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

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.

Keywords: Anelloviridae; immunocompromised patients; next-generation sequencing; stem cell transplant recipients; torque teno virus; viral metagenomics.

Figure 1

Proportion of anellovirus reads in NTC, HV, and ASCT recipients. The median of anellovirus reads proportion (among total viral reads) obtained from the 10 ASCT recipients and 8 HV is represented according to gender. One NTC (nuclease free-water processed through the metagenomics workflow) per batch was used to evaluate the contamination. The median value of anellovirus is also represented for the NTC. NTC: no-template control; HV: healthy volunteers; ASCT: autologous stem cell transplantation; F: female; M: male.

Figure 2

Anellovirus abundance and composition among the 10 ASCT recipients from diagnosis to 90 days post-ASCT (a) Kinetics of TTV, TTMV, and TTMDV (b) Kinetics of the 5 TTV genogroups. TTV: torque teno virus; TTMV: torque teno mini virus; TTMDV: torque teno midi virus; ASCT: autologous stem cell transplantation; F: female; M: male. RPM: reads per million mapped reads.

Figure 3

Correlation between the results of metagenomic NGS and TTV qPCR. Normalized number of reads obtained for torque teno virus (TTV) using mNGS are presented in function of the TTV viral load determined using qPCR. RPM: reads per million mapped reads.