Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.
Identifieur interne : 001309 ( PubMed/Corpus ); précédent : 001308; suivant : 001310Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.
Auteurs : Christine M. Malboeuf ; Xiao Yang ; Patrick Charlebois ; James Qu ; Aaron M. Berlin ; Monica Casali ; Kendra N. Pesko ; Christian L. Boutwell ; John P. Devincenzo ; Gregory D. Ebel ; Todd M. Allen ; Michael C. Zody ; Matthew R. Henn ; Joshua Z. LevinSource :
- Nucleic acids research [ 1362-4962 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA, Viral.
- genetics : HIV, Respiratory Syncytial Viruses, West Nile virus.
- Base Sequence, Genome, Viral, Humans, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA.
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.
DOI: 10.1093/nar/gks794
PubMed: 22962364
Links to Exploration step
pubmed:22962364Le document en format XML
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Levin</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Genome, Viral</term><term>HIV (genetics)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Amplification Techniques</term><term>RNA, Viral (chemistry)</term><term>Respiratory Syncytial Viruses (genetics)</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, RNA</term><term>West Nile virus (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>HIV</term><term>Respiratory Syncytial Viruses</term><term>West Nile virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Amplification Techniques</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, RNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22962364</PMID><DateCompleted><Year>2013</Year><Month>03</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>41</Volume><Issue>1</Issue><PubDate><Year>2013</Year><Month>Jan</Month><Day>07</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.</ArticleTitle><Pagination><MedlinePgn>e13</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gks794</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Malboeuf</LastName><ForeName>Christine M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. malboeuf@broadinstitute.org</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiao</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Charlebois</LastName><ForeName>Patrick</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Qu</LastName><ForeName>James</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Berlin</LastName><ForeName>Aaron M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Casali</LastName><ForeName>Monica</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Pesko</LastName><ForeName>Kendra N</ForeName><Initials>KN</Initials></Author><Author ValidYN="Y"><LastName>Boutwell</LastName><ForeName>Christian L</ForeName><Initials>CL</Initials></Author><Author ValidYN="Y"><LastName>DeVincenzo</LastName><ForeName>John P</ForeName><Initials>JP</Initials></Author><Author ValidYN="Y"><LastName>Ebel</LastName><ForeName>Gregory D</ForeName><Initials>GD</Initials></Author><Author ValidYN="Y"><LastName>Allen</LastName><ForeName>Todd M</ForeName><Initials>TM</Initials></Author><Author ValidYN="Y"><LastName>Zody</LastName><ForeName>Michael C</ForeName><Initials>MC</Initials></Author><Author ValidYN="Y"><LastName>Henn</LastName><ForeName>Matthew R</ForeName><Initials>MR</Initials></Author><Author ValidYN="Y"><LastName>Levin</LastName><ForeName>Joshua 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