In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses.

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 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 c

SUBMITTER: Nagy A 

PROVIDER: S-EPMC6367508 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature