PMID- 31554674 OWN - NLM STAT- MEDLINE DCOM- 20200716 LR - 20210521 IS - 1098-660X (Electronic) IS - 0095-1137 (Print) IS - 0095-1137 (Linking) VI - 57 IP - 12 DP - 2019 Dec TI - Metagenomic Next-Generation Sequencing for Identification and Quantitation of Transplant-Related DNA Viruses. LID - 10.1128/JCM.01113-19 [doi] LID - e01113-19 AB - 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 double-stranded DNA (dsDNA) viruses (adenovirus [ADV], BK virus [BKV], cytomegalovirus [CMV], Epstein-Barr virus [EBV], human herpesvirus 6A [HHV-6A], HHV-6B, herpes simplex virus 1 [HSV-1], HSV-2, JC virus [JCV], and varicella-zoster virus [VZV]). The mNGS 95% limit of detection ranged from 14 copies/ml (HHV-6) to 191 copies/ml (BKV), and the lower limit of quantitation ranged from 442 international units (IU)/ml (EBV) to 661 copies/ml (VZV). An 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 quantitative PCR (qPCR) of 89.2% (306/343), with a kappa statistic of 0.725. The positive percent agreement was 84.9% (73/86), and the negative percent agreement was 90.7% (233/257). Furthermore, mNGS detected seven subsequently confirmed coinfections that were not initially requested by qPCR. Passing-Bablok regression revealed a regression line of y = 0.953x + 0.075 (95% confidence interval [CI] of the slope, 0.883 to 1.011; intercept, -0.100 to 0.299), and Bland-Altman analysis (mNGS - qPCR) showed a slight positive bias (0.28 log(10) concentration; 95% limits of agreement, -0.62 to 1.18). In conclusion, the mNGS-based Galileo pipeline demonstrates analytical and clinical performance comparable to that of qPCR for transplant-related DNA viruses. CI - Copyright (c) 2019 Carpenter et al. FAU - Carpenter, Meredith L AU - Carpenter ML AD - Arc Bio, LLC, Scotts Valley, California, USA meredith@arcbio.com. FAU - Tan, Susanna K AU - Tan SK AUID- ORCID: 0000-0001-5835-8660 AD - Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA. FAU - Watson, Thomas AU - Watson T AD - Arc Bio, LLC, Cambridge, Massachusetts, USA. FAU - Bacher, Rowena AU - Bacher R AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Nagesh, Vaishnavi AU - Nagesh V AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Watts, Alain AU - Watts A AD - Arc Bio, LLC, Cambridge, Massachusetts, USA. FAU - Bentley, Gordon AU - Bentley G AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Weber, Jenna AU - Weber J AD - Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. FAU - Huang, ChunHong AU - Huang C AD - Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. FAU - Sahoo, Malaya K AU - Sahoo MK AD - Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. FAU - Hinterwirth, Armin AU - Hinterwirth A AD - Francis I Proctor Foundation, University of California San Francisco, San Francisco, California, USA. FAU - Doan, Thuy AU - Doan T AD - Francis I Proctor Foundation, University of California San Francisco, San Francisco, California, USA. AD - Department of Ophthalmology, University of California San Francisco, San Francisco, California, USA. FAU - Carter, Theodore AU - Carter T AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Dong, Queeny AU - Dong Q AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Gourguechon, Stephane AU - Gourguechon S AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Harness, Eric AU - Harness E AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Kermes, Sean AU - Kermes S AD - Arc Bio, LLC, Cambridge, Massachusetts, USA. FAU - Radhakrishnan, Srihari AU - Radhakrishnan S AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Wang, Gongbo AU - Wang G AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Quiroz-Zarate, Alejandro AU - Quiroz-Zarate A AD - Arc Bio, LLC, Cambridge, Massachusetts, USA. FAU - Ching, Jesus AU - Ching J AD - Arc Bio, LLC, Scotts Valley, California, USA. FAU - Pinsky, Benjamin A AU - Pinsky BA AUID- ORCID: 0000-0001-8751-4810 AD - Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA. AD - Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. LA - eng GR - R43 AI138864/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20191122 PL - United States TA - J Clin Microbiol JT - Journal of clinical microbiology JID - 7505564 SB - IM MH - Computational Biology/methods MH - DNA Virus Infections/*diagnosis MH - DNA Viruses/classification/genetics/*isolation & purification MH - High-Throughput Nucleotide Sequencing/*methods MH - Humans MH - Metagenomics/*methods MH - Molecular Diagnostic Techniques/*methods MH - Sensitivity and Specificity MH - Transplantation/*adverse effects PMC - PMC6879295 OTO - NOTNLM OT - DNA sequencing OT - genomics OT - transplant infectious diseases OT - virology EDAT- 2019/09/27 06:00 MHDA- 2020/07/17 06:00 PMCR- 2019/11/22 CRDT- 2019/09/27 06:00 PHST- 2019/07/09 00:00 [received] PHST- 2019/09/20 00:00 [accepted] PHST- 2019/09/27 06:00 [pubmed] PHST- 2020/07/17 06:00 [medline] PHST- 2019/09/27 06:00 [entrez] PHST- 2019/11/22 00:00 [pmc-release] AID - JCM.01113-19 [pii] AID - 01113-19 [pii] AID - 10.1128/JCM.01113-19 [doi] PST - epublish SO - J Clin Microbiol. 2019 Nov 22;57(12):e01113-19. doi: 10.1128/JCM.01113-19. Print 2019 Dec.