• Publicationsclose
• Research dataclose
• Other research productsclose
• 2018-2022close
• Preprint close
• FR close
• COVID-19 close

The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected COVID-19 spread in China. We use real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation on transmission in cities across China and ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was well explained by human mobility data. Following the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases are still indicative of local chains of transmission outside Wuhan. This study shows that the drastic control measures implemented in China have substantially mitigated the spread of COVID-19. One sentence summary: The spread of COVID-19 in China was driven by human mobility early on and mitigated substantially by drastic control measures implemented since the end of January.

Abstract Background: To compare the rate of postpartum depression (PPD) during the first COVID-19 lockdown with the rate observed prior to the pandemic, and to examine factors associated with PPD.Methods: This was a prospective study. Women who gave birth during the first COVID-19 lockdown (spring 2020) were offered call-interviews at 10 days and 6-8 weeks postpartum to assess PPD using the Edinburgh Postnatal Depression Scale (EPDS). Post-traumatic symptoms (Perinatal Post-traumatic Stress Disorder Questionnaire, PPQ), couple adjustment, and interaction and mother-to-infant bonding were also evaluated. The observed PPD rate was compared to the one reported before the pandemic. Factors associated with an increased risk of PPD were studied. The main outcome measures were comparison of the observed PPD rate (EPDS score>12) to pre-pandemic rate. Results: Of the 164 women included, 27 (16.5% [95%CI: 11.14 – 23.04]) presented an EPDS score>12 either at 10 days or 6-8 weeks postpartum. This rate was similar to the one of 15% reported prior to the pandemic (p=0.6). Combined EPDS>12 or PPQ>6 scores were observed in 20.7% of the mothers [95%CI: 14.8 – 0.28]. Maternal hypertension/preeclampsia (p=0.007), emergency cesarean section (p=0.03), and neonatal complications (p=0.008) were significantly associated with an EPDS>12 both in univariate and multivariate analysis (OR=10 [95%CI: 1.5 – 68.7], OR=4.09[95%CI: 1.2 – 14], OR=4.02[95%CI: 1.4 – 11.6], respectively).Conclusions: The rate of major PPD in our population did not increase during the first lockdown period. However, 20.7% of the women presented with post-traumatic/depressive symptoms.Trial Registration: NCT04366817

After steep drops and then rebounds in transportation-related CO$_2$ emissions over the first half of 2020, a second wave of COVID-19 this fall has caused further -- but less substantial -- emissions reductions. Here, we use near-real-time estimates of daily emissions to explore differences in human behavior and restriction policies over the course of 2020.

ABSTRACTThe novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

The model descibes the epidemic dynamics of Covid-19 in a population after vaccination. Using the maximum principale, our goal is to prove the existence of an optimal strategy such that it minimize the number of infected people after vaccination. Finally, some numerical results are provided.

ABSTRACTELISA and chemiluminescence serological assays for COVID-19 are currently incorporating only one or two SARS-CoV-2 antigens. We developed an automated Western immunoblotting as a complementary serologic assay for COVID-19. The Jess™ Simple Western system, an automated capillary-based assay was used, incorporating an inactivated SARS-CoV-2 lineage 20a strain as antigen, and IgT detection. In total, 602 sera were tested including 223 from RT-PCR-confirmed COVID-19 patients, 76 from patients diagnosed with seasonal HCoVs and 303 from coronavirus-negative control sera. We also compared this assay with the EUROIMMUN® SARS-CoV-2 IgG ELISA kit. Among 223 sera obtained from RT-PCR-confirmed COVID-19 patients, 180/223 (81%) exhibited reactivity against the nucleocapsid and 70/223 (31%) against the spike protein. Nucleocapsid reactivity was further detected in 9/76 (14%) samples collected from patients diagnosed with seasonal HCoVs and in 15/303 (5%) coronavirus-negative control samples. In the subset of sera collected more than 2 weeks after the onset of symptoms, the sensitivity was 94% and the specificity 93%, the latter value probably reflecting cross-reactivity of SARS-CoV-2 with other coronaviruses. The automated Western immunoblotting presented a substantial agreement (90%) with the compared ELISA (Cohen’s Kappa=0.64). Automated Western immunoblotting may be used as a second line test to monitor exposition of people to HCoVs including SARS-CoV-2.

AbstractCOVID-19 SARS-CoV-2 infection exhibits wide inter-individual clinical variability, from silent infection to severe disease and death. The identification of high-risk patients is a continuing challenge in routine care. We aimed to identify factors that influence clinical worsening. We analyzed 52 cell populations, 71 analytes, and RNA-seq gene expression in the blood of severe patients from the French COVID cohort upon hospitalization (n = 61). COVID-19 patients showed severe abnormalities of 27 cell populations relative to healthy donors (HDs). Forty-two cytokines, neutrophil chemo-attractants, and inflammatory components were elevated in COVID-19 patients. Supervised gene expression analyses showed differential expression of genes for neutrophil activation, interferon signaling, T- and B-cell receptors, EIF2 signaling, and ICOS-ICOSL pathways in COVID-19 patients. Unsupervised analysis confirmed the prominent role of neutrophil activation, with a high abundance of CD177, a specific neutrophil activation marker. CD177 was the most highly differentially-expressed gene contributing to the clustering of severe patients and its abundance correlated with CD177 protein serum levels. CD177 levels were higher in COVID-19 patients from both the French and “confirmatory” Swiss cohort (n = 203) than in HDs (P< 0.01) and in ICU than non-ICU patients (P< 0.001), correlating with the time to symptoms onset (P = 0.002). Longitudinal measurements showed sustained levels of serum CD177 to discriminate between patients with the worst prognosis, leading to death, and those who recovered (P = 0.01). These results highlight neutrophil activation as a hallmark of severe disease and CD177 assessment as a reliable prognostic marker for routine care.

AbstractBackgroundPublic health recommendations and governmental measures during the COVID-19 pandemic have enforced numerous restrictions on daily living including social distancing, isolation and home confinement. While these measures are imperative to abate the spreading of COVID-19, the impact of these restrictions on health behaviours and lifestyle at home is undefined. Therefore, an international online survey was launched in April 2020 in seven languages to elucidate the behavioral and lifestyle consequences of COVID-19 restrictions. This report presents the preliminary results from the first thousand responders on physical activity (PA) and nutrition behaviours.MethodsThirty-five research organisations from Europe, North-Africa, Western Asia and the Americas promoted the survey through their networks to the general society, in English, German, French, Arabic, Spanish, Portugese, and Slovenian languages. Questions were presented in a differential format with questions related to responses “before” and “during” confinement conditions.Results1047 replies (54% women) from Asia (36%), Africa (40%), Europe (21%) and other (3%) were included into a general analysis. The COVID-19 home confinement had a negative effect on all intensities of PA (vigorous, moderate, walking and overall). Conversely, daily sitting time increased from 5 to 8 hours per day. Additionally, food consumption and meal patterns (the type of food, eating out of control, snacks between meals, number of meals) were more unhealthy during confinement with only alcohol binge drink decreasing significantly.ConclusionWhile isolation is a necessary measure to protect public health, our results indicate that it alters physical activity and eating behaviours in a direction that would compromise health. A more detailed analysis of survey data will allow for a segregation of these responses in different age groups, countries and other subgroups which will help develop bespoke interventions to mitigate the negative lifestyle behaviors manifest during the COVID-19 confinement.

AbstractBackgroundCOVID-19 is spreading rapidly in nursing homes (NHs). It is urgent to evaluate the effect of infection prevention and control (IPC) measures to reduce COVID spreading.MethodsWe analysed COVID-19 outbreaks in 12 NH using rRT-PCR for SARS-CoV-2. We estimated secondary attack risks (SARs) and identified cofactors associated with the proportion of infected residents.ResultsThe SAR was below 5%, suggesting a high efficiency of IPC measures. Mask-wearing or establishment of COVID-19 zones for infected residents were associated with lower SAR.ConclusionsWearing masks and isolating potentially infected residents appear to limit SARS-CoV-2 spread in nursing homes.