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Monitoring of alphatorquevirus (torque teno virus [TTV]) DNA in plasma may prove to be useful to assess the net state of immune competence following allogeneic hematopoietic stem cell transplantation (allo‐HSCT). There are scarce data published on the prevalence of beta (torque teno mini virus [TTMV]) and gammatorqueviruses (torque teno midi virus [TTMDV]) and, in particular, on the dynamics of anelloviruses in allo‐HSCT patients. Twenty‐five allo‐HSCT recipients with available plasma specimens obtained before conditioning and after engraftment were included. Degenerated primers targeting a highly conserved genomic sequence across all anelloviruses were designed for genomic amplification and high‐throughput sequencing. Co‐detection of TTV, TTMV, and TTMDV both in pre‐transplant and post‐engraftment plasma specimens was documented in more than two‐thirds of patients. The use of quantitative real‐time polymerase chain reaction (PCR) assays targeting TTMV and TTMDV in addition to TTV may add value to TTV‐specific PCR assays in the inference of the net state of immunosuppresion or immune competence in this clinical setting. [ABSTRACT FROM AUTHOR]