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
Affiliations
Shivani Fox-Lewis
Microbiology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand; Corresponding author at: Microbiology Department, LabPLUS, Auckland City Hospital, Building 31, Gate 4 off Grafton Rd, Grafton, Auckland, New Zealand.
Andrew Fox-Lewis
Microbiology Department, Middlemore Hospital, Auckland District Health Board, Auckland, New Zealand
Jay Harrower
Auckland Regional Public Health Service, Auckland District Health Board, Auckland, New Zealand
Richard Chen
Jet Park Managed Isolation and Quarantine Facility, Auckland, New Zealand
Jing Wang
Institute of Environmental Science and Research (ESR), Wellington, New Zealand
Joep de Ligt
Institute of Environmental Science and Research (ESR), Wellington, New Zealand
Gary McAuliffe
Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
Susan Taylor
Microbiology Department, Middlemore Hospital, Auckland District Health Board, Auckland, New Zealand
Erasmus Smit
Institute of Environmental Science and Research (ESR), Wellington, New Zealand
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.
