Temporal dynamics of the lung and plasma viromes in lung transplant recipients

Abstract

The human virome plays an important role for the clinical outcome of lung transplant recipients (LTRs). While pathogenic viruses may cause severe infections, non-pathogenic viruses may serve as potential markers for the level of immunosuppression. However, neither the complexity of the virome in different compartments nor the dynamics of the virus populations posttransplantation are yet understood. Therefore, in this study the virome was analyzed by metagenomic sequencing in simultaneously withdrawn bronchoalveolar lavage (BAL) and plasma samples of 15 LTRs. In seven patients, also follow-up samples were investigated for abundance and dynamics of virus populations posttransplantation. Five eukaryotic and two prokaryotic virus families were identified in BAL, and nine eukaryotic and two prokaryotic families in plasma. Anelloviruses were the most abundant in both compartments, followed by Herpes- and Coronaviruses. Virus abundance was significantly higher in LTRs than in healthy controls (Kruskal-Wallis test, p<0.001). Up to 48 different anellovirus strains were identified within a single LTR. Analyses in the follow-up patients revealed for the first time a highly complex and unique dynamics of individual anellovirus strains in the posttransplantation period. The abundance of anelloviruses in plasma was inversely correlated with that of other eukaryotic viruses (Pearson correlation coefficient r = -0.605; p<0.05). A broad spectrum of virus strains co-exists in BAL and plasma of LTRs. Especially for the anelloviruses, a high degree of co-infections and a highly individual and complex dynamics after transplantation was observed. The biological impact of these findings and their relation to clinical variables remain to be elucidated by future analyses.

Fig 1. Viral families identified in 15 lung transplant recipients.

(A) Viral families identified in BAL samples, and (B) plasma samples obtained simultaneously at different time points after transplantation (F1-F7: LTRs with follow up samples; P1-P8: LTRs tested at only one time point). (C) Viral families identified in 7 healthy controls (C1-C7). Numbers after the patient identifier indicate days after transplantation for LTRs; and days between first and second sample for the healthy controls. Log10 abundance in reads per million.

Fig 2. Abundance of anelloviruses in different body compartments and number of strains by genogroup.

(A) Abundance of anelloviruses (number of sequencing reads per million) in BAL and plasma of 15 LTRs and in plasma of healthy controls (***:p<0.001; Kruskal-Wallis with post-hoc test). (B) Number of anellovirus strains in each genogroup normalized by the total number of reads sequenced for each sample and the total number of different strains identified per genogroup (*:p<0.05; Wilcoxon rank sum test).

Fig 3. Abundance and diversity of anellovirus strains in BAL and plasma.

(A) and (B) Average abundance of anellovirus strains found over all time points in BAL and plasma samples of LTRs. The strains are shown according to phylogenetic similarity and grouped by genogroup. Bar height indicates Log10 abundance (reads per million). (C) Shannon diversity indexes of LTR BAL samples based on TTV strains. (D) Shannon diversity indexes of LTR plasma samples based on TTV strains.

Fig 4. Within patient anellovirus isolates present at each time point after transplantation in BALs and plasma samples of LTRs (F1-F3).

C2 is a healthy control sample. *For C2, y-axis indicates day at which sample was taken. Blue lines: anellovirus strains detected simultaneously in BAL and plasma. Black lines: anellovirus strains present in only one body compartment.

Fig 5. Relation between the abundance of anelloviruses and of other eukaryotic viruses.

(A) and (B) Abundance of anelloviruses (Log10) versus the abundance of other eukaryotic viruses (non-anelloviruses) in BAL and plasma of 15 LTRs, respectively. Only one sample per patient was used for this analysis, for the time points closer to 87 days after transplantation.