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Background: Immunosuppressed individuals such as kidney transplant recipients (KTR) and hemodialysis patients (DP) show impaired immune responses to COVID-19 vaccination. Plasma Torque Teno Virus (TTV) DNA load is used as surrogate for the individual degree of immunosuppression. We now assessed the association of TTV load at time of COVID-19 vaccination with humoral and cellular immune response rates to vaccination in KTR, DP, and healthy medical personnel (MP)., Methods: A total of 100 KTR, 115 DP and 54 MP were included. All were SARS-CoV-2 seronegative at the time of vaccination with either BNT162b2 or mRNA-1273. Plasma TTV loads were assessed at the time of first vaccination. After two-dose vaccination, seroconversion (de novo detection of SARS-CoV-2 S1-IgA and/or IgG) was determined. In addition, cellular responses as assessed by interferon γ release and neutralizing antibodies were assessed in a subset of participants. ROC analyses were performed to define TTV load cut-offs predicting specific immune responses to vaccination., Results: Plasma TTV loads at the time of first vaccination were negatively associated with seroconversion after two-dose vaccination in KTR (OR 0.87, 95% CI 0.76-0.99). TTV loads were significantly lower in KTR who developed humoral and cellular immune responses to vaccination compared to non-responders (p = 0.0411 and 0.0030, respectively). Of patients with TTV loads above 10 6 copies/ml, none developed cellular immune responses against SARS-CoV-2, and only 2 of 17 (12%) seroconverted in response to vaccination., Conclusion: Plasma TTV loads at the time of first vaccination in immunosuppressed individuals may be useful to predict individual vaccine-specific immune responses., Competing Interests: Declaration of Competing Interest The authors declare no commercial or other association that might pose a conflict of interest., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: Torque Teno virus (TTV) is non-pathogenic, highly prevalent and reflects the immune status of its host. TTV plasma load was suggested for risk stratification of graft rejection and infection post kidney-transplantation, for which most studies applied an in-house PCR. Recently, a commercial PCR was CE-certified for clinical use. The present study was designed to assess the performance of TTV load as quantified by the commercial PCR in the prediction of graft rejection and infection., Methods: Patients and events were selected from the prospective TTV-POET trial, including 683 consecutive adult recipients of a kidney-graft transplanted at the Medical University Vienna, 2016-2020. TTV was quantified in plasma drawn in Months 4-12 post-transplant by in-house and commercial PCR and associated with consecutive infections and graft rejections until Month 12 post-transplantation., Results: A total of 342 samples from 314 patients with 85 biopsies (rejection, n = 18) and 79 infectious events were assessed. The two PCRs were highly associated (estimate 0.91, 95%CI 0.89-0.93), with a mean difference of 1.38 log 10 copies/mL (95%CI 1.46-1.30). The risk of rejection decreased by 25% with every log 10 increase in TTV load as quantified by commercial PCR (RR 0.75, 95%CI 0.67-0.85), and the risk of infection increased by 6% (RR 1.06, 95%CI 1.00-1.12)., Conclusion: These data support the value of TTV quantification by commercial PCR for the risk stratification of graft rejection and infection in the first year post kidney-transplantation. The test performance determined within this study may serve to design clinical trials and subsequently, support application in clinical routine., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Fanny Gelas, Dorian Kulifaj and Ludovic Brossault are employees of bioMérieux., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: The detection of SARS-CoV-2 vRNA in clinical samples has relied almost exclusively on RT-qPCR as the gold standard test. Published results from various external quality assessments ("ring trials") worldwide have shown that there is still a large variability in results reported for the same samples. As reference standards of SARS-CoV-2 RNA are available, we tested whether using standard curves to convert Ct values into copies/mL (cp/mL) improved harmonization., Methods: Nine laboratories using 23 test systems (15 of which were unique) prepared standard dilution curves to convert C t values of 13 SARS-CoV-2 positive samples to cp/mL (hereafter IU/mL). The samples were provided in three rounds of a virus genome detection external quality assessment (EQA) scheme. We tested the precision and accuracy of results reported in IU/mL, and attempted to identify the sources of variability., Results: Reporting results as IU/mL improved the precision of the estimated concentrations of all samples compared to reporting Ct values, although some inaccuracy remained. Variance analysis showed that nearly all variability in data was explained by individual test systems within individual laboratories. When controlling for this effect, there was no significant difference between all other factors tested (test systems, EQA rounds, sample material)., Conclusions: Converting results to copies/mL improved precision across laboratory test systems. However, it seems the results are still very specific to test systems within laboratories. Further efforts could be made to improve accuracy and achieve full harmonization across diagnostic laboratories., Competing Interests: Declaration of Competing Interest The authors declare no competing financial nor non-financial interests., (Copyright © 2022. Published by Elsevier B.V.)

Background: Human pegivirus 1 (HPgV1) may cause persistent infections in immunocompetent and immunosuppressed individuals. Its clinical relevance, however, has not been determined. Previous studies have described a higher prevalence of HPgV1 infection in organ transplant recipients compared to healthy controls, but its occurrence in lung transplant recipients (LTRs) and its association with immunosuppressive therapy has not been assessed., Objectives: The aim of this study was to evaluate the prevalence and clinical significance of HPgV1 infection in LTRs, and to compare HPgV1 loads and kinetics to Torque Teno Virus (TTV) kinetics, which reflects the level of immunosuppression., Study Design: From each of 110 LTRs, five consecutive plasma samples were collected within the first year after transplantation and tested for HPgV1 RNA and TTV DNA loads by quantitative PCR. Data were related to demographic data and clinical parameters followed up for 3 years post transplantation., Results: HPgV1 prevalence in LTRs was 18,2%. HPgV1 detection was significantly associated with younger age, but not with graft rejections or other microbial infections. The viral replication level remained unaffected by immunosuppressive therapy. This was in contrast to TTV loads which increased after initiation of immunosuppressive therapy, independent of the patients' HPgV1 infection status., Conclusions: In contrast to TTV, HPgV1 kinetics do not reflect the level of immunosuppression after lung transplantation, and there is no correlation between the replication of both persistent viruses in the post transplantation follow up. Thus the individual virus host interactions seem to differ substantially and require further investigation., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Different human cytomegalovirus (HCMV) strains may persistently coexist in the human host. In immunosuppressed patients infection with mixed HCMV populations was associated with a more severe course of infection. Congenital HCMV infection may lead to severe fetal disease and possibly mixed HCMV strain infections might have also impact on the clinical consequences for the newborn. Mixed HCMV strain populations were so far detected in saliva but only rarely in urine of congenitally infected newborns., Objectives: We have therefore analyzed the extent of mixed HCMV genotype populations in urine of congenitally infected newborns using a highly sensitive deep sequencing method., Study Design: Twenty urine samples (17 initial and 3 follow-up samples) from 17 congenitally infected newborns with a median HCMV DNA load of 7.5log10 copies/ml were included. Deep sequencing was applied for gO (UL74) genotyping and quantitative real-time PCR assays were used for gB (UL55) and gH (UL75) genotyping., Results: In none of the urine samples a gO genotype mixture was detected, although a mean of 10.000 sequence reads per amplicon was analyzed, which allows to explore gO genotypes down to less than 1% of the total gO sequences. Also only one gB genotype was detected in the patients' initial samples, while a gH genotype mixture was detected in one case using real time PCR with a sensitivity of 5% for minor populations., Conclusion: Mixed HCMV genotype populations are only rarely found in urine of congenitally infected newborns even when highly sensitive HCMV genotyping methods are applied., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Background: Immunocompetent individuals can harbor multiple human cytomegalovirus (HCMV) genotypes. However, little is known about the genotype populations acquired during primary HCMV infection., Objective: The aim of this study was to assess the HCMV genotype populations present in the blood of non-immunocompromised patients experiencing primary HCMV infection., Study Design: HCMV glycoprotein B (gB), glycoprotein H (gH), and UL10 genotyping was performed on HCMV-positive serum samples of 36 immunocompetent patients during primary infection by sensitive gB- and gH-genotype-specific real-time-PCR assays and by UL10 sequencing., Results: In all cases only one gB-gH-UL10 genotype was detected. In contrast, mixed-genotype infections were found in 4 of 14 immunocompetent patients experiencing HCMV reactivation/reinfection (P=0.004)., Conclusion: Thus, the data support the presumption that multiple HCMV genotypes in immunocompetent individuals are often a result of serial reinfection rather than primary coinfection with different strains., (Copyright 2010 Elsevier B.V. All rights reserved.)

Cytomegalovirus (CMV) as well as Epstein Barr virus (EBV) genomes include regions which show in part substantial polymorphisms. Characterization of several polymorphic regions led to the identification of various CMV and EBV subtypes. Within the last years there have been undertaken numerous efforts to find out whether the diverse subtypes differentially contribute to clinical manifestations. However, although some associations have been described so far between a certain virus subtype and the development of individual diseases these analyses were greatly complicated by the huge genomic background of CMV and EBV, by the large variety of individual host-virus relations and by differences in the geographic or demographic subtype distribution. In addition, it was shown meanwhile that a substantial proportion of virus infections is due to mixed infections with different subtypes. In this review we will give an overview of the current knowledge concerning the clinical significance of individual CMV and EBV subtypes, defined by characterization of selected polymorphisms. In addition, we also focus on recent analyses which show that infection with mixed virus subtype populations may be disadvantageous compared to single virus subtype infections.

Latent Epstein-Barr virus (EBV) nuclear antigens (EBNA)-3A, -3B, and -3C are involved in transcription regulation of both viral and cellular genes. In the present study, we chose functionally important regions within EBNA3A, -3B, and -3C genes with putative tumorigenic potential to investigate natural sequence variations among EBV Type I strains circulating in Europe. Based on the identification of linked EBNA3A, -3B, and -3C sequence patterns, we defined five EBNA3 variants in addition to the B95.8 prototype sequence. Phylogenetic analysis revealed that EBNA3 variant 5, the most diverged from the B95.8 sequence, showed an evolutionary history of intertypic recombination events occurring upstream and downstream of the C-terminus of EBNA3A. The frequency of occurrence of the five newly defined EBNA3 variants was similar for strains causing EBV primary infection or reactivation and was also similar within two of the European areas investigated. In addition, preferential linkages of certain EBNA3 variants to distinct latent membrane protein 1 (LMP1) groups were found to exist. Thus, a combination of more than one polymorphic site in the EBV genome might be involved in determining disease characteristics.