![]() The trees were visualized in Figtree ( Rambaut, 2018). A maximum likelihood phylogenetic tree, 1000 bootstrap replicates were constructed in PhyML ( Guindon and Gascuel, 2003 Lemoine et al., 2018) and a Bayesian tree using MrBayes ( Ronquist and Huelsenbeck, 2003) were constructed. The alignment was manually edited until a codon alignment was attained in all coding sequences (CDS). The 431 reference WGS were aligned with MUSCLE ( Edgar, 2004). The SARS-CoV-2 data generators are properly acknowledged in the acknowledgements section of this article and detailed information is provided in Supplementary Table S1. The SARS-CoV-2 sequences were downloaded from the GISAID database ( ) together with annotation of its original location, collection date and originating and submitting laboratory. To this reference dataset, we added 47 whole genomes of the current Coronavirus 2019 (SARS-CoV-2) outbreak that originated in Wuhan, China, in December 2019. These included 132 sequences of Severe Acute Respiratory Syndrome related Coronavirus (SARSr-CoV), 121 sequences of Beta coronavirus, 97 sequences of Middle East Respiratory Syndrome related Coronavirus (MERSr-CoV), 19 sequences of Human Coronavirus HKU1, 9 sequences of Murine Hepatitis Virus, 4 of Rousettus Bat Coronavirus HKU9, 3 of Rat Coronavirus and 1 WGS of Tylonycteris Bat Coronavirus HKU4, Zaria_bat_coronavirus and Longquan Rl Rat coronavirus. ![]() The tool also identifies changes at nucleotides, coding regions and proteins using a novel dynamic aligner to allow tracking new viral mutations ( Fig. 1).Ī reference dataset of previously published coronavirus whole-genome sequences (WGS) was compiled from the Virus Pathogen Resource (VIPR) database ( This dataset consisted of 386 WGS of nine important coronavirus species. The Genome Detective Coronavirus Typing Tool is a free-of-charge web-based bioinformatics pipeline that can accurately and quickly identify, assemble and classify coronaviruses genomes. Here, we present a new contribution that can speed up this communal effort. This has helped the understanding of the transmission dynamics, the development of rapid diagnostic and has informed public health response. They have openly and rapidly shared genomic and clinical data as never seen before allowing research results to be released almost instantaneously. This coronavirus outbreak has been unprecedented so too is the way that the scientific community has responded to it. It has high fatality rate ( Huang et al., 2020), can be transmitted from person to person, has infected over 70 000 individuals and has spread to over 30 countries in less than 2 months ( WHO, 2020). It causes severe respiratory illness, which the WHO recently named COVID-19 disease. ![]() The virus is a SARS-related coronavirus (SARSr-CoV), and it is genetically associated with SARSr-CoV strains that infect bats in China ( Lu et al., 2020 Zhu et al., 2020). The novel coronavirus (SARS-CoV-2), first isolated in Wuhan, China, has already caused more infections than the previous severe acute respiratory syndrome (SARS) outbreak of 20. In the end of January 2020, the WHO has declared it a global emergency ( WHO, 2020). We are currently faced with a potential global epidemic of a new coronavirus that has infected thousands of people in China and is spreading rapidly around the world. 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. 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 can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. 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. 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. ![]() This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets.
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