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

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.

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

“…Raw reads from Illumina sequencing were assembled using Genome Detective 1.126 (https://www.genomedetective.com/) and the coronavirus typing tool [16,17]. The initial assembly obtained from Genome Detective was polished by aligning mapped reads to the references and filtering out mutations with low genotype likelihoods using bcftools 1.7-2 mpileup method.…”

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

“…The urgency to develop an effective surveillance method that can be easily used in a variety of laboratory settings is underlined by the wide and rapid spreading of SARS-CoV-2 [28][29][30] . In addition, such method should also distinguish SARS-CoV-2 from other respiratory pathogens such as influenza virus, parainfluenza virus, adenovirus, respiratory syncytial virus, rhinovirus, human metapneumovirus, SARS coronavirus, etc., as well as mycoplasma pneumoniae, chlamydia pneumonia and bacterial pneumonia [31][32][33][34] . Furthermore, providing nucleotide sequence information through next generation sequencing (NGS) will prove to be essential for the surveillance of SARS-CoV-2's evolution [35][36][37][38] .…”

SARS-CoV-2 sequence typing, evolution and signatures of selection using CoVa, a Python-based command-line utility

“…Cova's speed, accuracy and breadth of analysis makes it an ideal tool for genome analysis of SARS-CoV-2. While several other genome analysis tools (35)(36)(37) have been developed for this virus, CoVa accomplishes all of these analyses in a short time and with minimum computational resources. As opposed to other web-based tools, CoVa can be run locally and, being a command-line utility, has the added advantage that it can be easily integrated into a larger workflow for bioinformatics research.…”