Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure
SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined u...
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MDPI AG
2023-05-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/45/5/262 |
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| author | Keita Yamashita Terumi Taniguchi Noriyasu Niizeki Yuki Nagao Akira Suzuki Akihiro Toguchi Shiori Takebayashi Jinko Ishikawa Osanori Nagura Kazuki Furuhashi Moriya Iwaizumi Masato Maekawa |
| author_facet | Keita Yamashita Terumi Taniguchi Noriyasu Niizeki Yuki Nagao Akira Suzuki Akihiro Toguchi Shiori Takebayashi Jinko Ishikawa Osanori Nagura Kazuki Furuhashi Moriya Iwaizumi Masato Maekawa |
| author_sort | Keita Yamashita |
| collection | DOAJ |
| description | SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert<sup>®</sup> System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents. |
| first_indexed | 2024-03-11T03:50:37Z |
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| id | doaj.art-5279cda3375c4d13a81ad122d8cf02af |
| institution | Directory Open Access Journal |
| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-03-11T03:50:37Z |
| publishDate | 2023-05-01 |
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| series | Current Issues in Molecular Biology |
| spelling | doaj.art-5279cda3375c4d13a81ad122d8cf02af2023-11-18T00:57:03ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452023-05-014554124413410.3390/cimb45050262Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene FailureKeita Yamashita0Terumi Taniguchi1Noriyasu Niizeki2Yuki Nagao3Akira Suzuki4Akihiro Toguchi5Shiori Takebayashi6Jinko Ishikawa7Osanori Nagura8Kazuki Furuhashi9Moriya Iwaizumi10Masato Maekawa11Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanDepartment of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, JapanSARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert<sup>®</sup> System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents.https://www.mdpi.com/1467-3045/45/5/262SARS-CoV-2GeneXpertCt valueG29179Tinfection controlquality control |
| spellingShingle | Keita Yamashita Terumi Taniguchi Noriyasu Niizeki Yuki Nagao Akira Suzuki Akihiro Toguchi Shiori Takebayashi Jinko Ishikawa Osanori Nagura Kazuki Furuhashi Moriya Iwaizumi Masato Maekawa Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure Current Issues in Molecular Biology SARS-CoV-2 GeneXpert Ct value G29179T infection control quality control |
| title | Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure |
| title_full | Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure |
| title_fullStr | Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure |
| title_full_unstemmed | Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure |
| title_short | Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert<sup>®</sup> System and a Mutation Associated with Different Target Gene Failure |
| title_sort | cycle threshold ct values of sars cov 2 detected with the genexpert sup r sup system and a mutation associated with different target gene failure |
| topic | SARS-CoV-2 GeneXpert Ct value G29179T infection control quality control |
| url | https://www.mdpi.com/1467-3045/45/5/262 |
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