Long term anti-SARS-CoV-2 antibody kinetics and correlate of protection against Omicron BA.1/BA.2 infection (preprint)

Binding antibody levels against SARS-CoV-2 have shown to be correlates of protection against infection with pre-Omicron lineages. This has been challenged by the emergence of immune-evasive variants, notably the Omicron sublineages, in an evolving immune landscape with high levels of cumulative incidence and vaccination coverage. This in turn limits the use of commercially available high-throughput methods to quantify binding antibodies as a tool to monitor protection at the population-level. In this work, we leverage repeated serological measurements between April 2020 and December 2021 on 1'083 participants of a population-based cohort in Geneva, Switzerland, to evaluate anti-Spike RBD antibody levels as a correlate of protection against Omicron BA.1/BA.2 infections during the December 2021-March 2022 epidemic wave. We do so by first modeling antibody dynamics in time with kinetic models. We then use these models to predict antibody trajectories into the time period where Omicron BA.1/BA.2 were the predominant circulating sub-lineages and use survival analyses to compare the hazard of having a positive SARS-CoV-2 test by antibody level, vaccination status and infection history. We find that antibody kinetics in our sample are mainly determined by infection and vaccination history, and to a lesser extent by demographics. After controlling for age and previous infections (based on anti-nucleocapsid serology), survival analyses show reveal a significant reduction in the hazard of having a documented positive SARS-CoV-2 infection during the Omicron BA.1/BA.2 wave with increasing antibody levels, reaching up to a three-fold reduction for anti-S antibody levels above 800 IU/mL (HR 0.30, 95% CI 0.22-0.41). However, we did not detect a reduction in hazard among uninfected participants. Taken together these results indicate that anti-Spike RBD antibody levels, as quantified by the immunoassay used in this study, are an indirect correlate of protection against Omicron BA.1/BA.2 for individuals with a history of previous SARS-CoV-2 infection. Despite the uncertainty in what SARS-COV-2 variant will come next, these results provide reassuring insights into the continued interpretation of SARS-CoV-2 binding antibody measurements as an independent marker of protection at both the individual and population levels.

Applying mixture model methods to SARS-CoV-2 serosurvey data from the SEROCoV-POP study (preprint)

Serosurveys are an important tool to estimate the true extent of the current SARS-CoV-2 pandemic. So far, most serosurvey data have been analysed with cut-off based methods, which dichotomize individual measurements into sero-positives or negatives based on a predefined cutoff. However, mixture model methods can gain additional information from the same serosurvey data. Such methods refrain from dichotomizing individual values and instead use the full distribution of the serological measurements from pre-pandemic and COVID-19 controls to estimate the cumulative incidence. This study presents an application of mixture model methods to SARS-CoV-2 serosurvey data from the SEROCoV-POP study from April and May 2020 (2766 individuals). Besides estimating the total cumulative incidence in these data (8.1% (95% CI: 6.8% - 9.8%)), we applied extended mixture model methods to estimate an indirect indicator of disease severity, which is the fraction of cases with a distribution of antibody levels similar to hospitalised COVID-19 patients. This fraction is 51.2% (95% CI: 15.2% - 79.5%) across the full serosurvey, but differs between three age classes: 21.4% (95% CI: 0% - 59.6%) for individuals between 5 and 40 years old, 60.2% (95% CI: 21.5% - 100%) for individuals between 41 and 65 years old and 100% (95% CI: 20.1% - 100%) for individuals between 66 and 90 years old. Additionally, we find a mismatch between the inferred negative distribution of the serosurvey and the validation data of pre-pandemic controls. Overall, this study illustrates that mixture model methods can provide additional insights from serosurvey data.

Persistence and detection of anti-SARS-CoV-2 antibodies: immunoassay heterogeneity and implications for serosurveillance (preprint)

Serologic studies have been critical in tracking the evolution of the COVID-19 pandemic. The reliability of serologic studies for quantifying the proportion of the population that have been infected depends on the extent of antibody decay as well as on assay performance in detecting both recent and older infections. Data on anti-SARS-CoV-2 antibodies persistence remain sparse, especially from infected individuals with few to no symptoms. In a cohort of mostly mild/asymptomatic SARS-CoV-2-infected individuals tested with three widely-used immunoassays, antibodies persisted for at least 8 months after infection, although detection depended on immunoassay choice, with one of them missing up to 40% of past infections. Simulations reveal that without appropriate adjustment for time-varying assay sensitivity, seroprevalence surveys may underestimate infection rates. As the immune landscape becomes more complex with naturally-infected and vaccinated individuals, assay choice and appropriate assay-performance-adjustment will become even more important for the interpretation of serologic studies.

SARS-CoV2- infection as a trigger of humoral response against apolipoprotein A-1 (preprint)

AimsUnravelling autoimmune targets triggered by SARS-CoV-2 infection may provide crucial insights in the physiopathology of the disease and foster the development of potential therapeutic candidate targets and prognostic tools. We want to determine whether SARS-CoV-2 exposure could trigger a humoral response against apolipoprotein A-1 (anti-apoA-1 IgG) through molecular mimicry and assess its relationship to patient prognosis. Methods and ResultsAnti-Spike domain 1 (SD1) IgGs, anti-apoA-1 IgGs and against mimic peptides, as well as cytokines were assessed by immunoassays on a case-control (n=101), an intensive care unit (ICU; n=126) with a 28-days follow-up, and a general population cohort (n=663) with available samples in the pre and post-pandemic period. Linear sequence homologies and antibodies cross-reactivity between apoA-1, TLR2, and Spike epitopes were identified. Overall, anti-apoA-1 IgG levels were higher in COVID-19 patients or anti-SARS-CoV-2 seropositive individuals than in healthy donors or anti-SARS-CoV-2 seronegative individuals (p<0.0001). Significant and similar associations were noted between anti-apoA-1, anti-SARS-CoV-2 IgG, cytokines, and lipid profile. In ICU patients, anti-SARS-CoV-2 and anti-apoA-1 seroconversion rates displayed similar 7-days kinetics, reaching 82% for anti-apoA-1 seropositivity. C-statistics (CS) indicated that anti-Spike/TLR2 mimic-peptide IgGs displayed a significant prognostic accuracy for overall mortality at 28 days (CS: 0.64; p=0.02). In the general population, SARS-CoV-2 exposure increased baseline anti-apoA-1 IgG levels. ConclusionsCOVID-19 induces a marked humoral response against the major protein of high-density lipoproteins. As a correlate of poorer prognosis in other clinical settings, such autoimmunity signatures may relate to long-term COVID-19 prognosis assessment and warrant further scrutiny in the current COVID-19 pandemic.

Antibody Persistence in the Six Months Following SARS-CoV-2 Infection Among Hospital Workers (preprint)

Background: Little is known about the duration and breadth of humoral immunity against SARS-CoV-2 to better inform appropriate pandemic control measures.Methods: We measured anti-RBD, -N and neutralizing antibodies at one, three and six months after mostly mild COVID-19 in 200 hospital workers using commercial ELISAs and a surrogate virus neutralization assay.Findings: Anti-RBD antibodies were detected in all participants at each timepoint. Geometric mean concentrations (GMCs) progressively increased between month one (74 . 2 U/ml [95%CI 62 . 7-87 . 8), three (103 . 2 U/ml [95%CI 87 . 9-121 . 2]; p<0 . 001), and six (123 . 3 U/ml [95%CI 103 . 4-147 . 0]; p<0 . 001) in the whole cohort. Anti-N antibodies were detectable in >97% at all times. Neutralizing antibodies were detectable in 92 . 5% (184/199), 94 . 4% (185/196) and 76 . 5% (150/196) participants at one, three and six months, respectively. Their GMC progressively decreased between months one (20 . 1 AU/ml [95%CI 16 . 9-24 . 0]), three (15 . 2 AU/ml [95%CI 13 . 2-17 . 6]; p<0 . 001) and six (9 . 4 AU/ml [95%CI 7 . 7-11 . 4]; p<0 . 001). Neutralizing antibody and anti-RBD concentrations strongly correlated at each timepoint (all r>0 . 86, p<0 . 001). Disease severity was associated with higher initial anti-RBD and neutralizing concentrations, but not with their kinetics.Interpretation: Neutralizing antibodies persisted at six months in most participants, indicating more durability than initially feared. Anti-RBD antibodies persisted better and even increased over time, possibly related to the preferential detection of progressively higher-affinity antibodies. Trial Registration: registered (NCT04329546)Funding: Pictet, Ancrage and Schmidheiny Foundations, Geneva University Hospitals’ Private Foundation, PRD, Center for Vaccinology and Centre for Emerging Viral Diseases.Declaration of Interests: The authors have no conflict of interest.Ethics Approval Statement: The study was approved by the local ethics committee (CCER 2020-00516) and registered (NCT04329546) prior to initiation. All hospital workers provided written informed consent before enrolment.

Validation and clinical evaluation of a SARS-CoV-2 Surrogate Virus Neutralization Test (sVNT) (preprint)

To understand SARS-CoV-2 immunity after natural infection or vaccination, functional assays such as virus neutralizing assays are needed. So far, assays to determine SARS-CoV-2 neutralizing antibodies rely on cell-culture based infection assays either using wild type SARS-CoV-2 or pseudotyped viruses. Such assays are labour-intensive, require appropriate biosafety facilities and are difficult to standardize. Recently, a new surrogate virus neutralisation assay (sVNT) was described that uses the principle of an ELISA to measure the neutralization capacity of anti-SARS-CoV-2 antibodies directed against the receptor binding domain. Here, we performed an independent evaluation of the robustness, specificity and sensitivity on an extensive panel of sera from 269 PCR-confirmed COVID-19 cases and 259 unmatched samples collected before 2020 and compared it to cell-based neutralization assays. We found a high specificity of 99.2 (95%CI: 96.9-99.9) and overall sensitivity of 80.3 (95%CI: 74.9-84.8) for the sVNT. Clinical sensitivity increased between early (<14 days post symptom onset or post diagnosis, dpos/dpd) and late sera (>14 dpos/dpd) from 75.0 (64.7-83.2) to 83.1 (76.5-88.1). Also, higher severity was associated with an increase in clinical sensitivity. Upon comparison with cell-based neutralisation assays we determined an analytical sensitivity of 74.3 (56.4-86.9) and 98.2 (89.4-99.9) for titres [≥]10 to <40 and [≥]40 to <160, respectively. Only samples with a titre [≥]160 were always positive in the sVNT. In conclusion, the sVNT can be used as an additional assay to determine the immune status of COVID-19 infected of vaccinated individuals but its value needs to be assessed for the specific context of use.

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.

Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma (preprint)

A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients, we identified immunodominant linear epitopes corresponding to key proteolytic sites on the spike protein.

Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from Geneva, Switzerland (preprint)

BackgroundAssessing the burden of COVID-19 based on medically-attended case counts is suboptimal given its reliance on testing strategy, changing case definitions and the wide spectrum of disease presentation. Population-based serosurveys provide one avenue for estimating infection rates and monitoring the progression of the epidemic, overcoming many of these limitations. MethodsTaking advantage of a pool of adult participants from population-representative surveys conducted in Geneva, Switzerland, we implemented a study consisting of 8 weekly serosurveys among these participants and their household members older than 5 years. We tested each participant for anti-SARS-CoV-2-IgG antibodies using a commercially available enzyme-linked immunosorbent assay (Euroimmun AG, Lubeck, Germany). We estimated seroprevalence using a Bayesian regression model taking into account test performance and adjusting for the age and sex of Genevas population. ResultsIn the first three weeks, we enrolled 1335 participants coming from 633 households, with 16% <20 years of age and 53.6% female, a distribution similar to that of Geneva. In the first week, we estimated a seroprevalence of 3.1% (95% CI 0.2-5.99, n=343). This increased to 6.1% (95% CI 2.69.33, n=416) in the second, and to 9.7% (95% CI 6.1-13.11, n=576) in the third week. We found that 5-19 year-olds (6.0%, 95% CI 2.3-10.2%) had similar seroprevalence to 20-49 year olds (8.5%, 95%CI 4.99-11.7), while significantly lower seroprevalence was observed among those 50 and older (3.7%, 95% CI 0.99-6.0, p=0.0008). InterpretationAssuming that the presence of IgG antibodies is at least in the short-term associated with immunity, these results highlight that the epidemic is far from burning out simply due to herd immunity. Further, no differences in seroprevalence between children and middle age adults are observed. These results must be considered as Switzerland and the world look towards easing restrictions aimed at curbing transmission.

Validation of a commercially available SARS-CoV-2 serological Immunoassay (preprint)

Aims: To validate the diagnostic accuracy of a Euroimmun SARS-CoV-2 IgG and IgA immunoassay for COVID-19 disease. Methods: In this unmatched (1:1) case-control validation study, we used sera of 181 laboratory-confirmed SARS-CoV-2 cases and 176 negative controls collected before the emergence of SARS-CoV-2. Diagnostic accuracy of the immunoassay was assessed against a whole spike protein-based recombinant immunofluorescence assay (rIFA) by receiver operating characteristic (ROC) analyses. Discrepant cases between ELISA and rIFA were further tested by pseudo-neutralization assay. Results: COVID-19 patients were more likely to be male and older than controls, and 50.3% of them were hospitalized. ROC curve analyses indicated that IgG and IgA had a high diagnostic accuracy with AUCs of 0.992 (95% Confidence Interval [95%CI]: 0.986-0.996) and 0.977 (95%CI: 0.963-0.990), respectively. IgG assays outperformed IgA assays (p=0.008). Considering optimized cut-offs taking the 15% inter-assay imprecision assessed into account, an IgG ratio cut-off > 1.5 displayed a 100% specificity (95%CI: 98-100) and a 100% positive predictive value (95%CI: 97-100). A 0.5 cut-off displayed a 97% sensitivity (95%CI: 93-99) and a 97% negative predictive value (95%CI: 93-99). Adopting these thresholds, rather than those of the manufacturer, improved assay performance, leaving 12% of IgG ratios ranging between 0.5-1.5 as indeterminate. Conclusions: The Euroimmun assay displays a nearly optimal diagnostic accuracy using IgG against SARS-CoV-2 in a samples of patients, without any obvious gains from considering IgA serology. The optimized cut-offs are fit for rule-in and rule-out purposes, allowing determination of whether individuals have been exposed to SARS-CoV-2 or not in our study population. They should however not be considered as a surrogate of protection at this stage.