Rapid screening assays of N501Y and E484K SARS-CoV-2 variants and identification of an emerging N501T variant in France (preprint)

From September 2020, new variants of concern of SARS-CoV-2 were detected in Europe. In this context, our hospital center has led us to be particularly vigilant in the search for and detection of these variants. To this end, two SARS-CoV-2 Mutation Discrimination assays for the detection of 501 and 484 mutations on spike protein were developed. It allowed to quickly identify the United Kingdom variant 20I/501Y.V1 and the south-african variant 20H/501Y.V2 that were circulating in our region and surprisingly identify a mutation of interest (N501T), which reported for the first time the A.28 lineage in France.

Pathology Assessments of Multiple Organs in Fatal COVID-19 in ICU vs. Non-ICU Patients (preprint)

Purpose: The objective of the present study was to provide a detailed histopathological description of fatal coronavirus disease 2019 (COVID 19), and compare the lesions in Intensive Care Unit (ICU) and non-ICU patients.Methods: In this prospective study we included adult patients who died in hospital after presenting with probable or confirmed COVID-19. Multiorgan biopsies were performed. Data generated with light microscopy, transmission electron microscopy (TEM) and RT-PCR assays were reviewed.Results20 patients were enrolled in the study and the main pulmonary finding was alveolar damage, which was focal in 11 patients and diffuse in 8 patients. Chronic fibrotic and inflammatory lesions were observed in 18 cases, with acute inflammatory lesions in 12 cases. Diffuse lesions, collapsed alveoli and dystrophic pneumocytes were more frequent in the ICU group (62.5%, vs. 25%; 63%, vs. 55%; 87.5%, vs. 54%). Acute lesions (82%, vs. 37.5%; p=0.07) with neutrophilic alveolitis (63.6% vs. 0%, respectively; p=0.01) were observed more frequently in the non-ICU group. Viral RNA was detected in 12 lung biopsies (60%) up to 56 days after disease upset. TEM detected viral particles in the lung and kidney biopsy samples up to 27 days after disease upset. Furthermore, abundant networks of double-membrane vesicles (DMVs, a hallmark of viral replication) were observed in proximal tubular epithelial cells.Conclusion: Lung injury was different in ICU and non-ICU patients. Extrapulmonary damage was also involved. Our TEM experiments provided the first description of SARS-CoV-2-induced DMVs in kidney biopsy samples – a sign of intense viral replication in this organ.Funding Information: This research did not receive any specific funding from agencies or organizations in the public, commercial, or not-for-profit sectors.Declaration of Interests: The authors report no disclosures of relevance to the manuscript.Ethics Approval Statement: The study was approved by the French Ministry of Health. Informed consent was obtained from all patient families.

COVID-19 or not COVID-19? Compared characteristics of patients hospitalized for suspected COVID-19.

During an epidemic period, we compared patients hospitalized for initial suspicion of COVID-19 but for whom an alternative diagnosis was finally retained (n = 152) with those who had COVID-19 (n = 222). Most common diagnoses were another infectious disease and heart failure. COVID-19-negative patients were more often active smokers had less often cough, fever, and digestive symptoms, as compared to the 222 COVID-19-positive patients. They had higher median neutrophil and lymphocyte counts and lower CRP level. In multivariate analysis, no current smoking, neurocognitive disorder, myalgia, and fibrinogen ≥4g/L were independently associated with a final diagnosis of COVID-19.

Anti-Spike, anti-Nucleocapsid and neutralizing antibodies in SARS-CoV-2 hospitalized patients and asymptomatic carriers (preprint)

ObjectiveThe objective of this study was to monitor the anti-SARS-CoV-2 antibody response in infected patients. MethodsIn order to assess the time of seroconversion, we used 151 samples from 30 COVID-19 inpatients and monitored the detection kinetics of anti-S1, anti-S2, anti-RBD and anti-N antibodies with in-house ELISAs. We also monitored the presence of neutralizing antibodies in these samples as well as 25 asymptomatic carrier samples using retroviral particles pseudotyped with the spike of the SARS-CoV-2. ResultsWe observed that specific antibodies were detectable in all inpatients two weeks post-symptom onset. The detection of the SARS-CoV-2 Nucleocapsid and RBD was more sensitive than the detection of the S1 or S2 subunits. Neutralizing antibodies reached a plateau two weeks post-symptom onset and then declined in the majority of inpatients. Furthermore, neutralizing antibodies were undetectable in 56% of asymptomatic carriers. ConclusionsOur results raise questions concerning the role played by neutralizing antibodies in COVID-19 cure and protection against secondary infection. They also suggest that induction of neutralizing antibodies is not the only strategy to adopt for the development of a vaccine. Finally, they imply that anti-SARS-CoV-2 neutralizing antibodies should be titrated to optimize convalescent plasma therapy. HighlightsO_LISpecific antibodies are detectable in 100% COVID-19 inpatients two weeks post-symptom onset. C_LIO_LIThe detection of the SARS-CoV-2 Nucleocapsid and Receptor Binding Domain is more sensitive than the detection of the S1 or S2 subunits. C_LIO_LINeutralizing antibodies reach a plateau two weeks post-symptom onset and then decline in the majority of inpatients. C_LIO_LINeutralizing antibodies are undetectable in the majority of asymptomatic carriers. C_LI