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

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

doi:10.1016/j.idcr.2021.e01233

Cited by 12 publications

(14 citation statements)

References 10 publications

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“…All nasopharyngeal swabs underwent routine rRT-PCR diagnostic testing by using the Cepheid Xpert Xpress SARS-CoV-2 assay (Cepheid, https://www.cepheid.com ) or an E gene rRT-PCR laboratory-developed test on the Panther Fusion platform (Hologic, https://www.hologic.com ) ( 10 , 11 ). WGS and phylogenetic analysis was undertaken as previously described ( 12 , 13 ).…”

Section: Methodsmentioning

confidence: 99%

“…Persons entering the country must complete a period of quarantine in one of several government-assigned managed quarantine facilities (MQFs) that form part of the border response ( 7 – 9 ). While in a MQF, asymptomatic persons undergo mandatory SARS-CoV-2 screening tests by real-time reverse transcription PCR (rRT-PCR) of nasopharyngeal swab samples routinely collected on days 0, 3, and 12 after arrival in New Zealand, or as close to these times as practical ( 10 ). Symptomatic persons and MQF room companions of SARS-CoV-2–positive persons are tested as soon as possible after symptom onset or case identification ( 7 , 10 ).…”

mentioning

confidence: 99%

“…While in a MQF, asymptomatic persons undergo mandatory SARS-CoV-2 screening tests by real-time reverse transcription PCR (rRT-PCR) of nasopharyngeal swab samples routinely collected on days 0, 3, and 12 after arrival in New Zealand, or as close to these times as practical ( 10 ). Symptomatic persons and MQF room companions of SARS-CoV-2–positive persons are tested as soon as possible after symptom onset or case identification ( 7 , 10 ). Persons who are identified as symptomatic at the border, have had a positive SARS-CoV-2 screening test, or who share the same MQF room as another SARS-CoV-2–positive person are immediately transferred from their respective MQF to a single dedicated managed isolation facility (MIF) for confirmed and suspected COVID-19 cases and close contacts.…”

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confidence: 99%

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Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Fox‐Lewis¹,

Williamson²,

Harrower³

et al. 2022

Emerg. Infect. Dis.

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In New Zealand, international arrivals are quarantined and undergo severe acute respiratory syndrome coronavirus 2 screening; those who test positive are transferred to a managed isolation facility (MIF). Solo traveler A and person E from a 5-person travel group (BCDEF) tested positive. After transfer to the MIF, person A and group BCDEF occupied rooms >2 meters apart across a corridor. Persons B, C, and D subsequently tested positive; viral sequences matched A and were distinct from E. The MIF was the only shared location of persons A and B, C, and D, and they had no direct contact. Security camera footage revealed 4 brief episodes of simultaneous door opening during person A’s infectious period. This public health investigation demonstrates transmission from A to B, C, and D while in the MIF, with airborne transmission the most plausible explanation. These findings are of global importance for coronavirus disease public health interventions and infection control practices.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Fox‐Lewis¹,

Williamson²,

Harrower³

et al. 2022

Emerg. Infect. Dis.

Self Cite

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“…Our data confirm that in places with a high level of SARS-CoV-2 infection rate, such as Moscow and the Moscow Region, and due to the high transmissibility of the virus and the spread of novel variants with mutations in a primer or probe location, the effectiveness of RT-PCR could be impaired. Several mutations in the binding sites of the target primers or probes in the N gene of SARS-CoV-2/SARS-CoV in almost all used diagnostic test systems for SARS-CoV-2 with the detection of gene N have been reported [ 13 , 22 , 23 , 24 ]. That leads to a decrease in the sensitivity of the assay and potentially underestimated diagnostics if only one detection target is used.…”

Section: Discussionmentioning

confidence: 99%

Identification of Hotspot Mutations in the N Gene of SARS-CoV-2 in Russian Clinical Samples That May Affect the Detection by Reverse Transcription-PCR

et al. 2022

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Sensitive and reliable diagnostic test systems based on real-time PCR are of great importance in the fight against the ongoing SARS-CoV-2 pandemic. The genetic variability of the SARS-CoV-2 virus leads to the accumulation of mutations, some of which may affect the sensitivity of modern PCR assays. The aim of this study was to search in Russian clinical samples for new mutations in SARS-CoV-2 gene N that can affect the detection by RT-PCR. In this study, the polymorphisms in the regions of the target gene N causing failed or poor detection of the target N in the RT-PCR assay on 12 selected samples were detected. Sequencing the entire N and E genes in these samples along with other 195 samples that were positive for both target regions was performed. Here, we identified a number of nonsynonymous mutations and one novel deletion in the N gene that affected the ability to detect a target in the N gene as well a few mutations in the E gene of SARS-CoV-2 that did not affect detection. Sequencing revealed that majority of the mutations in the N gene were located in the variable region between positions 193 and 235 aa, inside and nearby the phosphorylated serine-rich region of the protein N. This study highlights the importance of the further characterization of the genetic variability and evolution of gene N, the most common target for detecting SARS-CoV-2. The use of at least two targets for detecting SARS-CoV-2, including one for the E gene, will be necessary for reliable diagnostics.

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“…Two of these point mutations occur at the same nucleotide position, C29200T first described by Ziegler, Steininger [ 9 ], and C29200A described by Hasan, Sundararaju [ 10 ]. The fourth, and most recent mutation identified is C29197T [ 11 , 12 ]. Although there have been cases of target failure of the E-gene in the cobas SARS-CoV-2 test by Roche Diagnostics (Basel, Switzerland), to date there are no documented point mutations that cause failure of the E-gene target in either the Xpert Xpress SARS-CoV-2 or Xpert Omni SARS-CoV-2 assays [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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The C29197T mutation is one of 4 point mutations known to cause N-gene target failure (NGTF) in the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays from Cepheid (Sunnyvale, CA). We describe a high local prevalence in January of 8.5% (CI 4.9–14.2%) for the C29197T mutation, which was over 3-fold higher than the prevalence estimated statewide in California during the same time frame, 2.5% (CI 2.1–2.8%). Using phylogenetic analysis, we discovered that this increase in prevalence was due, at least in part, to a disproportionately large infection cluster of unknown origin. This study emphasizes the importance of sequencing at the local jurisdictional level and demonstrates the impact that regional variation can have when assessing risk due to point mutations that impact clinical test performance. It also reinforces the need for diligent reporting of abnormal test results by clinical laboratories, especially during Emergency Use Authorization (EUA) periods, as additional information is gathered about the target organism and the performance of EUA-authorized tests over time.

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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

Cited by 12 publications

References 10 publications

Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Identification of Hotspot Mutations in the N Gene of SARS-CoV-2 in Russian Clinical Samples That May Affect the Detection by Reverse Transcription-PCR

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

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