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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

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    30303 - Infectious Diseases

Result continuities

  • Project

  • 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

  • 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