Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection
Publication Date
May 25, 2017
Authors
Pierre H. H. Schneeberger, Joël F. Pothier, Andreas Bühlmann, Brion Duffy, et al
Volume
12
Issue
5
Pages
e0178195
DOI
https://dx.plos.org/10.1371/journal.pone.0178195
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0178195
Scopus
85019906733
Mendeley
http://www.mendeley.com/research/development-evaluation-bioinformatics-approach-designing-molecular-assays-viral-detection
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Mendeley | Further Information

{"title"=>"Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection", "type"=>"journal", "authors"=>[{"first_name"=>"Pierre H.H.", "last_name"=>"Schneeberger", "scopus_author_id"=>"56425762700"}, {"first_name"=>"Joël F.", "last_name"=>"Pothier", "scopus_author_id"=>"55796629973"}, {"first_name"=>"Andreas", "last_name"=>"Bühlmann", "scopus_author_id"=>"55073608300"}, {"first_name"=>"Brion", "last_name"=>"Duffy", "scopus_author_id"=>"7103040527"}, {"first_name"=>"Christian", "last_name"=>"Beuret", "scopus_author_id"=>"6602825110"}, {"first_name"=>"Jürg", "last_name"=>"Utzinger", "scopus_author_id"=>"7003667858"}, {"first_name"=>"Juèrg E.", "last_name"=>"Frey", "scopus_author_id"=>"55748868600"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"616372956", "pmid"=>"28542435", "doi"=>"10.1371/journal.pone.0178195", "issn"=>"19326203", "scopus"=>"2-s2.0-85019906733", "sgr"=>"85019906733", "isbn"=>"1111111111"}, "id"=>"f236b525-b455-38b2-b51d-9ce2c86d4de9", "abstract"=>"BACKGROUND Viruses belonging to the Flaviviridae and Bunyaviridae families show considerable genetic diversity. However, this diversity is not necessarily taken into account when developing diagnostic assays, which are often based on the pairwise alignment of a limited number of sequences. Our objective was to develop and evaluate a bioinformatics workflow addressing two recurrent issues of molecular assay design: (i) the high intraspecies genetic diversity in viruses and (ii) the potential for cross-reactivity with close relatives. METHODOLOGY The workflow developed herein was based on two consecutive BLASTn steps; the first was utilized to select highly conserved regions among the viral taxon of interest, and the second was employed to assess the degree of similarity of these highly-conserved regions to close relatives. Subsequently, the workflow was tested on a set of eight viral species, including various strains from the Flaviviridae and Bunyaviridae families. PRINCIPAL FINDINGS The genetic diversity ranges from as low as 0.45% variable sites over the complete genome of the Japanese encephalitis virus to more than 16% of variable sites on segment L of the Crimean-Congo hemorrhagic fever virus. Our proposed bioinformatics workflow allowed the selection-based on computing scores-of the best target for a diagnostic molecular assay for the eight viral species investigated. CONCLUSIONS/SIGNIFICANCE Our bioinformatics workflow allowed rapid selection of highly conserved and specific genomic fragments among the investigated viruses, while considering up to several hundred complete genomic sequences. The pertinence of this workflow will increase in parallel to the number of sequences made publicly available. We hypothesize that our workflow might be utilized to select diagnostic molecular markers for higher organisms with more complex genomes, provided the sequences are made available.", "link"=>"http://www.mendeley.com/research/development-evaluation-bioinformatics-approach-designing-molecular-assays-viral-detection", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Master"=>3, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Master"=>3, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>1, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"South Africa"=>1}, "group_count"=>0}

Scopus | Further Information

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