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

• Published in: Current Issues in Molecular Biology Vol. 45; no. 5; pp. 4124 - 4134
• Main Authors: Yamashita, Keita, Taniguchi, Terumi, Niizeki, Noriyasu, Nagao, Yuki, Suzuki, Akira, Toguchi, Akihiro, Takebayashi, Shiori, Ishikawa, Jinko, Nagura, Osanori, Furuhashi, Kazuki, Iwaizumi, Moriya, Maekawa, Masato
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 07.05.2023; MDPI
• Subjects: Ct value; DNA sequencing; G29179T; Genes; Genetic aspects; GeneXpert; Genomes; Genomics; Health aspects; infection control; Nucleotide sequencing; quality control; SARS-CoV-2; Japan; G29179T; SARS-CoV-2; infection control; Ct value; quality control; GeneXpert
• ISSN: 1467-3045; 1467-3037; 1467-3045
• DOI: 10.3390/cimb45050262

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 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.