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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
•Publicly available RT-PCR Panels detect SARS-CoV-2 targeting more than one genomic region.•Genetic variability observed until week 21 is predicted to have no effect on panel sensitivity.•The QIAstat-Dx SARS-CoV-2 Panel remains highly sensitive despite the nucleotide variations.•Combination of multi...
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Published in: | International journal of infectious diseases 2020-08, Vol.97, p.225-229 |
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Main Authors: | , , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
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Summary: | •Publicly available RT-PCR Panels detect SARS-CoV-2 targeting more than one genomic region.•Genetic variability observed until week 21 is predicted to have no effect on panel sensitivity.•The QIAstat-Dx SARS-CoV-2 Panel remains highly sensitive despite the nucleotide variations.•Combination of multiple assays in RT-PCR SARS-CoV-2 panels mitigate possible sensitivity loss.•Genetic variability assessment is critical to monitor sensitivity and specificity of the assays.
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.
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.
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.
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. |
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ISSN: | 1201-9712 1878-3511 |
DOI: | 10.1016/j.ijid.2020.06.027 |