Improved LNA probe-based assay for the detection of African and South American yellow fever virus strains
Abstract Background Real-time assays for Yellow fever virus (YFV) would help to improve acute diagnostics in outbreak investigations. Objectives To develop a real-time assay for YFV able to detect African and South American strains. Study design Three short probe (14–18 nt) formats were compared and...
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| Veröffentlicht in: | Journal of clinical virology 2010-07, Vol.48 (3), p.187-192 |
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| container_title | Journal of clinical virology |
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| creator | Weidmann, Manfred Faye, Ousmane Faye, Oumar Kranaster, Ramon Marx, Andreas Nunes, Marcio R.T Vasconcelos, Pedro F.C Hufert, Frank T Sall, Amadou A |
| description | Abstract Background Real-time assays for Yellow fever virus (YFV) would help to improve acute diagnostics in outbreak investigations. Objectives To develop a real-time assay for YFV able to detect African and South American strains. Study design Three short probe (14–18 nt) formats were compared and a plasmid-transcribed RNA standard was used to test the performance of the assays. Additionally the new TaqM1 enzyme was tested. Results A locked nucleotide probe (LNA probe) performed best with an analytical sensitivity of 10 RNA molecules detected. 44 African and 10 South American strains were detectable. One South American strain from 1984 had a one-nucleotide deviation in the hybridisation sequence for which the LNA probe had to be adapted. Comparison of enzymes revealed that not all enzymes are suitable for LNA probes. Conclusion The developed LNA probe based YFV real-time PCR performed best in an enzyme mix and less efficient using multifunctional enzymes. |
| doi_str_mv | 10.1016/j.jcv.2010.04.013 |
| format | Article |
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Objectives To develop a real-time assay for YFV able to detect African and South American strains. Study design Three short probe (14–18 nt) formats were compared and a plasmid-transcribed RNA standard was used to test the performance of the assays. Additionally the new TaqM1 enzyme was tested. Results A locked nucleotide probe (LNA probe) performed best with an analytical sensitivity of 10 RNA molecules detected. 44 African and 10 South American strains were detectable. One South American strain from 1984 had a one-nucleotide deviation in the hybridisation sequence for which the LNA probe had to be adapted. Comparison of enzymes revealed that not all enzymes are suitable for LNA probes. Conclusion The developed LNA probe based YFV real-time PCR performed best in an enzyme mix and less efficient using multifunctional enzymes.</description><identifier>ISSN: 1386-6532</identifier><identifier>EISSN: 1873-5967</identifier><identifier>DOI: 10.1016/j.jcv.2010.04.013</identifier><identifier>PMID: 20556888</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Allergy and Immunology ; Eclipse probe ; Humans ; Infectious Disease ; LNA probe ; MGB probe ; Molecular Diagnostic Techniques - methods ; Oligonucleotide Probes - genetics ; Real-time PCR ; Sensitivity and Specificity ; TaqM1 enzyme ; Virology - methods ; Yellow Fever - diagnosis ; Yellow Fever - virology ; Yellow fever virus ; Yellow fever virus - genetics ; Yellow fever virus - isolation & purification ; YFV</subject><ispartof>Journal of clinical virology, 2010-07, Vol.48 (3), p.187-192</ispartof><rights>Elsevier B.V.</rights><rights>2010 Elsevier B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c482t-fa5182985f35c4088076b45c08d855912a9ed9215af8dd5db995504602301e943</citedby><cites>FETCH-LOGICAL-c482t-fa5182985f35c4088076b45c08d855912a9ed9215af8dd5db995504602301e943</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1386653210001927$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20556888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Weidmann, Manfred</creatorcontrib><creatorcontrib>Faye, Ousmane</creatorcontrib><creatorcontrib>Faye, Oumar</creatorcontrib><creatorcontrib>Kranaster, Ramon</creatorcontrib><creatorcontrib>Marx, Andreas</creatorcontrib><creatorcontrib>Nunes, Marcio R.T</creatorcontrib><creatorcontrib>Vasconcelos, Pedro F.C</creatorcontrib><creatorcontrib>Hufert, Frank T</creatorcontrib><creatorcontrib>Sall, Amadou A</creatorcontrib><title>Improved LNA probe-based assay for the detection of African and South American yellow fever virus strains</title><title>Journal of clinical virology</title><addtitle>J Clin Virol</addtitle><description>Abstract Background Real-time assays for Yellow fever virus (YFV) would help to improve acute diagnostics in outbreak investigations. Objectives To develop a real-time assay for YFV able to detect African and South American strains. Study design Three short probe (14–18 nt) formats were compared and a plasmid-transcribed RNA standard was used to test the performance of the assays. Additionally the new TaqM1 enzyme was tested. Results A locked nucleotide probe (LNA probe) performed best with an analytical sensitivity of 10 RNA molecules detected. 44 African and 10 South American strains were detectable. One South American strain from 1984 had a one-nucleotide deviation in the hybridisation sequence for which the LNA probe had to be adapted. Comparison of enzymes revealed that not all enzymes are suitable for LNA probes. Conclusion The developed LNA probe based YFV real-time PCR performed best in an enzyme mix and less efficient using multifunctional enzymes.</description><subject>Allergy and Immunology</subject><subject>Eclipse probe</subject><subject>Humans</subject><subject>Infectious Disease</subject><subject>LNA probe</subject><subject>MGB probe</subject><subject>Molecular Diagnostic Techniques - methods</subject><subject>Oligonucleotide Probes - genetics</subject><subject>Real-time PCR</subject><subject>Sensitivity and Specificity</subject><subject>TaqM1 enzyme</subject><subject>Virology - methods</subject><subject>Yellow Fever - diagnosis</subject><subject>Yellow Fever - virology</subject><subject>Yellow fever virus</subject><subject>Yellow fever virus - genetics</subject><subject>Yellow fever virus - isolation & purification</subject><subject>YFV</subject><issn>1386-6532</issn><issn>1873-5967</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUsuO1DAQjBCIXRY-gAvyjVOG9iuxhYQ0WvFYaQSHhbPl2B2tQxIvdhI0f49Hs3DgACd3W9Wl7qqqqpcUdhRo82bYDW7bMSg9iB1Q_qi6pKrltdRN-7jUXDV1Izm7qJ7lPABQyUX7tLpgIGWjlLqsws10n-KGnhw-70kpO6w7m0tvc7ZH0sdEljskHhd0S4gziT3Z9yk4OxM7e3Ib1-WO7Cc8fx1xHONP0uOGiWwhrZnkJdkw5-fVk96OGV88vFfVtw_vv15_qg9fPt5c7w-1E4otdW8lVUwr2XPpBCgFbdMJ6UB5JaWmzGr0mlFpe-W99J3WUoJogHGgqAW_ql6fecsxP1bMi5lCdmUtO2NcsymErFzP4L_IlnMuaSN0QdIz0qWYc8Le3Kcw2XQ0FMzJCjOYYoU5WWFAmGJFmXn1wL52E_o_E7-1L4C3ZwAWNbaAyWQXcHboQypaGx_DP-nf_TXtxjAXD8bveMQ8xDXNRWZDTWYGzO0pC6coUCgx0KzlvwB5XKzu</recordid><startdate>20100701</startdate><enddate>20100701</enddate><creator>Weidmann, Manfred</creator><creator>Faye, Ousmane</creator><creator>Faye, Oumar</creator><creator>Kranaster, Ramon</creator><creator>Marx, Andreas</creator><creator>Nunes, Marcio R.T</creator><creator>Vasconcelos, Pedro F.C</creator><creator>Hufert, Frank T</creator><creator>Sall, Amadou A</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7U9</scope><scope>H94</scope></search><sort><creationdate>20100701</creationdate><title>Improved LNA probe-based assay for the detection of African and South American yellow fever virus strains</title><author>Weidmann, Manfred ; Faye, Ousmane ; Faye, Oumar ; Kranaster, Ramon ; Marx, Andreas ; Nunes, Marcio R.T ; Vasconcelos, Pedro F.C ; Hufert, Frank T ; Sall, Amadou A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c482t-fa5182985f35c4088076b45c08d855912a9ed9215af8dd5db995504602301e943</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Allergy and Immunology</topic><topic>Eclipse probe</topic><topic>Humans</topic><topic>Infectious Disease</topic><topic>LNA probe</topic><topic>MGB probe</topic><topic>Molecular Diagnostic Techniques - methods</topic><topic>Oligonucleotide Probes - genetics</topic><topic>Real-time PCR</topic><topic>Sensitivity and Specificity</topic><topic>TaqM1 enzyme</topic><topic>Virology - methods</topic><topic>Yellow Fever - diagnosis</topic><topic>Yellow Fever - virology</topic><topic>Yellow fever virus</topic><topic>Yellow fever virus - genetics</topic><topic>Yellow fever virus - isolation & purification</topic><topic>YFV</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Weidmann, Manfred</creatorcontrib><creatorcontrib>Faye, Ousmane</creatorcontrib><creatorcontrib>Faye, Oumar</creatorcontrib><creatorcontrib>Kranaster, Ramon</creatorcontrib><creatorcontrib>Marx, Andreas</creatorcontrib><creatorcontrib>Nunes, Marcio R.T</creatorcontrib><creatorcontrib>Vasconcelos, Pedro F.C</creatorcontrib><creatorcontrib>Hufert, Frank T</creatorcontrib><creatorcontrib>Sall, Amadou A</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><jtitle>Journal of clinical virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Weidmann, Manfred</au><au>Faye, Ousmane</au><au>Faye, Oumar</au><au>Kranaster, Ramon</au><au>Marx, Andreas</au><au>Nunes, Marcio R.T</au><au>Vasconcelos, Pedro F.C</au><au>Hufert, Frank T</au><au>Sall, Amadou A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improved LNA probe-based assay for the detection of African and South American yellow fever virus strains</atitle><jtitle>Journal of clinical virology</jtitle><addtitle>J Clin Virol</addtitle><date>2010-07-01</date><risdate>2010</risdate><volume>48</volume><issue>3</issue><spage>187</spage><epage>192</epage><pages>187-192</pages><issn>1386-6532</issn><eissn>1873-5967</eissn><abstract>Abstract Background Real-time assays for Yellow fever virus (YFV) would help to improve acute diagnostics in outbreak investigations. Objectives To develop a real-time assay for YFV able to detect African and South American strains. Study design Three short probe (14–18 nt) formats were compared and a plasmid-transcribed RNA standard was used to test the performance of the assays. Additionally the new TaqM1 enzyme was tested. Results A locked nucleotide probe (LNA probe) performed best with an analytical sensitivity of 10 RNA molecules detected. 44 African and 10 South American strains were detectable. One South American strain from 1984 had a one-nucleotide deviation in the hybridisation sequence for which the LNA probe had to be adapted. Comparison of enzymes revealed that not all enzymes are suitable for LNA probes. Conclusion The developed LNA probe based YFV real-time PCR performed best in an enzyme mix and less efficient using multifunctional enzymes.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>20556888</pmid><doi>10.1016/j.jcv.2010.04.013</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Allergy and Immunology Eclipse probe Humans Infectious Disease LNA probe MGB probe Molecular Diagnostic Techniques - methods Oligonucleotide Probes - genetics Real-time PCR Sensitivity and Specificity TaqM1 enzyme Virology - methods Yellow Fever - diagnosis Yellow Fever - virology Yellow fever virus Yellow fever virus - genetics Yellow fever virus - isolation & purification YFV |
| title | Improved LNA probe-based assay for the detection of African and South American yellow fever virus strains |
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