Humoral Immunity to SARS-CoV-2 and Inferred Protection from Infection in a French Longitudinal Community Cohort (preprint)

Population-level immunity to SARS-CoV-2 is growing through vaccination as well as ongoing circulation. Given waning immunity and emergence of new variants, it is important to dynamically determine the risk of re-infection in the population. For estimating immune protection, neutralization titers are most informative, but these assays are difficult to conduct at a population level. Measurement of antibody levels can be implemented at high throughput, but has not been robustly validated as a correlate of protection. Here, we have developed a method that predicts neutralization and protection based on variant-specific antibody measurements to SARS-CoV-2 antigens. This approach allowed us to estimate population-immunity in a longitudinal cohort from France followed for up to 2 years. Participants with a single vaccination or immunity caused by infection only are especially vulnerable to COVID-19 or hospitalization due to SARS-CoV-2. While the median reduced risk to COVID-19 in participants with 3 vaccinations was 96%, the median reduced risk among participants with infection-acquired immunity only was 42%. The results presented here are consistent with data from vaccine-effectiveness studies indicating robustness of our approach. Our multiplex serological assay can be readily optimized and employed to study any new variant and provides a framework for development of an assay that would include protection estimates.

SARS-CoV-2 Omicron neutralization and risk of infection among elderly after a booster dose of Pfizer vaccine (preprint)

Background: The protective immunity against Omicron following a BNT162b2 Pfizer booster dose among elderly is not well characterized. Methods: Thirty-eight residents from three nursing homes were recruited for the study. Antibodies targeting the Spike protein of SARS-CoV-2 were measured with the S-Flow assay. Neutralizing activities in sera were measured as effective dilution 50% (ED50) with the S-Fuse assay using authentic isolates of Delta and Omicron. Results: Among the 38 elderly included in the study, with median (inter-quartile range, IQR) age of 88 (81-92) years, 30 (78.9%) had been previously infected. The ED50 of neutralization were lower against Omicron than Delta, and higher among convalescent compared to naive residents. During an Omicron epidemic affecting two of the three nursing homes in December 2021-January 2022, 75% (6/8) of naive residents got infected, compared to 25% (6/24) of convalescents (P=0.03). Antibody levels to Spike and ED50 of neutralization against Omicron after the BNT162b2 booster dose were lower in those with breakthrough infection (n=12) compared to those without (n=20): median of 1256 vs 2523 BAU/mL (P=0.02) and median ED50 of 234 vs 1298 (P=0.0004), respectively. Conclusion: This study confirmed the importance of receiving at least three antigenic exposures to the SARS-CoV-2 Spike protein for achieving satisfactory neutralizing antibody levels. In this population, protection against Omicron infection was increased in individuals who had been previously infected in addition to the three vaccine doses. Thus, a fourth antigenic exposure may be useful in the elderly population to prevent infection with Omicron, a variant known for its high escape immunity properties.

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.

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