Real-time PCR Ct Values of Detection of Epstein-Barr Virus (EBV) EBNA1 Gene in Nasopharyngeal Swab Samples

Wardhana, Arroyan; Prayuni, Kinasih; Razari, Intan; Suseno, Dedy; Hidayati, Anggi Puspa Nur; Sari, Wening; Al-Fathani, Adilah Ulinnuha; Saputra, Zuki; Mahatmi, Karisma Prameswari Patria; Yossarsongko, Handoko Nugroho; Herawati, Cita; Saputra, Fahreza; Sutandyo, Noorwaty; Setiawan, Lyana; Susanti, Susanti; Akbariani, Gilang; Nurainy, Neni; Utomo, Ahmad Rusdan Handoyo

doi:10.31557/APJCP.2026.27.9.3179

Real-time PCR Ct Values of Detection of Epstein-Barr Virus (EBV) EBNA1 Gene in Nasopharyngeal Swab Samples

Document Type : Research Articles

Authors

¹ Graduate School of Biomedical Sciences, Universitas YARSI, Jakarta, Indonesia.

² Faculty of Medicine, Universitas YARSI, Jakarta, Indonesia.

³ Genomic Research Centre, Universitas YARSI, Jakarta, Indonesia.

⁴ YARSI Research Institute, Universitas YARSI, Jakarta, Indonesia.

⁵ Dharmais Cancer Hospital, Jakarta, Indonesia.

⁶ PathGen Diagnostik Teknologi, Cibinong, Indonesia.

⁷ Biofarma, Bandung, Indonesia.

10.31557/APJCP.2026.27.9.3179

Abstract

Objective: Nasopharyngeal cancer (NPC) is highly prevalent in Asia; however, no established screening program exists to identify high-risk individuals. This study evaluated the potential utility of real-time PCR cycle threshold (Ct) values of Epstein-Barr virus (EBV) DNA detection in nasopharyngeal swabs (NS) as a practical non-invasive screening approach. Methods: Nasopharyngeal cytobrush (CB) and swab (NS) samples were collected from 98 patients with NPC, and NS samples were collected from 174 non-NPC individuals. Real-time PCR targeted the EBNA1 gene, with a Ct cutoff < 35 defined as positive. Beta-globin amplification served as an internal control to verify sample adequacy. Results: In NPC patients, 79% and 81% were EBNA1 positive in CB and NS specimens, respectively. In non-NPC individuals, 10.3% were EBNA1 positive. Median Ct values were 24.4 in NPC patients and 34.4 in non-NPC individuals (p<0.001). Using a Ct cutoff of <35, the diagnostic performance of detecting EBNA1 in NS specimens showed 81% sensitivity, 90% specificity, and 90% accuracy. Conclusion: A real-time PCR Ct cutoff of< 35 for EBNA1 detection provides a practical and effective non-invasive screening tool for NPC in endemic populations. Further validation in prospective cohorts is required.

Keywords

Main Subjects