Comparison of Plasma Metagenomic Next-generation Sequencing and PCR Methods for Epstein-Barr Virus Viral Load Monitoring in Nasopharyngeal Carcinoma.

Abstract

Background/aim: Plasma Epstein-Barr virus (EBV) viral load measurement is prognostic in nasopharyngeal carcinoma (NPC) disease monitoring; however, a consensus measurement approach does not exist. This study characterized the clinical performance of metagenomic next-generation sequencing (mNGS), an unbiased sequencing-based assay distinct from polymerase chain reaction (PCR) or targeted sequencing approaches, in 73 peripheral blood specimens from 32 patients diagnosed with NPC.

Patients and methods: Samples were analyzed for plasma EBV viral load either by mNGS profiling or PCR-based assays (either LMP2 or BAMHI-W PCR) and compared to tumor presence by clinical assessment. Plasma mNGS-based EBV detection was quantified as reads per million (RPM).

Results: Plasma mNGS displayed similar overall performance (100% sensitivity, 86% specificity, 92% accuracy) to BAMHI-W PCR (100% sensitivity, 86% specificity, 94% accuracy) and superior performance to the LMP2 PCR assay (36% sensitivity, 56% specificity, 45% accuracy). In a subset of 13 patients who underwent longitudinal analysis, plasma mNGS EBV RPM correlated with cancer recurrence (95%CI Pre-CRT=232.10±214; 95%CI Post-CRT=0.34±0.32; 95%CI difference=-231.70±214; *p=0.03, paired t-test), suggesting plasma mNGS exhibits potential for monitoring recurrence.

Conclusion: Plasma mNGS is a distinct method for EBV titer measurement in NPC patients and more broadly, is a promising method for non-invasive monitoring of disease status for infection-associated malignancies.