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SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance
Ming-Jr Jian1, Hsing-Yi Chung1, Chih-Kai Chang1
1Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC.
Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with nucleocapsid (N) protein mutations may evade rapid antigen tests. Concomitant rapid antigen and RT-PCR testing is recommended for accurate COVID-19 diagnosis.
Area of Science:
- Virology
- Infectious Diseases
- Diagnostic Medicine
Background:
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants present diagnostic challenges.
- Mutations in spike (S) and nucleocapsid (N) proteins of SARS-CoV-2 impact diagnostic test accuracy.
- Rapid antigen tests targeting the N protein may be affected by viral mutations.
Purpose of the Study:
- To investigate the impact of SARS-CoV-2 N protein mutations on rapid antigen test performance.
- To compare the diagnostic accuracy of rapid antigen tests and RT-PCR for COVID-19 detection.
- To identify specific N protein mutations associated with discordant test results.
Main Methods:
- Simultaneous testing of patients with suspected COVID-19 using rapid antigen and RT-PCR assays.
- Whole genome sequencing to identify N protein variations in SARS-CoV-2 isolates.
- Comparison of sequenced viral genomes with global strains via GISAID.
- Analysis of N protein mutations, including T135I, in relation to test discordance.
Main Results:
- SARS-CoV-2 isolates belonged to the B.1.1.7 variant with multiple N protein mutations (D3L, R203K, G204R, S235F).
- A T135I mutation in the N protein was identified in a case with discordant results (negative rapid antigen, positive RT-PCR).
- This mutation may lead to SARS-CoV-2 variants being undetected by the Panbio COVID-19 rapid antigen test.
Conclusions:
- The T135I mutation in the SARS-CoV-2 N protein poses a diagnostic risk for specific antigen tests.
- Concomitant use of rapid antigen and molecular diagnostic methods is recommended for reliable SARS-CoV-2 detection.
- Confirmatory RT-PCR testing can correct false-negative antigen test results, preventing further outbreaks.
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