A recurrent mutation at position 1 26,340 of SARS-CoV-2 is associated with failure of the E-gene qRT-PCR utilized in a commercial dual-target diagnostic assay
[en] Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
pandemic requires accurate laboratory testing to identify infected individuals, while also
clearing essential staff to continue work. At the current time a number of qRT-PCR assays
have been developed to identify SARS-CoV-2, targeting multiple positions in the viral
genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of
transmission chains it is prudent to monitor circulating viruses for variants that might
compromise these assays. Here we report the identification of a C-to-U transition at
position 26,340 of the SARS-CoV-2 genome which is associated with failure of the cobas®
SARS-CoV-2 E-gene qRT-PCR in eight patients. As the cobas® SARS-CoV-2 assay
targets two positions in the genome, the individuals carrying this variant were still called as
SARS-CoV-2 positive. Whole genome sequencing of SARS-CoV-2 showed all to carry
closely related viruses. Examination of viral genomes deposited on GISAID showed this
mutation has arisen independently at least four times. This work highlights the necessity of
monitoring SARS-CoV-2 for the emergence of SNPs which might adversely affect RT
PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.
Disciplines :
Laboratory medicine & medical technology
Author, co-author :
Artesi, Maria ; Université de Liège - ULiège > Cancer-Human Genetics
Bontems, Sébastien ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Département des sciences biomédicales et précliniques
Göbbels, Paul
Franckh, M
Maes, Piet
BOREUX, Raphaël ; Centre Hospitalier Universitaire de Liège - CHU > Unilab > Laboratoire biologie moléculaire
MEEX, Cécile ; Centre Hospitalier Universitaire de Liège - CHU > Unilab > Laboratoire bactériologie
MELIN, Pierrette ; Centre Hospitalier Universitaire de Liège - CHU > Unilab > Service de microbiologie clinique
Hayette, Marie-Pierre ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Bact., mycologie, parasitologie, virologie, microbio.
Bours, Vincent ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Génétique humaine
Durkin, Keith ; Université de Liège - ULiège > Cancer-Human Genetics
Language :
English
Title :
A recurrent mutation at position 1 26,340 of SARS-CoV-2 is associated with failure of the E-gene qRT-PCR utilized in a commercial dual-target diagnostic assay
Alternative titles :
[en] Une mutation récurrente à la position 26 340 de SARS-CoV-2 est associée à l'échec de détection du gène E qRT-PCR utilisé dans un test de diagnostic commercial à double cible
Publication date :
20 July 2020
Journal title :
Journal of Clinical Microbiology
ISSN :
0095-1137
eISSN :
1098-660X
Publisher :
American Society for Microbiology, United States - District of Columbia
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