Shah, D;
Brown, JR;
Lee, JCD;
Carpenter, ML;
Wall, G;
Breuer, J;
(2022)
Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients.
Journal of Clinical Virology Plus
, 2
(2)
, Article 100073. 10.1016/j.jcvp.2022.100073.
(In press).
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Abstract
Background: Infections by several DNA viruses can severely impact outcomes in paediatric immunocompromised patients. Current testing, which is generally limited to singleplex qPCR assays, can miss both common and rarer viruses if they are not targeted. Objectives: To evaluate the performance of the Galileo Viral Panel (Galileo), a sample-to-result shotgun metagenomics platform for the detection and quantification of 12 DNA viruses, compared to standard of care qPCR assays. Study design: A clinical performance evaluation was carried out using 43 prospectively collected EDTA plasma samples positive for one or more DNA viruses. Agreement between assays was assessed by overall, positive, and negative percent agreement, as well as quantitative agreement by linear regression and Bland-Altman analysis. Results: Overall positive percent agreement was 84% (95% CI: 76%-90%), and negative percent agreement was 95% (95% CI: 92%-97%). There was a high correlation between Galileo and qPCR for ADV, CMV, EBV, and VZV (R2 = 0.91) and a mean difference by Bland Altman of -0.43 log10 IU or cp/ml (95% limits of agreement, -1.37 to 0.51). In addition, there was a high correlation between Galileo Signal Score and qPCR for TTV (R2 = 0.85). Conclusion: We observed high qualitative and quantitative agreement between qPCR and Galileo. Galileo identified additional viruses that were not tested with routine qPCR and could impact clinical outcomes.
| Type: | Article |
|---|---|
| Title: | Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.jcvp.2022.100073 |
| Publisher version: | https://doi.org/10.1016/j.jcvp.2022.100073 |
| Language: | English |
| Additional information: | © 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
| Keywords: | Metagenomics, Transplant viruses, Next-generation sequencing, Paediatric viral infection, qPCR |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10146983 |
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