Multiplexed measurement of binding- and neutralizing antibodies to SARS-CoV-2 variants in 12.000 post-vaccine sera

Diagnostic assays currently used to monitor the efficacy of COVID-19 vaccines measure levels of antibodies to the receptor-binding domain of ancestral SARS-CoV-2 (RBDwt). However, the predictive value for protection against new variants of concern (VOCs) has not been firmly established. Here, we used bead-based arrays and flow cytometry to measure binding of antibodies to spike proteins and receptor-binding domains (RBDs) from VOCs in 12,000 sera. Effects of sera on RBD-ACE2 interactions were measured as a proxy for neutralizing antibodies. The samples were obtained from healthy individuals or patients on immunosuppressive therapy who had received two to four doses of COVID-19 vaccines and from COVID-19 convalescents. The results show that anti-RBDwt titers correlate with the levels of binding- and neutralizing antibodies against the Alpha, Beta, Gamma, Delta, Epsilon and Omicron variants. The benefit of multiplexed analysis lies in the ability to measure a wide range of anti-RBD titers using a single dilution of serum for each assay. The reactivity patterns also yield an internal reference for neutralizing activity and binding antibody units per milliliter (BAU/ml). Results obtained with sera from vaccinated healthy individuals and patients confirmed and extended results from previous studies on time-dependent waning of antibody levels and effects of immunosuppressive agents. We conclude that anti-RBDwt titers correlate with levels of neutralizing antibodies against VOCs and propose that our method may be implemented to enhance the precision and throughput of immunomonitoring.

Breakthrough infections with the omicron and delta variants of SARS-CoV-2 result in similar re-activation of vaccine-induced immunity

BackgroundThe Omicron variant of SARS-CoV-2 is now overtaking the Delta variant in many countries. Results showing that sera from double vaccinated individuals have minimal neutralizing activity against Omicron may indicate that the higher rate of transmission is due to evasion from vaccine-induced immunity. However, there is little information about activation of recall responses to Omicron in vaccinated individuals. MethodsWe measured inflammatory mediators, antibodies to the SARS-CoV-2 spike and nucleocapsid proteins, and spike peptide-induced release of interferon gamma in whole blood in 51 vaccinated individuals infected with Omicron, in 14 infected with Delta, and in 18 healthy controls. The median time points for the first and second samples were 7 and 14 days after symptom onset, respectively. FindingsInfection with Omicron or Delta led to a rapid and similar increase in antibodies to the SARS-CoV-2 spike and nucleocapsid proteins and spike peptide-induced interferon gamma in whole blood. Both the Omicron and the Delta infected patients had a mild and transient increase in inflammatory parameters. InterpretationThe results suggest that vaccine-induced immunological memory yields similar coverage for the Omicron and Delta variants.

Public T-cell epitopes shared among SARS-CoV-2 variants are presented on prevalent HLA class I alleles

T-cell epitopes with broad population coverage may form the basis for a new generation of SARS-CoV-2 vaccines. However, published studies on immunoprevalence are limited by small test cohorts, low frequencies of antigen-specific cells and lack of data correlating eluted HLA ligands with T-cell responsiveness. As the protective role of pre-existing cross-reactivity to homologous peptides is unclear, we aimed to identify SARS-CoV-2-specific minimal epitopes recognized by CD8 T-cells among 48 peptides eluted from prevalent HLA alleles, and an additional 84 predicted binders, in a large cohort of convalescents (n=83) and pre-pandemic control samples (n=19). We identified nine conserved SARS-CoV-2-specific epitopes restricted by four of the most prevalent HLA class I alleles in the Norwegian study cohort, to which responding CD8 T cells were detected in 70-100% of convalescents expressing the relevant HLA allele. Only two of these were derived from the Spike protein, included in current vaccines. We found a strong correlation between immunoprevalence and immunodominance. Thus, the CD8 T-cell response to SARS-CoV-2 is more focused than previously believed. Using a new algorithm, we predict that a vaccine including these epitopes could induce a T-cell response in 83% of Caucasians.

Self-reported Memory Problems Eight Months after Non-Hospitalized COVID-19 in a Large Cohort

BackgroundNeurological manifestations of COVID-19 range from ageusia and anosmia, experienced by most patients, to altered consciousness and rare and severe encephalopathy. A direct affection of the central nervous system (CNS) in the disease has been supported by animal models and MRI findings in patients with mild and severe symptoms. Here we report eight-month data on memory problems for non-hospitalized COVID-19 patients compared to SARS-CoV-2 negative patients and untested volunteers. ObjectiveTo explore the association between non-hospitalized COVID-19 eight months previously and self-reported memory problems. MethodsWe followed a cohort of 13156 participants that was invited after (1) being tested for SARS-CoV-2 with a combined oropharyngeal- and nasopharyngeal swab or (2) randomly selected from the Norwegian population (untested). Participants completed online baseline- and follow-up questionnaires detailing underlying medical conditions, demographics, symptoms, and items from the RAND-36 questionnaire on health-related quality of life and known confounders for memory problems. ResultsAfter repeated invitations, the participation rate was 40% (N=794) of SARS-CoV-2 positive, 26% (N=7993) of negative, and 22% (N=4369) of untested randomly selected invitees. All participants completed the baseline questionnaire as a part of inclusion. The follow-up period was 248 days (SD=18) from baseline, and the follow-up questionnaire was completed by 75% of SARS-CoV-2 positive participants, 65% of negative participants, and 73% of untested randomly selected participants. At follow-up, 49 (11.5%) of the SARS-CoV-2 positive participants reported memory problems in contrast to 173 (4.1%) of the SARS-CoV-2 negative participants and 65 (2.4%) of the untested randomly selected participants. In a multivariate model, SARS-CoV-2 positivity remained strongly associated with reporting memory problems at eight months follow-up compared to the SARS-CoV-2 negative group (odds ratio (OR) 4.0, 95% confidence interval (CI) 2.8-5.2) and the untested group (OR 4.9, 95% CI 3.4-7.2). Compared to the other groups, SARS-CoV-2 positive participants also reported more concentration problems and a significant worsening of health compared to one year ago at follow-up. Feeling depressed, less energy, or pain were reported relatively equally by the different groups. SummaryWe find that 11.5% of COVID-19 patients experience memory problems eight months after the disease. SARS-CoV-2 is a new virus, and the long-term consequences of infections are therefore unknown. Our results show that a relatively high proportion of non-hospitalized COVID-19 patients report memory problems eight months after the disease.

Risk factors for community transmission of SARS-CoV-2. A cross-sectional study in 116,678 people.

BackgroundThe risk factors for SARS-CoV-2 transmission are not well characterised in Western populations. We sought to identify potential risk factors for transmission and actionable information to prevent for SARS-CoV-2. MethodsIndividuals tested for SARS-CoV-2 at four major laboratories were invited. In addition, participants were sampled by convenience after a media campaign. Self-reported test results were compared with laboratory results, demographic data and behavioural facts were collected using a digital platform. In a cross-sectional design positive cases were compared with negative and untested control groups. FindingsApproximately 14 days after a countrywide lockdown in Norway, 116,678 participants were included. Median age was 46 years, 44% had children in preschool or in school; 18% were practicing health professionals. International flights, contact with infected, and gatherings of more than 50 people, were associated with high risk. Health professionals who used public transport were at higher risk of testing positive than those who did not. Having undergone light infections, the last six months was strongly associated with lower odds ratio of SARS-CoV-2 positivity. Contact with children, use of hand sanitiser and use of protective gloves in private were also associated with lower odds ratio of testing positive for SARS-CoV-2. InterpretationFurther research is needed to explore if being a parent or looking after children is associated with lower risk of SARS-CoV-2 positivity in the next phases of the pandemic. Immunological research should be done to determine the effects of prior trivial infections on SARS-CoV-2 infection. We confirm that large gatherings during the pandemic should be avoided and those who are infected, or under suspicion thereof, posed very high risks to others this population.