2026-06-08T04:19:27Zhttps://docta.ucm.es/rest/oai/request
oai:docta.ucm.es:20.500.14352/1199632025-07-30T17:40:42Zcom_20.500.14352_14col_20.500.14352_15
Docta Complutense author Peñas-Utrilla, Daniel author Sanz, Amadeo author Catalán Alonso, Pilar author Veintimilla, Cristina author Alcalá, Luis author Alonso Fernández, Roberto Alfonso author Muñoz García, Patricia Carmen author Pérez-Lago, Laura author García de Viedma, Darío 2025-05-09T16:06:26Z 2025-05-09T16:06:26Z 2023 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). 1471-2180 10.1186/S12866-023-02924-8 https://hdl.handle.net/20.500.14352/119963 https://doi.org/10.1186/S12866-023-02924-8 37460980 https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02924-8 Background COVID-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). Results We 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. Conclusions We 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. eng Attribution 4.0 International A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic. journal article 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URL https://docta.ucm.es/bitstreams/2a1da34b-c3c2-43fa-8a64-6ced4e4f2729/download File MD5 3fa71050db84dd68d337e8afcd78b818 1005122 application/pdf A_mutation_responsible_for_impaired_detection-by_the_ Xpert.pdf