Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.
Identifieur interne : 001406 ( PubMed/Checkpoint ); précédent : 001405; suivant : 001407Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.
Auteurs : Eunice C. Chen [États-Unis] ; Steve A. Miller ; Joseph L. Derisi ; Charles Y. ChiuSource :
- Journal of visualized experiments : JoVE [ 1940-087X ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- diagnostic : Maladies virales.
- génétique : Virus.
- isolement et purification : Virus.
- virologie : Maladies virales.
- Enfant, Humains, Hybridation d'acides nucléiques, Réaction de polymérisation en chaîne, Séquençage par oligonucléotides en batterie, Virologie.
English descriptors
- KwdEn :
- MESH :
- diagnosis : Virus Diseases.
- genetics : Viruses.
- isolation & purification : Viruses.
- methods : Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Virology.
- virology : Virus Diseases.
- Child, Humans, Nucleic Acid Hybridization.
Abstract
The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology. Using the Virochip, we have identified the full spectrum of viruses associated with respiratory infections, including cases of unexplained critical illness in hospitalized patients, with a sensitivity equivalent to or superior to conventional clinical testing. The Virochip has also been used to identify novel viruses, including the SARS coronavirus, a novel rhinovirus clade, XMRV (a retrovirus linked to prostate cancer), avian bornavirus (the cause of a wasting disease in parrots), and a novel cardiovirus in children with respiratory and diarrheal illness. The current version of the Virochip has been ported to an Agilent microarray platform and consists of ~36,000 probes derived from over ~1,500 viruses in GenBank as of December of 2009. Here we demonstrate the steps involved in processing a Virochip assay from start to finish (~24 hour turnaround time), including sample nucleic acid extraction, PCR amplification using random primers, fluorescent dye incorporation, and microarray hybridization, scanning, and analysis.
DOI: 10.3791/2536
PubMed: 21559002
Affiliations:
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Derisi</name></author><author><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y" last="Chiu">Charles Y. 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Chiu</name></author></analytic><series><title level="j">Journal of visualized experiments : JoVE</title><idno type="eISSN">1940-087X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Child</term><term>Humans</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Polymerase Chain Reaction (methods)</term><term>Virology (methods)</term><term>Virus Diseases (diagnosis)</term><term>Virus Diseases (virology)</term><term>Viruses (genetics)</term><term>Viruses (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Enfant</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Maladies virales (diagnostic)</term><term>Maladies virales (virologie)</term><term>Réaction de polymérisation en chaîne ()</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Virologie ()</term><term>Virus (génétique)</term><term>Virus (isolement et purification)</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Maladies virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term><term>Polymerase Chain Reaction</term><term>Virology</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Maladies virales</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Child</term><term>Humans</term><term>Nucleic Acid Hybridization</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Enfant</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Réaction de polymérisation en chaîne</term><term>Séquençage par oligonucléotides en batterie</term><term>Virologie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology. Using the Virochip, we have identified the full spectrum of viruses associated with respiratory infections, including cases of unexplained critical illness in hospitalized patients, with a sensitivity equivalent to or superior to conventional clinical testing. The Virochip has also been used to identify novel viruses, including the SARS coronavirus, a novel rhinovirus clade, XMRV (a retrovirus linked to prostate cancer), avian bornavirus (the cause of a wasting disease in parrots), and a novel cardiovirus in children with respiratory and diarrheal illness. The current version of the Virochip has been ported to an Agilent microarray platform and consists of ~36,000 probes derived from over ~1,500 viruses in GenBank as of December of 2009. Here we demonstrate the steps involved in processing a Virochip assay from start to finish (~24 hour turnaround time), including sample nucleic acid extraction, PCR amplification using random primers, fluorescent dye incorporation, and microarray hybridization, scanning, and analysis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21559002</PMID><DateCompleted><Year>2011</Year><Month>08</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1940-087X</ISSN><JournalIssue CitedMedium="Internet"><Issue>50</Issue><PubDate><Year>2011</Year><Month>Apr</Month><Day>27</Day></PubDate></JournalIssue><Title>Journal of visualized experiments : JoVE</Title><ISOAbbreviation>J Vis Exp</ISOAbbreviation></Journal><ArticleTitle>Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.3791/2536</ELocationID><ELocationID EIdType="pii" ValidYN="Y">2536</ELocationID><Abstract><AbstractText>The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology. Using the Virochip, we have identified the full spectrum of viruses associated with respiratory infections, including cases of unexplained critical illness in hospitalized patients, with a sensitivity equivalent to or superior to conventional clinical testing. The Virochip has also been used to identify novel viruses, including the SARS coronavirus, a novel rhinovirus clade, XMRV (a retrovirus linked to prostate cancer), avian bornavirus (the cause of a wasting disease in parrots), and a novel cardiovirus in children with respiratory and diarrheal illness. The current version of the Virochip has been ported to an Agilent microarray platform and consists of ~36,000 probes derived from over ~1,500 viruses in GenBank as of December of 2009. 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IdType="pubmed">18768820</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region><settlement><li>San Francisco</li></settlement></list><tree><noCountry><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y" last="Chiu">Charles Y. Chiu</name><name sortKey="Derisi, Joseph L" sort="Derisi, Joseph L" uniqKey="Derisi J" first="Joseph L" last="Derisi">Joseph L. Derisi</name><name sortKey="Miller, Steve A" sort="Miller, Steve A" uniqKey="Miller S" first="Steve A" last="Miller">Steve A. Miller</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Chen, Eunice C" sort="Chen, Eunice C" uniqKey="Chen E" first="Eunice C" last="Chen">Eunice C. Chen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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