Longitudinal monitoring of DNA viral loads in transplant patients using quantitative metagenomic next-generation sequencing

Abstract

Introduction Immunocompromised patients are prone to reactivations of multiple latent DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metagenomic next-generation sequencing (mNGS) approach was used for identification and load monitoring of transplantation-related DNA viruses. Methods Longitudinal plasma samples from six patients that were qPCR-positive for cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyoma virus (BKV, adenovirus (ADV), parvovirus B19 (B19V), and torque teno-virus (TTV) were sequenced using the quantitative metagenomic Galileo Viral Panel Solution (Arc Bio, LLC) reagents and bioinformatics pipeline combination. Qualitative and quantitative performance was analysed with focus on viral load ranges relevant for clinical decision-making. Results All pathogens identified by qPCR were also identified by mNGS. In addition, BKV, CMV, and HHV6B were detected by mNGS which were not ordered initially but could be confirmed by qPCR. Viral loads determined by mNGS correlated with the qPCR results, with inter-method differences in viral load per virus ranging from 0.19 log10 IU/ml for EBV to 0.90 log10 copies/ml for ADV. TTV, analysed by mNGS in a semi-quantitative way, showed a mean difference of 3.0 log10 copies/ml. Trends over time in viral load determined by mNGS and qPCR were comparable, and clinical thresholds for initiation of treatment were equally indicated by mNGS. Conclusion The Galileo Viral Panel for quantitative mNGS performed comparable to qPCR with regard to detection and viral load determination, within clinically relevant ranges of patient management algorithms.