Azlan, Adlina Sarah and Shahdan, Intan Azura and Kamarudin, Norhidayah (2025) Assessment on residual buffer sample mixture of rapid antigen assay performance in SARS-CoV-2 genomic surveillance: a cross-sectional study in a Malaysian teaching hospital. Malaysian Journal of Microbiology, 21 (1). pp. 19-23. ISSN 1823-8262 E-ISSN 2231-7538
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Abstract
Aims: Initially, COVID-19 PCR samples were frequently collected for genetic sequencing, thereby prolonging the processing time for diagnosing, screening and surveillance of SARS-CoV-2 virus. The direct utilisation of residual buffer sample mixtures (RBSM) from COVID-19 antigen rapid test kits for whole genome sequencing (WGS) offers a potential solution to expedite processing time. Thus, this study aimed to perform genomic surveillance of SARS-CoV-2 variants utilising samples obtained from RBSM of rapid antigen test kits. Methodology and results: For sample collection, nasopharyngeal swabs were collected from inpatients and outpatients of a teaching hospital in Pahang, Malaysia, between October 2022 and April 2023. Antigen fluorescent immunoassays (Ag-FIA) were conducted on all samples. RNA extraction and SARS-CoV-2 real-time PCR (RT-PCR) were then performed on positive Ag-FIA RBSM. Subsequently, variant analysis was carried out using GISAID (https://gisaid.org/). A total of 12,059 swabs were collected, with an Ag-FIA positivity rate of 2.7% (321/12059). Upon RT-PCR, 224/321 (69.8%) samples met the sequencing criteria with a Ct value of less than 30. To date, 66 samples have been completely sequenced, with less than half of the total samples (45.5%) revealing the presence of Omicron subvariants (BA.1.1.529, BA.2.75, XBB and XBB.1.5). Conclusion, significance and impact of study: All in all, this study demonstrates that the RBSM from Ag-FIA generates valid sequencing results and hence, can be optimised for rapid detection of viral variants.
| Item Type: | Article (Journal) |
|---|---|
| Uncontrolled Keywords: | Diagnostic testing, genome sequencing, reagent kit, RT-PCR, SARS-CoV-2 |
| Subjects: | Q Science > QR Microbiology R Medicine > RB Pathology R Medicine > RJ Pediatrics > RJ50 Examination. Diagnosis > RJ51.A-Z Special diagnostic methods, A-Z R Medicine > RT Nursing > RT48 Nursing assessment > RT48.5 Diagnostic techniques, Laboratory tests, etc. |
| Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button): | Kulliyyah of Allied Health Sciences Kulliyyah of Allied Health Sciences > Department of Biomedical Science (Effective:1st July 2011) Kulliyyah of Medicine Kulliyyah of Medicine > Department of Pathology & Lab Medicine |
| Depositing User: | Dr Norhidayah Kamarudin |
| Date Deposited: | 10 Nov 2025 16:38 |
| Last Modified: | 10 Nov 2025 16:38 |
| URI: | http://irep.iium.edu.my/id/eprint/124283 |
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