Background: The DiagCORE® Respiratory Panel is a fast qualitative test based on RT-qPCR used to analyze nasopharyngeal swab in transport medium samples taken from patients with respiratory symptoms for the presence of the most relevant viral or bacterial pathogens: Influenza A and B, different Coronavirus strains, Parainfluenza virus strains 1 to 4, Respiratory Syncytial virus, human Metapneumovirus, Adenovirus, Bocavirus, Rhinovirus, Enterovirus, Mycoplasma pneumoniae, Legionella pneumophila, and Bordetella pertussis. The present study was performed to analyze a bioinformatic analysis to assess the specificity of the DiagCORE® Respiratory Panel, and the corresponding in vitro amplification using whole viral and bacterial samples to corroborate specificity and avoid cross-reactivity.
Materials/methods: Inclusivity tests were performed to detect specificity for all strains, genotypes and subtypes of relevance of pathogens included in the DiagCORE® Respiratory Panel. In silico homology analysis was performed individually for all oligo sets designed for all pathogens, and hits obtained were filtered to obtain unique sequences with potential PCR amplification. A second approach constructing a sequence alignment including all annotated target gene sequences available in databases was performed for each pathogen to characterize possible mismatches between primers and probes to optimize the detection of all clinically relevant strains and subtypes of all the respiratory pathogens detected in the DiagCORE® Respiratory Panel. In addition to in silico analysis, in vitro testing has been performed to corroborate specificity and sensitivity of the assay.
Results: It can be concluded that all the clinically prevalent and relevant strains for each target are represented into the inclusivity analysis. Parallelly, no potential cross-reaction with unspecific targets was detected in any primer/probe set of the DiagCORE® Respiratory Panel. In addition, no significant mismatches between primer sets and target gene sequences affecting specificity of the assay were detected for any of the main strains of all pathogens. Finally, in vitro testing demonstrated the specificity of the assay with high sensitivity levels in almost all pathogens.
Conclusions: The clinical prevalent and relevant respiratory pathogens including all strains, genotypes and subtypes strains can be successfully detected by the DiagCORE® Respiratory Panel design.
Authors: Peñarrubia L, Márquez Y, Turmo D, Cerdán M, Van de Sand C*.