Serodiagnostics for SARS-CoV-2
Bibliographic record
Abstract
LettersFebruary 2021Serodiagnostics for SARS-CoV-2FREEJesse Papenburg, MD, MSc, Cedric P. Yansouni, MD, Chelsea Caya,, MScPH, Matthew P. Cheng, MDCMJesse Papenburg, MD, MScMcGill Interdisciplinary Initiative in Infection and Immunity, School of Population and Global Health, McGill University, and Montreal Children's Hospital, Montreal, Quebec, Canada, Cedric P. Yansouni, MDMcGill University Health Centre, McGill Interdisciplinary Initiative in Infection and Immunity, and J.D. MacLean Centre for Tropical Diseases, McGill University, Montreal, Quebec, Canada, Chelsea Caya,, MScPHMcGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, Canada, Matthew P. Cheng, MDCMMcGill University Health Centre and McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, CanadaAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/L20-1396 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail IN RESPONSE:We would like to clarify our statement on the importance of accounting for the prevalence of prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the population when interpreting serologic test results. We apologize that we unintentionally omitted the value of test sensitivity necessary for calculation of the example, for which we were using an estimate of 95%. Furthermore, the use of the term “false-positive rate” may have led to confusion, because it is sometimes used to refer to (1 − specificity) (1). However, we were using a common statistical definition of this term, whereby “the false positive rate [emphasis added] is the percentage of people who test positive but do not actually have the disease” (2).Nevertheless, the key concept expressed in this section of our review is that imperfect test specificity can introduce important bias when prior infection prevalence is very low, where the number of false-positive results could equal or even outnumber true-positive results. Drs. Harada Sassa and Harada have also explored this issue in their own work using lateral-flow and enzyme-linked immunosorbent assays on pre–coronavirus disease 2019 sera in Japan, showing the risk of overestimating SARS-CoV-2 seroprevalence when using these tools (3). Investigators should be encouraged to use analytical methods that adjust for imperfect test sensitivity and specificity and disease prevalence when estimating SARS-CoV-2 seroprevalence (4).References1. Casscells W, Schoenberger A, Graboys TB. Interpretation by physicians of clinical laboratory results. N Engl J Med. 1978;299:999-1001. [PMID: 692627] CrossrefMedlineGoogle Scholar2. King AP, Eckersley RJ. Descriptive Statistics III: ROC Analysis. In: King AP, Eckersley RJ, eds. Statistics for Biomedical Engineers and Scientists. How to Visualize and Analyze Data: Academic Pr; 2019:57-69. Google Scholar3. Lyu Z, Harada Sassa, Fujitani T, et al. Serological tests for SARS-CoV-2 coronavirus by commercially available point-of-care and laboratory diagnostics in pre-COVID-19 samples in Japan. Diseases. 2020;8. [PMID: 32977485] doi:10.3390/diseases8040036 CrossrefMedlineGoogle Scholar4. Clapham H, Hay J, Routledge I, et al. Seroepidemiologic study designs for determining SARS-COV-2 transmission and immunity. Emerg Infect Dis. 2020;26:1978-86. [PMID: 32544053] doi:10.3201/eid2609.201840 CrossrefMedlineGoogle Scholar Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAuthors: Jesse Papenburg, MD, MSc; Cedric P. Yansouni, MD; Chelsea Caya,, MScPH; Matthew P. Cheng, MDCMAffiliations: McGill Interdisciplinary Initiative in Infection and Immunity, School of Population and Global Health, McGill University, and Montreal Children's Hospital, Montreal, Quebec, CanadaMcGill University Health Centre, McGill Interdisciplinary Initiative in Infection and Immunity, and J.D. MacLean Centre for Tropical Diseases, McGill University, Montreal, Quebec, CanadaMcGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, CanadaMcGill University Health Centre and McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec, CanadaDisclosures: Disclosures can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=M20-2854. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetailsSee AlsoSerodiagnostics for Severe Acute Respiratory Syndrome–Related Coronavirus 2 Matthew P. Cheng , Cedric P. Yansouni , Nicole E. Basta , Michaël Desjardins , Sanjat Kanjilal , Katryn Paquette , Chelsea Caya , Makeda Semret , Caroline Quach , Michael Libman , Laura Mazzola , Jilian A. Sacks , Sabine Dittrich , and Jesse Papenburg Serodiagnostics for SARS-CoV-2 Mariko Harada Sassa , Kouji H. Harada Metrics Cited byTwo‐phase Bayesian latent class analysis to assess diagnostic test performance in the absence of a gold standard: COVID ‐19 serological assays as a proof of conceptDiagnostic accuracy of rapid one-step PCR assays for detection of herpes simplex virus-1 and -2 in cerebrospinal fluid: a systematic review and meta-analysis February 2021Volume 174, Issue 2Page: 287-288KeywordsCOVID-19DisclosureEnzyme linked immunosorbent assaySpecificityUpper respiratory tract infections ePublished: 16 February 2021 Issue Published: February 2021 Copyright & PermissionsCopyright © 2021 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.007 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.021 | 0.007 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".