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Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management

1
Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, 69004 Lyon, France
2
Univ Lyon, Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69372 Lyon, France
3
Laboratoire Commun de Recherche HCL-bioMerieux, Centre Hospitalier Lyon Sud, 69495 Pierre-Bénite, France
4
Service d’Hématologie Clinique, Centre Hospitalier Lyon Sud, Pierre-Bénite, 69495 Lyon, France
5
Bioaster, Genomics and Transcriptomics Technological Unit, 69007 Lyon, France
*
Author to whom correspondence should be addressed.
Viruses 2018, 10(11), 633; https://doi.org/10.3390/v10110633
Received: 21 October 2018 / Revised: 6 November 2018 / Accepted: 9 November 2018 / Published: 14 November 2018
(This article belongs to the Special Issue Viromics: Approaches, Advances, and Applications)
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Abstract

Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence. View Full-Text
Keywords: next-generation sequencing; viral metagenomics; immunocompromised patients; stem cell transplant recipients; Anelloviridae; torque teno virus next-generation sequencing; viral metagenomics; immunocompromised patients; stem cell transplant recipients; Anelloviridae; torque teno virus
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Bal, A.; Sarkozy, C.; Josset, L.; Cheynet, V.; Oriol, G.; Becker, J.; Vilchez, G.; Sesques, P.; Mallet, F.; Pachot, A.; Morfin, F.; Lina, B.; Salles, G.; Reynier, F.; Trouillet-Assant, S.; Brengel-Pesce, K. Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management. Viruses 2018, 10, 633.

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