Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak
Autor
Peñarrubia, Luis
Ruiz, Maria
Porco, Roberto
Rao, Sonia N.
Juanola-Falgarona, Martí
Manissero, Davide
López-Fontanals, Marta
Pareja, Josep
Institución
Resumen
Objectives: In this study, five SARS-CoV-2 PCR assay panels were evaluated against the accumulated
genetic variability of the virus to assess the effect on sensitivity of the individual assays.
Design or methods: As of week 21, 2020, the complete set of available SARS-CoV-2 genomes from GISAID
and GenBank databases were used in this study. SARS-CoV-2 primer sequences from publicly available
panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx were included in the alignment, and accumulated
genetic variability affecting any oligonucleotide annealing was annotated.
Results: A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR
assay. Variations in 8,773 (25.94%) genomes were considered as high risk, whereas additional 2,854
(8.43%) genomes presented low frequent single mutations and were predicted to yield no impact on
sensitivity. In case of the QIAstat-Dx SARS-CoV-2 Panel, 99.11% of the genomes matched with a 100%
coverage all oligonucleotides, and critical variations were tested in vitro corroborating no loss of
sensitivity.
Conclusions: This analysis stresses the importance of targeting more than one region in the viral genome
for SARS-CoV-2 detection to mitigate the risk of loss of sensitivity due to the unknown mutation rate
during this SARS-CoV-2 outbreak.