{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:08:23Z","timestamp":1772168903600,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.22507.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T00:00:00Z","timestamp":1586822400000}}],"reference-count":10,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T00:00:00Z","timestamp":1586822400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    We report\n                    <ns4:italic>in silico<\/ns4:italic>\n                    identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a\n                    <ns4:italic>de novo<\/ns4:italic>\n                    search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.22507.2","type":"journal-article","created":{"date-parts":[[2020,4,17]],"date-time":"2020-04-17T14:15:21Z","timestamp":1587132921000},"page":"145","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":60,"title":["In silico identification of vaccine targets for 2019-nCoV"],"prefix":"10.12688","volume":"9","author":[{"given":"Chloe H.","family":"Lee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3640-7043","authenticated-orcid":false,"given":"Hashem","family":"Koohy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2020,4,14]]},"reference":[{"key":"ref-1","article-title":"2019-NCoV Outbreak Is an Emergency of International Concern.","year":"2020"},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"e87-e88","DOI":"10.1016\/S2542-5196(20)30035-8","article-title":"2019-nCoV in context: lessons learned?","volume":"4","author":"R Kock","year":"2020","journal-title":"Lancet Planet Health."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"D339-D343","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update.","volume":"47","author":"R Vita","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref-4","article-title":"In silico identification of vaccine targets for 2019-nCoV (Custom code).","author":"C Lee","year":"2020","journal-title":"Zenodo."},{"key":"ref-5","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-018-0577-7","article-title":"Exploring the pre-immune landscape of antigen-specific T cells.","volume":"10","author":"M Pogorelyy","year":"2018","journal-title":"Genome Med."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"3360-3368","DOI":"10.4049\/jimmunol.1700893","article-title":"NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.","volume":"199","author":"V Jurtz","year":"2017","journal-title":"J Immunol."},{"key":"ref-7","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02501","article-title":"TCR Fingerprinting and Off-Target Peptide Identification.","volume":"10","author":"A Karapetyan","year":"2019","journal-title":"Front Immunol."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"290-6","DOI":"10.1038\/351290a0","article-title":"Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules.","volume":"351","author":"K Falk","year":"1991","journal-title":"Nature."},{"key":"ref-9","doi-asserted-by":"publisher","DOI":"10.1101\/2020.02.03.933226","article-title":"Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies","author":"S Ahmed","year":"2020"},{"key":"ref-10","article-title":"In silico identification of vaccine targets for 2019-nCoV (Data tables).","author":"C Lee","year":"2020","journal-title":"Zenodo."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/9-145\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/9-145\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/9-145\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,17]],"date-time":"2020-04-17T14:15:58Z","timestamp":1587132958000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/9-145\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,4,14]]},"references-count":10,"URL":"https:\/\/doi.org\/10.12688\/f1000research.22507.2","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.25726.r61739","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.25726.r61739","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,14]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/9-145\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.24839.r60504, Katalin Wilkinson, Tuberculosis Laboratory, The Francis Crick Institute, London, UK, 05 Mar 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-145\/v1#referee-response-60504","order":0,"name":"referee-response-60504","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Hashem Koohy<\/b>; \n<i>Posted: 07 Apr 2020<\/i>; Dear Prof&nbsp;Wilkinson, Thank you so much for your time and valuable suggestions. In our new and revised version we have taken your suggestions into consideration. Best regards Hashem Koohy","URL":"https:\/\/f1000research.com\/articles\/9-145\/v2#referee-comment-5404","order":1,"name":"referee-comment-5404","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.24839.r60502, Raffaele De Palma, DIMI, Department of Internal Medicine, University of Genova, Genova, Italy, 31 Mar 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-145\/v1#referee-response-60502","order":2,"name":"referee-response-60502","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.25726.r61739, Angelika Riemer, Maria Bonsack, Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany, 14 Apr 2020, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/9-145\/v2#referee-response-61739","order":3,"name":"referee-response-61739","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This study was funded by the Medical Research Council Human Immunology Unit.","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"}]}}