Evaluation of SARS-CoV-2 RT-PCR test using swabs after quantitative antigen test

• Published in: Japanese Journal of Medical Technology Vol. 74; no. 1; pp. 118 - 123
• Main Authors: YANAGITA, Mitsutoshi, IWASAKI, Seiji, OZAWA, Tetsuo, GOTOU, Masashi, AIDA, Izumi, NAKAJIMA, Ryo
• Format: Journal Article
• Language: Japanese
• Published: Japanese Association of Medical Technologists 25.01.2025; 一般社団法人 日本臨床衛生検査技師会
• Subjects: melting curve analysis; nasopharyngeal swab; quantative antigen test; real-time reverse transcription PCR; SARS-CoV-2; 使用済みスワブ; 抗原定量検査; 融解曲線解析
• ISSN: 0915-8669; 2188-5346
• DOI: 10.14932/jamt.24-45

Since the onset of COVID-19 pandemic in Japan, we launched both a quantitative antigen test and a real-time reverse transcription PCR test (RT-PCR) for SARS-CoV-2. We confirmed that the accuracy of the two tests was sufficient for clinical use. Initially, two nasopharyngeal swabs were collected separately for each test. Subsequently, we tried to perform these tests using a single nasopharyngeal swab to alleviate the stress on patients associated with sample collection. First, we extracted RNA from the remaining liquid sample for the antigen test and performed RT- PCR testing on 122 subjects. However, all results were negative, including 28 subjects positive for RT-PCR test using fresh nasopharyngeal swabs (nasopharyngeal RT-PCR test). We assumed that an unidentified PCR inhibitory factor contained in the sample treatment reagent caused the false negative results. Therefore, we extracted the viral RNA from the cotton swab used for the antigen test and ran the RT-PCR (used swab RT-PCR test). The results of the used swab and the nasopharyngeal RT-PCR tests were completely consistent on 228 samples. However, the Cp values in the used swab RT-PCR test (25.3 ± 4.2) were significantly higher than those in the nasopharyngeal RT-PCR test (22.9 ± 4.4) (t-test, p < 0.05). In addition, we performed identification of omicron variant BA.1 and BA.2 using both the nasopharyngeal and the used swab RT-PCR tests with melting curve analysis, and the results were completely consistent on 26 studied samples. In conclusion, the used swab RT-PCR test showed approximately equivalent assay performance to the nasopharyngeal RT-PCR test.