About: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

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About: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
Creator	Yang, Xiao Casali, Monica Charlebois, Patrick Qu, James Allen, Todd Ebel, Gregory Berlin, Aaron Boutwell, Christian Henn, Matthew Levin, Joshua Malboeuf, Christine Pesko, Kendra Zody, Michael Devincenzo, John
Source	PMC
abstract	RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and de novo assembly optimized for viral genomes. With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination.
has issue date	2012-09-08(xsd:dateTime)
bibo:doi	10.1093/nar/gks794
bibo:pmid	22962364
has license	cc-by-nc
sha1sum (hex)	9d651ee3cc003d22f9ffff68394494087112ec45
schema:url	https://doi.org/10.1093/nar/gks794
resource representing a document's title	Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
has PubMed Central identifier	PMC3592391
has PubMed identifier	22962364
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:9d651ee3cc003d22f9ffff68394494087112ec45#body_text
is schema:about of	named entity 'INDEPENDENT' named entity 'ULTRA' named entity 'HOST' named entity 'ASSEMBLY' named entity 'CLONE' named entity 'LARGE' named entity 'CAPTURE' named entity 'INFECTIOUS AGENTS' named entity 'HERE' named entity 'PANDEMIC' named entity 'AIDS' named entity 'VIRAL' named entity 'SEQUENCE' named entity 'PRIOR' named entity 'APPLICABLE' named entity 'DESCRIBE' named entity 'FULLY' named entity 'LOW' named entity 'de novo assembly' named entity 'sequence' named entity 'viral' named entity 'HIV' named entity 'contamination' named entity 'RNA' named entity 'amplification' named entity 'COPY' named entity 'SEQUENCE' named entity 'SAMPLES' named entity 'DETECTION METHODS' named entity 'INFORMATION' named entity 'INFLUENZA' named entity 'VIRAL RNA' named entity 'UNDERSTAND' named entity 'GENOME SEQUENCING' named entity 'CONTAINING' named entity 'NUMBERS' named entity 'SAMPLES' named entity 'PRESENCE OF' named entity 'GENERATING' named entity 'PATHOGENS' named entity 'GENOME SEQUENCING' named entity 'COMPLETE' named entity 'LOW' named entity 'AMPLIFICATION' named entity 'PROTEIN CODING REGION' named entity 'SYNCYTIAL' named entity '100' named entity 'WEST' named entity 'HIV' named entity 'THESE' named entity 'READS' named entity 'COPIES' named entity 'ANTIGEN' named entity 'KNOWLEDGE' named entity 'SURVEILLANCE' named entity 'CONTAMINATION' named entity 'METHODS' named entity 'LENGTH' named entity 'COMPLETE' named entity '100%' named entity 'DEVELOPMENT' named entity 'AMOUNTS' named entity 'VIRAL RNA' named entity 'HEALTH' named entity 'STUDY' named entity 'GENOMES' named entity 'VIRAL DETECTION' named entity 'SARS'

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