Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jul 17;23(1):190.
doi: 10.1186/s12866-023-02924-8.

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

Daniel Peñas-Utrilla  1   2 , Amadeo Sanz  1   2 , Pilar Catalán  1   2 , Cristina Veintimilla  1   2 , Luis Alcalá  1   2 , Roberto Alonso  1   2   3 , Patricia Muñoz  1   2   3   4 , Laura Pérez-Lago  1   2 , Darío García de Viedma  5   6   7 ; Gregorio Marañón Microbiology-ID COVID 19 Study Group
Collaborators, Affiliations

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

Daniel Peñas-Utrilla et al. BMC Microbiol. .

Abstract

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.

Keywords: C29200T; COVID-19; Cepheid Xpert; Detection impairment; N gene.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Graphic representation of the findings (waves sampled, number of lineages and specimens identified harboring it) extracted from the literature and from our study regarding C29200T SNP
See this image and copyright information in PMC

References

    1. Rodríguez-Grande C, Alcalá L, Estévez A, Sola-Campoy PJ, Buenestado-Serrano S, Martínez-Laperche C, et al. Systematic genomic and clinical analysis of severe acute respiratory syndrome coronavirus 2 reinfections and recurrences involving the same strain. Emerg Infect Dis. 2022;28(1):85. - PMC - PubMed
    1. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20(4):1160–1166. doi: 10.1093/bib/bbx108. - DOI - PMC - PubMed
    1. Kuraku S, Zmasek CM, Nishimura O, Katoh K. aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Res. 2013;41(Web Server issue):W22. doi: 10.1093/nar/gkt389. - DOI - PMC - PubMed
    1. Ziegler K, Steininger P, Ziegler R, Steinmann J, Korn K, Ensser A. SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene. Eurosurveillance. 2020;25(39):2001650. doi: 10.2807/1560-7917.ES.2020.25.39.2001650. - DOI - PMC - PubMed
    1. Leelawong M, Mitchell SL, Fowler RC, Gonzalez E, Hughes S, Griffith MP, et al. SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States. Diagn Microbiol Infect Dis. 2021;101(3):115468. doi: 10.1016/j.diagmicrobio.2021.115468. - DOI - PMC - PubMed

Publication types

Supplementary concepts