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

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 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.

Availability and implementation: https://www.genomedetective.com/app/typingtool/cov.

Contact: koen@emweb.be or deoliveira@ukzn.ac.za.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Genome Detective Coronavirus Typing Tool assembles genomes from next-generation sequencing (NGS) in FASTAQ format or assembled genomes in FASTA format. A user can submit up to 1 Gb of NGS data or 2000 assembled genomic sequences. For each assembled genomic sequence, the tool identifies the virus species, constructs a phylogenetic tree and identifies phylogenetic clusters, which includes the novel coronavirus identified in Wuhan, China in 2019 (SARS-CoV-2). The tool identifies changes at nucleotides, coding regions and proteins using a novel dynamic aligner and display all of the mutations in detailed tables and reports

Fig. 2.

Output from Genome Detective Coronavirus Typing Tool showing: (A) SARS-CoV-2 complete genome map. Top bar represents the genome (nucleotide positions 1 to 29 903). Bottom segments represent the open reading frames (ORFs). (B) Amino-acid alignment of the spike protein highlighting a four amino acid insertion (PRRA), which creates a new polybase cleavage site (RRAR) for SARS-CoV-2. Amino acid (aa) alignment is compared with four-related coronaviruses. The tool also calculates the percentage aa identities with reference to SARS-CoV-2 as shown here for the complete (1274 aa) spike protein