Publication

Title: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Authors: Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T.
Journal: Bioinformatics,btaa145, https://doi.org/10.1093/bioinformatics/btaa145: (2020)

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 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..

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

Supplementary information: Supplementary data is available online.

Open Reviewers Comments: Reviewers comments on the paper (deposited by senior author on 17 Feb 2020).

Download: Full text paper

Citation: Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes Bioinformatics,btaa145, https://doi.org/10.1093/bioinformatics/btaa145: (2020).

Printed and Online Media Coverage

Independent on Saturday

Social media helped scientists with coronavirusIndependent on Saturday - 2020-02-15

The huge amount of knowledge gathered in six short weeks on the coronavirus outbreak (Covid19 or SarsCoV2) was a first for the global scientific community. That was the opinion of University of KwaZulu-Natal Professor Tulio De Oliveira from the KZN Research Innovation and Sequencing Platform (KRISP) at a public talk attended by 120 people at the Nelson Mandela Medical School, 15 feb 2020.


Bioinformatics

KRISP work to produce a bioinformatics software for coronavirus COVID-19 rapid identification and characterizationBioinformatics - 2020-03-04

We developed an rapid bioinformatics tool for the identification and characterization of novel coronavirus genomes. The tool was released in January 2020 and published in Bioinformatics in February 2020 as an open access tool to help to characterise genomes of COVID-19 viruses.


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KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).


Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira