About: Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses

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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	Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses
Creator	Wang, Zheng Lin, Baochuan Tibbetts, Clark Kidd, Carolyn Malanoski, Anthony Stenger, David Blaney, Kate Long, Nina Thach, Dzung
Source	Medline; PMC
abstract	BACKGROUND: Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. RESULTS: Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. CONCLUSION: This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
has issue date	2008-12-01(xsd:dateTime)
bibo:doi	10.1186/1471-2164-9-577
bibo:pmid	19046445
has license	cc-by
sha1sum (hex)	9693080ead2c95fe79e8bf077637b5585cac664f
schema:url	https://doi.org/10.1186/1471-2164-9-577
resource representing a document's title	Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses
has PubMed Central identifier	PMC2607299
has PubMed identifier	19046445
schema:publication	BMC Genomics
resource representing a document's body	covid:9693080ead2c95fe79e8bf077637b5585cac664f#body_text
is schema:about of	named entity 'TYPING' named entity 'MICROARRAY PROBE DESIGN' named entity 'BUT' named entity 'PARTICULAR' named entity 'CHALLENGE' covid:arg/9693080ead2c95fe79e8bf077637b5585cac664f named entity 'RHINOVIRUSES' named entity 'CAUSES' named entity 'HIGH CONFIDENCE' named entity 'DIVERSE' named entity 'POTENTIAL' named entity 'RESPIRATORY PATHOGENS' named entity 'VIRUSES' named entity 'DIVERSE' named entity 'PATHOGEN' named entity 'GLOBAL' named entity 'DIFFICULT' named entity 'HUMAN' named entity 'GENOMICS' named entity 'RESEQUENCING' named entity 'BMC' named entity 'RESPIRATORY ILLNESS' named entity 'RESEQUENCING' named entity 'BACKGROUND' named entity 'DEMONSTRATED' named entity 'DIFFERENTIAL DIAGNOSIS' named entity 'DESIGN' named entity 'RHINOVIRUSES' named entity 'PATHOGENS' named entity 'METHOD' named entity 'IMPACT' named entity 'FRI' named entity 'FREQUENT' named entity 'FEBRILE' named entity 'LACKING' named entity 'PUBLIC HEALTH' named entity 'SIMULTANEOUSLY' named entity 'PROBES' named entity 'VIRUSES' named entity 'ISSUE' named entity 'ECONOMICS' named entity 'DETECTION' named entity 'HIGH' named entity 'HUMAN' named entity 'ENTEROVIRUSES' named entity 'ENTEROVIRUSES' named entity 'MICROARRAY TECHNOLOGY' named entity 'SELECT' named entity 'gene sequences' named entity '5'UTR' named entity 'assay' named entity 'genetically diverse' named entity 'differential diagnosis' named entity 'Pathogen' named entity 'Febrile' named entity 'public health' named entity 'HRV' named entity 'BMC Genomics' named entity 'microarray' named entity '5'UTR' named entity '5'UTR' named entity '5'UTR' named entity 'hybridization' named entity 'American Type Culture Collection' named entity 'genetic diversity' named entity 'pathogens' named entity 'RPM' named entity 'ATCC' named entity '5'UTR' named entity 'serotypes' named entity 'serotype' named entity 'VP1' named entity 'nucleotide sequence'

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