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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, View ORCID ProfileTulio de Oliveira
doi: https://doi.org/10.1101/2020.01.31.928796
Sara Cleemput
1Emweb bv, Herent, Belgium
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Wim Dumon
1Emweb bv, Herent, Belgium
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Vagner Fonseca
2KwaZulu-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
3Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
4Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Brazil
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Wasim Abdool Karim
2KwaZulu-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
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Marta Giovanetti
5Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Luiz Carlos Alcantara
3Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
5Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Koen Deforche
1Emweb bv, Herent, Belgium
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Tulio de Oliveira
2KwaZulu-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
6Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
7Department of Global Health, University of Washington, Seattle, USA
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  • ORCID record for Tulio de Oliveira
  • For correspondence: tuliodna@gmail.com
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ABSTRACT

Summary 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 novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for 2019-nCoV. 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.

Availability Available online: https://www.genomedetective.com/app/typingtool/cov

Contact koen{at}emweb.be and deoliveira{at}ukzn.ac.za

Supplementary information Supplementary data is available online.

Footnotes

  • http://www.genomedetective.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 02, 2020.
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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, Tulio de Oliveira
bioRxiv 2020.01.31.928796; doi: https://doi.org/10.1101/2020.01.31.928796
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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, Tulio de Oliveira
bioRxiv 2020.01.31.928796; doi: https://doi.org/10.1101/2020.01.31.928796

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