Genome Detective: an automated system for virus identification from high-throughput sequencing data

Vilsker, Michael; Moosa, Yumna; Nooij, Sam; Fonseca, Vagner; Ghysens, Yoika; Dumon, Korneel; Pauwels, Raf; Alcântara, Luíz Carlos Júnior; Eynden, Ewout Vanden; Vandamme, Anne‐Mieke; Deforche, Koen; Oliveira, Túlio de

doi:10.1093/bioinformatics/bty695

Cited by 305 publications

(275 citation statements)

References 16 publications

(20 reference statements)

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“…This tool allows the analysis of whole or partial viral genomes within minutes. It accepts assembled genomes in FASTA format or raw NGS data in FASTQ format from Illumina, Ion Torrent, PACBIO or Oxford Nanopore Technologies (ONT) can be submitted to the Genome Detective Virus Tool (Vilsker et al, 2019) to automatically assemble the consensus genome prior to executing the Coronavirus Typing Tool. User effort is minimal, and a user can submit multiple FASTA sequences at once.…”

Section: Discussionmentioning

confidence: 99%

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

Cleemput

Dumon

Fonseca

et al. 2020

Preprint

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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 novel coronavirus (2019-nCoV) 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 2019-nCoV. 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.

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Section: Discussionmentioning

confidence: 99%

“…The phylogenetic reference dataset was used to create an automated Coronavirus Typing Tool using the Genome Detective framework (Vilsker et al, 2019. To determine the accuracy of this tool, each of the 431 test WGS was considered for evaluation (i.e.…”

Section: Systems and Methodsmentioning

confidence: 99%

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

Cleemput

Dumon

Fonseca

et al. 2020

Preprint

Self Cite

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“…Unprocessed paired‐end reads were first de novo assembled with the Genome Detective application . Binary sequence alignment map files were downloaded from each sample sequence run in Genome Detective and imported into the Geneious software suite.…”

Section: Methodsmentioning

confidence: 99%

“…Unprocessed paired-end reads were first de novo assembled with the Genome Detective application. 21 Binary sequence alignment map files were downloaded from each sample sequence run in Genome Detective and imported into the Geneious software suite. Consensus fasta files were extracted and analyzed in the jumping profile Hidden Markov Model tool 22 to determine the subtype composition of the viral sample.…”

Section: Genotyping and Phylogeneticsmentioning

confidence: 99%

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

Msomi

Ndlovu

Giandhari

et al. 2019

Journal of Medical Virology

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Occult hepatitis B virus (HBV) infection (OBI) is defined as the presence of HBV DNA in the liver with or without detectable HBV DNA in the serum of individuals testing HBV surface antigen (HBsAg) negative using currently available assays. The prevalence of OBI among patients receiving hemodialysis (HD) treatment remains poorly characterized in South Africa despite the high prevalence of HBV. We sought to determine the prevalence of OBI in HD units in tertiary hospitals of KwaZulu‐Natal and to characterize the HBV S gene mutations potentially responsible for OBI. A cross‐sectional descriptive study of residual diagnostic plasma samples from 85 HBsAg‐negative patients receiving HD treatment was included. The PreS/S gene was amplified with a nested HBV polymerase chain reaction for downstream next‐generation sequencing, to determine the viral genotype and identify S gene mutations associated with OBI. Nine of the 85 samples had OBI, based on detectable HBV DNA. The point prevalence of OBI was 10.6% (95% control interval: 5.5%‐19.1%). Phylogenetic analysis of the samples with OBI showed that all belonged to genotype A. Three (~33%) samples had mutations in the major hydrophilic region (MHR) within the S gene, three (~33%) had mutations within the S gene but outside the MHR, whilst the remaining three had no mutations observed. The prevalence of OBI in HBsAg‐negative patients undergoing HD was 10.6%, suggesting that OBI is a clinically significant problem in patients with HD in this region. The screening methods for HBV infection need to be revised to include nucleic acid testing.

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“…The centroids were then subjected to sequential BLAST searches against the NCBI nucleotide database and NCBI RefSeq viral protein database using BLASTn and BLASTx, respectively. C) The adaptor and quality trimmed data were uploaded to Genome Detective [42], a web base software that assembles viral genomes from NGS data. The software first groups reads into different buckets based on the proteins similarity to different viral hits.…”

Section: Data Analysis and Bioinformatics Pipelinesmentioning

confidence: 99%

Non-invasive surveys of mammalian viruses using environmental DNA

Alfano

Dayaram

Axtner

et al. 2020

Preprint

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SummaryEnvironmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence.HighlightsEnvironmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for virusesA comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversityLeech blood meal host determination and viruses identified were congruentViruses determined from water correlated with known and observed species visiting the water sourcesIn briefAlfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence.

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Genome Detective: an automated system for virus identification from high-throughput sequencing data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 305 publications

References 16 publications

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

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

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

Non-invasive surveys of mammalian viruses using environmental DNA

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