About: Comparative Evaluation of Commercially Available Manual and Automated Nucleic Acid Extraction Methods for Rotavirus RNA Detection in Stool

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Comparative Evaluation of Commercially Available Manual and Automated Nucleic Acid Extraction Methods for Rotavirus RNA Detection in Stool
Creator	Kamili, Shifaq Gautam, Rashi Kerin, Tara Bowen, Michael Esona, Mathew Mcdonald, Sharla
source	Elsevier; Medline; PMC
abstract	Rotaviruses are a major cause of viral gastroenteritis in children. For accurate and sensitive detection of rotavirus RNA from stool samples by reverse transcription-polymerase chain reaction (RT-PCR), the extraction process must be robust. However, some extraction methods may not remove the strong RT-PCR inhibitors known to be present in stool samples. The objective of this study was to evaluate and compare the performance of six extraction methods used commonly for extraction of rotavirus RNA from stool, which have never been formally evaluated: the MagNA Pure Compact, KingFisher Flex and NucliSENS® easyMAG® instruments, the NucliSENS® miniMAG® semi-automated system, and two manual purification kits, the QIAamp Viral RNA kit and a modified RNaid® kit. Using each method, total nucleic acid or RNA was extracted from eight rotavirus-positive stool samples with enzyme immunoassay optical density (EIA OD) values ranging from 0.176 to 3.098. Extracts prepared using the MagNA Pure Compact instrument yielded the most consistent results by qRT-PCR and conventional RT-PCR. When extracts prepared from a dilution series were extracted by the 6 methods and tested, rotavirus RNA was detected in all samples by qRT-PCR but by conventional RT-PCR testing, only the MagNA Pure Compact and KingFisher Flex extracts were positive in all cases. RT-PCR inhibitors were detected in extracts produced with the QIAamp Viral RNA Mini kit. The findings of this study should prove useful for selection of extraction methods to be incorporated into future rotavirus detection and genotyping protocols.
has issue date	2013-12-01(xsd:dateTime)
bibo:doi	10.1016/j.jviromet.2013.08.023
bibo:pmid	24036075
has license	green-oa
sha1sum (hex)	988eb76f99bdb20992a35c3e9e5bdcd5105d58e5
schema:url	https://doi.org/10.1016/j.jviromet.2013.08.023
resource representing a document's title	Comparative Evaluation of Commercially Available Manual and Automated Nucleic Acid Extraction Methods for Rotavirus RNA Detection in Stool
has PubMed Central identifier	PMC4603280
has PubMed identifier	24036075
schema:publication	Journal of Virological Methods
resource representing a document's body	covid:988eb76f99bdb20992a35c3e9e5bdcd5105d58e5#body_text
is schema:about of	named entity 'remove' named entity 'RT-PCR' named entity 'accurate' named entity 'extracts' named entity 'objective' named entity 'Flex' named entity 'protocols' named entity 'commonly' named entity 'dilution series' named entity 'genotyping' named entity 'acid' named entity 'A MAJOR' named entity 'FUTURE' named entity 'VIRAL GASTROENTERITIS' named entity 'NUCLEIC ACID' named entity 'NEVER' named entity 'STUDY' named entity 'STOOL' named entity 'CAUSE' named entity 'OBJECTIVE' named entity 'OPTICAL DENSITY' named entity 'CHILDREN' named entity 'USED' named entity 'MAGNA' named entity 'ROTAVIRUSES' named entity 'EXTRACTED' named entity 'CASES' named entity 'AUTOMATED' named entity 'PERFORMANCE' named entity 'GENOTYPING' named entity 'MANUAL' named entity 'DETECTION' named entity 'POSITIVE' named entity 'INHIBITORS' named entity 'EXTRACTION' named entity 'STOOLS' named entity 'AVAILABLE' named entity 'DETECTION' named entity 'ROTAVIRUS RNA' named entity 'NUCLEIC ACID EXTRACTION' named entity 'COMPARATIVE EVALUATION' named entity 'METHODS' named entity 'COMPARE' named entity 'POLYMERASE CHAIN REACTION' named entity 'USING' named entity 'ROTAVIRUS DETECTION' named entity 'DETECTED' named entity 'PREPARED' named entity 'FISHER' named entity 'ACCURATE' named entity 'USEFUL' named entity 'SAMPLES' named entity 'PROCESS' named entity 'SYSTEM' named entity 'VALUES' named entity 'SELECTION' named entity 'BUT' named entity 'FLEX' named entity 'PURE' named entity 'CONVENTIONAL' named entity 'EVALUATE' named entity 'INSTRUMENT' named entity 'INSTRUMENTS' named entity 'RT-PCR' named entity 'EXTRACTION METHODS' named entity 'REMOVE' named entity 'ENZYME IMMUNOASSAY' named entity 'EXTRACTION METHODS' named entity 'VIRAL RNA' named entity 'PCR' named entity 'COMPACT' named entity 'TESTING' named entity 'PURIFICATION' named entity 'EXTRACTS' named entity 'CONSISTENT' named entity 'KING'

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