About: An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection

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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	An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection
Creator	Wang, Jing Canuti, Marta Liu, Bo Su, Haoxiang Dong, Jie Sun, Lilian Yang, Fan Li, Li Zhang, Ting Yang, Li, Sun Garcia, Manuel Shao, Nan Cn, Fan Martinez-Hernandez, Francisco Zhou, Siyu
Source	Medline; PMC
abstract	Respiratory virus infections are one of the major causes of acute respiratory disease or exacerbation of chronic obstructive pulmonary disease (COPD). However, next-generation sequencing has not been used for routine viral detection in clinical respiratory samples owing to its sophisticated technology. Here, several pharyngeal samples with COPD were collected to enrich viral particles using an optimized method (M3), which involved M1 with centrifugation, filtration, and concentration, M2 (magnetic beads) combined with mixed nuclease digestion, and M4 with no pretreatment as a control. Metagenomic sequencing and bioinformatics analyses showed that the M3 method for viral enrichment was superior in both viral sequencing composition and viral taxa when compared to M1, M2, and M4. M3 acquired the most viral reads and more complete sequences within 15-h performance, indicating that it might be feasible for viral detection in multiple respiratory samples in clinical practice. Based on sequence similarity analysis, 12 human viruses, including nine Anelloviruses and three coronaviruses, were characterized. Coronavirus OC43 with the largest number of viral reads accounted for nearly complete (99.8%) genome sequences, indicating that it may be a major viral pathogen involved in exacerbation of COPD.
has issue date	2020-07-10(xsd:dateTime)
bibo:doi	10.3389/fmicb.2020.01552
bibo:pmid	32754134
has license	cc-by
sha1sum (hex)	b53f98a28198d869f567e568e7b121e25849cc9d
schema:url	https://doi.org/10.3389/fmicb.2020.01552
resource representing a document's title	An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection
has PubMed Central identifier	PMC7366072
has PubMed identifier	32754134
schema:publication	Front Microbiol
resource representing a document's body	covid:b53f98a28198d869f567e568e7b121e25849cc9d#body_text
is schema:about of	named entity 'sequences' named entity 'chronic obstructive pulmonary disease (COPD)' named entity 'superior' named entity 'mixed' named entity 'genome' named entity 'pharyngeal' named entity 'composition' named entity 'SUPERIOR' named entity 'VIRAL DETECTION' named entity 'VIRAL SEQUENCING' named entity 'PERFORMANCE' named entity 'ONE OF' named entity 'COMBINED' named entity 'ROUTINE' named entity 'READS' named entity 'ACQUIRED' named entity 'CONTROL' named entity 'SAMPLES' named entity 'nuclease' named entity 'reads' named entity 'viral' named entity 'complete' named entity 'viral' named entity 'enrich' named entity 'magnetic' named entity 'sequencing' named entity 'coronaviruses' named entity 'taxa' named entity 'Coronavirus' named entity 'taxa' named entity 'Anelloviruses' named entity 'nuclease' named entity 'COPD' named entity 'virus infections' named entity 'combined' named entity 'taxonomic' named entity 'polymerase chain reaction' named entity 'HCov-OC43' named entity 'genus' named entity 'virus' named entity 'Capital Medical University' named entity '99.9%' named entity 'metagenomic data' named entity 'RT-PCR' named entity 'human reference' named entity 'nuclease' named entity 'DNase' named entity 'coronaviruses' named entity 'Inoviridae' named entity 'NGS' named entity 'nucleotide sequences' named entity 'Beijing Union Medical College' named entity 'cDNA' named entity 'LCA' named entity 'NGS' named entity 'lowest common ancestor' named entity 'polyvinylidene difluoride' named entity 'Paramyxoviruses' named entity 'genomes' named entity 'transcriptome' named entity 'virus' named entity 'primers' named entity 'Orthomyxoviruses' named entity 'Assay' named entity 'Herpesviridae' named entity 'Picornaviridae'

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