as high (20·4%, 15·6-26·3) in 20-49-year-olds than in individuals aged 50 years or older (9·7%, 6·9-14·1). 40·2% (34·3-46·3) of infections in adults were detected in June to August, 2020, compared with 49·3% (42·9-55·9) in November, 2020, to January, 2021. Our regional estimates of seroprevalence were strongly correlated with the external validation dataset (coefficient of correlation 0·89). INTERPRETATION: Our simple approach to estimate the proportion of adults that have been infected with SARS-CoV-2 can help to characterise the burden of SARS-CoV-2 infection, epidemic dynamics, and the performance of surveillance in different regions. FUNDING: EU RECOVER, Agence Nationale de la Recherche, Fondation pour la Recherche Médicale, Institut National de la Santé et de la Recherche Médicale (Inserm)

Etude des déterminants individuels, collectifs et environnementaux du risque d'infection par le virus grippal pandémique A/H1N1

Les facteurs liés à la transmission du virus grippal et à la susceptibilité à l infection sont encore peu documentés. Le risque d infection peut être considéré comme la résultante d une interaction de facteurs liés à l agent infectieux, à l hôte (dont les défenses immunitaires) et aux caractéristiques de l exposition (paramètres environnementaux et contacts interhumains). L émergence d un nouveau variant du virus A/H1N1, lors de la pandémie de 2009, a offert un terrain de recherche particulièrement prometteur, en permettant d étudier les déterminants habituellement associés à l ensemble des infections grippales et le cas particulier d un virus envers lequel la susceptibilité de la population était très variable et liée à l exposition préalable des sujets à des virus génétiquement proches. Afin d étudier les infections liées à ce virus et leurs déterminants, une cohorte de 601 ménages (1450 sujets) en population générale française a été constituée fin 2009 en vue d une approche pluridsciplinaire. Le suivi de cette cohorte, impliquant des collections biologiques et un suivi actif des symptômes grippaux, comprend notamment un recueil de données épidémio-cliniques détaillées. L analyse de cette vaste base de données offre une opportunité nouvelle d étudier le risque d infection comme résultant d une interaction complexe de facteurs appartenant à des dimensions habituellement étudiées indépendamment. La réalisation de ce travail implique le recours à de nouvelles méthodes d analyse, inspirées des approches omiques déjà utilisées pour l étude simultanée d un grand nombre de covariables.Factors associated with influenza virus transmission and susceptibility to infection still remain not well understood. The risk for infection can be considered as the result of an interaction between factors linked to the pathogen, the host (including the immune system) and the characteristics of exposure (environmental parameters and interhuman contacts). The emergence of the novel A/H1N1 virus, causing the 2009 pandemic, had offered a promising research opportunity to study the determinants usually associated with influenza infections in general and in particular regarding a virus for which the susceptibility of the population was very variable and linked with previous exposure of subjects to viruses that were genetically close. To study influenza infections and their determinants, a cohort of 601 households (1450 subjects) in the French general population was established in late 2009 using a multidisciplinary approach. The follow-up of this cohort, which involves the collection of biological samples and an active tracking of influenza-like symptoms, notably consists of a detailed collection of clinical and epidemiological data (including information regarding the subjects environment, their contacts, and their risk perception likely to impact their behavior). The analysis of this massive database offers a novel opportunity to study the risk of infection as a result of a complex interaction of factors which have previously been studied separately. This project implicated the use of new analytical methods, inspired by the omics approach already used for the simultaneous study of a large number of covariates.PARIS-BIUSJ-Biologie recherche (751052107) / SudocSudocFranceF

Biased and unbiased estimation of the average length of stay in intensive care units in the Covid-19 pandemic

International audienceBackground: The average length of stay (LOS) in the intensive care unit (ICU_ALOS) is a helpful parameter summarizing critical bed occupancy. During the outbreak of a novel virus, estimating early a reliable ICU_ALOS estimate of infected patients is critical to accurately parameterize models examining mitigation and preparedness scenarios. Methods: Two estimation methods of ICU_ALOS were compared: the average LOS of already discharged patients at the date of estimation (DPE), and a standard parametric method used for analyzing time-to-event data which fits a given distribution to observed data and includes the censored stays of patients still treated in the ICU at the date of estimation (CPE). Methods were compared on a series of all COVID-19 consecutive cases (n = 59) admitted in an ICU devoted to such patients. At the last follow-up date, 99 days after the first admission, all patients but one had been discharged. A simulation study investigated the generalizability of the methods' patterns. CPE and DPE estimates were also compared to COVID-19 estimates reported to date. Results: LOS ≥ 30 days concerned 14 out of the 59 patients (24%), including 8 of the 21 deaths observed. Two months after the first admission, 38 (64%) patients had been discharged, with corresponding DPE and CPE estimates of ICU_ALOS (95% CI) at 13.0 days (10.4-15.6) and 23.1 days (18.1-29.7), respectively. Series' true ICU_ALOS was greater than 21 days, well above reported estimates to date. Conclusions: Discharges of short stays are more likely observed earlier during the course of an outbreak. Cautious unbiased ICU_ALOS estimates suggest parameterizing a higher burden of ICU bed occupancy than that adopted to date in COVID-19 forecasting models

Les types de protéines et les macronutriments énergétiques expliquent les relations entre la végétalisation des régimes et leur qualité et valeur santé

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Vaccination and COVID-19 Dynamics in Dialysis Patients

International audienceBackground and objectives Dialysis patients have a high mortality risk after coronavirus disease 2019 (COVID-19) and an altered immunologic response to vaccines, but vaccine clinical effectiveness remains unknown in this population. Design, setting, participants, & measurements Using Bayesian multivariable spatiotemporal models, we estimated the association between vaccine exposure and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) severe infections (with hospital admission) in dialysis patients from simultaneous incidence in the general population. For dialysis patients, cases were reported within the French end-stage kidney disease REIN registry from March 11, 2020, to April 29, 2021, and vaccine exposure (first dose) was reported in weekly national surveys since January 2021. Cases in the general population were obtained from the national exhaustive inpatient surveillance system (SI-VIC database), and vaccination coverage (first dose) was obtained from the national surveillance system (VAC-SI database). Results During the first wave, incidence in dialysis patients was approximately proportional to the general population. However, we showed a lower relative incidence for dialysis patients during the second wave (compared with that observed in nondialysis patients), suggesting an effect of prevention measures. Moreover, from the beginning of the vaccination rollout, incidence in dialysis patients was lower compared with predictions based on the first and second waves. Adding vaccination coverages in dialysis and nondialysis patients as predictors allowed the reported cases to be fit correctly (3685 predicted cases, 95% confidence interval, 3552 to 3816, versus 3620 reported). Incidence rate ratios were 0.37 (95% confidence interval, 0.18 to 0.71) for vaccine exposure in dialysis patients and 0.50 (95% confidence interval, 0.40 to 0.61) per 10% higher in vaccination coverage in the same-age general population, meaning that vaccine exposure in dialysis patients and the general population was independently associated with lower hospitalization rate of dialysis patients. Conclusions Our findings suggest that vaccination may yield a protective effect against severe forms of COVID-19 in dialysis patients, despite altered immunologic vaccine responses

Plant and Animal Protein Intakes Largely Explain the Nutritional Quality and Health Value of Diets Higher in Plants: A Path Analysis in French Adults

International audienceDiets higher in plants are associated with lower risks of chronic diseases. However, animal foods, which are rich in protein, are also rich in some important minerals and vitamins. Using data from a representative survey in France (INCA3, n = 1,125), we used path analyses as a mediation-like approach to decipher the importance of plant and animal proteins in the relationship between the plant-based diet index (PDI) and diet quality. We used three types of diet quality scores, namely, nutrient security, positive nutrient adequacy, and long-term mortality risk of four diet-related diseases (i.e., coronary heart disease, stroke, type 2 diabetes, and colorectal cancer). We identified positive and negative mediations, i.e., changes in plant/animal protein intake that are associated with changes in PDI, and favor or limit the association with the diet quality score. The PDI was positively associated with the risk of long-term mortality but not significantly with nutrient adequacy or nutrient security. A positive mediation by plant protein was found for all diet quality scores (specific indirect effects (SIEs) ranging from 0.04 to 0.10 SD). Conversely, the association between PDI and nutrient adequacy (but not nutrient security) was negatively mediated by animal protein intake (SIE: −0.06 SD). In further detailed models, the association between PDI and diet quality was mainly positively mediated by protein foods from the fruit-vegetables-legumes group (0.01 SD for the nutrient security and 0.02 SD for the nutrient adequacy) and whole grains (0.02 SD for the nutrient adequacy). Our data suggest that the positive impact of plant-based diets on diet quality is largely driven by higher intakes of plant protein foods, especially from fruits-vegetables-legumes and whole grains. Conversely, lower animal protein intake tends to limit the positive impact of plant-based diets on overall positive nutrient adequacy but not security. Protein sources appear critical to healthy plant-based diets

Hospital admissions and mortality for acute exacerbations of COPD during the COVID-19 pandemic: A nationwide study in France

Background: A global reduction in hospital admissions for acute exacerbations of chronic obstructive pulmonary disease (AECOPD) was observed during the first months of the COVID-19 pandemic. Large-scale studies covering the entire pandemic period are lacking. We investigated hospitalizations for AECOPD and the associated in-hospital mortality at the national level in France during the first 2 years of the pandemic. Methods: We used the French National Hospital Database to analyse the time trends in (1) monthly incidences of hospitalizations for AECOPD, considering intensive care unit (ICU) admission and COVID-19 diagnoses, and (2) the related in-hospital mortality, from January 2016 to November 2021. Pandemic years were compared with the pre-pandemic years using Poisson regressions. Results: The database included 565,890 hospitalizations for AECOPD during the study period. The median age at admission was 74 years (interquartile range 65–83), and 37% of the stays concerned women. We found: (1) a dramatic and sustainable decline in hospitalizations for AECOPD over the pandemic period (from 8,899 to 6,032 monthly admissions, relative risk (RR) 0.65, 95% confidence interval (CI) 0.65–0.66), and (2) a concomitant increase in in-hospital mortality for AECOPD stays (from 6.2 to 7.6% per month, RR 1.24, 95% CI 1.21–1.27). The proportion of stays yielding ICU admission was similar in the pre-pandemic and pandemic years, 21.5 and 21.3%, respectively. In-hospital mortality increased to a greater extent for stays without ICU admission (RR 1.39, 95% CI 1.35–1.43) than for those with ICU admission (RR 1.09, 95% CI 1.05–1.13). Since January 2020, only 1.5% of stays were associated with a diagnosis of COVID-19, and their mortality rate was nearly three-times higher than those without COVID-19 (RR 2.66, 95% CI 2.41–2.93). Conclusion: The decline in admissions for AECOPD during the pandemic could be attributed to a decrease in the incidence of exacerbations for COPD patients and/or to a possible shift from hospital to community care. The rise in in-hospital mortality is partially explained by COVID-19, and could be related to restricted access to ICUs for some patients and/or to greater proportions of severe cases among the patients hospitalized during the pandemic

Epidemiology, risk factors and prognosis of ventilator-associated pneumonia during severe COVID-19: Multicenter observational study across 149 European Intensive Care Units

International audienceBackground: COVID-19 patients requiring mechanical ventilation are particularly at risk of developing ventilator-associated pneumonia (VAP). Risk factors and the prognostic impact of developing VAP during critical COVID-19 have not been fully documented.Methods: Patients invasively ventilated for at least 48 h from the prospective multicentre COVID-ICU database were included in the analyses. Cause-specific Cox regression models were used to determine factors associated with the occurrence of VAP. Cox-regression multivariable models were used to determine VAP prognosis. Risk factors and the prognostic impact of early vs. late VAP, and Pseudomonas-related vs. non-Pseudomonas-related VAP were also determined.Main findings: 3388 patients were analysed (63 [55-70] years, 75.8% males). VAP occurred in 1523/3388 (45.5%) patients after 7 [5-9] days of ventilation. Identified bacteria were mainly Enterobacteriaceae followed by Staphylococcus aureus and Pseudomonas aeruginosa. VAP risk factors were male gender (Hazard Ratio (HR) 1.26, 95% Confidence Interval [1.09-1.46]), concomitant bacterial pneumonia at ICU admission (HR 1.36 [1.10-1.67]), PaO2/FiO2 ratio at intubation (HR 0.99 [0.98-0.99] per 10 mmHg increase), neuromuscular-blocking agents (HR 0.89 [0.76-0.998]), and corticosteroids (HR 1.27 [1.09-1.47]). VAP was associated with 90-mortality (HR 1.34 [1.16-1.55]), predominantly due to late VAP (HR 1.51 [1.26-1.81]). The impact of Pseudomonas-related and non-Pseudomonas-related VAP on mortality was similar.Conclusion: VAP affected almost half of mechanically ventilated COVID-19 patients. Several risk factors have been identified, among which modifiable risk factors deserve further investigation. VAP had a specific negative impact on 90-day mortality, particularly when it occurred between the end of the first week and the third week of ventilation

Predictors of IV behaviors during and after the 2009 influenza pandemic in France

International audienceBackgroundControversies about the 2009 H1N1 pandemic influenza vaccination might have impacted the motivational processes that underlie individual immunization against seasonal influenza. The purpose of this article is to investigate correlates of vaccine uptake during and after the pandemic.MethodsData from the 1174 subjects of the CoPanFlu France cohort aged 15 and over were used. We used logistic regression models to identify social and behavioral predictors of getting vaccinated against seasonal influenza in 2009–2010 and in 2010–2011 and against H1N1 influenza in 2009–2010.ResultsThis study points out that correlates of vaccination behaviors varied according to the vaccine. Respondents under 65 years who adopted the seasonal influenza vaccine were, as usual, more likely to belong to a target group and have a lower education, contrary to subjects who chose the pandemic vaccine. Exceptionally during the pandemic, a higher socioeconomic status also led to adoption of either vaccine. Motivational processes differed by vaccine. Uptaking the “new” pandemic vaccine was the result of a deliberative decision-making process, influenced by cognitive factors related to the pandemic context (such as perceived severity of the H1N1 flu strain and trust in public health authorities). In contrast, respondents got the seasonal flu vaccine without relying on explicit justifications, but instead through habit of performing this behavior in the past.ConclusionsTarget groups for seasonal influenza but not those for pandemic influenza were more likely to adopt the pandemic vaccine, which is a cause for great concern. This may be due to large extent to the automatic and habitual nature of influenza vaccination decisions. Public health authorities, should pay more attention to situational than informational cues to facilitate vaccine uptake among priority groups, especially in case of mild pandemic influenza