Viral metagenomics analysis of kidney donors and recipients: Torque teno virus genotyping and prevalence

Abstract

The viral load of the ubiquitous and nonpathogenic torque teno virus (TTV) is associated with the grade of immunosuppression of its host. The development of next‐generation sequencing (NGS) allowed to describe the human virome of the blood compartment in transplanted patients, and showed that TTV is the most important part of the virome. This study is a descriptive retrospective pilot study of sequencing plasma samples from 15 matched donors and recipients. After sample processing, nucleic acids were amplified by rolling circle amplification and submitted to NGS by ion proton sequencing technology. Results were analyzed after mapping of reads on the 29 TTV reference genomes and de novo assembling of the reads with MIRA software. The number of TTV species present in donors and recipients was, on average, 12 in donors and 33 in recipients. TTV species predominantly present in donors were TTV‐13 and TTV‐18; and in recipients were TTV‐P15‐2, TTV‐27, TTV‐HD14a, and TTV‐22. We highlighted a significant variability in abundance and composition in sequential samples from recipients. Temporal evolution of TTV populations was clearly observed in recipients, but no preferential transmission of a species from donor to recipient was evidenced. Diversity and population expansion were observed in kidney recipients. Further study of TTV species could help assess the potential impact of each species of this virus.

Comparative metavirome analysis in polytransfused patients

“…In blood donors, the most abundant TTV type was 24. Nevertheless, the obtained TTV composition in patients and blood donors seems to be similar to other studies that examined plasma virome not only of blood donors ( 11 ) but also of patients undergoing solid organ transplantation ( 12 ) and in kidney donors and recipients ( 13 ). Based on the above cited studies and the obtained results from our study, we believe that some TTV types might be more broadly adapted to the human blood environment despite the clinical condition of the host.…”

Clinical Relevance of Torque Teno Virus (TTV) in HIV/HCV Coinfected and HCV Monoinfected Patients Treated with Direct-Acting Antiviral Therapy

“…The assay limit of detection is 167 copies/mL and the linearity range is 1.61–10.61 Log copies/mL [ 39 ]. This assay can detect and quantify a broad range of human alpha-torquetenovirus genotypes (TTV genotypes 1/3/6–8/10/12/15/16/19/27/28) [ 39 , 40 ] belonging to genogroups 1–5. All DAA-treated patients had their serum tested at EOT.…”

Genomic Diversity of Torque Teno Virus in Blood Samples from Febrile Paediatric Outpatients in Tanzania: A Descriptive Cohort Study

“…Next-generation sequencing (NGS) technologies have made it possible to investigate intra-host genomic diversity at an unprecedented level of granularity. It is now established that humans are very frequently co-infected by several species and genotypes [ 16 , 17 , 18 ], with the possible detection of a considerable number of genotypes within a single individual and that this diversity may remain stable over time [ 19 ]. The reason for this genetic diversity is not yet clear.…”