The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction

Abstract

Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. Thus far, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 month post-transplant and found that levels of Anellovirus, mainly Torque teno viruses (TTV), were significantly higher than in non-transplant healthy controls. Here we used quantitative PCR to analyze TTV and shotgun metagenomics to characterize full viral communities in acellular bronchoalveolar lavage from donor organs and post-reperfusion allografts in PGD and non-PGD lung transplant recipient pairs. Unexpectedly, TTV DNA levels were 100-fold elevated in donor lungs compared with healthy adults (p=0.0026). Although absolute TTV levels did not differ by PGD status, PGD cases showed a smaller increase in TTV levels from pre- to post-transplant than did control recipients (p=0.041). Metagenomic sequencing revealed mainly TTV and bacteriophages of respiratory tract bacteria, but no viral taxa distinguished PGD cases from controls. These findings suggest that conditions associated with brain death promote TTV replication, and that greater immune activation or tissue injury associated with PGD may restrict TTV abundance in the lung.

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

“…Linkeramplified shotgun library (LASL) was applied for virus sequencing from marine water samples [8]. The anchored random PCR approach, as used in our study, has been frequently used and described in detail in previous studies [16,[36][37][38][39][40][41][42].…”

Anellovirus loads are associated with outcomes in pediatric lung transplantation

“…15 Patients who developed PGD after lung transplantation underwent a smaller increase in anellovirus levels from before to after transplant, as compared to non-PGD controls (P = .0026). 27 In another study of lung transplant recipients, alphatorquevirus levels assessed prior to the diagnosis of CLAD were significantly lower in patients who subsequently developed CLAD (P = .020). 17 While no association between alphatorqueviruses and CLAD (defined in the current analysis as either BO or BOS) was established in the current study, the different results may be due to differences in the cohorts or in the timing of the samples tested.…”

“…Low blood anellovirus loads were reported in heart transplant recipients with moderate‐to‐severe graft rejection, as compared to non‐rejecting patients ( P = .011) . Patients who developed PGD after lung transplantation underwent a smaller increase in anellovirus levels from before to after transplant, as compared to non‐PGD controls ( P = .0026) . In another study of lung transplant recipients, alphatorquevirus levels assessed prior to the diagnosis of CLAD were significantly lower in patients who subsequently developed CLAD ( P = .020) .…”

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

“…The prevalence of each microbe in each respiratory sample was described using 2 criteria: abundance relative to other microbes in the same sample, wherein we normalized sequencing reads per million total sequencing reads (rpm), and (2) abundance relative to the same microbe in other samples in the cohort, wherein we normalized sequencing reads as the number of standard deviations above or below the mean log 10 -transformed rpm for the total cohort (Z-score). Given the anticipated wide array of respiratory bacteria and the paucity of knowledge regarding the significance of low-level viruses and fungi, we aimed to maximize specificity for bacterial pathogens and to maximize sensitivity for viral and fungal pathogens [15,23,24]. Therefore, we defined microbial outliers as those with Z-score ≥2 and ≥10 rpm (bacteria) or ≥1 rpm (viruses/fungi).…”