About: Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses

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About: Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses
Creator	Zlateva, Kalina Lauber, Chris Spaan, Willy Gorbalenya, Alexander Claas, Eric Crusio, Kelly Kravchenko, Alexander Leontovich, Andrey
Source	Elsevier; Medline; PMC
abstract	The ssRNA+ family Coronaviridae includes two subfamilies prototyped by coronaviruses and toroviruses that cause respiratory and enteric infections. To facilitate the identification of new distantly related members of the family Coronaviridae, we have developed a molecular assay with broad specificity. The consensus-degenerated hybrid oligonucleotide primer (CODEHOP) strategy was modified to design primers targeting the most conserved motifs in the RNA-dependent RNA polymerase locus. They were evaluated initially on RNA templates from virus-infected cells using a two-step RT-PCR protocol that was further advanced to a one-step assay. The sensitivity of the assay ranged from 10(2) to 10(6) and from 10(5) to 10(9) RNA copy numbers for individual corona-/torovirus templates when tested, respectively, with and without an excess of RNA from human cells. This primer set compared to that designed according to the original CODEHOP rules showed 10–10(3) folds greater sensitivity for 5 of the 6 evaluated corona-/torovirus templates. It detected 57% (32 of 56) of the respiratory specimens positive for 4 human coronaviruses, as well as stool specimens positive for a bovine torovirus. The high sensitivity and broad virus range of this assay makes it suitable for screening biological specimens in search for new viruses of the family Coronaviridae.
has issue date	2011-08-11(xsd:dateTime)
bibo:doi	10.1016/j.jviromet.2011.08.005
bibo:pmid	21864579
has license	no-cc
sha1sum (hex)	f558e3046f1472abb3df752a61adc9215467718f
schema:url	https://doi.org/10.1016/j.jviromet.2011.08.005
resource representing a document's title	Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses
has PubMed Central identifier	PMC7112876
has PubMed identifier	21864579
schema:publication	J Virol Methods
resource representing a document's body	covid:f558e3046f1472abb3df752a61adc9215467718f#body_text
is schema:about of	named entity 'DETECTION' named entity 'CONSENSUS' named entity 'biological specimens' named entity 'locus' named entity 'respiratory' named entity 'screening' named entity 'positive' named entity 'This' named entity 'viruses' named entity 'advanced' named entity 'respiratory' named entity 'sensitive' named entity 'SENSITIVE' named entity 'RNA' named entity 'RNA-DEPENDENT RNA POLYMERASE' named entity 'HAVE' named entity 'DEGENERATE' named entity 'RULES' named entity 'GREATER' named entity 'BROAD' named entity 'PROTOCOL' named entity 'VIRUS' named entity 'DEGENERATED' named entity 'INFECTED' named entity 'SPECIMENS' named entity 'FOLDS' named entity 'OLIGONUCLEOTIDE PRIMER' named entity 'COPY' named entity 'ENTERIC' named entity 'SET' named entity 'DESIGN' named entity 'MODIFIED' named entity 'MEMBERS' named entity 'HUMAN' named entity 'BOVINE TOROVIRUS' named entity 'INITIALLY' named entity 'SCREENING' covid:arg/f558e3046f1472abb3df752a61adc9215467718f named entity 'VALIDATION' named entity 'TEMPLATES' named entity 'TARGETING' named entity 'STEP' named entity 'ORIGINAL' named entity 'PRIMER' named entity 'SSRNA' named entity 'EVALUATED' named entity 'SUITABLE' named entity 'STRATEGY' named entity 'HYBRID' named entity 'SENSITIVITY' named entity 'ASSAY' named entity 'HUMAN CELLS' named entity 'POSITIVE FOR' named entity 'RESPIRATORY' named entity 'HIGH SENSITIVITY' named entity 'INDIVIDUAL' named entity 'DESIGN' named entity 'OLIGONUCLEOTIDE' named entity 'TOROVIRUSES' named entity 'BROAD' named entity 'NEW' named entity 'BIOLOGICAL' named entity 'CAUSE' named entity 'RELATED' named entity 'PRIMERS' named entity 'CORONA' named entity 'HYBRID' named entity 'FAMILY CORONAVIRIDAE' named entity 'RT-PCR' named entity 'TOROVIRUSES' named entity 'INCLUDES' named entity 'DETECTED' named entity 'ADVANCED' named entity 'TESTED'

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