About: Reliable typing of MERS-CoV variants with a small genome fragment

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About: Reliable typing of MERS-CoV variants with a small genome fragment Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Reliable typing of MERS-CoV variants with a small genome fragment
Creator	Koopmans, Marion Reusken, Chantal Farag, Elmoubasher Alhajri, Mohd Mohran, Khaled Haagmans, Bart Al-Romaihi, Hamad Pas, Suzan Smits, Saskia Stalin Raj, V
topic	covid:534ed7010e58f80e4298a57981b1d01e5e992e99#this
source	Elsevier; Medline; PMC
abstract	BACKGROUND: Middle East Respiratory Syndrome coronavirus (MERS-CoV) is an emerging pathogen that causes lower respiratory tract infection in humans. Camels are the likely animal source for zoonotic infection, although exact transmission modes remain to be determined. Human-to-human transmission occurs sporadically. The wide geographic distribution of MERS-CoV among dromedary camels and ongoing transmissions to humans provides concern for the evolution of a MERS-CoV variant with efficient human-to-human transmission capabilities. Phylogenetic analysis of MERS-CoV has occurred by analysis of full-length genomes or multiple concatenated genome fragments, which is time-consuming, costly and limited to high viral load samples. OBJECTIVE: To develop a simple, reliable MERS-CoV variant typing assay to facilitate monitoring of MERS-CoV diversity in animals and humans. STUDY DESIGN: Phylogenetic analysis of presently known full-length MERS-CoV genomes was performed to identify genomic regions with sufficient phylogenetic content to allow reliable MERS-CoV variant typing. RT-PCR assays targeting these regions were designed and optimized. RESULTS: A reverse-transcription PCR assay for MERS-CoV targeting a 615 bp spike fragment provides a phylogenetic clustering of MERS-CoV variants comparable to that of full-length genomes. The detection limit corresponds to a cycle treshold value of ∼35 with standard upE real time PCR assays on RNA isolated from MERS-CoV EMC. Nasal swabs from RT-PCR positive camels (Ct values 12.9–32.2) yielded reliable sequence information in 14 samples. CONCLUSIONS: We developed a simple, reliable MERS-CoV variant typing assay which is crucial in monitoring MERS-CoV circulation in real time with relatively little investment on location.
has issue date	2014-12-15(xsd:dateTime)
bibo:doi	10.1016/j.jcv.2014.12.006
bibo:pmid	25728084
has license	no-cc
sha1sum (hex)	534ed7010e58f80e4298a57981b1d01e5e992e99
schema:url	https://doi.org/10.1016/j.jcv.2014.12.006
resource representing a document's title	Reliable typing of MERS-CoV variants with a small genome fragment
has PubMed Central identifier	PMC7106551
has PubMed identifier	25728084
schema:publication	J Clin Virol
resource representing a document's body	covid:534ed7010e58f80e4298a57981b1d01e5e992e99#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/534ed7010e58f80e4298a57981b1d01e5e992e99
is schema:about of	named entity 'VARIANTS' named entity 'camels' named entity 'The' named entity 'regions' named entity 'genomes' named entity 'MERS-CoV' named entity 'limited' named entity 'genomes' named entity 'Background' named entity 'genome' named entity 'ASSAY' named entity 'ZOONOTIC INFECTION' named entity 'CONTENT' named entity 'EXACT' named entity 'RELIABLE' named entity 'EFFICIENT' named entity 'PERFORMED' named entity 'SOURCE' named entity 'CAUSES' named entity 'EVOLUTION' named entity '32.2' named entity 'UPE' named entity 'DETERMINED' named entity 'EMC' named entity 'VALUES' covid:arg/534ed7010e58f80e4298a57981b1d01e5e992e99 named entity 'LOWER RESPIRATORY TRACT INFECTION' named entity 'VARIANT' named entity 'RESULTS' named entity 'TIME-CONSUMING' named entity 'SPORADICALLY' named entity 'KNOWN' named entity 'CYCLE' named entity 'WIDE' named entity 'TO IDENTIFY' named entity 'RNA' named entity 'ONGOING' named entity '615' named entity 'LOCATION' named entity 'ANALYSIS' named entity 'PCR POSITIVE' named entity 'PRESENTLY' named entity 'HUMAN' named entity 'SAMPLES' named entity 'THESE' named entity 'MERS-COV' named entity 'SPIKE' named entity 'LENGTH' named entity 'SIMPLE' named entity 'PROVIDES' named entity 'STANDARD' named entity 'CAMELS' named entity 'ANIMALS' named entity 'HUMANS' named entity 'DROMEDARY' named entity 'REVERSE-TRANSCRIPTION' named entity 'LIMITED' named entity 'INVESTMENT' named entity 'GEOGRAPHIC DISTRIBUTION' named entity 'CONCLUSIONS' named entity 'ISOLATED' named entity 'SMALL' named entity 'HIGH' named entity 'OCCURRED' named entity 'REGIONS' named entity 'NASAL SWABS' named entity 'FRAGMENT' named entity 'EMERGING PATHOGEN' named entity 'GENOMIC' named entity 'CIRCULATION'

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