About: Rhinovirus identification by BglI digestion of picornavirus RT-PCR amplicons

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About: Rhinovirus identification by BglI digestion of picornavirus RT-PCR amplicons 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
has title	Rhinovirus identification by BglI digestion of picornavirus RT-PCR amplicons
Creator	Sanderson, G Johnston, S Papadopoulos, N Hunter, J Meyer, J
topic	covid:a4680d5422c0ce9ae5d8e189fc2b2408d371a408#this
Source	Elsevier; Medline; PMC
abstract	Abstract Rhinoviruses are the main cause of the common cold and precipitate the majority of asthma exacerbations. RT-PCR followed by internal probe hybridisation or Southern blotting, or nested PCRs are currently the most sensitive methods for their identification. However, none of the published techniques can differentiate satisfactorily rhinoviruses from other picornaviruses. Examination of the restriction maps of sequenced rhinoviruses, revealed a highly conserved BglI restriction site (GCCnnnnnGGC), located exactly in the middle of the 380-bp amplicon generated with the OL26–OL27 primer pair, which has been used extensively in the past to identify picornaviruses. Such a site was either not present, or positioned differently in other picornaviruses of known sequence. It was, therefore, considered that digestion of rhinovirus amplicons with this enzyme would result in two equal length fragments, generating a single 190-bp band in gel electrophoresis. In contrast, either one undigested 380-bp band or a double-band pattern would appear in amplicons from other picornaviruses. To test this hypothesis, Bgl digestions of OL26–OL27 amplicons from cultured and wild-type rhinoviruses, whose identity was confirmed by acid lability, as well as from echo, polio and coxsackie viruses were carried out. All rhinovirus samples were digested successfully generating single bands. Among the other picornaviruses, only 6.6% presented a single band pattern, while the rest were as predicted from the model. With a sensitivity of 100% and a specificity over 90%, the method described, which is rapid and remarkably easy to perform, can be used to distinguish rhinoviruses from other picornaviruses to a considerable extent.
has issue date	1999-07-31(xsd:dateTime)
bibo:doi	10.1016/s0166-0934(99)00045-2
bibo:pmid	10471027
has license	els-covid
sha1sum (hex)	a4680d5422c0ce9ae5d8e189fc2b2408d371a408
schema:url	https://doi.org/10.1016/s0166-0934%2899%2900045-2
resource representing a document's title	Rhinovirus identification by BglI digestion of picornavirus RT-PCR amplicons
has PubMed Central identifier	PMC7172259
has PubMed identifier	10471027
schema:publication	Journal of Virological Methods
resource representing a document's body	covid:a4680d5422c0ce9ae5d8e189fc2b2408d371a408#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/a4680d5422c0ce9ae5d8e189fc2b2408d371a408
is schema:about of	named entity 'gel electrophoresis' named entity 'result' named entity 'confirmed' named entity 'carried' named entity 'picornaviruses' named entity 'amplicons' named entity 'TO TEST' named entity 'NESTED' named entity 'ASTHMA EXACERBATIONS' named entity 'REVEALED' covid:arg/a4680d5422c0ce9ae5d8e189fc2b2408d371a408 named entity 'rapid' named entity 'pattern' named entity 'revealed' named entity 'fragments' named entity 'polio' named entity 'probe' named entity 'sensitive' named entity 'sensitivity' named entity 'rhinovirus' named entity 'acid' named entity 'pair' named entity 'coxsackie' named entity 'picornaviruses' named entity 'amplicons' named entity 'picornaviruses' named entity 'picornaviruses' named entity 'restriction site' named entity 'enzyme' named entity 'asthma exacerbations' named entity 'digestion' named entity 'rhinovirus' named entity 'precipitate' named entity 'picornavirus' named entity 'amplicons' named entity 'agarose gel' named entity 'viruses' named entity 'restriction site' named entity 'PCR' named entity 'rhinovirus' named entity 'amplicons' named entity 'fetal calf serum' named entity 'cDNA' named entity 'ethidium bromide' named entity 'clinical presentation' named entity 'asthma attacks' named entity 'enterovirus' named entity 'wild type' named entity 'infection' named entity 'PBS' named entity 'viruses' named entity 'sodium bicarbonate' named entity 'nested PCR' named entity 'viruses' named entity 'amplicon' named entity 'Electrophoresis' named entity 'enteroviruses' named entity 'serotypes' named entity 'digestion' named entity 'restriction fragment length polymorphism' named entity '37°C' named entity 'antigenic' named entity 'polioviruses' named entity 'amplicons' named entity 'Triton X-100' named entity 'picornaviruses' named entity 'upper respiratory infections' named entity 'asthma exacerbations' named entity 'reproducibility' named entity 'PCR' named entity 'pH 3' named entity 'Public Health Laboratory Service' named entity '37°C' named entity 'asthma exacerbations' named entity 'upper respiratory infections'

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