1
|
Rahmasari R, Raekiansyah M, Aliyah SH, Yodi P, Baihaqy F, Irhamsyah M, Sari KCDP, Suryadi H, Moi ML, Sauriasari R. Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting. Sci Rep 2024; 14:1817. [PMID: 38245603 PMCID: PMC10799953 DOI: 10.1038/s41598-024-52250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.
Collapse
Affiliation(s)
- Ratika Rahmasari
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia.
| | | | - Siti Hana Aliyah
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Priska Yodi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Fathan Baihaqy
- Helix Laboratory & Clinic, Depok, West Java, Indonesia
- Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung, West Java, Indonesia
| | | | | | - Herman Suryadi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Meng Ling Moi
- School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rani Sauriasari
- Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| |
Collapse
|