Immune escape of Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, XBB.1.5, EG.5.1 and JN.1.1 after vaccination, infection and hybrid immunity (preprint)

Since their emergence in late 2021, SARS-CoV-2 Omicron replaced earlier variants of concern and marked a new phase in the SARS-CoV-2 pandemic. Until the end of 2023, Omicron lineages continue to circulate and continue to evolve, with new lineages causing infection waves throughout 2022 and 2023. In the population, this leads to a complex immunological exposure background, characterized by immunity derived through vaccination, in the 5th year of the pandemic in the majority of individuals followed by at least one or even multiple infections or only natural infection in individuals that did not receive a vaccine. In this study, we use eight authentic SARS-CoV-2 isolates (ancestral lineage B.1 and the seven Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, XBB.1.5, EG.5.1 and JN.1.1) in a live virus neutralization assay to study immune escape in 97 human sera or plasma of different immunological backgrounds (vaccination, hybrid immunity due to one or two natural infections and natural infection without vaccination in children and adults). We showed a gradually increasing immune escape after vaccination and hybrid immunity in from B.1 to BA.1/BA.2 to BA.5.1 to BQ.1 to XBB.1.5 to EG.5.1, but remarkably, no more enhanced immune escape of JN.1.1 compared to EG.5.1, with the latter two showing almost identical neutralization titers in individuals with hybrid immunity due to one or more infections. In vaccinated but never infected individuals, neutralization was markedly reduced or completely lost for XBB.1.5., EG.5.1 and JN.1.1, while in those with hybrid immunity, titers were reduced but almost all sera still showed some degree of neutralization. After a single infection without vaccination, reduced or complete loss of neutralization occurred for BQ.1, XBB.1.5, EG.5.1 and JN.1.1 compared to BA.1/BA.2. Furthermore, we observed that, although absolute titers differed between groups, the pattern of immune escape between the variants remains comparable across groups, with strongest loss of neutralization for BQ.1, XBB.1.5, EG.5.1 and JN.1.1 was observed across the different immunological backgrounds. Our results show gradually increasing antibody escape of evolving Omicron lineages over the last two years of Omicron circulation until variant EG.5.1, but not anymore for the currently dominant lineages JN.1.1, suggesting other mechanisms than immune escape to be behind the rapid global emergence of JN.1.

SARS-CoV-2 convalescence and hybrid immunity elicits mucosal immune responses (preprint)

Mucosal antibodies play a key role in the protection against SARS-CoV-2 infection in the upper respiratory tract, and potentially in limiting virus replication and therefore onward transmission. While systemic immunity to SARS-CoV-2 is well understood, little is known about the antibodies present on the nasal mucosal surfaces. In this study, we evaluated SARS-CoV-2 mucosal antibodies in response to infection, vaccination, or a combination of both. Paired nasal fluid and serum samples were collected from 136 individuals, which include convalescent, vaccinated, or breakthrough infections. We detected a high correlation between IgG responses in serum and nasal fluids, which were higher in both compartments in vaccinated compared to convalescent participants. Contrary, nasal and systemic SARS-CoV-2 IgA responses were weakly correlated, indicating a compartmentalization between the local and systemic IgA responses. SARS-CoV-2 secretory component IgA (s-IgA) antibodies, present exclusively on mucosal surfaces, were detected in the nasal fluid only in a minority of vaccinated subjects and were significantly higher in previously infected individuals. s-IgA binding antibodies showed significant correlation with neutralizing activity of nasal fluids against SARS-CoV-2 ancestral B.1 and Omicron-BA.5 variant, indicating that s-IgA is the crucial contributor to neutralization in the nasal mucosa. Neutralization against both SARS-CoV-2 strains was higher in the mucosa of subjects with previous SARS-CoV-2 infections compared to vaccinated participants. In summary, we demonstrate that currently available vaccines elicit strong systemic antibody responses, but SARS-CoV-2 infection generates more potent binding and neutralizing mucosal antibodies. Our results support the importance to develop SARS-CoV-2 vaccines that elicit mucosal antibodies.

Clinical sensitivity and specificity of a high-throughput microfluidic nano-immunoassay combined with capillary blood microsampling for the identification of anti-SARS-CoV-2 Spike IgG serostatus (preprint)

Background: We evaluate the diagnostic performance of dried blood microsampling combined with a high-throughput microfluidic nano-immunoassay (NIA) for the identification of anti-SARS-CoV-2 Spike IgG seropositivity. Methods: We conducted a serological study among 192 individuals with documented prior SARS-CoV- 2 infection and 44 SARS-CoV-2 negative individuals. Participants with prior SARS-CoV-2 infection had a long interval of 11 months since their qRT-PCR positive test. Serum was obtained after venipuncture and tested with an automated electrochemiluminescence anti-SARS-CoV-2 S total Ig reference assay, a commercial ELISA anti-S1 IgG assay, and the index test NIA. 109 participants from the positive co- hort and 44 participants from the negative cohort also participated in capillary blood collection using three microsampling devices: Mitra, repurposed glucose test strips, and HemaXis. Samples were dried, shipped by regular mail, extracted, and measured with NIA. Findings: Using serum samples, we achieve a clinical sensitivity of 98.33% and specificity of 97.62% on NIA, affirming the high performance of NIA in participants 11 months post infection. Combining microsampling with NIA, we obtain a clinical sensitivity of 95.05% using Mitra, 61.11% using glucose test strips, 83.16% using HemaXis, and 91.49% for HemaXis after automated extraction, without any drop in specificity. Interpretation: High sensitivity and specificity was demonstrated when testing micro-volume capillary dried blood samples using NIA, which is expected to facilitate its use in large-scale studies using home- based sampling or samples collected in the field. Funding: Swiss National Science Foundation NRP 78 Covid-19 grant 198412 and Private Foundation of the Geneva University Hospital.

Epidemiological, virological and serological investigation into a SARS-CoV-2 outbreak (Alpha variant) in a primary school in Geneva, Switzerland: a prospective longitudinal study (preprint)

Background Twenty-one months into the pandemic, the extent to which young children get infected and transmit SARS-CoV-2 in school settings remains controversial, in particular with variants of concern. We report a prospective epidemiological, virological and serological investigation of a SARS-CoV-2 outbreak in a primary school in Geneva, Switzerland, in April-May 2021. Methods This outbreak investigation is part of a longitudinal, prospective, primary school-based surveillance study (SEROCoV-Schools). It involved repeated testing of pupils and teachers and household members of participants who tested positive. Rapid antigen tests and/or real-time reverse transcription polymerase chain reaction were performed at Day 0-2 and Day 5-7; serologies on dried capillary blood samples were performed at Day 0-2 and Day 30. Contact tracing interviews and SARS-CoV-2 whole genome sequencing were carried out for positive cases. Results This SARS-CoV-2 outbreak caused by the Alpha variant involved 20 children aged 4 to 6 years from 4 classes, 2 teachers and 3 household members. Infection attack rates were between 11.8 and 62.0% among pupils from the 4 classes, 22.2% among teachers and 0% among non-teaching staff. Secondary attack rate among household members was 10.7%. Symptoms were reported by 63% of infected children, 100% of teachers and 66.7% of household members. All analysed sequences but one showed 100% identity. Serological tests detected 8 seroconversions unidentified by SARS-CoV-2 virological tests. Conclusions This study confirmed child-to-child and child-to-adult transmission of the infection. SARS-CoV-2 can spread rapidly between children and adults in school settings, and is thereby introduced into households. Effective measures to limit transmission in schools have the potential to reduce the overall community circulation.

SARS-CoV-2 viral load in the upper respiratory tract of children and adultswith early acute COVID-19 (preprint)

The role of children in the transmission of SARS-CoV-2 is unclear. We analysed viral load at the time of diagnosis in 53 children vs. 352 adults with COVID-19 in the first 5 days post symptom onset. No significant differences in SARS-CoV-2 RNA loads were seen between children and adults.