About: Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples
Creator	Liu, Lei Ma, Xuejun Zhang, Yanjun Li, Junping Lou, Xiuyu Mao, Haiyan Pan, Junhang Shu, Yan Tang, Hongfeng Yan, Hao Zhang, Dan Zhao, Yun Chen, Jiang
Source	Medline; PMC
abstract	BACKGROUND: Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly. RESULTS: In this study, we performed qRT-PCR and viral metagenomic analysis of the extraction efficiency of four commonly used Qiagen extraction kits: QIAamp Viral RNA Mini Kit (VRMK), QIAamp MinElute Virus Spin Kit (MVSK), RNeasy Mini Kit (RMK), and RNeasy Plus Micro Kit (RPMK), using a mixed respiratory clinical sample without any pre-treatment. This sample contained an adenovirus (ADV), influenza virus A (Flu A), human parainfluenza virus 3 (PIV3), human coronavirus OC43 (OC43), and human metapneumovirus (HMPV). The quantity and quality of the viral extracts were significantly different among these kits. The highest threshold cycle(Ct)values for ADV and OC43 were obtained by using the RPMK. The MVSK had the lowest Ct values for ADV and PIV3. The RMK revealed the lowest detectability for HMPV and PIV3. The most effective rate of NGS data at 67.47% was observed with the RPMK. The other three kits ranged between 12.1–26.79% effectiveness rates for the NGS data. Most importantly, compared to the other three kits the highest proportion of non-host reads was obtained by the RPMK. The MVSK performed best with the lowest Ct value of 20.5 in the extraction of ADV, while the RMK revealed the best extraction efficiency by NGS analysis. CONCLUSIONS: The evaluation of viral nucleic acid extraction efficiency is different between NGS and qRT-PCR analysis. The RPMK was most applicable for the metagenomic analysis of viral RNA and enabled more sensitive identification of the RNA virus genome in respiratory clinical samples. In addition, viral RNA extraction kits were also applicable for metagenomic analysis of the DNA virus. Our results highlighted the importance of nucleic acid extraction kit selection, which has a major impact on the yield and number of viral reads by NGS analysis. Therefore, the choice of extraction method for a given viral pathogen needs to be carefully considered. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5152-5) contains supplementary material, which is available to authorized users.
has issue date	2018-10-25(xsd:dateTime)
bibo:doi	10.1186/s12864-018-5152-5
bibo:pmid	30359242
has license	cc-by
sha1sum (hex)	9fd83230962e678e8ec4d5dffee0bb431e19c2d9
schema:url	https://doi.org/10.1186/s12864-018-5152-5
resource representing a document's title	Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples
has PubMed Central identifier	PMC6202819
has PubMed identifier	30359242
schema:publication	BMC Genomics
resource representing a document's body	covid:9fd83230962e678e8ec4d5dffee0bb431e19c2d9#body_text
is schema:about of	named entity 'specimens' named entity 'viral' named entity 'extracts' named entity 'extraction' named entity 'efficiency' named entity 'ADV' named entity 'RNA' named entity 'sample' named entity 'Our' named entity 'metagenomic analysis' named entity 'Kit' named entity 'CLINICAL' named entity 'EXTRACTION METHODS' covid:arg/9fd83230962e678e8ec4d5dffee0bb431e19c2d9 named entity 'EFFECTIVENESS' named entity 'QUALITY' named entity 'A MAJOR' named entity 'INFLUENZA VIRUS A' named entity 'SAMPLES' named entity 'CLINICAL' named entity 'HUMAN METAPNEUMOVIRUS' named entity 'SPECIMENS' named entity 'OC43' named entity 'MIXED' named entity 'VIRAL RNA EXTRACTION' named entity 'CONCLUSIONS' named entity 'IDENTIFICATION' named entity 'RESULTS' named entity 'CONSIDERED' named entity 'VIRAL' named entity 'STUDY' named entity 'LOWEST' named entity '20.5' named entity 'ENRICHMENT' named entity 'USING' named entity 'BEST' named entity 'NEXT-GENERATION SEQUENCING' named entity 'SPIN' named entity 'QIAGEN' named entity 'VIRUS' named entity 'NUMBER OF' named entity 'MINI' named entity 'AMPLIFICATION' named entity 'VIRAL RNA' named entity 'GENOME' named entity 'ADV' named entity 'QUANTITY' named entity 'EXTRACTS' named entity 'SELECTED' named entity 'PIV3' named entity 'ADENOVIRUS' named entity 'EXTRACTION' named entity 'SELECTION' named entity 'CHALLENGES' named entity 'TREATMENT' named entity 'DNA VIRUS' named entity 'THESE' named entity 'HUMAN PARAINFLUENZA VIRUS 3' named entity 'OBSERVED' named entity 'HAVE' named entity 'USED' named entity 'OUR' named entity 'QRT-PCR' named entity 'ADDITION' named entity 'EVALUATE' named entity 'ANALYSIS' named entity 'CT VALUE' named entity 'MICRO' named entity 'CHOICE'

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