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A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic.

dc.contributor.authorPeñas-Utrilla, Daniel
dc.contributor.authorSanz, Amadeo
dc.contributor.authorCatalán Alonso, Pilar
dc.contributor.authorVeintimilla, Cristina
dc.contributor.authorAlcalá, Luis
dc.contributor.authorAlonso Fernández, Roberto Alfonso
dc.contributor.authorMuñoz García, Patricia Carmen
dc.contributor.authorPérez-Lago, Laura
dc.contributor.authorGarcía de Viedma, Darío
dc.date.accessioned2025-05-09T16:06:26Z
dc.date.available2025-05-09T16:06:26Z
dc.date.issued2023-07-17
dc.description.abstractBackground 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.
dc.description.departmentDepto. de Enfermería
dc.description.facultyFac. de Enfermería, Fisioterapia y Podología
dc.description.refereedTRUE
dc.description.sponsorshipInstituto 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
dc.description.statuspub
dc.identifier.citationPeñas-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).
dc.identifier.doihttps://doi.org/10.1186/S12866-023-02924-8
dc.identifier.issn1471-2180
dc.identifier.officialurlhttps://doi.org/10.1186/S12866-023-02924-8
dc.identifier.pmid37460980
dc.identifier.relatedurlhttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02924-8
dc.identifier.urihttps://hdl.handle.net/20.500.14352/119963
dc.issue.number1
dc.journal.titleBMC Microbiology
dc.language.isoeng
dc.page.final6
dc.page.initial1
dc.publisherBioMed Central Ltd
dc.rightsAttribution 4.0 Internationalen
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subject.cdu61
dc.subject.keywordC29200T
dc.subject.keywordCOVID-19
dc.subject.keywordCepheid Xpert
dc.subject.keywordDetection impairment
dc.subject.keywordN gene
dc.subject.ucmCiencias Biomédicas
dc.subject.unesco3299 Otras Especialidades Médicas
dc.titleA mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic.
dc.typejournal article
dc.type.hasVersionVoR
dc.volume.number23
dspace.entity.typePublication
relation.isAuthorOfPublication39395567-f35a-4917-83d2-1b2a7f0af5a4
relation.isAuthorOfPublicationfd62e7d5-ce12-40bd-bdd5-eceb530d66c0
relation.isAuthorOfPublication057f539e-41b0-4a1e-b97b-204a23ead398
relation.isAuthorOfPublication.latestForDiscovery39395567-f35a-4917-83d2-1b2a7f0af5a4

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