About: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
Creator	Balmaseda, A Nl, Harris, E Skewes-Cox, P Stenglein, M
Source	PMC
abstract	Dengue virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness.
has issue date	2012-02-07(xsd:dateTime)
bibo:doi	10.1371/journal.pntd.0001485
bibo:pmid	22347512
has license	cc-by
sha1sum (hex)	9692bb55e1e2eec083333ee2139137e6ddf3a4d8
schema:url	https://doi.org/10.1371/journal.pntd.0001485
resource representing a document's title	Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
has PubMed Central identifier	PMC3274504
has PubMed identifier	22347512
schema:publication	PLoS Negl Trop Dis
resource representing a document's body	covid:9692bb55e1e2eec083333ee2139137e6ddf3a4d8#body_text
is schema:about of	named entity 'CASES' named entity 'ANELLOVIRIDAE' named entity 'ADDRESS' named entity 'ILLNESSES' named entity 'DIAGNOSTIC' named entity 'MILLION' named entity 'APPROACHES' named entity 'GENERATING' named entity 'SEQUENCE' named entity 'READS' named entity 'PATHOGEN' named entity 'VIRAL' named entity 'PATHOGEN DETECTION' named entity 'DEEP SEQUENCING' named entity 'TO DETECT' named entity 'DATABASE' named entity 'DEEP' named entity 'LIKE' named entity 'SIMILARITY' named entity 'CASES' named entity 'FLAVIVIRIDAE' named entity 'NEGATIVE' named entity 'PATIENTS' named entity 'ANNUALLY' named entity 'QUALITY' named entity 'BARCODING' named entity 'MICROARRAYS' named entity 'INFECTS' named entity 'TROPICAL' named entity 'SERA' named entity 'NON-' named entity 'INFECTIOUS AGENT' named entity 'SPECIMENS' named entity 'MULTIPLE' named entity 'BIOINFORMATIC' named entity 'FEBRILE ILLNESS' named entity 'VIRUS IDENTIFICATION' named entity 'USING' named entity 'TOOLS' named entity 'USED' named entity 'LOW' named entity 'BUT' named entity 'TESTING' named entity 'DISEASE' named entity 'STRATEGY' named entity 'MICROARRAY' named entity 'VIRUSES' named entity 'INCLUDED' named entity 'SAMPLES' named entity 'NICARAGUAN' named entity 'SUBSEQUENT' named entity 'TO REMOVE' named entity 'SAMPLE' named entity 'TO CHARACTERIZE' named entity 'SYMPTOMS' named entity 'IDENTICAL' named entity 'FILTERING' named entity 'DEEP SEQUENCING' named entity 'PRESENT' named entity 'STUDY' named entity 'MAJORITY' named entity 'UTILITY' named entity 'TROPICAL' named entity 'SIMULTANEOUSLY' named entity 'HERPESVIRIDAE' named entity 'HUMAN' named entity 'ACCURACY' named entity 'CHALLENGES' named entity 'FAMILIES' named entity '100' named entity 'WORLDWIDE' named entity 'CIRCOVIRIDAE' named entity 'PARVOVIRIDAE' named entity 'PEOPLE' named entity 'CONTAINED' named entity 'PREVIOUSLY' named entity 'SPEED'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software