The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern
ABSTRACT: Objectives: We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). Methods: This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single react...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-02-01
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| Series: | International Journal of Infectious Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971222006191 |
| _version_ | 1797943118073430016 |
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| author | Hsing-Yi Chung Ming Jian, Jr Chih-Kai Chang Chi-Sheng Chen Shih-Yi Li Jung-Chung Lin Kuo-Ming Yeh Ya-Sung Yang Chien-Wen Chen Shan-Shan Hsieh Sheng-Hui Tang Cherng-Lih Perng Kuo-Sheng Hung Feng-Yee Chang Hung-Sheng Shang |
| author_facet | Hsing-Yi Chung Ming Jian, Jr Chih-Kai Chang Chi-Sheng Chen Shih-Yi Li Jung-Chung Lin Kuo-Ming Yeh Ya-Sung Yang Chien-Wen Chen Shan-Shan Hsieh Sheng-Hui Tang Cherng-Lih Perng Kuo-Sheng Hung Feng-Yee Chang Hung-Sheng Shang |
| author_sort | Hsing-Yi Chung |
| collection | DOAJ |
| description | ABSTRACT: Objectives: We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). Methods: This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be used to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. Results: The limit of detection of each gene locus was 80 copies per polymerase chain reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. Conclusion: The assay can also be applied in a commercial platform with the completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours. |
| first_indexed | 2024-04-10T20:18:13Z |
| format | Article |
| id | doaj.art-ceb5baa8564341c6a04ee1b053650715 |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-04-10T20:18:13Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-ceb5baa8564341c6a04ee1b0536507152023-01-26T04:44:31ZengElsevierInternational Journal of Infectious Diseases1201-97122023-02-011275662The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concernHsing-Yi Chung0Ming Jian, Jr1Chih-Kai Chang2Chi-Sheng Chen3Shih-Yi Li4Jung-Chung Lin5Kuo-Ming Yeh6Ya-Sung Yang7Chien-Wen Chen8Shan-Shan Hsieh9Sheng-Hui Tang10Cherng-Lih Perng11Kuo-Sheng Hung12Feng-Yee Chang13Hung-Sheng Shang14Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan; Graduate Institute of Medical Science, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanCenter for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, TaiwanDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan; Corresponding author.ABSTRACT: Objectives: We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). Methods: This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be used to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. Results: The limit of detection of each gene locus was 80 copies per polymerase chain reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. Conclusion: The assay can also be applied in a commercial platform with the completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours.http://www.sciencedirect.com/science/article/pii/S1201971222006191SARS-CoV-2 variantVariant of concernsCOVID-19High-throughputOmicron |
| spellingShingle | Hsing-Yi Chung Ming Jian, Jr Chih-Kai Chang Chi-Sheng Chen Shih-Yi Li Jung-Chung Lin Kuo-Ming Yeh Ya-Sung Yang Chien-Wen Chen Shan-Shan Hsieh Sheng-Hui Tang Cherng-Lih Perng Kuo-Sheng Hung Feng-Yee Chang Hung-Sheng Shang The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern International Journal of Infectious Diseases SARS-CoV-2 variant Variant of concerns COVID-19 High-throughput Omicron |
| title | The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern |
| title_full | The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern |
| title_fullStr | The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern |
| title_full_unstemmed | The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern |
| title_short | The application of a novel 5-in-1 multiplex reverse transcriptase–polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern |
| title_sort | application of a novel 5 in 1 multiplex reverse transcriptase polymerase chain reaction assay for rapid detection of sars cov 2 and differentiation between variants of concern |
| topic | SARS-CoV-2 variant Variant of concerns COVID-19 High-throughput Omicron |
| url | http://www.sciencedirect.com/science/article/pii/S1201971222006191 |
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