RT Journal Article
T1 A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic.
A1 Peñas-Utrilla, Daniel
A1 Sanz, Amadeo
A1 Catalán Alonso, Pilar
A1 Veintimilla, Cristina
A1 Alcalá, Luis
A1 Alonso Fernández, Roberto Alfonso
A1 Muñoz García, Patricia Carmen
A1 Pérez-Lago, Laura
A1 García de Viedma, Darío
AB BackgroundCOVID-19 diagnosis lies on the detection of SARS-CoV-2 on nasopharyngeal specimens by RT-PCR. The Xpert-Xpress SARS-CoV-2 assay provides results in less than one hour from specimen reception, which makes it suitable for clinical/epidemiological circumstances that require faster responses. The analysis of a COVID-19 outbreak suspected in the neonatology ward from our institution showed that the Ct values obtained for the targeted genes in the Xpert assay were markedly different within each specimen (N Ct value > 20 cycles above the E Ct value).ResultsWe identified the mutation C29200T in the N gene as responsible for an impairment in the N gene amplification by performing whole genome sequencing of the specimens involved in the outbreak (Omicron variant). Subsequently, a retrospective analysis of all specimens sequenced in our institution allowed us to identify the same SNP as responsible for similar impairments in another 12 cases (42% of the total cases reported in the literature). Finally, we found that the same SNP emerged in five different lineages independently, throughout almost all the COVID-19 pandemic.ConclusionsWe demonstrated for the first time the impact of this SNP on the Xpert assay, when harbored by new Omicron variants. We extend our observation period throughout almost all the COVID-19 pandemic, offering the most updated observations of this phenomenon, including sequences from the seventh pandemic wave, until now absent in the reports related to this issue. Continuous monitoring of emerging SNPs that could affect the performance of the most commonly used diagnostic tests, is required to redesign the tests to restore their correct performance.
PB BioMed Central Ltd
SN 1471-2180
YR 2023
FD 2023-07-17
LK https://hdl.handle.net/20.500.14352/119963
UL https://hdl.handle.net/20.500.14352/119963
LA eng
NO Peñas-Utrilla D, Sanz A, Catalán P, Veintimilla C, Alcalá L, Alonso R, et al. A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic. BMC Microbiology. 2023;23(1).
NO Instituto de Salud Carlos III (PI21/01823), FEDER fund “A way of making Europe”, the CIBER -Consorcio Centro de Investigación Biomédica en Red (CB06/06/0058, CB21/13/00044), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea- European Regional Development Fund, and the ECDC (2021/PHF/23776). Miguel Servet Contract (CPII20/00001) to LPL
DS Docta Complutense
RD 13 may 2025