Abstract
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Open-Reading Frame 1a (ORF1a) Gene Target Failure with Omicron BA.5.2.1 Caused by Partial Deletion of the ORF1a Gene
by Hirofumi Toda, Yuki Yamamoto, Yuji Tanaka, Kenji Yamade, Tomohisa Kawabata, Kazue Yoshitomi, Toshinori Kamisako
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Background: We identified two cases of Omicron BA.5.2.1 that exhibited characteristics of open-reading frame 1a (ORF1a) gene target failure (OGTF) in RNA detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The purpose of this study was to determine the cause of the OGTF in the two samples.
Method: Samples were specimens obtained from a 37-year-old male and a 43-year-old female who were suspected to have Coronavirus disease 2019. SARS-CoV-2 RNA detection using μTAS Wako g1 system (FUJIFILM Wako Pure Chemical, Osaka, Japan) was performed and it detected S gene but did not detect ORF1a gene.
Results: The results of whole genome sequencing of these samples showed that SARS-CoV-2 genome in these two samples matched to Omicron BA.5.2.1. SARS-CoV-2 genomes in the two samples had a deletion of 15 bases and a deletion of 9 bases, so that they overlapped with the 3'-terminal side of the primer binding region in ORF1a gene, and these deletions were considered to be the cause of OGTF.
Conclusions: Since such a gene target failure due to base deletion is not considered rare, it was considered desirable to implement a multi-target detection in SARS-CoV-2 RNA molecular diagnostic system to address the mutation or deletion of the viral gene.
DOI: 10.7754/Clin.Lab.2024.240913
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