Metagenomic Next-Generation Sequencing for the Identification and Quantitation of Transplant-Related DNA Viruses. Journal of clinical microbiology Carpenter, M. L., Tan, S. K., Watson, T., Bacher, R., Nagesh, V., Watts, A., Bentley, G., Weber, J., Huang, C., Sahoo, M. K., Hinterwirth, A., Doan, T., Carter, T., Dong, Q., Gourguechon, S., Harness, E., Kermes, S., Radhakrishnan, S., Wang, G., Quiroz-Zarate, A., Ching, J., Pinsky, B. A. 2019


Infections with DNA viruses are frequent causes of morbidity and mortality in transplant recipients. This study describes the analytical and clinical performance characteristics of the Arc Bio Galileo Pathogen Solution, an all-inclusive metagenomic next-generation sequencing (mNGS) reagent and bioinformatics pipeline that allows the simultaneous quantitation of 10 transplant-related dsDNA viruses (ADV, BKV, CMV, EBV, HHV-6A, HHV-6B, HSV-1, HSV-2, JCV, and VZV). The mNGS 95% limit of detection ranged from 14 international units (IU)/mL (HHV-6) to 191 copies/mL (BKV), and the lower limit of quantitation ranged from 442 IU/mL (EBV) to 661 copies/mL (VZV). Evaluation of 50 residual plasma samples with at least one DNA virus detected in prior clinical testing showed a total percent agreement of mNGS and qPCR of 89.2% (306/343), with a kappa statistic of 0.725. The positive percent agreement was 84.9% (73/86) and negative percent agreement was 90.7% (233/257). Furthermore, mNGS detected seven subsequently confirmed co-infections that were not initially requested by qPCR. Passing-Bablok regression revealed a regression line of Y = 0.953*X + 0.075 [95% CI of the slope (0.883 to 1.011) and intercept (-0.100 to 0.299)], and Bland-Altman analysis (mNGS - qPCR) showed a slight positive bias (0.28 log10 concentration, 95% limits of agreement of -0.62 to 1.18). In conclusion, the mNGS-based Galileo pipeline demonstrates comparable analytical and clinical performance to qPCR for transplant-related DNA viruses.

View details for DOI 10.1128/JCM.01113-19

View details for PubMedID 31554674