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

Shivani Fox-Lewis; Andrew Fox-Lewis; Jay Harrower; Richard Chen; Jing Wang; Joep de Ligt; Gary McAuliffe; Susan Taylor; Erasmus Smit

doi:10.1016/j.idcr.2021.e01233

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

IDCases. 2021:25:e01233. doi: 10.1016/j.idcr.2021.e01233. Epub 2021 Jul 24.

Authors

Shivani Fox-Lewis¹, Andrew Fox-Lewis², Jay Harrower³, Richard Chen⁴, Jing Wang⁵, Joep de Ligt⁵, Gary McAuliffe⁶, Susan Taylor², Erasmus Smit⁵

Affiliations

¹ Microbiology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand.
² Microbiology Department, Middlemore Hospital, Auckland District Health Board, Auckland, New Zealand.
³ Auckland Regional Public Health Service, Auckland District Health Board, Auckland, New Zealand.
⁴ Jet Park Managed Isolation and Quarantine Facility, Auckland, New Zealand.
⁵ Institute of Environmental Science and Research (ESR), Wellington, New Zealand.
⁶ Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand.

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.

Keywords: COVID-19; Mutations; PCR; SARS-CoV-2; Single nucleotide polymorphisms; Xpert.

Publication types

Case Reports