Antibody Responses to SARS-CoV-2 Infection—Comparative Determination of Seroprevalence in Two High-Throughput Assays versus a Sensitive Spike Protein ELISA

Robust assay development for SARS-CoV-2 serological testing requires assessment of asymptomatic and non-hospitalised individuals to determine if assays are sensitive to mild antibody responses. Our study evaluated the performance characteristics of two high-throughput SARS-CoV-2 IgG nucleocapsid assays (Abbott Architect and Roche) and The Binding Site (TBS) Anti-Spike IgG/A/M ELISA kit in samples from healthcare workers (HCWs). The 252 samples were collected from multi-site NHS trusts and analysed for SARS-CoV-2 serology. Assay performance was evaluated between these three platforms and ROC curves were used to redefine the Abbott threshold. Concordance between Abbott and TBS was 66%. Any discrepant results were analysed using Roche, which showed 100% concordance with TBS. Analysis conducted in HCWs within 58 days post-PCR result demonstrated 100% sensitivity for both Abbott and Roche. Longitudinal analysis for >100 days post-PCR led to sensitivity of 77.2% and 100% for Abbott and Roche, respectively. A redefined Abbott threshold (0.64) increased sensitivity to 90%, producing results comparable to TBS and Roche. The manufacturer’s threshold set by Abbott contributes to lower sensitivity and elevated false-negative occurrences. Abbott performance improved upon re-optimisation of the cut-off threshold. Our findings provided evidence that TBS can be used as bespoke alternative for SARS-CoV-2 serology analysis where high-throughput platforms are not feasible on site.

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Comparative assessment of SARS-CoV-2 serology in healthcare workers with Abbott Architect, Roche Elecsys and The Binding site ELISA immunoassays.

10.1101/2021.03.19.21253518 ◽

2021 ◽

Author(s):

Dinesh Mohanraj ◽

Alison Whitelegg ◽

Kelly Bicknell ◽

Malini Bhole ◽

Caroline Webber ◽

...

Keyword(s):

Binding Site ◽

High Throughput ◽

Roc Curves ◽

Epidemiological Surveillance ◽

Lower Sensitivity ◽

Post Vaccination ◽

Population Immunity ◽

Assay Performance ◽

Assay Result ◽

Serology Testing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology testing is key for assessing seroprevalence and antibody response post-vaccination in immunocompromised patients. Here we performed a comparison between two high-throughput nucleocapsid assays (Abbott SARS-CoV-2 IgG and Roche Elecsys Anti-SARS-CoV-2) and The Binding Site (TBS) anti-Spike IgG/A/M- SARS-CoV-2 ELISA kit. 236 samples were collected across 2 sites, Portsmouth Hospital University NHS Trust (PHU) and The Dudley Group NHS Trust. We derived concordance, agreement and assay performance as well as using receiver operating characteristic (ROC) curves to redefine the assay threshold of the Abbott assay. Result concordance between the Abbott and TBS was 66%. Discrepant samples were analysed using the Roche assay which showed 100% agreement with the TBS assay. In samples analysed >58 days post-PCR, the sensitivity of Abbott and Roche was 100%. In samples analysed >100 days post-PCR the sensitivity of the Abbott assay dropped to 77.2% but remained at 100% for the Roche assay. A redefined Abbott threshold of 0.64 increased the sensitivity to 90% giving results similar to the Roche and TBS assays. In conclusion, this study demonstrated Abbott assay had a lower sensitivity in comparison to TBS and Roche. This study established TBS can be implemented as a viable alternative for SARS-CoV-2 serology testing where high-throughput assays are not available on site. Furthermore, anti-spike assays, such as TBS, could be used to monitor vaccination responses to deduce SARS-CoV-2 population-immunity. Further optimization studies are required to evaluate the performance characteristics of these assays which could facilitate widescale sero-epidemiological surveillance.

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From Multiplex Serology to Serolomics—A Novel Approach to the Antibody Response against the SARS-CoV-2 Proteome

Viruses ◽

10.3390/v13050749 ◽

2021 ◽

Vol 13 (5) ◽

pp. 749

Author(s):

Julia Butt ◽

Rajagopal Murugan ◽

Theresa Hippchen ◽

Sylvia Olberg ◽

Monique van Straaten ◽

...

Keyword(s):

Antibody Response ◽

High Throughput ◽

Large Population ◽

High Sensitivity ◽

Population Based ◽

Antibody Responses ◽

Hek293 Cells ◽

Novel Approach ◽

Assay Performance ◽

Multiplex Serology

The emerging SARS-CoV-2 pandemic entails an urgent need for specific and sensitive high-throughput serological assays to assess SARS-CoV-2 epidemiology. We, therefore, aimed at developing a fluorescent-bead based SARS-CoV-2 multiplex serology assay for detection of antibody responses to the SARS-CoV-2 proteome. Proteins of the SARS-CoV-2 proteome and protein N of SARS-CoV-1 and common cold Coronaviruses (ccCoVs) were recombinantly expressed in E. coli or HEK293 cells. Assay performance was assessed in a COVID-19 case cohort (n = 48 hospitalized patients from Heidelberg) as well as n = 85 age- and sex-matched pre-pandemic controls from the ESTHER study. Assay validation included comparison with home-made immunofluorescence and commercial enzyme-linked immunosorbent (ELISA) assays. A sensitivity of 100% (95% CI: 86–100%) was achieved in COVID-19 patients 14 days post symptom onset with dual sero-positivity to SARS-CoV-2 N and the receptor-binding domain of the spike protein. The specificity obtained with this algorithm was 100% (95% CI: 96–100%). Antibody responses to ccCoVs N were abundantly high and did not correlate with those to SARS-CoV-2 N. Inclusion of additional SARS-CoV-2 proteins as well as separate assessment of immunoglobulin (Ig) classes M, A, and G allowed for explorative analyses regarding disease progression and course of antibody response. This newly developed SARS-CoV-2 multiplex serology assay achieved high sensitivity and specificity to determine SARS-CoV-2 sero-positivity. Its high throughput ability allows epidemiologic SARS-CoV-2 research in large population-based studies. Inclusion of additional pathogens into the panel as well as separate assessment of Ig isotypes will furthermore allow addressing research questions beyond SARS-CoV-2 sero-prevalence.

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From multiplex serology to serolomics – a novel approach to the antibody response against the SARS-CoV-2 proteome

10.1101/2020.10.19.20214916 ◽

2020 ◽

Author(s):

Julia Butt ◽

Rajagopal Murugan ◽

Theresa Hippchen ◽

Sylvia Olberg ◽

Monique van Straaten ◽

...

Keyword(s):

Antibody Response ◽

High Throughput ◽

Large Population ◽

High Sensitivity ◽

Population Based ◽

Antibody Responses ◽

Hek293 Cells ◽

Novel Approach ◽

Assay Performance ◽

Multiplex Serology

ABSTRACTBackgroundThe emerging SARS-CoV-2 pandemic entails an urgent need for specific and sensitive high-throughput serological assays to assess SARS-CoV-2 epidemiology. We therefore aimed at developing a fluorescent-bead based SARS-CoV-2 multiplex serology assay for detection of antibody responses to the SARS-CoV-2 proteome.MethodsProteins of the SARS-CoV-2 proteome and protein N of SARS-CoV-1 and common cold Coronaviruses (ccCoVs) were recombinantly expressed in E. coli or HEK293 cells. Assay performance was assessed in a Covid-19 case cohort (n=48 hospitalized patients from Heidelberg) as well as n=85 age- and sex-matched pre-pandemic controls from the ESTHER study. Assay validation included comparison with home-made immunofluorescence and commercial Enzyme-linked immunosorbent (ELISA) assays.ResultsA sensitivity of 100% (95% CI: 86%-100%) was achieved in Covid-19 patients 14 days post symptom onset with dual sero-positivity to SARS-CoV-2 N and the receptor-binding domain of the spike protein. The specificity obtained with this algorithm was 100% (95% CI: 96%-100%). Antibody responses to ccCoVs N were abundantly high and did not correlate with those to SARS-CoV-2 N. Inclusion of additional SARS-CoV-2 proteins as well as separate assessment of immunoglobulin (Ig) classes M, A, and G allowed for explorative analyses regarding disease progression and course of antibody response.ConclusionThis newly developed SARS-CoV-2 multiplex serology assay achieved high sensitivity and specificity to determine SARS-CoV-2 sero-positivity. Its high throughput ability allows epidemiologic SARS-CoV-2 research in large population-based studies. Inclusion of additional pathogens into the panel as well as separate assessment of Ig isotypes will furthermore allow addressing research questions beyond SARS-CoV-2 sero-prevalence.

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Evaluation of commercially available high-throughput SARS-CoV-2 serological assays for serosurveillance and related applications

10.1101/2021.09.04.21262414 ◽

2021 ◽

Author(s):

Mars Stone ◽

Eduard Grebe ◽

Hasan Sulaeman ◽

Clara Di Germanio ◽

Honey Dave ◽

...

Keyword(s):

High Throughput ◽

High Sensitivity ◽

Antibody Responses ◽

Antibody Detection ◽

Laboratory Evaluation ◽

Assay Performance ◽

Testing Algorithm ◽

Sensitivity Specificity ◽

Intended Use

SARS-CoV-2 serosurveys can estimate cumulative incidence for monitoring epidemics but require characterization of employed serological assays performance to inform testing algorithm development and interpretation of results. We conducted a multi-laboratory evaluation of 21 commercial high-throughput SARS-CoV-2 serological assays using blinded panels of 1,000 highly-characterized blood-donor specimens. Assays demonstrated a range of sensitivities (96%-63%), specificities (99%-96%) and precision (IIC 0.55-0.99). Durability of antibody detection in longitudinal samples was dependent on assay format and immunoglobulin target, with anti-spike, direct, or total Ig assays demonstrating more stable, or increasing reactivity over time than anti-nucleocapsid, indirect, or IgG assays. Assays with high sensitivity, specificity and durable antibody detection are ideal for serosurveillance. Less sensitive assays demonstrating waning reactivity are appropriate for other applications, including characterizing antibody responses after infection and vaccination, and detection of anamnestic boosting by reinfections and vaccine breakthrough infections. Assay performance must be evaluated in the context of the intended use.

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Software-guided microscale flow calorimeter for efficient acquisition of thermokinetic data

Journal of Flow Chemistry ◽

10.1007/s41981-021-00145-6 ◽

2021 ◽

Author(s):

Timothy Aljoscha Frede ◽

Marlene Dietz ◽

Norbert Kockmann

Keyword(s):

Design Of Experiments ◽

Process Development ◽

Reaction Conditions ◽

Experimental Conditions ◽

Flow Calorimeter ◽

Microscale Flow ◽

Increased Sensitivity ◽

Important Time ◽

Optimal Reaction

AbstractFast chemical process development is inevitably linked to an optimized determination of thermokinetic data of chemical reactions. A miniaturized flow calorimeter enables increased sensitivity when examining small amounts of reactants in a short time compared to traditional batch equipment. Therefore, a methodology to determine optimal reaction conditions for calorimetric measurement experiments was developed and is presented in this contribution. Within the methodology, short-cut calculations are supplemented by computational fluid dynamics (CFD) simulations for a better representation of the hydrodynamics within the microreactor. This approach leads to the effective design of experiments. Unfavourable experimental conditions for kinetics experiments are determined in advance and therefore, need not to be considered during design of experiments. The methodology is tested for an instantaneous acid-base reaction. Good agreement of simulations was obtained with experimental data. Thus, the prediction of the hydrodynamics is enabled and the first steps towards a digital twin of the calorimeter are performed. The flow rates proposed by the methodology are tested for the determination of reaction enthalpy and showed that reasonable experimental settings resulted. Graphical abstract A methodology is suggested to evaluate optimal reaction conditions for efficientacquisition of kinetic data. The experimental design space is limited by thestepwise determination of important time scales based on specified input data.

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nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽

10.1186/s12864-020-07182-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Surajit Bhattacharya ◽

Hayk Barseghyan ◽

Emmanuèle C. Délot ◽

Eric Vilain

Keyword(s):

De Novo ◽

Genome Mapping ◽

Gene List ◽

Sufficient Information ◽

Rna Seq ◽

Structural Variants ◽

De Novo Genome Assembly ◽

Pathogenic Variants ◽

Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

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TIRADS, SRE and SWE in INDETERMINATE thyroid nodule characterization: Which has better diagnostic performance?

La radiologia medica ◽

10.1007/s11547-021-01349-5 ◽

2021 ◽

Author(s):

Ilaria Celletti ◽

Daniele Fresilli ◽

Corrado De Vito ◽

Marco Bononi ◽

Sara Cardaccio ◽

...

Keyword(s):

Thyroid Nodule ◽

Preoperative Staging ◽

Shear Wave Elastography ◽

Roc Curves ◽

Strain Ratio ◽

Multicenter Studies ◽

Increased Sensitivity ◽

Bonferroni Test ◽

Indeterminate Cytology ◽

Sensitivity Specificity

Abstract Purpose To assess Strain Ratio (SRE) and Shear Wave Elastography (SWE) accuracy alone and with TIRADS classification, for the risk stratification of indeterminate thyroid nodules. Materials and methods 128 Patients with 128 indeterminate nodules candidates for thyroidectomy underwent preoperative staging neck ultrasound and were classified according to K-TIRADS score. After TIRADS evaluation, semi-quantitative (SRE) and quantitative (SWE expressed in kPa) elastosonography were performed and relative diagnostic performances, alone and in combination, were compared through ROC curves analysis. In order to maximize the SRE and SWE sensitivity and specificity, their cut-off values were calculated using the Liu test. Bonferroni test was used to evaluate statistically significant differences with a p value < 0.05. Results Sensitivity, specificity, PPV and NPV were, respectively, 71.4%, 82.4%, 62.5%, 87.5% for K-TIRADS baseline US, 85.7%, 94.1%, 85.7%, 94.1% for SRE and 57.1%, 79.4%, 53.3%, 81.8% for SWE (kPa expressed). SRE evaluation showed the best diagnostic accuracy compared to the SWE (kPa expressed) (p < 0.05) and to the K-TIRADS (p > 0.05). The association of SRE with conventional ultrasound with K-TIRADS score increased sensitivity (92.9% vs 71.4%) but decreased the specificity than conventional US alone (76.5% vs 82.4%). Conclusion Strain Elastosonography can be associated with K-TIRADS US examination in the thyroid nodule characterization with indeterminate cytology; in fact, adding the SRE to K-TIRADS assessment significantly increases its sensitivity and negative predictive value. However, further multicenter studies on larger population are warranted.

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