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

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 buffersample 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.