{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:08:40Z","timestamp":1772168920733,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.51061.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T00:00:00Z","timestamp":1644969600000}},{"DOI":"10.12688\/f1000research.51061.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T00:00:00Z","timestamp":1644969600000}}],"reference-count":29,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T00:00:00Z","timestamp":1644969600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>The performance of diagnostic tests crucially depends on\u00a0the disease\u00a0prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab\u00a0procedures\u00a0which make the rating of the test results somewhat problematic. A current example is\u00a0the mass\u00a0testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results\u00a0have\u00a0a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is\u00a0in the nature of wet\u00a0lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols,\u00a0and analytical reagents. These limitations in sensitivity and specificity\u00a0have to\u00a0be\u00a0taken into account\u00a0when calculating\u00a0the real\u00a0test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for\u00a0analyzing\u00a0disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative,\u00a0and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented\u00a0on\u00a0any system supporting SQL. We provide\u00a0an example of influenza test results from California, USA, as well as\u00a0two\u00a0examples of SARS-CoV-2 test results from official government reports from The Netherlands and\u00a0Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we\u00a0discuss\u00a0this tool\u2019s multiple applications, including its putative importance for informing policy decisions.<\/ns4:p>","DOI":"10.12688\/f1000research.51061.3","type":"journal-article","created":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T10:00:06Z","timestamp":1645005606000},"page":"369","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Bayes Lines Tool (BLT):\u00a0a\u00a0SQL-script for\u00a0analyzing\u00a0diagnostic test results with an application to SARS-CoV-2-testing"],"prefix":"10.12688","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7650-0093","authenticated-orcid":false,"given":"Wouter","family":"Aukema","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2644-3438","authenticated-orcid":false,"given":"Bobby Rajesh","family":"Malhotra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Goddek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2311-6984","authenticated-orcid":false,"given":"Ulrike","family":"K\u00e4mmerer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5635-6351","authenticated-orcid":false,"given":"Peter","family":"Borger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3908-1122","authenticated-orcid":false,"given":"Kevin","family":"McKernan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1401-4270","authenticated-orcid":false,"given":"Rainer Johannes","family":"Klement","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2022,2,16]]},"reference":[{"key":"ref1","first-page":"1015-24","article-title":"Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study.","volume":"133","author":"L Ren","year":"2020","journal-title":"Chin Med J (Engl)."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"727-33","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019.","volume":"382","author":"N Zhu","year":"2020","journal-title":"N Engl J Med."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"536-44","DOI":"10.1038\/s41564-020-0695-z","article-title":"The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.","volume":"5","author":"A Gorbalenya","year":"2020","journal-title":"Nat Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1-8","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","article-title":"Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR.","volume":"25","author":"V Corman","year":"2020","journal-title":"Euro Surveill."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"465-9","DOI":"10.1038\/s41586-020-2196-x","article-title":"Virological assessment of hospitalized patients with COVID-2019.","volume":"581","author":"R W\u00f6lfel","year":"2020","journal-title":"Nature."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"2309","DOI":"10.3390\/ijerph17072309","article-title":"Corona Virus (COVID-19) \u201cInfodemic\u201d and Emerging Issues through a Data Lens: The Case of China.","volume":"17","author":"J Hua","year":"2020","journal-title":"Int J Environ Res Public Health."},{"key":"ref7","article-title":"WHO Director-General\u2019s opening remarks at the media briefing on COVID-19-11 March 2020.","year":"2020 cited 2021 Feb 6"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"260-4","DOI":"10.1177\/2043820620935355","article-title":"The dashboard pandemic.","volume":"10","author":"J Everts","year":"2020","journal-title":"Dialogues Hum Geogr."},{"key":"ref9","article-title":"Case definition for coronavirus disease 2019 (COVID-19), as of 3 December 2020.","year":"2020 cited 2021 Jan 22"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1-7","DOI":"10.1002\/rmv.2052","article-title":"Lessons in diagnostic virology: expected and unexpected sources of error.","volume":"29","author":"G van Zyl","year":"2019","journal-title":"Rev Med Virol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"582","DOI":"10.3390\/v12060582","article-title":"Challenges in Laboratory Diagnosis of the Novel.","volume":"12","author":"N Younes","year":"2020","journal-title":"Viruses."},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.13684","article-title":"Pitfalls in SARS-CoV-2 PCR diagnostics.","author":"K Wernike","year":"2020","journal-title":"Transbound Emerg Dis."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e0242958","DOI":"10.1371\/journal.pone.0242958","article-title":"False-negative results of initial RT-PCR assays for COVID-19: A systematic review.","volume":"15","author":"I Arevalo-Rodriguez","year":"2020","journal-title":"PLoS One."},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1007\/s10441-020-09393-w","article-title":"The Epistemology of a Positive SARS-CoV-2 Test.","author":"R Klement","year":"2020","journal-title":"Acta Biotheor."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"15438-53","DOI":"10.1074\/jbc.RA120.015434","article-title":"A blueprint for academic laboratories to produce SARS-cov-2 quantitative RT-PCR test kits.","volume":"295","author":"S Mascuch","year":"2020","journal-title":"J Biol Chem."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"715-21","DOI":"10.1021\/acs.analchem.0c03996","article-title":"A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests.","volume":"93","author":"H Zhou","year":"2020","journal-title":"Anal Chem."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"598-602","DOI":"10.7326\/0003-4819-137-7-200210010-00011","article-title":"Spectrum Bias or Spectrum Effect? Subgroup Variation in Diagnostic.","volume":"137","author":"S Mulherin","year":"2002","journal-title":"Ann Intern Med."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"125-35","DOI":"10.1002\/sim.1591","article-title":"Spectrum bias: A quantitative and graphical analysis of the variability of medical diagnostic test performance.","volume":"23","author":"C Goehring","year":"2004","journal-title":"Stat Med."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"211-33","DOI":"10.1016\/0001-6918(80)90046-3","article-title":"The base-rate fallacy in probability judgments.","volume":"44","author":"M Bar-Hillel","year":"1980","journal-title":"Acta Psychol (Amst)."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1-12","DOI":"10.1038\/s41467-020-19509-y","article-title":"Infection fatality rate of SARS-CoV2 in a super-spreading event in Germany.","volume":"11","author":"H Streeck","year":"2020","journal-title":"Nat Commun."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1-8","DOI":"10.2807\/1560-7917.ES.2020.25.47.2001752","article-title":"Serology- And PCR-based cumulative incidence of SARS-cov-2 infection in adults in a successfully contained early hotspot (CoMoLo study), Germany, May to June 2020.","volume":"25","author":"C Santos-H\u00f6vener","year":"2020","journal-title":"Euro Surveill."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"E96-100","DOI":"10.1055\/a-1197-4293","article-title":"Screening of Mothers in a COVID-19 Low-Prevalence Region: Determination of SARS-CoV-2 Antibodies in 401 Mothers from Rostock by ELISA and Confirmation by Immunofluorescence.","volume":"145","author":"E Reisinger","year":"2020","journal-title":"Dtsch Medizinische Wochenschrift."},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1101\/2020.04.24.20078949","article-title":"Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19.","author":"N Padhye","year":"2020","journal-title":"medRxiv."},{"key":"ref24","article-title":"WHO Information Notice for IVD Users 2020\/05.","year":"2021 cited 2021 Jan 22"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"330-6","DOI":"10.1155\/2006\/152612","article-title":"An outbreak of human coronavirus OC43 infection and serological cross-reactivity with SARS coronavirus.","volume":"17","author":"D Patrick","year":"2006","journal-title":"Can J Infect Dis Med Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2020.10.017","article-title":"Ct values from SARS-CoV-2 diagnostic PCR assays should not be used as direct estimates of viral load.","author":"E Dahdouh","year":"2020","journal-title":"J Infect."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"e38","DOI":"10.1056\/NEJMp2015897","article-title":"False Negative Tests for SARS-CoV-2 Infection \u2014 Challenges and Implications.","volume":"383","author":"S Woloshin","year":"2020","journal-title":"N Engl J Med."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"262-7","DOI":"10.7326\/M20-1495","article-title":"Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction\u2014Based SARS-CoV-2 Tests by Time Since Exposure.","volume":"173","author":"L Kucirka","year":"2020","journal-title":"Ann Intern Med."},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.4594210","article-title":"Bayes Lines Tool (BLT) - A SQL-script for analysing diagnostic test results with an application to SARS-CoV-2-testing (Version 4.2).","author":"W Aukema","year":"2021, March 10","journal-title":"Zenodo."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/10-369\/v3\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/10-369\/v3\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/10-369\/v3\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,2]],"date-time":"2022-03-02T05:20:12Z","timestamp":1646198412000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/10-369\/v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,16]]},"references-count":29,"URL":"https:\/\/doi.org\/10.12688\/f1000research.51061.3","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.121230.r123945","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.121230.r123945","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,16]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/10-369\/v3#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.57358.r87900, Phillip M. Bentley, European Spallation Source ESS, Lund, Sweden, 27 Aug 2021, version 2, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/10-369\/v2#referee-response-87900","order":0,"name":"referee-response-87900","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.121230.r123945, Mariska M G Leeflang, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands, 02 Mar 2022, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/10-369\/v3#referee-response-123945","order":1,"name":"referee-response-123945","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The author(s) declared that no grants were involved in supporting this work","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}