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2.
Nat Commun ; 13(1): 6025, 2022 Oct 12.
Article in English | MEDLINE | ID: covidwho-2062212

ABSTRACT

Infection with SARS-CoV-2 variant Omicron is considered to be less severe than infection with variant Delta, with rarer occurrence of severe disease requiring intensive care. Little information is available on comorbid factors, clinical conditions and specific viral mutational patterns associated with the severity of variant Omicron infection. In this multicenter prospective cohort study, patients consecutively admitted for severe COVID-19 in 20 intensive care units in France between December 7th 2021 and May 1st 2022 were included. Among 259 patients, we show that the clinical phenotype of patients infected with variant Omicron (n = 148) is different from that in those infected with variant Delta (n = 111). We observe no significant relationship between Delta and Omicron variant lineages/sublineages and 28-day mortality (adjusted odds ratio [95% confidence interval] = 0.68 [0.35-1.32]; p = 0.253). Among Omicron-infected patients, 43.2% are immunocompromised, most of whom have received two doses of vaccine or more (85.9%) but display a poor humoral response to vaccination. The mortality rate of immunocompromised patients infected with variant Omicron is significantly higher than that of non-immunocompromised patients (46.9% vs 26.2%; p = 0.009). In patients infected with variant Omicron, there is no association between specific sublineages (BA.1/BA.1.1 (n = 109) and BA.2 (n = 21)) or any viral genome polymorphisms/mutational profile and 28-day mortality.


Subject(s)
COVID-19 , SARS-CoV-2 , Critical Illness , Humans , Phenotype , Prospective Studies , SARS-CoV-2/genetics
3.
Microbiol Spectr ; 10(4): e0115722, 2022 08 31.
Article in English | MEDLINE | ID: covidwho-1950017

ABSTRACT

Large-scale head-to-head assessment of the performance of lateral-flow tests (LFTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen is required in the context of the continuous emergence of new viral variants. The aim of this study was to evaluate the performance of 22 rapid LFTs for the detection of SARS-CoV-2 antigens. The clinical performance of 22 LFTs was evaluated in 1,157 samples collected in the Greater Paris area. The 8 best-performing LFTs were further assessed for their ability to detect 4 variants of concern (VOC), including the alpha, beta, delta, and omicron (BA.1) variants. The specificity of SARS-CoV-2 LFTs was generally high (100% for 15 of them) but was insufficient (<75%) for 3 tests. Sensitivity of the LFTs varied from 30.0% to 79.7% compared to nucleic acid amplification testing (NAAT). Using a cycle threshold (CT) cutoff of ≤25, sensitivity of the assays ranged from 59.7% to 100%. The 8 best-performing assays had a sensitivity of ≥80% for the detection of the 4 VOC when the CT was ≤25. Falsely negative SARS-CoV-2 antigen LFT results were observed with omicron, due to the occurrence of low viral loads (CT > 30 in 32% of samples) during the two first days following symptom onset. Several LFTs exhibited satisfactory sensitivity and specificity, whereas a few others yielded an unacceptable proportion of false-positive results and/or lacked sensitivity. The sensitivity of the best-performing assays was not influenced by VOC, including alpha, beta, delta, and omicron variants. The ability of LFTs to detect the omicron variant could be reduced during the first days following symptom onset due to lower viral loads than with other variants. IMPORTANCE The use of lateral-flow tests (LFTs) to detect SARS-CoV-2 has expanded worldwide. LFTs detect SARS-CoV-2 viral antigen and are less sensitive than nucleic acid amplification testing (NAAT). Their performance must be evaluated independently of the manufacturers. Our study assessed the performance of 22 SARS-CoV-2 antigen LFTs in large panels of well-characterized samples. The majority of LFTs tested exhibited satisfactory sensitivity and specificity, while some assays yielded unacceptable proportions of false-positive results, and others lacked sensitivity for samples containing large amounts of virus. The sensitivity of the best-performing assays did not vary according to the VOC, including the alpha, beta, delta, and omicron variants.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , Humans , SARS-CoV-2/genetics , Serologic Tests/methods
4.
Viruses ; 14(7)2022 Jul 13.
Article in English | MEDLINE | ID: covidwho-1939016

ABSTRACT

The SARS-CoV-2 variant of concern, α, spread worldwide at the beginning of 2021. It was suggested that this variant was associated with a higher risk of mortality than other variants. We aimed to characterize the genetic diversity of SARS-CoV-2 variants isolated from patients with severe COVID-19 and unravel the relationships between specific viral mutations/mutational patterns and clinical outcomes. This is a prospective multicenter observational cohort study. Patients aged ≥18 years admitted to 11 intensive care units (ICUs) in hospitals in the Greater Paris area for SARS-CoV-2 infection and acute respiratory failure between 1 October 2020 and 30 May 2021 were included. The primary clinical endpoint was day-28 mortality. Full-length SARS-CoV-2 genomes were sequenced by means of next-generation sequencing (Illumina COVIDSeq). In total, 413 patients were included, 183 (44.3%) were infected with pre-existing variants, 197 (47.7%) were infected with variant α, and 33 (8.0%) were infected with other variants. The patients infected with pre-existing variants were significantly older (64.9 ± 11.9 vs. 60.5 ± 11.8 years; p = 0.0005) and had more frequent COPD (11.5% vs. 4.1%; p = 0.009) and higher SOFA scores (4 [3-8] vs. 3 [2-4]; 0.0002). The day-28 mortality was no different between the patients infected with pre-existing, α, or other variants (31.1% vs. 26.2% vs. 30.3%; p = 0.550). There was no association between day-28 mortality and specific variants or the presence of specific mutations. At ICU admission, the patients infected with pre-existing variants had a different clinical presentation from those infected with variant α, but mortality did not differ between these groups. There was no association between specific variants or SARS-CoV-2 genome mutational pattern and day-28 mortality.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Adult , Critical Illness , Genomics , Humans , Prospective Studies , SARS-CoV-2/genetics
5.
BMJ Open ; 12(4): e059383, 2022 04 26.
Article in English | MEDLINE | ID: covidwho-1816767

ABSTRACT

INTRODUCTION: COVID-19 induces venous, arterial and microvascular thrombosis, involving several pathophysiological processes. In patients with severe COVID-19 without macrovascular thrombosis, escalating into high-dose prophylactic anticoagulation (HD-PA) or therapeutic anticoagulation (TA) could be beneficial in limiting the extension of microvascular thrombosis and forestalling the evolution of lung and multiorgan microcirculatory dysfunction. In the absence of data from randomised trials, clinical practice varies widely. METHODS AND ANALYSIS: This is a French multicentre, parallel-group, open-label, randomised controlled superiority trial to compare the efficacy and safety of three anticoagulation strategies in patients with COVID-19. Patients with oxygen-treated COVID-19 showing no pulmonary artery thrombosis on computed tomography with pulmonary angiogram will be randomised to receive either low-dose PA, HD-PA or TA for 14 days. Patients attaining the extremes of weight and those with severe renal failure will not be included. We will recruit 353 patients. Patients will be randomised on a 1:1:1 basis, and stratified by centre, use of invasive mechanical ventilation, D-dimer levels and body mass index. The primary endpoint is a hierarchical criterion at day 28 including all-cause mortality, followed by the time to clinical improvement defined as the time from randomisation to an improvement of at least two points on the ordinal clinical scale. Secondary outcomes include thrombotic and major bleeding events at day 28, individual components of the primary endpoint, number of oxygen-free, ventilator-free and vasopressor-free days at day 28, D-dimer and sepsis-induced coagulopathy score at day 7, intensive care unit and hospital stay at day 28 and day 90, and all-cause death and quality of life at day 90. ETHICS AND DISSEMINATION: The study has been approved by an ethical committee (Ethics Committee, Ile de France VII, Paris, France; reference 2020-A03531-38). Patients will be included after obtaining their signed informed consent. The results will be submitted for publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT04808882.


Subject(s)
COVID-19 , Anticoagulants/therapeutic use , Blood Coagulation , Humans , Microcirculation , Multicenter Studies as Topic , Quality of Life , Randomized Controlled Trials as Topic
6.
Respir Res ; 23(1): 68, 2022 Mar 22.
Article in English | MEDLINE | ID: covidwho-1759751

ABSTRACT

BACKGROUND: Patient hospitalized for coronavirus disease 2019 (COVID-19) pulmonary infection can have sequelae such as impaired exercise capacity. We aimed to determine the frequency of long-term exercise capacity limitation in survivors of severe COVID-19 pulmonary infection and the factors associated with this limitation. METHODS: Patients with severe COVID-19 pulmonary infection were enrolled 3 months after hospital discharge in COVulnerability, a prospective cohort. They underwent cardiopulmonary exercise testing, pulmonary function test, echocardiography, and skeletal muscle mass evaluation. RESULTS: Among 105 patients included, 35% had a reduced exercise capacity (VO2peak < 80% of predicted). Compared to patients with a normal exercise capacity, patients with reduced exercise capacity were more often men (89.2% vs. 67.6%, p = 0.015), with diabetes (45.9% vs. 17.6%, p = 0.002) and renal dysfunction (21.6% vs. 17.6%, p = 0.006), but did not differ in terms of initial acute disease severity. An altered exercise capacity was associated with an impaired respiratory function as assessed by a decrease in forced vital capacity (p < 0.0001), FEV1 (p < 0.0001), total lung capacity (p < 0.0001) and DLCO (p = 0.015). Moreover, we uncovered a decrease of muscular mass index and grip test in the reduced exercise capacity group (p = 0.001 and p = 0.047 respectively), whilst 38.9% of patients with low exercise capacity had a sarcopenia, compared to 10.9% in those with normal exercise capacity (p = 0.001). Myocardial function was normal with similar systolic and diastolic parameters between groups whilst reduced exercise capacity was associated with a slightly shorter pulmonary acceleration time, despite no pulmonary hypertension. CONCLUSION: Three months after a severe COVID-19 pulmonary infection, more than one third of patients had an impairment of exercise capacity which was associated with a reduced pulmonary function, a reduced skeletal muscle mass and function but without any significant impairment in cardiac function.


Subject(s)
COVID-19/complications , Exercise Tolerance/physiology , Pneumonia/physiopathology , Aged , COVID-19/physiopathology , Cohort Studies , Echocardiography/methods , Echocardiography/statistics & numerical data , Exercise Test/methods , Exercise Test/statistics & numerical data , Exercise Tolerance/immunology , Female , Follow-Up Studies , France , Humans , Lung/physiopathology , Male , Middle Aged , Pneumonia/etiology , Prospective Studies , Respiratory Function Tests/methods , Respiratory Function Tests/statistics & numerical data , Respiratory Insufficiency/etiology , Respiratory Insufficiency/physiopathology
7.
Int J Cancer ; 150(10): 1609-1618, 2022 05 15.
Article in English | MEDLINE | ID: covidwho-1615974

ABSTRACT

The SARS-Cov2 may have impaired care trajectories, patient overall survival (OS), tumor stage at initial presentation for new colorectal cancer (CRC) cases. This study aimed at assessing those indicators before and after the beginning of the pandemic in France. In this retrospective cohort study, we collected prospectively the clinical data of the 11.4 million of patients referred to the Greater Paris University Hospitals (AP-HP). We identified new CRC cases between 1 January 2018 and 31 December 2020, and compared indicators for 2018-2019 to 2020. pTNM tumor stage was extracted from postoperative pathology reports for localized colon cancer, and metastatic status was extracted from CT-scan baseline text reports. Between 2018 and 2020, 3602 and 1083 new colon and rectal cancers were referred to the AP-HP, respectively. The 1-year OS rates reached 94%, 93% and 76% for new CRC patients undergoing a resection of the primary tumor, in 2018-2019, in 2020 without any Sars-Cov2 infection and in 2020 with a Sars-Cov2 infection, respectively (HR 3.78, 95% CI 2.1-7.1). For patients undergoing other kind of anticancer treatment, the percentages are 64%, 66% and 27% (HR 2.1, 95% CI 1.4-3.3). Tumor stage at initial presentation, emergency level of primary tumor resection, delays between the first multidisciplinary meeting and the first anticancer treatment did not differ over time. The SARS-Cov2 pandemic has been associated with less newly diagnosed CRC patients and worse 1-year OS rates attributable to the infection itself rather than to its impact on hospital care delivery or tumor stage at initial presentation.


Subject(s)
COVID-19 , Colonic Neoplasms , Colorectal Neoplasms , COVID-19/epidemiology , Cohort Studies , Colorectal Neoplasms/epidemiology , Colorectal Neoplasms/therapy , Hospitals, University , Humans , Pandemics , RNA, Viral , Retrospective Studies , SARS-CoV-2
8.
Trials ; 23(1): 4, 2022 Jan 03.
Article in English | MEDLINE | ID: covidwho-1606541

ABSTRACT

BACKGROUND: Cardiogenic shock (CS) is a life-threatening condition characterized by circulatory insufficiency caused by an acute dysfunction of the heart pump. The pathophysiological approach to CS has recently been enriched by the tissue consequences of low flow, including inflammation, endothelial dysfunction, and alteration of the hypothalamic-pituitary-adrenal axis. The aim of the present trial is to evaluate the impact of early low-dose corticosteroid therapy on shock reversal in adults with CS. METHOD/DESIGN: This is a multicentered randomized, double-blind, placebo-controlled trial with two parallel arms in adult patients with CS recruited from medical, cardiac, and polyvalent intensive care units (ICU) in France. Patients will be randomly allocated into the treatment or control group (1:1 ratio), and we will recruit 380 patients (190 per group). For the treatment group, hydrocortisone (50 mg intravenous bolus every 6 h) and fludrocortisone (50 µg once a day enterally) will be administered for 7 days or until discharge from the ICU. The primary endpoint is catecholamine-free days at day 7. Secondary endpoints include morbidity and all-cause mortality at 28 and 90 days post-randomization. Pre-defined subgroups analyses are planned, including: postcardiotomy, myocardial infarction, etomidate use, vasopressor use, and adrenal profiles according the short corticotropin stimulation test. Each patient will be followed for 90 days. All analyses will be conducted on an intention-to-treat basis. DISCUSSION: This trial will provide valuable evidence about the effectiveness of low dose of corticosteroid therapy for CS. If effective, this therapy might improve outcome and become a therapeutic adjunct for patients with CS. TRIAL REGISTRATION: ClinicalTrials.gov , NCT03773822 . Registered on 12 December 2018.


Subject(s)
COVID-19 , Shock, Cardiogenic , Adult , Humans , Hypothalamo-Hypophyseal System , Multicenter Studies as Topic , Pituitary-Adrenal System , Randomized Controlled Trials as Topic , SARS-CoV-2 , Shock, Cardiogenic/diagnosis , Shock, Cardiogenic/drug therapy , Treatment Outcome
9.
J Clin Virol ; 146: 105048, 2022 01.
Article in English | MEDLINE | ID: covidwho-1540751

ABSTRACT

Direct detection of SARS-CoV-2 viral antigens could replace RT-PCR, provided that its clinical performance is validated in different epidemiological settings. Here, we evaluated the performance of the VITROS Antigen test, an enzyme immunoassay detecting a SARS-CoV-2 antigen, in NPSs from 3 cohorts of patients. METHODS: Three cohorts including SARS-CoV-2 RNA-positive samples collected during the first and second wave of the French epidemic between March 2020 and February 2021 (including variant B.1.1.7/α and variant B.1.351/ß). RESULTS: Among the 1763 prospectively tested subjects, 8.2% (145/1763) were SARS-CoV-2 RNA-positive by RT-PCR. Using Ct ≤ 30 and Ct ≤ 35 as thresholds, the sensitivities of the antigen assay were 98.8% (93.6-100%) and 93.5% (87.0-97.3%), respectively. The overall specificity of the assay was 100% (1614/1614; 99.8-100%). In a retrospective cohort of subjects infected with variants of concern, 90.4% (47/52) of NPSs containing B. B.1.1.7/α (Ct ≤ 35) and 100% (7/7) of those containing B.1.351/ß were positive with the VITROS EIA SARS-CoV-2 Antigen test. CONCLUSION: The excellent performance of the EIA Antigen test reported here, including in patients infected with viral "variants of concern", support the use of high-throughput, EIA-based SARS-CoV-2 antigen assays as an alternative or complement to nucleic acid testing in order to scale-up laboratory screening and diagnostic capacities.


Subject(s)
COVID-19 , SARS-CoV-2 , Antigens, Viral , Humans , Immunoassay , Immunoenzyme Techniques , RNA, Viral , Retrospective Studies , Sensitivity and Specificity
10.
J Clin Virol ; 142: 104930, 2021 09.
Article in English | MEDLINE | ID: covidwho-1356292

ABSTRACT

BACKGROUND: Direct detection of SARS-CoV-2 viral proteins in nasopharyngeal swabs using lateral flow immunoassays is a simple, fast and cheap approach to diagnose the infection. AIMS AND METHODS: The performance of 6 SARS-CoV-2 antigen rapid diagnostic tests has been assessed in 634 hospitalized patients or outpatients including 297 patients found to be positive for SARS-CoV-2 RNA by means of RT-PCR and 337 patients presumed to be SARS-CoV-2 RNA-negative. RESULTS: The specificity of SARS-CoV-2 RDTs was generally high (398.5%). One assay had a lower specificity of 93.2%. The overall sensitivity of the 6 RDTs was variable, from 32.3% to 61.7%. Sensitivity correlated with the delay of sampling after the onset of symptoms and the viral load estimated by the Ct value in RT-PCR. Four out of 6 RDTs tested achieved sensitivities 380% when clinical specimens were collected during the first 3 days following symptom onset or with a Ct value ≤25. CONCLUSIONS: The present study shows that SARS-CoV-2 antigen can be easily and reliably detected by RDTs. These tests are easy and rapid to perform. However, the specificity and sensitivity of COVID-19 antigen RDTs may widely vary across different tests and must therefore be carefully evaluated before releasing these assays for realworld applications.


Subject(s)
COVID-19 , SARS-CoV-2 , Antigens, Viral , Diagnostic Tests, Routine , Humans , RNA, Viral , Sensitivity and Specificity
12.
Eur J Cancer ; 150: 260-267, 2021 06.
Article in English | MEDLINE | ID: covidwho-1101196

ABSTRACT

INTRODUCTION: The dissemination of SARS-Cov2 may have delayed the diagnosis of new cancers. This study aimed at assessing the number of new cancers during and after the lockdown. METHODS: We prospectively collected the clinical data of the 11.4 million patients referred to the Assistance Publique Hôpitaux de Paris Teaching Hospital. We identified new cancer cases between 1st January 2018 and 31st September 2020 and compared indicators for 2018 and 2019 to 2020 with a focus on the French lockdown (17th March to 11th May 2020) across cancer types and patient age classes. RESULTS: Between January and September, 28,348, 27,272 and 23,734 new cancer cases were identified in 2018, 2019 and 2020, respectively. The monthly median number of new cases reached 3168 (interquartile range, IQR, 3027; 3282), 3054 (IQR 2945; 3127) and 2723 (IQR 2085; 2,863) in 2018, 2019 and 2020, respectively. From March 1st to May 31st, new cancer decreased by 30% in 2020 compared to the 2018-19 average; then by 9% from 1st June to 31st September. This evolution was consistent across all tumour types: -30% and -9% for colon, -27% and -6% for lung, -29% and -14% for breast, -33% and -12% for prostate cancers, respectively. For patients aged <70 years, the decrease of colorectal and breast new cancers in April between 2018 and 2019 average and 2020 reached 41% and 39%, respectively. CONCLUSION: The SARS-Cov2 pandemic led to a substantial decrease in new cancer cases. Delays in cancer diagnoses may affect clinical outcomes in the coming years.


Subject(s)
COVID-19 , Neoplasms/epidemiology , Aged , Female , France/epidemiology , Health Policy , Humans , Male , Middle Aged , Neoplasms/diagnosis , Quarantine , SARS-CoV-2
13.
Am J Respir Crit Care Med ; 202(11): 1509-1519, 2020 12 01.
Article in English | MEDLINE | ID: covidwho-952528

ABSTRACT

Rationale: Uncontrolled inflammatory innate response and impaired adaptive immune response are associated with clinical severity in patients with coronavirus disease (COVID-19).Objectives: To compare the immunopathology of COVID-19 acute respiratory distress syndrome (ARDS) with that of non-COVID-19 ARDS, and to identify biomarkers associated with mortality in patients with COVID-19 ARDS.Methods: Prospective observational monocenter study. Immunocompetent patients diagnosed with RT-PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and ARDS admitted between March 8 and March 30, 2020, were included and compared with patients with non-COVID-19 ARDS. The primary clinical endpoint of the study was mortality at Day 28. Flow cytometry analyses and serum cytokine measurements were performed at Days 1-2 and 4-6 of ICU admission.Measurements and Main Results: As compared with patients with non-COVID-19 ARDS (n = 36), those with COVID-19 (n = 38) were not significantly different regarding age, sex, and Sequential Organ Failure Assessment and Simplified Acute Physiology Score II scores but exhibited a higher Day-28 mortality (34% vs. 11%, P = 0.030). Patients with COVID-19 showed profound and sustained T CD4+ (P = 0.002), CD8+ (P < 0.0001), and B (P < 0.0001) lymphopenia, higher HLA-DR expression on monocytes (P < 0.001) and higher serum concentrations of EGF (epithelial growth factor), GM-CSF, IL-10, CCL2/MCP-1, CCL3/MIP-1a, CXCL10/IP-10, CCL5/RANTES, and CCL20/MIP-3a. After adjusting on age and Sequential Organ Failure Assessment, serum CXCL10/IP-10 (P = 0.047) and GM-CSF (P = 0.050) were higher and nasopharyngeal RT-PCR cycle threshold values lower (P = 0.010) in patients with COVID-19 who were dead at Day 28.Conclusions: Profound global lymphopenia and a "chemokine signature" were observed in COVID-19 ARDS. Increased serum concentrations of CXCL10/IP-10 and GM-CSF, together with higher nasopharyngeal SARS-CoV-2 viral load, were associated with Day-28 mortality.


Subject(s)
Antibodies, Viral/blood , COVID-19/immunology , COVID-19/physiopathology , Chemokines/blood , Immunity, Innate , Respiratory Distress Syndrome/immunology , Respiratory Distress Syndrome/physiopathology , Adult , Aged , COVID-19/blood , COVID-19/epidemiology , Female , France/epidemiology , Humans , Male , Middle Aged , Pandemics , Prospective Studies , Respiratory Distress Syndrome/blood , Respiratory Distress Syndrome/epidemiology , Viral Load
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