Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Front Microbiol
2023 Jan 01;14:1248323. doi: 10.3389/fmicb.2023.1248323.
Show Gene links
Show Anatomy links
Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals.
Vigil K
,
Aw TG
.
???displayArticle.abstract???
INTRODUCTION: Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals.
METHODS: In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals.
RESULTS: Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species.
DISCUSSION: Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.
Adewale,
Will long-read sequencing technologies replace short-read sequencing technologies in the next 10 years?
2020, Pubmed
Adewale,
Will long-read sequencing technologies replace short-read sequencing technologies in the next 10 years?
2020,
Pubmed
Allen,
Single virus genomics: a new tool for virus discovery.
2011,
Pubmed
Bacqué-Cazenave,
Social harassment induces anxiety-like behaviour in crayfish.
2017,
Pubmed
Bettarel,
A comparison of methods for counting viruses in aquatic systems.
2000,
Pubmed
Bieringer,
Experimental adaptation of wild-type canine distemper virus (CDV) to the human entry receptor CD150.
2013,
Pubmed
Bochow,
First complete genome of an Ambidensovirus; Cherax quadricarinatus densovirus, from freshwater crayfish Cherax quadricarinatus.
2015,
Pubmed
,
Echinobase
Bogomolni,
Saxitoxin increases phocine distemper virus replication upon in-vitro infection in harbor seal immune cells.
2016,
Pubmed
Bonny,
Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams.
2021,
Pubmed
Bossart,
Marine mammals as sentinel species for oceans and human health.
2011,
Pubmed
Brancaccio,
MinION nanopore sequencing and assembly of a complete human papillomavirus genome.
2021,
Pubmed
Breitbart,
ICTV Virus Taxonomy Profile: Circoviridae.
2017,
Pubmed
Breitbart,
Genomic analysis of uncultured marine viral communities.
2002,
Pubmed
Briese,
Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis.
2015,
Pubmed
Brown,
Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing.
2021,
Pubmed
Burek,
Effects of climate change on Arctic marine mammal health.
2008,
Pubmed
Canova,
Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast.
2021,
Pubmed
Carbo,
Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness.
2020,
Pubmed
Carducci,
Epidemiological surveillance of human enteric viruses by monitoring of different environmental matrices.
2006,
Pubmed
Castinel,
Neonatal mortality in New Zealand sea lions (Phocarctos hookeri) at Sandy Bay, Enderby Island, Auckland Islands from 1998 to 2005.
2007,
Pubmed
Cebriá-Mendoza,
Exploring the Diversity of the Human Blood Virome.
2021,
Pubmed
Chen,
The Microbiome Structure of a Rice-Crayfish Integrated Breeding Model and Its Association with Crayfish Growth and Water Quality.
2022,
Pubmed
Chin,
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
2013,
Pubmed
Chin,
Phased diploid genome assembly with single-molecule real-time sequencing.
2016,
Pubmed
Chiu,
Viral pathogen discovery.
2013,
Pubmed
Clark,
Human sealpox resulting from a seal bite: confirmation that sealpox virus is zoonotic.
2005,
Pubmed
Cohen,
Divergent impacts of warming weather on wildlife disease risk across climates.
2020,
Pubmed
Compeau,
How to apply de Bruijn graphs to genome assembly.
2011,
Pubmed
Cotmore,
ICTV Virus Taxonomy Profile: Parvoviridae.
2019,
Pubmed
Crum,
Coliphages of the human urinary microbiota.
2023,
Pubmed
Dayaram,
Diverse small circular DNA viruses circulating amongst estuarine molluscs.
2015,
Pubmed
Dida,
Empirical evaluation of methods for de novo genome assembly.
2021,
Pubmed
Doszpoly,
Full genome sequence of a novel circo-like virus detected in an adult European eel Anguilla anguilla showing signs of cauliflower disease.
2014,
Pubmed
Duignan,
Phocine distemper virus: current knowledge and future directions.
2014,
Pubmed
Fire,
Comparison of during-bloom and inter-bloom brevetoxin and saxitoxin concentrations in Indian River Lagoon bottlenose dolphins, 2002-2011.
2020,
Pubmed
Flewelling,
Brevetoxicosis: red tides and marine mammal mortalities.
2005,
Pubmed
Fontenele,
Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil.
2019,
Pubmed
Garalde,
Highly parallel direct RNA sequencing on an array of nanopores.
2018,
Pubmed
Garcia-Heredia,
Benchmarking of single-virus genomics: a new tool for uncovering the virosphere.
2021,
Pubmed
Goldsmith,
Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes.
2021,
Pubmed
Griffin,
Torque teno virus: an improved indicator for viral pathogens in drinking waters.
2008,
Pubmed
Hamza,
Evaluation of pepper mild mottle virus, human picobirnavirus and Torque teno virus as indicators of fecal contamination in river water.
2011,
Pubmed
Haramoto,
Quantification and genotyping of torque teno virus at a wastewater treatment plant in Japan.
2008,
Pubmed
Haramoto,
A review on recent progress in the detection methods and prevalence of human enteric viruses in water.
2018,
Pubmed
Hayashida,
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing.
2019,
Pubmed
Hendrix,
Ice seals as sentinels for algal toxin presence in the Pacific Arctic and subarctic marine ecosystems.
2021,
Pubmed
Hewson,
Densovirus associated with sea-star wasting disease and mass mortality.
2014,
Pubmed
,
Echinobase
Hino,
Torque teno virus (TTV): current status.
2007,
Pubmed
Hsiao,
Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population.
2021,
Pubmed
Hu,
Next-generation sequencing technologies: An overview.
2021,
Pubmed
Huang,
Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing.
2021,
Pubmed
Huber,
Drug-sensitive reward in crayfish: an invertebrate model system for the study of SEEKING, reward, addiction, and withdrawal.
2011,
Pubmed
Idury,
A new algorithm for DNA sequence assembly.
1995,
Pubmed
Jackson,
Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin.
2020,
Pubmed
,
Echinobase
Jiang,
Transcriptome analysis of red swamp crawfish Procambarus clarkii reveals genes involved in gonadal development.
2014,
Pubmed
Jung,
Comparative Evaluation of Genome Assemblers from Long-Read Sequencing for Plants and Crops.
2020,
Pubmed
Kamath,
HINGE: long-read assembly achieves optimal repeat resolution.
2017,
Pubmed
Kang,
Densoviruses in oyster Crassostrea ariakensis.
2017,
Pubmed
,
Echinobase
Kolmogorov,
metaFlye: scalable long-read metagenome assembly using repeat graphs.
2020,
Pubmed
Kolmogorov,
Assembly of long, error-prone reads using repeat graphs.
2019,
Pubmed
Kono,
Nanopore sequencing: Review of potential applications in functional genomics.
2019,
Pubmed
Koren,
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
2017,
Pubmed
LaRocca,
Viral Shedding in Mice following Intravenous Adenovirus Injection: Impact on Biosafety Classification.
2023,
Pubmed
Lee,
Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis.
2021,
Pubmed
Lefebvre,
Detection of domoic acid in northern anchovies and California sea lions associated with an unusual mortality event.
1999,
Pubmed
Lefebvre,
Prevalence of algal toxins in Alaskan marine mammals foraging in a changing arctic and subarctic environment.
2016,
Pubmed
Li,
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
2016,
Pubmed
Li,
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.
2012,
Pubmed
Liu,
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes.
2022,
Pubmed
Lolomadze,
Constant companion: clinical and developmental aspects of torque teno virus infections.
2020,
Pubmed
Manni,
Detecting recombination in TT virus: a phylogenetic approach.
2002,
Pubmed
Martínez-Puchol,
Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals.
2022,
Pubmed
Martínez-Puchol,
Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens.
2020,
Pubmed
Miller,
Aggressive assembly of pyrosequencing reads with mates.
2008,
Pubmed
Munang'andu,
Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms.
2017,
Pubmed
Myers,
A whole-genome assembly of Drosophila.
2000,
Pubmed
Neill,
Genetic relatedness of the caliciviruses: San Miguel sea lion and vesicular exanthema of swine viruses constitute a single genotype within the Caliciviridae.
1995,
Pubmed
Noble,
Virus decay and its causes in coastal waters.
1997,
Pubmed
Patterson,
Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica.
2021,
Pubmed
Pevzner,
An Eulerian path approach to DNA fragment assembly.
2001,
Pubmed
Pop,
Bioinformatics challenges of new sequencing technology.
2008,
Pubmed
Pugh,
The Current State of Nanopore Sequencing.
2023,
Pubmed
Quick,
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
2017,
Pubmed
Roe,
Septicaemia and meningitis caused by infection of New Zealand sea lion pups with a hypermucoviscous strain of Klebsiella pneumoniae.
2015,
Pubmed
Roess,
Sealpox virus in marine mammal rehabilitation facilities, North America, 2007-2009.
2011,
Pubmed
Ruan,
Fast and accurate long-read assembly with wtdbg2.
2020,
Pubmed
Sakai,
Canine distemper virus associated with a lethal outbreak in monkeys can readily adapt to use human receptors.
2013,
Pubmed
Sanderson,
Unchartered waters: Climate change likely to intensify infectious disease outbreaks causing mass mortality events in marine mammals.
2020,
Pubmed
Saranathan,
Capturing Structural Variants of Herpes Simplex Virus Genome in Full Length by Oxford Nanopore Sequencing.
2022,
Pubmed
Siebert,
BACTERIAL MICROBIOTA IN HARBOR SEALS (PHOCA VITULINA) FROM THE NORTH SEA OF SCHLESWIG-HOLSTEIN, GERMANY, AROUND THE TIME OF MORBILLIVIRUS AND INFLUENZA EPIDEMICS.
2017,
Pubmed
Smith,
Calicivirus emergence from ocean reservoirs: zoonotic and interspecies movements.
1998,
Pubmed
Takahashi,
Identification of a new human DNA virus (TTV-like mini virus, TLMV) intermediately related to TT virus and chicken anemia virus.
2000,
Pubmed
Tavakoli Nick,
Occurrence and molecular characterization of Torque teno virus (TTV) in a wastewater treatment plant in Tehran.
2019,
Pubmed
Tørresen,
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
2019,
Pubmed
Vigil,
Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals.
2023,
Pubmed
Wang,
Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm.
2021,
Pubmed
Wang,
Microarray-based detection and genotyping of viral pathogens.
2002,
Pubmed
Wang,
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
2018,
Pubmed
Wang,
Viral discovery and sequence recovery using DNA microarrays.
2003,
Pubmed
Webster,
Conjunctivitis in human beings caused by influenza A virus of seals.
1981,
Pubmed
Webster,
Characterization of an influenza A virus from seals.
1981,
Pubmed
Wick,
Trycycler: consensus long-read assemblies for bacterial genomes.
2021,
Pubmed
Yahara,
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.
2021,
Pubmed
Yu,
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.
2023,
Pubmed
Zimin,
The MaSuRCA genome assembler.
2013,
Pubmed