Application of Molecular Diagnostic Techniques for Viral Testing
Identifieur interne : 000971 ( Pmc/Curation ); précédent : 000970; suivant : 000972Application of Molecular Diagnostic Techniques for Viral Testing
Auteurs : Fernando CoboSource :
- The Open Virology Journal [ 1874-3579 ] ; 2012.
Abstract
Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory.
Url:
DOI: 10.2174/1874357901206010104
PubMed: 23248732
PubMed Central: 3522074
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Application of Molecular Diagnostic Techniques for Viral Testing</title><author><name sortKey="Cobo, Fernando" sort="Cobo, Fernando" uniqKey="Cobo F" first="Fernando" last="Cobo">Fernando Cobo</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23248732</idno><idno type="pmc">3522074</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522074</idno><idno type="RBID">PMC:3522074</idno><idno type="doi">10.2174/1874357901206010104</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000971</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000971</idno><idno type="wicri:Area/Pmc/Curation">000971</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000971</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Application of Molecular Diagnostic Techniques for Viral Testing</title><author><name sortKey="Cobo, Fernando" sort="Cobo, Fernando" uniqKey="Cobo F" first="Fernando" last="Cobo">Fernando Cobo</name></author></analytic><series><title level="j">The Open Virology Journal</title><idno type="eISSN">1874-3579</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hayden, R" uniqKey="Hayden R">R Hayden</name></author><author><name sortKey="Persing, Dh" uniqKey="Persing D">DH Persing</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huizing, Kmn" uniqKey="Huizing K">KMN Huizing</name></author><author><name sortKey="Swanink, Cma" uniqKey="Swanink C">CMA Swanink</name></author><author><name sortKey="Landstra, Am" uniqKey="Landstra A">AM Landstra</name></author><author><name sortKey="Van Zwet, Aa" uniqKey="Van Zwet A">AA van Zwet</name></author><author><name sortKey="Van Setten, Pa" uniqKey="Van Setten P">PA van Setten</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Open Virol J</journal-id><journal-id journal-id-type="iso-abbrev">Open Virol J</journal-id><journal-id journal-id-type="publisher-id">TOVJ</journal-id><journal-title-group><journal-title>The Open Virology Journal</journal-title></journal-title-group><issn pub-type="epub">1874-3579</issn><publisher><publisher-name>Bentham Open</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23248732</article-id><article-id pub-id-type="pmc">3522074</article-id><article-id pub-id-type="publisher-id">TOVJ-6-104</article-id><article-id pub-id-type="doi">10.2174/1874357901206010104</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group><series-title>Suppl 1</series-title></article-categories><title-group><article-title>Application of Molecular Diagnostic Techniques for Viral Testing</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Cobo</surname><given-names>Fernando</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff>Microbiology Unit (Biotechnology Area), Hospital de Poniente. Ctra de Almerimar S/N, El Ejido 04700, Almería, Spain</aff><author-notes><corresp id="cor1"><label>*</label>Address correspondence to this author at the Microbiology Unit (Biotechnology Area), Hospital de Poniente. Ctra de Almerimar S/N, El Ejido 04700, Almería, Spain; Tel: +34950022638; E-mail: <email xlink:href="fernando.cobo.sspa@juntadeandalucia.es">fernando.cobo.sspa@juntadeandalucia.es</email></corresp></author-notes><pub-date pub-type="epub"><day>30</day><month>11</month><year>2012</year></pub-date><pub-date pub-type="collection"><year>2012</year></pub-date><volume>6</volume><fpage>104</fpage><lpage>114</lpage><history><date date-type="received"><day>22</day><month>6</month><year>2012</year></date><date date-type="rev-recd"><day>17</day><month>8</month><year>2012</year></date><date date-type="accepted"><day>23</day><month>8</month><year>2012</year></date></history><permissions><copyright-statement>© Fernando Cobo; Licensee Bentham Open.</copyright-statement><copyright-year>2012</copyright-year><copyright-holder>Fernando Cobo</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/"><license-p>This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (<uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</uri>) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.</license-p></license></permissions><abstract><p>Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory.</p></abstract><kwd-group><title>Keywords</title><kwd>Automation methods</kwd><kwd>molecular diagnosis</kwd><kwd>molecular microbiology</kwd><kwd>nucleic acid techniques</kwd><kwd>PCR techniques</kwd><kwd>viral laboratory diagnosis.</kwd></kwd-group></article-meta></front><floats-group><table-wrap id="T1" orientation="portrait" position="float"><label>Table 1.</label><caption><p>Summary of Main Molecular Testing Techniques for Viruses</p></caption><table frame="border" rules="cols" width="100%"><thead><tr><th rowspan="1" colspan="1">Technique</th><th rowspan="1" colspan="1">Format</th><th rowspan="1" colspan="1">Examples of viruses</th></tr><tr><th colspan="3" rowspan="1"><hr></hr></th></tr></thead><tbody><tr><td rowspan="3" colspan="1"><bold>NON AMPLIFIED NUCLEIC ACID PROBES</bold></td><td rowspan="1" colspan="1">Liquid-phase</td><td rowspan="3" colspan="1">HPV, CMV</td></tr><tr><td rowspan="1" colspan="1">Solid-phase</td></tr><tr><td rowspan="1" colspan="1"><italic>In situ</italic> hybridization</td></tr><tr><td rowspan="2" colspan="1"><bold>AMPLIFIED NUCLEIC ACID TECHNIQUES</bold><break></break><bold>Signal amplification techniques</bold></td><td rowspan="1" colspan="1"><break></break>bDNA assays</td><td rowspan="1" colspan="1"><break></break>HCV, HBV, HIV</td></tr><tr><td rowspan="1" colspan="1">Hybrid capture assays</td><td rowspan="1" colspan="1">HPV, CMV</td></tr><tr><td rowspan="9" colspan="1"><bold>Target amplification techniques</bold></td><td rowspan="1" colspan="1">PCR techniques</td><td rowspan="1" colspan="1">Most of viruses</td></tr><tr><td rowspan="1" colspan="1">RT-PCR</td><td rowspan="1" colspan="1">RNA virus (HCV, HIV)</td></tr><tr><td rowspan="1" colspan="1">Nested PCR</td><td rowspan="1" colspan="1">Herpesviruses</td></tr><tr><td rowspan="1" colspan="1">Multiplex PCR</td><td rowspan="1" colspan="1">Herpesviruses, respiratory viruses</td></tr><tr><td rowspan="1" colspan="1">Real-time PCR</td><td rowspan="1" colspan="1">Most of viruses</td></tr><tr><td rowspan="1" colspan="1">Transcriptional-based amplification methods</td><td rowspan="1" colspan="1">HCV (TMA-based), HIV (TMAbased, NASBA), CMV (NASBA) Enterovirus (NASBA), RSV (NASBA)</td></tr><tr><td rowspan="1" colspan="1">Strand displacement amplification </td><td rowspan="1" colspan="1">HIV</td></tr><tr><td rowspan="1" colspan="1">LAMP</td><td rowspan="1" colspan="1">Influenza A and B, CMV, HSV, VZV, BK virus, HPV</td></tr><tr><td rowspan="1" colspan="1">HDA</td><td rowspan="1" colspan="1">HIV-1, HSV 1 and 2</td></tr><tr><td rowspan="3" colspan="1"><bold>Probe amplification techniques</bold></td><td rowspan="1" colspan="1">Ligase chain reaction</td><td rowspan="3" valign="bottom" colspan="1">HCV, HPV</td></tr><tr><td rowspan="1" colspan="1">Cycling probe technology</td></tr><tr><td rowspan="1" colspan="1">Cleavase-invader technology</td></tr><tr><td rowspan="2" colspan="1"><bold>MICROARRAYS</bold></td><td rowspan="1" colspan="1">DNA microarrays</td><td rowspan="1" colspan="1">Respiratory viruses, HCV, HPV, HIV, CNS infection viruses</td></tr><tr><td rowspan="1" colspan="1">Multiplexed microsphere-based array</td><td rowspan="1" colspan="1">HIV, HCV, HSV</td></tr></tbody></table><table-wrap-foot><fn id="T1F1"><p><bold>HPV:</bold> human papillomavirus; <bold>CMV:</bold> cytomegalovirus; <bold>HCV:</bold> hepatitis C virus; <bold>HBV:</bold> hepatitis B virus; <bold>HIV:</bold> human immunodeficiency virus; <bold>TMA:</bold> transcription-mediated
amplification; <bold>NASBA:</bold> nucleic acid sequence-based amplification; <bold>RSV:</bold> respiratory syncytial virus; <bold>DNA:</bold> deoxyribonucleic acid; <bold>RNA:</bold> ribonucleic acid; <bold>LAMP:</bold> loop-mediated
isothermal amplification; <bold>HDA:</bold> helicase-dependent amplification.</p></fn></table-wrap-foot></table-wrap><table-wrap id="T2" orientation="portrait" position="float"><label>Table 2.</label><caption><p>Main Viruses, Samples and Molecular Techniques Used for Viral Diagnosis</p></caption><table frame="border" rules="cols" width="100%"><thead><tr><th rowspan="1" colspan="1">Viruses</th><th rowspan="1" colspan="1">Samples</th><th rowspan="1" colspan="1">Techniques</th><th rowspan="1" colspan="1">Infections</th></tr><tr><th colspan="4" rowspan="1"><hr></hr></th></tr></thead><tbody><tr><td rowspan="3" colspan="1">CMV</td><td rowspan="1" colspan="1">CSF</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="1" colspan="1">CNS infection</td></tr><tr><td rowspan="2" colspan="1">Blood</td><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Congenital infection</td></tr><tr><td rowspan="1" colspan="1">Hybrid capture assay</td><td rowspan="1" colspan="1">CMV immunosuppressed infections</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="5" colspan="1">HSV</td><td rowspan="1" colspan="1">CSF</td><td rowspan="1" colspan="1">Nested PCR</td><td rowspan="1" colspan="1">Meningo-encephalitis</td></tr><tr><td rowspan="1" colspan="1">Blood</td><td rowspan="1" colspan="1">Multiplex PCR</td><td rowspan="1" colspan="1">Neonatal herpes infection</td></tr><tr><td rowspan="1" colspan="1">Leucocytes</td><td rowspan="1" colspan="1">Hybrid capture assay</td><td rowspan="2" colspan="1">Generalized and visceral herpes infection in immunosuppressed patients</td></tr><tr><td rowspan="2" colspan="1">Specimens from genital ulcers or muco-cutaneous lesions</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td></tr><tr><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Dermal and genital diseases</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="4" colspan="1">VZV</td><td rowspan="1" colspan="1">CSF</td><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">CNS infection</td></tr><tr><td rowspan="1" colspan="1">Exudate from skin lesions</td><td rowspan="3" colspan="1">Multiplex PCR</td><td rowspan="1" colspan="1">Cutaneous lesions</td></tr><tr><td rowspan="1" colspan="1">Broncho-alveolar lavage</td><td rowspan="1" colspan="1">Pulmonary infections</td></tr><tr><td rowspan="1" colspan="1">Amniotic fluid</td><td rowspan="1" colspan="1">Congenital and neonatal infections</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="4" colspan="1">EBV</td><td rowspan="1" colspan="1">CSF</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="1" colspan="1">Infectious mononucleosis</td></tr><tr><td rowspan="1" colspan="1">Blood</td><td rowspan="1" colspan="1"><italic>In situ</italic> hybridization</td><td rowspan="1" colspan="1">Encephalitis</td></tr><tr><td rowspan="1" colspan="1">Lymphocytes</td><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="2" colspan="1">Tumors</td></tr><tr><td rowspan="1" colspan="1">Tissue</td><td rowspan="1" colspan="1">NASBA, Southern blot, dot blot</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="4" colspan="1">Parvovirus B19</td><td rowspan="1" colspan="1">Blood</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="4" colspan="1">Perinatal and neonatal infections</td></tr><tr><td rowspan="1" colspan="1">Bone marrow</td><td rowspan="3" colspan="1">Real time quantitative PCR</td></tr><tr><td rowspan="1" colspan="1">Placental and fetal tissue</td></tr><tr><td rowspan="1" colspan="1">Amniotic fluid</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="2" colspan="1">Polyomavirus JC</td><td rowspan="2" colspan="1">CSF</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="2" colspan="1">Leukoencephalopathy</td></tr><tr><td rowspan="1" colspan="1">Real time quantitative PCR</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="2" colspan="1">Polyomavirus BK</td><td rowspan="1" colspan="1">Urine</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="2" colspan="1">Nephropathy</td></tr><tr><td rowspan="1" colspan="1">Blood samples</td><td rowspan="1" colspan="1">Real time quantitative PCR</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="4" colspan="1">Influenza and parainfluenza viruses</td><td rowspan="4" colspan="1">Respiratory samples</td><td rowspan="1" colspan="1">RT-PCR</td><td rowspan="1" colspan="1">Flu</td></tr><tr><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Bronchiolitis</td></tr><tr><td rowspan="1" colspan="1">Multiplex PCR</td><td rowspan="1" colspan="1">Croup</td></tr><tr><td rowspan="1" colspan="1">Microarrays</td><td rowspan="1" colspan="1">Pneumonia</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="3" colspan="1">Adenovirus</td><td rowspan="3" colspan="1">Several clinical samples</td><td rowspan="1" colspan="1">Conventional qualitative PCR</td><td rowspan="1" colspan="1">Respiratory infections</td></tr><tr><td rowspan="2" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Ocular infections</td></tr><tr><td rowspan="1" colspan="1">Gastrointestinal infections</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="2" colspan="1">Enterovirus</td><td rowspan="2" colspan="1">CSF</td><td rowspan="1" colspan="1">RT-PCR</td><td rowspan="2" colspan="1">CNS infection</td></tr><tr><td rowspan="1" colspan="1">Real time quantitative PCR</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="5" colspan="1">HPV</td><td rowspan="1" colspan="1">Cervical exudates and biopsies</td><td rowspan="1" colspan="1">Type-specific PCR</td><td rowspan="1" colspan="1">Cervical lesions</td></tr><tr><td rowspan="1" colspan="1">Warts biopsies</td><td rowspan="1" colspan="1">General primers PCR</td><td rowspan="4" colspan="1">Warts</td></tr><tr><td rowspan="3" colspan="1">Other biopsies</td><td rowspan="1" colspan="1">Liquid hybridization</td></tr><tr><td rowspan="1" colspan="1">HPV mRNA detection</td></tr><tr><td rowspan="1" colspan="1">Microarrays</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="3" colspan="1">Hepatitis viruses</td><td rowspan="1" colspan="1">Serum or plasma</td><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Chronic infections (viral load)</td></tr><tr><td rowspan="2" colspan="1">Liver tissue</td><td rowspan="1" colspan="1">Hybridization</td><td rowspan="2" colspan="1">Genotyping</td></tr><tr><td rowspan="1" colspan="1">Sequencing</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td rowspan="1" colspan="1">HIV</td><td rowspan="1" colspan="1">Plasma</td><td rowspan="1" colspan="1">Real time quantitative PCR</td><td rowspan="1" colspan="1">Viral load detection</td></tr></tbody></table><table-wrap-foot><fn id="T2F1"><p><bold>CMV:</bold> cytomegalovirus; <bold>CSF:</bold> cerebrospinal fluid; <bold>PCR:</bold> polymerase chain reaction; <bold>CNS:</bold> central nervous system; <bold>HSV:</bold> virus herpes simplex; <bold>VZV:</bold> virus varicella-zoster; <bold>EBV:</bold> virus Epstein-Barr; <bold>NASBA:</bold> nucleic acid sequence-based amplification; <bold>HPV:</bold> human papillomavirus; <bold>HIV:</bold> human immunodeficiency virus; <bold>RNA:</bold> ribonucleic acid.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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