About: Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010

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

About: Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013 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	Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013
Creator	Lon, Chanthap Saunders, David Fernandez, Stefan Klungthong, Chonticha Manasatienkij, Wudtichai Thaisomboonsuk, Butsaya Yoon, In-Kyu Simasathien, Sriluck Mark, John Ajariyakhajorn, Chuanpis Buddhari, Darunee Chinnawirotpisan, Piyawan Phonpakobsin, Thipwipha Rutvisuttinunt, Wiriya Wangchuk, Sonam Jarman, Richard Alera, P Macareo, Louis Shrestha, Sanjaya Theresa, Maria Velasco, S
Source	Elsevier; Medline; PMC
abstract	BACKGROUND: Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010–2013. Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. OBJECTIVE: To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. STUDY DESIGN: The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2–26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. RESULTS: WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%).
has issue date	2017-07-14(xsd:dateTime)
bibo:doi	10.1016/j.jcv.2017.07.004
bibo:pmid	28779659
has license	no-cc
sha1sum (hex)	c2033bc278a4005808e5338b3a0ffbdfdb92411b
schema:url	https://doi.org/10.1016/j.jcv.2017.07.004
resource representing a document's title	Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013
has PubMed Central identifier	PMC7106496
has PubMed identifier	28779659
schema:publication	J Clin Virol
resource representing a document's body	covid:c2033bc278a4005808e5338b3a0ffbdfdb92411b#body_text
is schema:about of	named entity 'INFLUENZA-LIKE ILLNESS' named entity 'USE OF' named entity 'INCONCLUSIVE' named entity 'BACKGROUND' named entity 'RESPIRATORY PATHOGENS' named entity 'FINDINGS' named entity 'GENERALLY' named entity 'SEROLOGICAL TESTING' named entity 'LABORATORY' named entity 'LEADS' named entity 'TRADITIONAL' named entity 'TESTING' named entity 'OCCASIONALLY' named entity 'CLINICAL INFORMATION' named entity 'LIMITED' named entity 'REVEALS' named entity 'REPRESENT' named entity 'DETERMINATION' named entity 'PRESENCE OF' named entity 'NEXT-GENERATION SEQUENCING' named entity 'EAST ASIA' named entity 'ENTEROVIRUSES' named entity 'MOLECULAR' named entity 'INCREASING' named entity 'PUBLIC HEALTH' named entity 'OUTBREAKS' named entity 'RETROSPECTIVE' named entity 'THREAT' named entity 'RESPIRATORY SAMPLES' named entity 'SOUTH' named entity 'ACUTE' named entity 'COLLECTED' named entity 'Background' named entity 'traditional' named entity 'occasionally' named entity 'molecular' named entity 'Emerging' named entity 'laboratory' named entity 'Enteroviruses' named entity 'leads' named entity 'IFV' named entity 'serotypes' named entity 'influenza-like illness' named entity 'viruses' named entity 'Viral' named entity 'Sanger' named entity 'upper respiratory' named entity 'PCR tests' named entity 'subclinical' named entity 'HSV-1' named entity 'BLASTn' named entity 'host cells' named entity 'Agilent' named entity 'bioinformatics' named entity 'viruses' named entity 'Thailand' named entity 'PCR' named entity 'HEp-2' named entity 'HSV-1' named entity 'virus' named entity 'Philippines'

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