{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T11:44:05Z","timestamp":1774266245932,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,2,28]],"date-time":"2020-02-28T00:00:00Z","timestamp":1582848000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","award":["MRC-RFA-UFSP-01-2013"],"award-info":[{"award-number":["MRC-RFA-UFSP-01-2013"]}],"id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","award":["UKZN HIVEPI"],"award-info":[{"award-number":["UKZN HIVEPI"]}],"id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme","award":["634650"],"award-info":[{"award-number":["634650"]}]},{"name":"National Human Genome Research Institute of the National Institutes of Health","award":["U24HG006941"],"award-info":[{"award-number":["U24HG006941"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/www.genomedetective.com\/app\/typingtool\/cov<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>koen@emweb.be or deoliveira@ukzn.ac.za<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa145","type":"journal-article","created":{"date-parts":[[2020,2,25]],"date-time":"2020-02-25T15:16:28Z","timestamp":1582643788000},"page":"3552-3555","source":"Crossref","is-referenced-by-count":131,"title":["Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes"],"prefix":"10.1093","volume":"36","author":[{"given":"Sara","family":"Cleemput","sequence":"first","affiliation":[{"name":"Emweb bv , Herent, Belgium"}]},{"given":"Wim","family":"Dumon","sequence":"additional","affiliation":[{"name":"Emweb bv , Herent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5521-6448","authenticated-orcid":false,"given":"Vagner","family":"Fonseca","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) , School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"},{"name":"Laborat\u00f3rio de Gen\u00e9tica Celular e Molecular , Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"},{"name":"Coordena\u00e7\u00e3o Geral dos Laborat\u00f3rios de Sa\u00fade P\u00fablica\/Secretaria de Vigil\u00e2ncia em Sa\u00fade , Minist\u00e9rio da Sa\u00fade, (CGLAB\/SVS-MS), Bras\u00edlia, Brazil"}]},{"given":"Wasim","family":"Abdool Karim","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) , School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"}]},{"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Flaviv\u00edrus , Instituto Oswaldo Cruz, Funda\u00e7\u00e3o Oswaldo Cruz, Rio de Janeiro, RJ, Brazil"}]},{"given":"Luiz Carlos","family":"Alcantara","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Gen\u00e9tica Celular e Molecular , Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"},{"name":"Laborat\u00f3rio de Flaviv\u00edrus , Instituto Oswaldo Cruz, Funda\u00e7\u00e3o Oswaldo Cruz, Rio de Janeiro, RJ, Brazil"}]},{"given":"Koen","family":"Deforche","sequence":"additional","affiliation":[{"name":"Emweb bv , Herent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3027-5254","authenticated-orcid":false,"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) , School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"},{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA) , Durban, South Africa"},{"name":"Department of Global Health , University of Washington, Seattle, WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,2,28]]},"reference":[{"key":"2023062300082226700_btaa145-B1","author":"Deforche","year":"2017"},{"key":"2023062300082226700_btaa145-B2","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023062300082226700_btaa145-B3","doi-asserted-by":"crossref","first-page":"e0007231","DOI":"10.1371\/journal.pntd.0007231","article-title":"A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes","volume":"13","author":"Fonseca","year":"2019","journal-title":"PLoS Negl. 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