Torque Teno Virus Viral Load as a Marker of Immune Function in Allogeneic Haematopoietic Stem Cell Transplantation Recipients

Torquetenovirus from bronchoalveolar lavage fluid as a biomarker for lung infection among immunocompromised hosts

Aim: Torquetenovirus (TTV) was a promising biomarker for immunity, while lung regional TTV for evaluating the opportunistic infection among immunocompromised hosts (ICH) was unclear. Materials & methods: In the ICH and non-ICH populations, we compared the susceptibility to opportunistic infections, clinical severity and the prognosis between subgroups, respectively. Results: ICH with detectable bronchoalveolar lavage fluid (BALF)-TTV were more susceptible to lung aspergillosis and Mycobacterium infections. Furthermore, our data demonstrated that the ICH cohort with detectable BALF-TTV represented a higher clinical severity and a worse prognosis, while the above findings were not found in the non-ICH population. Conclusion: Our findings demonstrated that the BALF-TTV could act as an effective predictor for opportunistic infection for ICH that complemented the CD4+ T cell counts.

Torque Teno Virus DNA Load in Blood as an Immune Status Biomarker in Adult Hematological Patients: The State of the Art and Future Prospects

A solid body of scientific evidence supports the assumption that Torque teno virus (TTV) DNA load in the blood compartment may behave as a biomarker of immunosuppression in solid organ transplant recipients; in this clinical setting, high or increasing TTV DNA levels precede the occurrence of infectious complications, whereas the opposite anticipates the development of acute rejection. The potential clinical value of the TTV DNA load in blood to infer the risk of opportunistic viral infection or immune-related (i.e., graft vs. host disease) clinical events in the hematological patient, if any, remains to be determined. In fact, contradictory data have been published on this matter in the allo-SCT setting. Studies addressing this topic, which we review and discuss herein, are highly heterogeneous as regards design, patient characteristics, time points selected for TTV DNA load monitoring, and PCR assays used for TTV DNA quantification. Moreover, clinical outcomes are often poorly defined. Prospective, ideally multicenter, and sufficiently powered studies with well-defined clinical outcomes are warranted to elucidate whether TTV DNA load monitoring in blood may be of any clinical value in the management of hematological patients.

High Torque teno virus load and outcome of patients undergoing allogeneic hematopoietic cell transplantation

Quantification of Torque teno virus (TTV) load emerged as a marker of immunosuppression. Associations of TTV load with complications and survival after allogeneic hematopoietic cell transplantation (allo-HCT) were controversial in published studies. In this prospective study, we aimed to identify factors influencing TTV load after allo-HCT and to determine whether the TTV load is associated with complications or outcomes. Seventy allo-HCT recipients were included. TTV DNA load was quantified in 469 plasma samples of 70 patients from Day (D) 15 before D120 after transplantation. The influence of transplant characteristics on TTV load and the associations of TTV load with viral infections, acute graft versus host disease, mortality, and relapse were analyzed. More than 80% of patients were TTV DNA positive from D30 after transplantation onwards. Median TTV load increased between D30 and D60 post-transplantation. Patients with lymphoid malignancies had higher TTV load than those with myeloid malignancies. Myeloablative conditioning was associated with higher TTV loads. Patients with no measurable residual disease at transplant had higher TTV loads. High TTV load at D90 post-transplantation was associated with lower overall survival and at D120 post-transplantation was associated with higher relapse rate. In conclusion, TTV load at time points later than D90 after allo-HCT may be useful to assess prognosis.

Viral DNAemia and DNA Virus Seropositivity and Mortality in Pediatric Sepsis

Importance

Sepsis is a leading cause of pediatric mortality. Little attention has been paid to the association between viral DNA and mortality in children and adolescents with sepsis.

Objective

To assess the association of the presence of viral DNA with sepsis-related mortality in a large multicenter study.

Design, Setting, and Participants

This cohort study compares pediatric patients with and without plasma cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), human herpesvirus 6 (HHV-6), parvovirus B19 (B19V), BK polyomavirus (BKPyV), human adenovirus (HAdV), and torque teno virus (TTV) DNAemia detected by quantitative real-time polymerase chain reaction or plasma IgG antibodies to CMV, EBV, HSV-1, or HHV-6. A total of 401 patients younger than 18 years with severe sepsis were enrolled from 9 pediatric intensive care units (PICUs) in the Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network. Data were collected from 2015 to 2018. Samples were assayed from 2019 to 2022. Data were analyzed from 2022 to 2023.

Main Outcomes and Measures

Death while in the PICU.

Results

Among the 401 patients included in the analysis, the median age was 6 (IQR, 1-12) years, and 222 (55.4%) were male. One hundred fifty-four patients (38.4%) were previously healthy, 108 (26.9%) were immunocompromised, and 225 (56.1%) had documented infection(s) at enrollment. Forty-four patients (11.0%) died in the PICU. Viral DNAemia with at least 1 virus (excluding TTV) was detected in 191 patients (47.6%) overall, 63 of 108 patients (58.3%) who were immunocompromised, and 128 of 293 (43.7%) who were not immunocompromised at sepsis onset. After adjustment for age, Pediatric Risk of Mortality score, previously healthy status, and immunocompromised status at sepsis onset, CMV (adjusted odds ratio [AOR], 3.01 [95% CI, 1.36-6.45]; P = .007), HAdV (AOR, 3.50 [95% CI, 1.46-8.09]; P = .006), BKPyV (AOR. 3.02 [95% CI, 1.17-7.34]; P = .02), and HHV-6 (AOR, 2.62 [95% CI, 1.31-5.20]; P = .007) DNAemia were each associated with increased mortality. Two or more viruses were detected in 78 patients (19.5%), with mortality among 12 of 32 (37.5%) who were immunocompromised and 9 of 46 (19.6%) who were not immunocompromised at sepsis onset. Herpesvirus seropositivity was common (HSV-1, 82 of 246 [33.3%]; CMV, 107 of 254 [42.1%]; EBV, 152 of 251 [60.6%]; HHV-6, 253 if 257 [98.4%]). After additional adjustment for receipt of blood products in the PICU, EBV seropositivity was associated with increased mortality (AOR, 6.10 [95% CI, 1.00-118.61]; P = .049).

Conclusions and Relevance

The findings of this cohort study suggest that DNAemia for CMV, HAdV, BKPyV, and HHV-6 and EBV seropositivity were independently associated with increased sepsis mortality. Further investigation of the underlying biology of these viral DNA infections in children with sepsis is warranted to determine whether they only reflect mortality risk or contribute to mortality.

Diagnostic performance and clinical impacts of metagenomic sequencing after allogeneic hematopoietic stem cell transplantation

BACKGROUND

Metagenomic Next-Generation Sequencing (mNGS) is a rapid, non-culture-based, high-throughput technique for pathogen diagnosis. Despite its numerous advantages, only a few studies have investigated its use in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS

We conducted a retrospective analysis of 404 mNGS tests performed on 264 patients after allo-HSCT. The tests were divided into three groups (Phase A, B, C) based on the time spent hospitalized post-transplantation, and we evaluated the analytical performance of mNGS in comparison with conventional microbiological tests (CMT), while also analyzing its clinical utility for clinical impacts.

RESULTS

Metagenomic sequencing demonstrated a significantly higher rate of positive microbiological findings as compared to CMT (334/404 (82.7 %) vs. 159/404 (39.4 %), respectively, P < 0.001). The detection rates by both mNGS and CMT varied across the three-phase (mNGS: A-60/89 (67.4 %), B-147/158 (93.0 %), C-125/157 (79.6 %), respectively, P < 0.001; CMT: A-21/89 (23.6 %), B-79/158 (50.0 %), C-59/157 (37.6 %), respectively, P < 0.001). The infection sites and types of pathogens were also different across the three phases. Compared to non-GVHD cases, mNGS detected more Aspergillus spp. and Mucorales in GVHD patients (Aspergillus: 12/102 (11.8 %) vs. 8/158 (5.1 %), respectively, P = 0.048; Mucorales: 6/102 (5.9 %) vs. 2/158 (1.3 %), respectively, P = 0.035). Forty-five (181/404) percent of mNGS tests yielded a positive impact on the clinical diagnosis, while 24.3 % (98/404) of tests benefited the patients in antimicrobial treatment.

CONCLUSION

mNGS is an indispensable diagnostic tool in identifying pathogens and optimizing antibiotic therapy for hematological patients receiving allo-HSCT.

Torque Teno Virus plasma DNA load: a novel prognostic biomarker in CAR-T therapy

Torque Teno Virus (TTV) is a single-stranded circular DNA virus which has been identified as a surrogate marker of immune competence in transplantation. In this study we investigated the dynamics of plasma TTV DNAemia in 79 adult patients undergoing chimeric antigen receptor T-cell (CAR-T) therapy for relapsed or refractory large B-cell lymphoma, also evaluating the impact of TTV on immunotoxicities, response and survival outcomes. After lymphodepleting therapy, TTV DNA load was found to decrease slightly until reaching nadir around day 10, after which it increased steadily until reaching maximum load around day 90. TTV DNA load < 4.05 log10 copies/ml at immune effector cell-associated neurotoxicity syndrome (ICANS) onset identified patients at risk of progressing to severe forms of ICANS (OR 16.68, P = 0.048). Finally, patients who experienced falling or stable TTV DNA load between lymphodepletion and CAR-T infusion had better progression-free survival than those with ascending TTV DNA load (HR 0.31, P = 0.006). These findings suggest that TTV monitoring could serve as a surrogate marker of immune competence, enabling predictions of CAR-T efficacy and toxicity. This could pave the way for the development of TTV-guided therapeutic strategies that modulate clinical patient management based on plasma TTV load, similar to suggested strategies in solid organ transplant recipients.

Torque Teno Virus (TTV)-A Potential Marker of Immunocompetence in Solid Organ Recipients

Torque Teno Virus (TTV), first discovered in 1997, is a non-pathogenic, highly prevalent virus with a notable presence in the human virome. TTV has garnered attention as a potential indicator of immunocompetence in recipients of solid organ transplants. In this review, we discuss the role of TTV as a potential marker for immunosuppression optimization, prediction of graft rejection, and as an indicator of opportunistic infections. We discuss TTV's behavior over the course of time after transplantation, TTV's implications in different immunosuppressive regimens, and potential utility in vaccinations. The review synthetizes findings from various studies depicting its potential clinical utility for future personalized patient care.

Torque teno virus-DNA load as individual cytomegalovirus risk assessment parameter upon allogeneic hematopoietic stem cell transplantation

BACKGROUND

Immune recovery following allogeneic hematopoietic stem cell transplantation (allo-HSCT) decisively influences the occurrence of opportunistic infections, one of the leading causes of death among this group of patients. Yet, today, there are no laboratory parameters mirroring immune function sufficiently. Torque teno virus (TTV) has already proven itself as a functional immune marker in other settings.

AIMS

In this analysis, we investigated whether monitoring of TTV-DNA load in whole blood is able to provide additional information on the capacity of the immune system to control cytomegalovirus (CMV) replication in allo-HSCT recipients.

METHODS

Whole blood samples from 59 patients were collected upon allo-HSCT (between Day -7 and +10), on Day +14, +21, +28, +56, +90, and +365 post-transplant. TTV-DNA loads and other relevant clinical information were correlated with the risk of CMV infections or reactivations, defined by evidence of viral replication in blood.

RESULTS

CMV serostatus of the recipient and a TTV load below 1000 copies/mL upon allo-HSCT were significantly associated with an increased incidence of CMV infection or reactivation.

CONCLUSIONS

Quantification of TTV load in the early phase of allo-HSCT procedure could provide additional information in order to identify patients at risk for CMV infection or reactivation.

Kinetics of TTV Loads in Peripheral Blood Mononuclear Cells of Early Treated Acute HIV Infections

Torquetenovirus (TTV) is the most abundant component of the human blood virome and its replication is controlled by a functioning immune system. In this study, TTV replication was evaluated in 21 people with acute HIV infection (AHI) and immune reconstitution following antiretroviral therapy (ART). PBMC-associated TTV and HIV-1 DNA, as well as plasma HIV-1 RNA, were measured by real-time PCR. CD4 and CD8 differentiation, activation, exhaustion, and senescence phenotypes were analyzed by flow cytometry. Thirteen healthy donors (HD) and twenty-eight chronically infected HIV individuals (CHI), late presenters at diagnosis, were included as control groups. TTV replication in AHI seems to be controlled by the immune system being higher than in HD and lower than in CHI. During ART, a transient increase in TTV DNA levels was associated with a significant perturbation of activation and senescence markers on CD8 T cells. TTV loads were positively correlated with the expansion of CD8 effector memory and CD57+ cells. Our results shed light on the kinetics of TTV replication in the context of HIV acute infection and confirm that the virus replication is strongly regulated by the modulation of the immune system.

SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.

Quantification of Torque Teno Virus (TTV) in plasma and saliva of individuals with liver cirrhosis: a cross sectional study

Introduction

Torque teno virus (TTV) has been pointed as an endogenous marker of immune function, the objective of this study was to investigate the TTV viral load in plasma and saliva of cirrhotic individuals and correlate it with clinical characteristics.

Methods

Blood, saliva, clinical data from records and laboratory tests were collected from 72 cirrhotic patients. Plasma and saliva were submitted to real-time polymerase chain reaction for quantification of TTV viral load.

Results

The majority of the patients presented decompensated cirrhosis (59.7%) and 47.2% had alterations in the white blood series. TTV was identified in 28 specimens of plasma (38.8%) and in 67 specimens of saliva (93.0%), with median values of TTV copies/mL of 90.6 in plasma and 245.14 in saliva. All the patients who were positive for TTV in plasma were also positive in saliva, with both fluids having a moderately positive correlation for the presence of TTV. There was no correlation between TTV viral load, either in plasma or in saliva, and any of the variables studied.

Conclusion

TTV is more frequently found and in greater amount in the saliva than in the plasma of cirrhotic patients. There was no correlation between TTV viral load and clinical parameters.

Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma

Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 10⁵ copies/mL) and HPgV-1 (median 1.18 × 10⁶ copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.

Impact of polymorphisms in genes orchestrating innate immune responses on replication kinetics of Torque teno virus after kidney transplantation

Background: Torque teno virus (TTV) DNAemia has been proposed as a surrogate marker of immunosuppression after kidney transplantation (KT), under the assumption that the control of viral replication is mainly exerted by T-cell-mediated immunity. However, Tthe impact on post-transplant TTV kinetics of single genetic polymorphisms (SNPs) in genes orchestrating innate responses remains unknown. We aimed to characterize the potential association between 14 of these SNPs and TTV DNA levels in a single-center cohort of KT recipients.

Methods: Plasma TTV DNAemia was quantified by real-time PCR in 221 KT recipients before transplantation (baseline) and regularly through the first 12 post-transplant months. We performed genotyping of the following SNPs: CTLA4 (rs5742909, rs231775), TLR3 (rs3775291), TLR9 (rs5743836, rs352139), CD209 (rs735240, rs4804803), IFNL3 (rs12979860, rs8099917), TNF (rs1800629), IL10 (rs1878672, rs1800872), IL12B (rs3212227) and IL17A (rs2275913).

Results: The presence of the minor G allele of CD209 (rs4804803) in the homozygous state was associated with undetectable TTV DNAemia at the pre-transplant assessment (adjusted odds ratio: 36.96; 95% confidence interval: 4.72–289.67; p-value = 0.001). After applying correction for multiple comparisons, no significant differences across SNP genotypes were observed for any of the variables of post-transplant TTV DNAemia analyzed (mean and peak values, areas under the curve during discrete periods, or absolute increments from baseline to day 15 and months 1, 3, 6 and 12 after transplantation).

Conclusion: The minor G allele of CD209 (rs4804803) seems to exert a recessive protective effect against TTV infection in non-immunocompromised patients. However, no associations were observed between the SNPs analyzed and post-transplant kinetics of TTV DNAemia. These negative results would suggest that post-transplant TTV replication is mainly influenced by immunosuppressive therapy rather than by underlying genetic predisposition, reinforcing its clinical application as a biomarker of adaptive immunity.

Viral Metagenomics for Identification of Emerging Viruses in Transfusion Medicine

Viral metagenomics has revolutionized our understanding for identification of unknown or poorly characterized viruses. For that reason, metagenomic studies gave been largely applied for virus discovery in a wide variety of clinical samples, including blood specimens. The emerging blood-transmitted virus infections represent important problem for public health, and the emergence of HIV in the 1980s is an example for the vulnerability of Blood Donation systems to such infections. When viral metagenomics is applied to blood samples, it can give a complete overview of the viral nucleic acid abundance, also named "blood virome". Detailed characterization of the blood virome of healthy donors could identify unknown (emerging) viral genomes that might be assumed as hypothetic transfusion threats. However, it is impossible only by application of viral metagenomics to assign that one viral agent could impact blood transfusion. That said, this is a complex issue and will depend on the ability of the infectious agent to cause clinically important infection in blood recipients, the viral stability in blood derivatives and the presence of infectious viruses in blood, making possible its transmission by transfusion. This brief review summarizes information regarding the blood donor virome and some important challenges for use of viral metagenomics in hemotherapy for identification of transfusion-transmitted viruses.

The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases

Background

Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging.

Methods

From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed.

Results

Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3”)-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3”)-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains.

Conclusion

In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.

Pathogen detection by metagenomic next generation sequencing during neutropenic fever in patients with hematological malignancies

Background

Febrile neutropenia (FN) following chemotherapy is a major cause of morbidity during cancer treatment. The performance of metagenomic next-generation sequencing (mNGS) of circulating cell-free DNA from plasma may be superior to blood culture (BC) diagnostics for identification of causative pathogens. The aim of this study was to validate mNGS (DISQVER test) for the detection of pathogens in hematologic patients with FN.

Methods

We collected paired whole blood specimens from central venous catheter and peripheral vein during FN for BC and mNGS testing. We repeated paired sampling at the earliest after 3 days of fever, which was defined as one FN episode. All clinical data were retrospectively reviewed by an infectious disease expert panel. We calculated percent positive agreement (PPA), percent negative agreement (PNA), percent overall agreement (POA), and sensitivity and specificity.

Results

We analyzed a total of 98 unselected FN episodes in 61 patients who developed predominantly FN after conditioning therapy for allogeneic (n = 22) or autologous (n = 21) hematopoietic stem cell transplantation. Success rate of mNGS was 99% (97/98). Positivity rate of mNGS was 43% (42/97) overall and 32% (31/97) excluding viruses compared to 14% (14/98) in BC. PPA, PNA and POA between mNGS and BC were 84.6% (95% CI, 54.6% to 98.1%), 63.1% (51.9% to 73.4%) and 66% (55.7% to 75.3%), respectively. Sensitivity for bacteria or fungi was 40% (28.0% to 52.9%) and 18.5% (9.9% to 30.0%), respectively.

Conclusion

Pathogen detection by mNGS (DISQVER) during unselected FN episodes shows twofold higher sensitivity and a broader pathogen spectrum than BC.

The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation

The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interactions between the residents of the various human microbiotas and the human body. Since the gut microbiota is the densest, most popular, and most studied human microbiota, the impact of other human microbiotas such as the oral, lung, urinary, and genital microbiotas is often overshadowed. However, these microbiotas also provide critical and unique insights pertaining to transplantation success, rejection risk, and overall host health, across multiple different transplantation scenarios. Organ transplantation as well as the pre-, peri-, and post-transplant pharmacological regimens patients undergo is known to adversely impact the microbiotas, thereby increasing the risk of adverse patient outcomes. Over the past decade, holistic approaches to post-transplant patient care such as the administration of clinical and dietary interventions aiming at restoring deranged microbiota community structures have been gaining momentum. Examples of these include prebiotic and probiotic administration, fecal microbial transplantation, and bacteriophage-mediated multidrug-resistant bacterial decolonization. This review will discuss these perspectives and explore the role of different human microbiotas in the context of various transplantation scenarios.

Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients

•

The Galileo Viral Panel metagenomic sequencing platform was compared to singleplex qPCR for the detection and quantification of DNA viruses in immunocompromised paediatric patients.

•

Galileo had high qualitative and quantitative agreement with qPCR.

•

Galileo was able to detect additional viruses not targeted in routine testing.

Background

Infections by several DNA viruses can severely impact outcomes in paediatric immunocompromised patients. Current testing, which is generally limited to singleplex qPCR assays, can miss both common and rarer viruses if they are not targeted.

Objectives

To evaluate the performance of the Galileo Viral Panel (Galileo), a sample-to-result shotgun metagenomics platform for the detection and quantification of 12 DNA viruses, compared to standard of care qPCR assays.

Study design

A clinical performance evaluation was carried out using 43 prospectively collected EDTA plasma samples positive for one or more DNA viruses. Agreement between assays was assessed by overall, positive, and negative percent agreement, as well as quantitative agreement by linear regression and Bland-Altman analysis.

Results

Overall positive percent agreement was 84% (95% CI: 76%-90%), and negative percent agreement was 95% (95% CI: 92%-97%). There was a high correlation between Galileo and qPCR for ADV, CMV, EBV, and VZV (R² = 0.91) and a mean difference by Bland Altman of -0.43 log₁₀ IU or cp/ml (95% limits of agreement, -1.37 to 0.51). In addition, there was a high correlation between Galileo Signal Score and qPCR for TTV (R² = 0.85).

Conclusion

We observed high qualitative and quantitative agreement between qPCR and Galileo. Galileo identified additional viruses that were not tested with routine qPCR and could impact clinical outcomes.

Viruses, friends and foes: The case of Torque Teno virus and the net state of immunosuppression

New reliable biomarkers are needed to improve individual risk assessment for post-transplant infection, acute graft rejection and other immune-related complications after solid organ transplantation (SOT) and allogeneic hematopoietic stem cell transplantation (allo-HSCT). One promising strategy relies on the monitoring of replication kinetics of virome components as functional surrogate for the net state of immunosuppression. Torque Teno Virus (TTV) is a small, non-enveloped, circular, single-stranded DNA anellovirus with no attributable pathological effects. A major component of the human blood virome, TTV exhibits various features that facilitate its application as immune biomarker: high prevalence rates, nearly ubiquitous distribution, stable viral loads with little intra-individual variability, insensitivity to antiviral drugs, and availability of commercial PCR assays for DNA quantification. The present review summarizes the available studies supporting the use of post-transplant TTV viremia to predict patient and graft outcomes after SOT and allo-HSCT. Taken together, this evidence suggests that high or increasing TTV DNA levels precede the occurrence of infectious complications in the SOT setting, whereas low or decreasing viral loads are associated with the development of acute rejection. The interpretation in allo-HSCT recipients is further complicated by complex interplay with the underlying disease, conditioning regimen and timing of recovery of lymphocyte counts, although TTV kinetics may act as a marker of immunological reconstitution at the early post-transplant period. The standardization of PCR methods and reporting units for TTV DNAemia and the results from ongoing interventional trials evaluating a TTV load-guided strategy to adjust immunosuppressive therapy are achievements expected in the coming years. This article is protected by copyright. All rights reserved.

Diagnosis of infectious diseases in immunocompromised hosts using metagenomic next generation sequencing-based diagnostics

The diagnosis of infectious diseases in immunocompromised hosts presents unique challenges for the clinician. Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples (mNGS for pathogen identification or mNGSpi) may be a useful tool in addressing some of these challenges. Studies of mNGSpi in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. While these studies provide proof of concept for mNGSpi utility, they have a number of limitations, which make it difficult to confidently assess test performance and clinical impact based on current data. Future studies will likely feature larger cohort sizes and controlled interventional study designs that assess the impact of mNGSpi on clinical endpoints. They will also likely include assessments of the clinical value of data generated by mNGS beyond pathogen identification.