Titers of antibodies the receptor-binding domain (RBD) of ancestral SARS-CoV-2 are predictive for levels of neutralizing antibodies to multiple variants (preprint)

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.

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

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 (preprint)

Background: The 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. Methods: We 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. Findings: Infection 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. Interpretation: The results suggest that vaccine-induced immunological memory yields similar coverage for the Omicron and Delta variants.

Use of Public Transport and Contraction of SARS-CoV-2 in a Large Prospective Cohort in Norway. (preprint)

Background: For many people public transport is the only mode of travel, and it can be challenging to keep the necessary distances in such a restricted space. The exact role of public transportation and risk of SARS-CoV-2 transmission is not known. Methods: : Participants (n=121 374) were untested adult Norwegian residents recruited through social media who in the spring of 2020 completed a baseline questionnaire on demographics and use of public transport. Incident cases (n=1069) had a positive SARS-CoV-2 polymerase chain reaction test registered at the Norwegian Messaging System for Infectious Diseases by January 27, 2021. We investigated the association between use of public transport and SARS-CoV-2 using logistic regression. Odds ratios (ORs) with 95% confidence intervals (CIs) adjusted for age, calendar time, gender, municipality, smoking, income level, fitness and underlying medical conditions were estimated. Frequency of use of public transport was reported for 2 week-periods. Results: : Before lockdown, those who tested positive on SARS-CoV-2 were more likely to have used public transport 1-3 times (OR =1.28, CI 1.09-1.51), 4-10 times (OR=1.49, CI 1.26-1.77) and ≥11 times (OR=1.50, CI 1.27-1.78, p for trend<0.0001) than those who had not tested positive. Conclusion: Use of public transport was positively associated with contracting SARS-CoV-2 both before and after lockdown.

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

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. Here, we investigate CD8 T-cell responses to 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 identify nine conserved SARS-CoV-2 specific epitopes restricted by four of the most prevalent HLA class I alleles in Caucasians, to which responding CD8 T cells are detected in 70-100% of convalescents expressing the relevant HLA allele, including two novel epitopes. We find a strong correlation between immunoprevalence and immunodominance. Using a new algorithm, we predict that a vaccine including these epitopes would induce a T cell response in 83% of Caucasians. Significance Statement: Vaccines that induce broad T-cell responses may boost immunity as protection from current vaccines against SARS-CoV-2 is waning. From a manufacturing standpoint, and to deliver the highest possible dose of the most immunogenic antigens, it is rational to limit the number of epitopes to those inducing the strongest immune responses in the highest proportion of individuals in a population. Our data show that the CD8 T cell response to SARS-CoV-2 is more focused than previously believed. We identify nine conserved SARS-CoV-2 specific CD8 T cell epitopes restricted by four of the most prevalent HLA class I alleles in Caucasians and demonstrate that seven of these are endogenously presented.

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

Background: Neurological 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. Objective: To explore the association between non-hospitalized COVID-19 eight months previously and self-reported memory problems. Methods: We 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. Results: After 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. Summary: We 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.

Preexisting Cross-Reactive T Cells are Boosted and Comprise Significant Immunity in COVID-19 Recovered Patients (preprint)

Most SARS-CoV-2 infected individuals develop symptoms that do not require medical management. We hypothesized that pre-existing cross-reactive T cell responses could protect the majority from severe disease. Here we found that CTL and Th cells specific for seasonal human coronaviruses (HCoV) were significantly expanded in recovered COVID-19 donors and that CTL responses were significantly higher than responses to private SARS-CoV-2 peptides not shared with seasonal HCoV. A third of the SARS-CoV-2 peptide:HLA ligandome was matched by highly similar peptide mimics from seasonal HCoV, constituting a common HCoV peptide pool. CTL immunity was significantly skewed to the common HCoV peptide pool in age groups 20-70y, but not >70y-old donors. Over 40% of recovered donors lacked neutralizing antibodies, highlighting the role of T cell immunity in COVID-19. Results suggest a protective pre-acquired T cell immunity to SARS-CoV-2 and identify epitopes that may help boost vaccine responses and ensure broad protection against this family of viruses.Trial Registration: ClinicalTrials.gov: NCT04320732.Funding: This study was funded by The Health-South East Health Authority (Project 29286), the Research Council of Norway (Project 312693), the Oslo University Hospital, the KG Jebsen Foundation (grant 19), the University of Oslo, The Norwegian Cancer Society.Conflict of Interest: The authors declare that we have no competing interests.

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

Background The risk factors for SARS-CoV-2 transmission are not well characterised. We sought to identify potential risk factors for transmission and actionable information that can be used to prevent SARS-CoV-2. Methods Individuals tested for SARS-CoV-2 at four accredited laboratories were invited. In addition, participants were recruited through a media campaign. Self-reported SARS-CoV-2 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. Findings Approximately 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 individuals, and gatherings of more than 50 people, were associated with increased risk of testing positive. Health professionals who treated COVID-19 patients 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. Interpretation Further 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 in this population. Registration: Trial registration: ClinicalTrials.gov: NTC 04320732, March 25, 2020.

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

Background The 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. Methods Individuals tested for SARS-CoV-2 at three 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. Findings Approximately than 14 days after lockdown, 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. Interpretation Further 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.