{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T17:16:06Z","timestamp":1792602966498,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/f1000research.52412.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T00:00:00Z","timestamp":1629417600000}}],"reference-count":79,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T00:00:00Z","timestamp":1629417600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006756","name":"Brigham Young University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006756","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    <ns3:bold>Background:<\/ns3:bold>\n                    Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of coronavirus disease-2019 (COVID-19), is a novel Betacoronavirus that was first reported in Wuhan, China in December of 2019. The virus has since caused a worldwide pandemic that highlights the need to quickly identify potential prophylactic or therapeutic treatments that can reduce the signs, symptoms, and\/or spread of disease when dealing with a novel infectious agent. To combat this problem, we constructed a computational pipeline that uniquely combines existing tools to predict drugs and biologics that could be repurposed to combat an emerging pathogen.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Methods:<\/ns3:bold>\n                    Our workflow analyzes RNA-sequencing data to determine differentially expressed genes, enriched Gene Ontology (GO) terms, and dysregulated pathways in infected cells, which can then be used to identify US Food and Drug Administration (FDA)-approved drugs that target human proteins within these pathways. We used this pipeline to perform a meta-analysis of RNA-seq data from cells infected with three Betacoronavirus species including severe acute respiratory syndrome coronavirus (SARS-CoV; SARS), Middle East respiratory syndrome coronavirus (MERS-CoV; MERS), and SARS-CoV-2, as well as respiratory syncytial virus and influenza A virus to identify therapeutics that could be used to treat COVID-19.\u00a0\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Results:<\/ns3:bold>\n                    This analysis identified twelve existing drugs, most of which already have FDA-approval, that are predicted to counter the effects of SARS-CoV-2 infection. These results were cross-referenced with interventional clinical trials and other studies in the literature to identify drugs on our list that had previously been identified or used as treatments for COIVD-19 including canakinumab, anakinra, tocilizumab, sarilumab, and baricitinib.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Conclusions:<\/ns3:bold>\n                    While the results reported here are specific to Betacoronaviruses, such as SARS-CoV-2, our bioinformatics pipeline can be used to quickly identify candidate therapeutics for future emerging infectious diseases.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.52412.2","type":"journal-article","created":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T08:40:15Z","timestamp":1629448815000},"page":"330","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases"],"prefix":"10.12688","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6209-8301","authenticated-orcid":false,"given":"Tiana M.","family":"Scott","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Jensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7930-8160","authenticated-orcid":false,"given":"Brett E.","family":"Pickett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2021,8,20]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"163-88","DOI":"10.1016\/bs.aivir.2018.01.001","article-title":"Hosts and Sources of Endemic Human Coronaviruses.","volume":"100","author":"V Corman","year":"2018","journal-title":"Adv Virus Res."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"325-8","DOI":"10.1016\/j.chom.2020.02.001","article-title":"Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China.","volume":"27","author":"A Wu","year":"2020","journal-title":"Cell Host Microbe."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"181-92","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses.","volume":"17","author":"J Cui","year":"2019","journal-title":"Nat Rev Microbiol."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.3390\/jcm9041225","article-title":"The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control.","volume":"9","author":"Y Helmy","year":"2020","journal-title":"J Clin Med."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"105955","DOI":"10.1016\/j.ijantimicag.2020.105955","article-title":"The epidemiology, diagnosis and treatment of COVID-19.","volume":"55","author":"P Zhai","year":"2020","journal-title":"Int J Antimicrob Agents."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"755-69","DOI":"10.1002\/jmv.25813","article-title":"Epidemiological analysis of COVID-19 and practical experience from China.","volume":"92","author":"Q Ye","year":"2020","journal-title":"J Med Virol."},{"key":"ref-7","article-title":"Weekly epidemiological update - 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.55686.r85467, Jos\u00e9 Pedro Cer\u00f3n-Carrasco, Bioinformatics and High Performance Computing Research Group (BIO-HPC), Faculty of Polytechnic Science, UCAM Catholic University of Murcia, Murcia, Spain, 02 Jun 2021, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/10-330\/v1#referee-response-85467","order":0,"name":"referee-response-85467","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Brett Pickett<\/b>; \n<i>Posted: 17 Aug 2021<\/i>; We thank the reviewer for their helpful comment and agree that researchers would could indeed make good use of the complete list of drugs that we predicted to be useful against SARS-CoV-2. To address this comment we will update Table 4 in the next manuscript version to now include not only all of the predicted drugs, but also summaries of how each drug ranks across all analyzed Coronavirus datasets and also across all SARS-CoV-2 datasets. We believe that this change will improve the readability and relevance of our study.","URL":"https:\/\/f1000research.com\/articles\/10-330\/v2#referee-comment-7043","order":1,"name":"referee-comment-7043","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.55686.r89746, Babatunde Joseph Oso, Department of Biochemistry, McPherson University, Seriki Sotayo, Nigeria, 02 Aug 2021, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/10-330\/v1#referee-response-89746","order":2,"name":"referee-response-89746","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.76722.r99992, Soumya Lipsa Rath, National Institute of Technology, Warangal, Telangana, India, 19 Nov 2021, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/10-330\/v2#referee-response-99992","order":3,"name":"referee-response-99992","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This research was funded by a startup package from Brigham Young University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"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"}]}}