In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses
Identifieur interne : 000113 ( Main/Exploration ); précédent : 000112; suivant : 000114In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses
Auteurs : Alexander Nagy [République tchèque] ; Tomáš Ji Inec [République tchèque] ; Helena Ji Incová [République tchèque] ; Lenka Erníková [République tchèque] ; Martina Havlí Ková [République tchèque]Source :
- Scientific Reports [ 2045-2322 ] ; 2019.
Abstract
The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed
Url:
DOI: 10.1038/s41598-018-37869-w
PubMed: 30733500
PubMed Central: 6367508
Affiliations:
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when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000202</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000202</idno><idno type="wicri:Area/Pmc/Curation">000202</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000202</idno><idno type="wicri:Area/Pmc/Checkpoint">000091</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000091</idno><idno type="wicri:Area/Ncbi/Merge">000F65</idno><idno type="wicri:Area/Ncbi/Curation">000F65</idno><idno type="wicri:Area/Ncbi/Checkpoint">000F65</idno><idno type="wicri:Area/Main/Merge">000113</idno><idno type="wicri:Area/Main/Curation">000113</idno><idno type="wicri:Area/Main/Exploration">000113</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>In silico</italic> re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses</title><author><name sortKey="Nagy, Alexander" sort="Nagy, Alexander" uniqKey="Nagy A" first="Alexander" last="Nagy">Alexander Nagy</name><affiliation wicri:level="3"><nlm:aff id="Aff1">State Veterinary Institute Prague, Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>State Veterinary Institute Prague, Prague</wicri:regionArea><placeName><settlement type="city">Prague</settlement><region type="région" nuts="2">Bohême centrale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2184 1595</institution-id><institution-id institution-id-type="GRID">grid.425485.a</institution-id><institution>National Institute of Public Health, National Reference Laboratory for Influenza,</institution></institution-wrap>Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Prague</wicri:regionArea></affiliation></author><author><name sortKey="Ji Inec, Tomas" sort="Ji Inec, Tomas" uniqKey="Ji Inec T" first="Tomáš" last="Ji Inec">Tomáš Ji Inec</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2184 1595</institution-id><institution-id institution-id-type="GRID">grid.425485.a</institution-id><institution>National Institute of Public Health, National Reference Laboratory for Influenza,</institution></institution-wrap>Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Prague</wicri:regionArea></affiliation></author><author><name sortKey="Ji Incova, Helena" sort="Ji Incova, Helena" uniqKey="Ji Incova H" first="Helena" last="Ji Incová">Helena Ji Incová</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2184 1595</institution-id><institution-id institution-id-type="GRID">grid.425485.a</institution-id><institution>National Institute of Public Health, National Reference Laboratory for Influenza,</institution></institution-wrap>Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Prague</wicri:regionArea></affiliation></author><author><name sortKey=" Ernikova, Lenka" sort=" Ernikova, Lenka" uniqKey=" Ernikova L" first="Lenka" last=" Erníková">Lenka Erníková</name><affiliation wicri:level="3"><nlm:aff id="Aff1">State Veterinary Institute Prague, Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>State Veterinary Institute Prague, Prague</wicri:regionArea><placeName><settlement type="city">Prague</settlement><region type="région" nuts="2">Bohême centrale</region></placeName></affiliation></author><author><name sortKey="Havli Kova, Martina" sort="Havli Kova, Martina" uniqKey="Havli Kova M" first="Martina" last="Havlí Ková">Martina Havlí Ková</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2184 1595</institution-id><institution-id institution-id-type="GRID">grid.425485.a</institution-id><institution>National Institute of Public Health, National Reference Laboratory for Influenza,</institution></institution-wrap>Prague, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea>Prague</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="Par1">The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed <italic>in silico</italic> on public sequences to evaluate the ability to detect actually circulating strains and to infer potentially escaping variants. In the work presented we re-assessed a RT-qPCR assay for the universal detection of influenza A (IA) viruses currently recommended by the European Union Reference Laboratory for Avian Influenza. To this end, the primers and probe sequences were challenged against more than 99,000 M-segment sequences in five data pools. To streamline this process, we developed a simple algorithm called the SequenceTracer designed for alignment stratification, compression, and personal sequence subset selection and also demonstrated its utility. The re-assessment confirmed the high inclusivity of the assay for the detection of avian, swine and human pandemic H1N1 IA viruses. On the other hand, the analysis identified human H3N2 strains with a critical probe-interfering mutation circulating since 2010, albeit with a significantly fluctuating proportion. Minor variations located in the forward and reverse primers identified in the avian and swine data were also considered.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Holland, Pm" uniqKey="Holland P">PM Holland</name></author><author><name sortKey="Abramson, Rd" uniqKey="Abramson R">RD Abramson</name></author><author><name sortKey="Watson, R" uniqKey="Watson R">R Watson</name></author><author><name sortKey="Gelfand, Dh" uniqKey="Gelfand D">DH Gelfand</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lemmon, Gh" uniqKey="Lemmon G">GH Lemmon</name></author><author><name sortKey="Gardner, Sn" uniqKey="Gardner S">SN Gardner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stevenson, J" uniqKey="Stevenson J">J Stevenson</name></author><author><name sortKey="Hymas, W" uniqKey="Hymas W">W Hymas</name></author><author><name sortKey="Hillyard, D" uniqKey="Hillyard D">D 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uniqKey="Larsson A">A Larsson</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République tchèque</li></country><region><li>Bohême centrale</li></region><settlement><li>Prague</li></settlement></list><tree><country name="République tchèque"><region name="Bohême centrale"><name sortKey="Nagy, Alexander" sort="Nagy, Alexander" uniqKey="Nagy A" first="Alexander" last="Nagy">Alexander Nagy</name></region><name sortKey=" Ernikova, Lenka" sort=" Ernikova, Lenka" uniqKey=" Ernikova L" first="Lenka" last=" Erníková">Lenka Erníková</name><name sortKey="Havli Kova, Martina" sort="Havli Kova, Martina" uniqKey="Havli Kova M" first="Martina" last="Havlí Ková">Martina Havlí Ková</name><name sortKey="Ji Incova, Helena" sort="Ji Incova, Helena" uniqKey="Ji Incova H" first="Helena" last="Ji Incová">Helena Ji Incová</name><name sortKey="Ji Inec, Tomas" sort="Ji Inec, Tomas" uniqKey="Ji Inec T" first="Tomáš" last="Ji Inec">Tomáš Ji Inec</name><name sortKey="Nagy, Alexander" sort="Nagy, Alexander" uniqKey="Nagy A" first="Alexander" last="Nagy">Alexander Nagy</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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