Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/40347

Type
Article
Copyright
Open access
Collections
Share

Statistics
Metadata
Show full item record

GENOME DETECTIVE CORONAVIRUS TYPING TOOL FOR RAPID IDENTIFICATION AND CHARACTERIZATION OF NOVEL CORONAVIRUS GENOMES
Cleemput, Sara et al. | Date Issued: 2020
Author
Cleemput, Sara
Dumon, Wim
Fonseca, Vagner
Karim, Wasim Abdool
Giovanetti, Marta
Alcantara, Luiz Carlos
Deforche, Koen
Oliveira, Tulio de
Affilliation
Emweb bv, Herent, Belgium.
Emweb bv, Herent, Belgium.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). School of Laboratory Medicine and Medical Sciences. University of KwaZulu-Natal. College of Health Sciences. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular Belo Horizonte, MG, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Coordenação Geral dos Laboratórios de Saúde Pública. Brasília, DF, Brasil.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). School of Laboratory Medicine and Medical Sciences. University of KwaZulu-Natal. College of Health Sciences. Durban, South Africa.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular Belo Horizonte, MG, Brasil / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Laboratório de Genética Celular e Molecular Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.
Emweb bv, Herent, Belgium.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). School of Laboratory Medicine and Medical Sciences. University of KwaZulu-Natal. College of Health Sciences. Durban, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA). Durban, South Africa / University of Washington. Department of Global Health. Seattle, USA.
Abstract
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 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 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.
Keywords in Portuguese
Coronavírus
Tipagem
Genoma
Identificaçao
Caracterização
Ferramenta
 
Keywords
Coronavirus Typing Tool
Identification and characterization
Genomes
COVID-19
 
Publisher
Oxford University Press
Citation
CLEEMPUT, Sara et al. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics, btaa145, p. 1-4, Feb. 2020.
DOI
10.1093/bioinformatics/btaa145
ISSN
1460-2059
Notes
Devido a pandemia mundial do COVID-19, o artigo da revista foi liberado em acesso aberto durante o ano de 2020, visando divulgação e disseminação.
Em decorrência da pandemia decretada pela OMS em 2020, o artigo encontra-se em acesso aberto.