Alpha 2.0
Login Register
» Articles » PMID: 34336597

Lack of N2-gene Amplification on the Cepheid Xpert Xpress SARS-CoV-2 Assay and Potential Novel Causative Mutations: A Case Series from Auckland, New Zealand

Overview
Journal IDCases
Specialty Infectious Diseases
Date 2021 Aug 2
PMID 34336597
Citations 8
Authors
Shivani Fox-Lewis
Andrew Fox-Lewis
Jay Harrower
Richard Chen
Jing Wang
Joep de Ligt
Gary McAuliffe
Susan Taylor
Erasmus Smit
Affiliations
Soon will be listed here.
Abstract

We describe three cases with viral strains that demonstrate impaired N2-gene detection on the Cepheid Xpert Xpress SARS-CoV-2 assay, with two previously undescribed single nucleotide polymorphisms (SNPs): C29197T and G29227T. We propose that these SNPs are likely responsible since they are in close proximity to the previously described C29200T/C29200A SNPs, already shown to abolish N2-gene detection by the Xpert assay. Whether these SNPs abolish N2-gene detection by the Xpert assay individually or only in combination requires more work to elucidate.

Citing Articles

Partial N-gene target failure in the Seegene Allplex SARS-CoV-2 Master Assay as a proxy of SARS-CoV-2 BA.2.86.

Valli M, Schiavone M, Rueca M, Berno G, Spezia P, Gruber C Microbiol Spectr. 2024; 12(6):e0017924.

PMID: 38647335 PMC: 11237703. DOI: 10.1128/spectrum.00179-24.

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

Penas-Utrilla D, Sanz A, Catalan P, Veintimilla C, Alcala L, Alonso R BMC Microbiol. 2023; 23(1):190.

PMID: 37460980 PMC: 10351113. DOI: 10.1186/s12866-023-02924-8.

Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert System and a Mutation Associated with Different Target Gene Failure.

Yamashita K, Taniguchi T, Niizeki N, Nagao Y, Suzuki A, Toguchi A Curr Issues Mol Biol. 2023; 45(5):4124-4134.

PMID: 37232731 PMC: 10217001. DOI: 10.3390/cimb45050262.

Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection.

Kami W, Kinjo T, Hashioka H, Arakaki W, Uechi K, Takahashi A J Virol Methods. 2023; 314:114692.

PMID: 36796678 PMC: 9930255. DOI: 10.1016/j.jviromet.2023.114692.

Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2.

Lopez D, Roberts J, Bourgeois M, Kootstra J, Minnick S, Black A PLoS One. 2022; 17(2):e0264008.

PMID: 35171960 PMC: 8849547. DOI: 10.1371/journal.pone.0264008.

References
1.
Corman V, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D . Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020; 25(3). PMC: 6988269. DOI: 10.2807/1560-7917.ES.2020.25.3.2000045. View
2.
Wang R, Hozumi Y, Yin C, Wei G . Mutations on COVID-19 diagnostic targets. Genomics. 2020; 112(6):5204-5213. PMC: 7502284. DOI: 10.1016/j.ygeno.2020.09.028. View
3.
Loeffelholz M, Alland D, Butler-Wu S, Pandey U, Perno C, Nava A . Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test. J Clin Microbiol. 2020; 58(8). PMC: 7383535. DOI: 10.1128/JCM.00926-20. View
4.
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. Euro Surveill. 2020; 25(39). PMC: 7531073. DOI: 10.2807/1560-7917.ES.2020.25.39.2001650. View
5.
Mostafa H, Carroll K, Hicken R, Berry G, Manji R, Smith E . Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test. J Clin Microbiol. 2020; 59(3). PMC: 8106732. DOI: 10.1128/JCM.02955-20. View