In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F75010330%3A_____%2F19%3A00012606" target="_blank" >RIV/75010330:_____/19:00012606 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41598-018-37869-w" target="_blank" >https://www.nature.com/articles/s41598-018-37869-w</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41598-018-37869-w" target="_blank" >10.1038/s41598-018-37869-w</a>
Alternative languages
Result language
angličtina
Original language name
In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses
Original language description
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 in silico 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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
30303 - Infectious Diseases
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Scientific Reports
ISSN
2045-2322
e-ISSN
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Volume of the periodical
9
Issue of the periodical within the volume
February
Country of publishing house
GB - UNITED KINGDOM
Number of pages
10
Pages from-to
1630
UT code for WoS article
000458017800098
EID of the result in the Scopus database
2-s2.0-85061276289