Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region

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1. Version published to 10.1016/j.isci.2023.105928

   Feb 1, 2023
2. 

   Version published to 10.1101/2020.05.31.20118554v5 on medRxiv

   Aug 23, 2022
3. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.05.31.20118554: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement

   IRB: Human specimens and data: All experiments and analyses involving samples from human donors were conducted with the approval of the local ethics committee (KEK-ZH-Nr. 2015-0561, BASEC-Nr. 2018-01042, and BASEC-Nr. 2020-01731), in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation. Consent: EDTA plasma from healthy donors was obtained from the Blutspendedienst (blood donation service) Kanton Zürich and Kanton Luzern from donors who signed the consent that their samples can be used for conducting research.

   Randomization

   Additionally, we added 52 and 70 randomly …

   SciScore for 10.1101/2020.05.31.20118554: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Human specimens and data: All experiments and analyses involving samples from human donors were conducted with the approval of the local ethics committee (KEK-ZH-Nr. 2015-0561, BASEC-Nr. 2018-01042, and BASEC-Nr. 2020-01731), in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation. Consent: EDTA plasma from healthy donors was obtained from the Blutspendedienst (blood donation service) Kanton Zürich and Kanton Luzern from donors who signed the consent that their samples can be used for conducting research.
   Randomization	Additionally, we added 52 and 70 randomly selected prepandemic samples for the BDS and the USZ cohort respectively.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   High-throughput serological screening: In order to test the samples for the presence of IgG antibodies directed against SARS-CoV-2 antigens, high-binding 1536-well plates (Perkin Elmer, SpectraPlate 1536 HB) were coated with 1 μg/mL S or RBD or NC in PBS at 37 °C for 1 h, followed by 3 washes with PBS-T (using Biotek El406) and by blocking with 5% milk in PBS-T (using Biotek MultifloFX peristaltic pumps) for 1.5 h.	SARS-CoV-2 suggested: None
   After the sample incubation for 2 h at RT, the wells were washed five times with wash buffer and the presence of IgGs directed against above-defined SARS-CoV-2 antigens was detected using an HRP-linked anti-human IgG antibody (Peroxidase AffiniPure Goat Anti-Human IgG, Fcγ Fragment Specific, Jackson, 109-035-098, at 1:4000 dilution in sample buffer).	Anti-Human IgG suggested: (Jackson ImmunoResearch Labs Cat# 109-035-098, RRID:AB_2337586)
   The day after, membranes were washed four times with PBS-T and incubated for 1 hours with an anti-human secondary antibody, HRP-conjugated, diluted 1:10000 in 1% SureBlock.	anti-human secondary antibody, HRP-conjugated, suggested: None
   As a positive control, one membrane was incubated overnight with mouse anti-Histag antibody (ThermoFisher, dilution 1:10000 in 1% SureBlock) and subsequently with anti-mouse secondary antibody, HRP-conjugated (Jackson, dilution 1:10000 in 1% SureBlock).	anti-Histag suggested: (RevMAb Biosciences Cat# 54-1161-00, RRID:AB_2716428) anti-mouse suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Details of viral proteins used for this study: For high-throughput serology, the following proteins were used: SARS-CoV-2 S (pHL-Sec; aa. 11208, C-terminal 8His-Twin-Strep) and RBD (pOPINTTGNeo; aa. 330-532, C-terminal 6His) pro at the SGC in Oxford and the nucleocapsid protein from AcroBiosystems (AA Met 1 - Ala 419, C-terminal his-tag, NUN-C5227).	SARS-CoV-2 S suggested: None
   Software and Algorithms
   Sentences	Resources
   The SARS-CoV-2 chemiluminescent microparticle immunoassay from Abbott (Abbott Park, IL, USA) detects IgG against the nucleocapsid antigen and was performed on an Architect™ analyser.	Abbott suggested: (Abbott, RRID:SCR_010477)
   For competitive ELISA, we used: The prefusion ectodo of the SARS-CoV-2 S protein (Lausanne, EPFL SV PTECH PTPSP), the RBD from Tren- zyme (C-terminal his-tag, P2020-001) and the nucleocapsid protein from AcroBiosystems (AA Met 1 - Ala 419, C-terminal his-tag, NUN-C5227).	AcroBiosystems suggested: (ACRObiosystems, RRID:SCR_012550)

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   Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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4. 

   Version published to 10.1101/2020.05.31.20118554v4 on medRxiv

   Aug 7, 2020
5. 

   Version published to 10.1101/2020.05.31.20118554v3 on medRxiv

   Aug 5, 2020
6. 

   Version published to 10.1101/2020.05.31.20118554v2 on medRxiv

   Jun 22, 2020
7. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.31.20118554: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement

   Let 's study immune responses , but let 's not create a dystopian society based on them . Materials and Methods Human specimens and data All experiments and analyses involving samples from human donors were conducted with the approval of the local ethics committee ( KEK-ZH-Nr . 2015-0561 , BASEC-Nr . 2018-01042 , and BASEC 2020-00802) , in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation .

   Randomization

   To directly validate our method , we selected 210 high scoring samples and 122 random samples from known negatives and aimed to reproduce our results …

   SciScore for 10.1101/2020.05.31.20118554: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement

   Let 's study immune responses , but let 's not create a dystopian society based on them . Materials and Methods Human specimens and data All experiments and analyses involving samples from human donors were conducted with the approval of the local ethics committee ( KEK-ZH-Nr . 2015-0561 , BASEC-Nr . 2018-01042 , and BASEC 2020-00802) , in accordance with the provisions of the Declaration of Helsinki and the Good Clinical Practice guidelines of the International Conference on Harmonisation .

   Randomization

   To directly validate our method , we selected 210 high scoring samples and 122 random samples from known negatives and aimed to reproduce our results .

   Blinding

   A blinded comparison with commercial test kits showed that our approach – combining three individual assays into one single score – was suitable for large-scale epidemiologic studies .

   Power Analysis

   not detected.

   Sex as a biological variable

   Lastly , seropositivity can be found across all age groups and in both genders , with more male individuals affected in the USZ and BDS cohorts ( Fig . 3A , B , Table S1) .

   Cell Line Authentication

   not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Solution-equilibrium measurements revealed immunodominant antibodies with nanomolar affinity in COVID samples, whereas prepandemic plasma showed lower affinities despite similar titers for individual SARS2 antigens.	SARS2 suggested: None
   However , those with strong binding properties to SARS2 RBD ( > 2.5 ) cluster at high values for SARS1 RBD , indicating that some anti-SARS2 RBD antibodies are likely cross-reactive to SARS1 RBD .	anti-SARS2 RBD suggested: None
   Anti-his-tag antibody was included as a positive control .	Anti-his-tag suggested: None
   In a comparative approach , we investigated IgG and IgA antibodies to S , RBD , and NC as well as responses to multiple control antigens , in four asymptomatic blood donors and 4 convalescent individuals recruited to the BDS for a plasmapheresis study .	IgA suggested: None
   Counter screening using commercial and custom-designed platforms We used the following commercial tests for the detection of anti-SARS-SARS2 antibodies in 56 plasma samples of 27 patients who were diagnosed by RT-PCR to be infected by SARS-SARS2 as well as 83-90 plasma samples which were collected before December 2019 and , hence , before the start of the COVID19 pandemics: The double-antigen sandwich electro-chemiluminescence immunoassay from Roche diagnostics ( Rotkreuz , Switzerland ) was performed with the E801 of the COBAS8000® system ( Roche diagnostics , Rotkreuz , Switzerland) .	anti-SARS-SARS2 suggested: None
   The test detects any antibody against the nucleocapsid antigen .	antibody against the nucleocapsid antigen . suggested: None
   Baseline and plateau values are fixed by the respective positive and negative controls in a plate-wise fashion and the signal is fitted following these equations: 1 = 1 − ( + + 1 − √ ( + )2 + 2 ( − ) + 1 ) , 2 where cbound , ca and c are concentration of the antigen-antibody , antigen , and blood concentration respectively .	+ + 1 − √ ( + )2 + 2 ( − ) + 1 ) , 2 suggested: None
   Assume that we have data for samples with known serostatus and antibody measurements , that is , we have ( , ) , = 1 , . . , , where is the vector of size ( in our case our antigen measurements ) and is a Boolean variable defining group membership ( in our case , whether the individual is seropositive or not) .	we have ( , ) , = 1 , . . , suggested: None
   The day after, membranes were washed four times with PBS-T and incubated for 1 hours with an anti-human secondary antibody, HRP-conjugated, diluted 1:10000 in 1% SureBlock.	anti-human secondary antibody, HRP-conjugated, suggested: None
   As a positive control, one membrane was incubated overnight with mouse anti-Histag antibody (ThermoFisher, dilution 1:10000 in 1% SureBlock) and subsequently with anti-mouse secondary antibody, HRP-conjugated (Jackson, dilution 1:10000 in 1% SureBlock).	anti-Histag suggested: (RevMAb Biosciences Cat# 54-1161-00, AB_2716428) <div style="margin-bottom:8px"> <div><b>anti-mouse</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, the plates were washed five times with PBS-T and the presence of IgGs was detected using an HRP-linked anti-human IgG antibody (Peroxidase AffiniPure Goat Anti-Human IgG, Fcγ Fragment Specific, Jackson, 109-035-098, at 1:4000 dilution in sample buffer).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Anti-Human IgG</b></div> <div>suggested: (Jackson ImmunoResearch Labs Cat# 109-035-098, <a href="https://scicrunch.org/resources/Any/search?q=AB_2337586">AB_2337586</a>)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We confirmed these findings by using the samples of the asymptomatic and convalescent individuals as primary antibodies in Western Blot and detected bands for both S and the NC in the Expi293 cells overexpressing the viral proteins but not in the Expi293 control lysate ( Fig . 5B) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Expi293</b></div> <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_D615">CVCL_D615</a></div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To benchmark TRABI, we compared the results with an in-house high-throughput assay under development at the University of Oxford (optimizations ongoing at the time of data acquisition), the Roche Elecsys, the DiaSorin, the EuroImmun, and the Abbott systems (Fig. 1C), using 139 of 149 samples (10 were removed from the analysis because of insufficient sample volume to perform all tests).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Abbott systems</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">COVID and prepandemic samples were used to assess the performance of TRABI, commercial tests (Roche, DiaSorin, Abbott, Euroimmun) and an early version of an assay under development at the Target Discovery Institute (Oxford).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Abbott</b></div> <div>suggested: (Abbott, <a href="https://scicrunch.org/resources/Any/search?q=SCR_010477">SCR_010477</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Details of viral proteins used for this study For high-throughput serology , the following proteins were used: SARS-CoV-2 S ( pHL-Sec; aa . 11208 , C-terminal 8His-Twin-Strep ) and RBD ( pOPINTTGNeo; aa . 330-532 , C-terminal 6His ) produced at the SGC in Oxford and the nucleocapsid protein from AcroBiosystems ( AA Met 1 - Ala 419 , C-terminal his-tag , NUN-C5227) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>AcroBiosystems</b></div> <div>suggested: (ACRObiosystems, <a href="https://scicrunch.org/resources/Any/search?q=SCR_012550">SCR_012550</a>)</div> </div> </td></tr></table> Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog). About SciScore SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

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8. 

   Version published to 10.1101/2020.05.31.20118554v1 on medRxiv

   Jun 2, 2020