About: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition

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About: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition 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	Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition
Creator	Hindiyeh, Musa Mendelson, Ella Cohen, Dani Muhsen, Khitam Sofer, Danit Shulman, Lester
topic	covid:08dd1169c7aa45621e5f48bf6246b049e071e445#this
Source	PMC
abstract	Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system’s lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples.
has issue date	2012-07-16(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0039455
bibo:pmid	22815706
has license	cc-by
sha1sum (hex)	08dd1169c7aa45621e5f48bf6246b049e071e445
schema:url	https://doi.org/10.1371/journal.pone.0039455
resource representing a document's title	Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition
has PubMed Central identifier	PMC3397973
has PubMed identifier	22815706
schema:publication	PLoS One
resource representing a document's body	covid:08dd1169c7aa45621e5f48bf6246b049e071e445#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/08dd1169c7aa45621e5f48bf6246b049e071e445
is schema:about of	named entity 'SYSTEMS' named entity 'enterovirus' named entity 'spiked' named entity 'systems' named entity 'suspension' named entity 'suspensions' named entity 'good' named entity 'Automatic' named entity 'interfere' named entity 'thresholds' named entity 'extracted' named entity 'RT-PCR' named entity 'Inhibition' named entity 'USING' named entity 'STOOL' named entity 'EXOGENOUS' named entity 'REAL-TIME' named entity 'CONTAINING' named entity 'EXTENT' named entity 'CO-PURIFICATION' named entity 'PREDICTOR' named entity 'SUSPENSION' named entity 'IS A' named entity 'STOOL' named entity 'EXOGENOUS' named entity 'RT-PCR' named entity 'SYSTEMS' named entity 'EVALUATION' named entity 'DIAGNOSTIC' named entity 'EXTRACTOR' named entity 'SECOND' named entity '28A' named entity 'DETERMINED' named entity 'CYCLE' named entity 'UNKNOWN' named entity 'LC2' named entity 'SYSTEM' named entity 'GROUP' named entity 'SUITABLE' named entity 'INTACT' named entity 'INHIBITIONS' named entity 'PROVIDED' named entity 'INHIBITORS' named entity 'EXTRACTION METHODS' named entity 'EXTERNAL' named entity 'USING' named entity 'EVALUATED' named entity 'CONTROL' named entity 'ENTEROVIRUS' named entity '2859' named entity 'KIT' named entity 'SAMPLES' named entity 'IDENTIFIED' named entity 'COLIPHAGE' named entity 'EFFICIENCY' named entity 'MAGNA' named entity 'EXTRACTION' named entity 'EXTRACTS' named entity 'CONCLUSION' named entity '287' named entity 'VIRAL RNA' named entity 'USED' named entity 'REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION' named entity 'MINI' named entity 'DIFFERENT' named entity 'INHIBITION' named entity 'RNA' named entity 'SUSPENSIONS' named entity 'CONTROL' named entity 'VIRUS PARTICLES' named entity 'MS2' named entity 'COLIPHAGE' named entity 'DIFFERENT' named entity 'RT-PCR'

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