SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic. Diagnostic testing for SARS-CoV-2 has continuously been challenged due to several variants with diverse spike (S) and nucleocapsid (N) protein mutations []. SARS-CoV-2 variant proliferation potentially affects N prot...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | International Journal of Infectious Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971221008535 |
| _version_ | 1819097789661970432 |
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| author | Ming-Jr Jian Hsing-Yi Chung Chih-Kai Chang Jung-Chung Lin Kuo-Ming Yeh Chien-Wen Chen De-Yu Lin Feng-Yee Chang Kuo-Sheng Hung Cherng-Lih Perng Hung-Sheng Shang |
| author_facet | Ming-Jr Jian Hsing-Yi Chung Chih-Kai Chang Jung-Chung Lin Kuo-Ming Yeh Chien-Wen Chen De-Yu Lin Feng-Yee Chang Kuo-Sheng Hung Cherng-Lih Perng Hung-Sheng Shang |
| author_sort | Ming-Jr Jian |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic. Diagnostic testing for SARS-CoV-2 has continuously been challenged due to several variants with diverse spike (S) and nucleocapsid (N) protein mutations []. SARS-CoV-2 variant proliferation potentially affects N protein-targeted rapid antigen testing. In this study, rapid antigen and reverse transcription PCR (RT-PCR) tests were performed simultaneously in patients with suspected coronavirus disease 2019 (COVID-19). Direct whole genome sequencing was performed to determine the N protein variations, and the viral assemblies were uploaded to GISAID. The genomes were then compared with those of global virus strains from GISAID. These isolates belonged to the B.1.1.7 variant, exhibiting several amino acid substitutions, including D3L, R203K, G204R, and S235F N protein mutations. The T135I mutation was also identified in one variant case in which the rapid antigen test and RT-PCR test were discordantly negative and positive, respectively. These findings suggest that the variants undetected by the Panbio COVID-19 rapid antigen test may be due to the T135I mutation in the N protein, posing a potential diagnostic risk for commercially available antigen tests. Hence, we recommend concomitant paired rapid antigen tests and molecular diagnostic methods to detect SARS-CoV-2. False-negative results could be rapidly corrected using confirmatory RT-PCR results to prevent future COVID-19 outbreaks. |
| first_indexed | 2024-12-22T00:20:41Z |
| format | Article |
| id | doaj.art-38d454027a0c4adeb2e5f1ea07400fdc |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-12-22T00:20:41Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-38d454027a0c4adeb2e5f1ea07400fdc2022-12-21T18:45:10ZengElsevierInternational Journal of Infectious Diseases1201-97122022-01-01114112114SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performanceMing-Jr Jian0Hsing-Yi Chung1Chih-Kai Chang2Jung-Chung Lin3Kuo-Ming Yeh4Chien-Wen Chen5De-Yu Lin6Feng-Yee Chang7Kuo-Sheng Hung8Cherng-Lih Perng9Hung-Sheng Shang10Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCCenter for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROCDivision of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC; Corresponding author: Hung-Sheng Shang, Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan, ROC. Tel: +886 920713130. Fax: +886 287927226.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic. Diagnostic testing for SARS-CoV-2 has continuously been challenged due to several variants with diverse spike (S) and nucleocapsid (N) protein mutations []. SARS-CoV-2 variant proliferation potentially affects N protein-targeted rapid antigen testing. In this study, rapid antigen and reverse transcription PCR (RT-PCR) tests were performed simultaneously in patients with suspected coronavirus disease 2019 (COVID-19). Direct whole genome sequencing was performed to determine the N protein variations, and the viral assemblies were uploaded to GISAID. The genomes were then compared with those of global virus strains from GISAID. These isolates belonged to the B.1.1.7 variant, exhibiting several amino acid substitutions, including D3L, R203K, G204R, and S235F N protein mutations. The T135I mutation was also identified in one variant case in which the rapid antigen test and RT-PCR test were discordantly negative and positive, respectively. These findings suggest that the variants undetected by the Panbio COVID-19 rapid antigen test may be due to the T135I mutation in the N protein, posing a potential diagnostic risk for commercially available antigen tests. Hence, we recommend concomitant paired rapid antigen tests and molecular diagnostic methods to detect SARS-CoV-2. False-negative results could be rapidly corrected using confirmatory RT-PCR results to prevent future COVID-19 outbreaks.http://www.sciencedirect.com/science/article/pii/S1201971221008535COVID-19SARS-CoV-2Rapid antigen testB.1.1.7 variantN protein |
| spellingShingle | Ming-Jr Jian Hsing-Yi Chung Chih-Kai Chang Jung-Chung Lin Kuo-Ming Yeh Chien-Wen Chen De-Yu Lin Feng-Yee Chang Kuo-Sheng Hung Cherng-Lih Perng Hung-Sheng Shang SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance International Journal of Infectious Diseases COVID-19 SARS-CoV-2 Rapid antigen test B.1.1.7 variant N protein |
| title | SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance |
| title_full | SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance |
| title_fullStr | SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance |
| title_full_unstemmed | SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance |
| title_short | SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance |
| title_sort | sars cov 2 variants with t135i nucleocapsid mutations may affect antigen test performance |
| topic | COVID-19 SARS-CoV-2 Rapid antigen test B.1.1.7 variant N protein |
| url | http://www.sciencedirect.com/science/article/pii/S1201971221008535 |
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