Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels

The Effect of Immunosuppressive Treatment on Torque Teno Virus Load in Lung Transplant Recipients: A Preliminary Study

After transplantation, systematically monitoring and assessing the risk of transplanted organ rejection is crucial. Current methods involving immunosuppressant monitoring, the assessment of organ function, and biopsies are insufficient for predicting rejection. However, regular determination of torque teno virus (TTV) load after transplantation may prove to be a useful parameter for monitoring immunosuppression efficacy. Therefore, we aimed to evaluate TTV load in patients before and after lung transplantation and the kinetics of TTV growth in relation to immunosuppression strength. We included 14 patients (mean age: 49.4 ± 14.0 years) undergoing lung transplantation and determined TTV copy numbers using the commercial ARGENE TTV-R-GENE kit from BioMerieux from the day of transplantation to 180 days post-transplantation. We also developed an empirical immunosuppression unit scale to calculate immunosuppression strength. We observed an average positive correlation between log10 TTV and immunosuppression strength, with significant increases in log10 TTV depending on the duration of immunosuppression. These results indicate the potential of TTV as a new parameter to assess the possibility of transplanted organ rejection.

Assessing Torquetenovirus (TTV) as a Biomarker for Immune Responses to SARS-CoV-2 mRNA Vaccines in People Living with HIV and Healthy Individuals

Background: Torquetenovirus (TTV) viremia is increasingly recognized as a marker of immune competence. In the context of COVID-19, TTV viral load (VL) has been shown to predict anti-Spike antibody levels in severely immunocompromised patients. This study aimed to evaluate whether pre-vaccine TTV VL could predict humoral and cellular immune responses to SARS-CoV-2 mRNA vaccines in people living with HIV (PLWH) and healthy individuals (HP). Methods: TTV VL was measured via real-time PCR in serum samples collected before the second and third doses of mRNA vaccines in 93 PLWH and 48 HP (second dose) and 255 PLWH and 48 HP (third dose). Immune responses were assessed through anti-SARS-CoV-2 receptor-binding domain (RBD) IgG, neutralizing antibodies, and IFN-γ release. Statistical analyses included correlation studies between TTV VL and vaccine-induced immune responses. Results: TTV VL did not significantly correlate with anti-RBD IgG or neutralizing antibody levels in either cohort; highlighting its limited predictive value for humoral responses in relatively immunocompetent populations. However, a strong inverse correlation was observed between TTV VL and IFN-γ release after the third, but not the second, vaccine dose. These findings suggest that higher TTV VL, indicative of reduced immune competence, may impair T-cell-mediated immunity to vaccines. Conclusions: In virologically suppressed PLWH and HP, TTV VL is not a reliable predictor of humoral immune responses to COVID-19 vaccines. However, its inverse relationship with cellular responses warrants further investigation in more immunosuppressed populations. These results reinforce the continuum model of TTV VL as a biomarker, with predictive utility increasing alongside the degree of immunosuppression.

Plasma Virome of HIV-infected Subjects on Suppressive Antiretroviral Therapy Reveals Association of Differentially Abundant Viruses with Distinct T-cell Phenotypes and Inflammation

Background

The plasma virome represents the overall composition of viral sequences present in it. Alteration in plasma virome has been reported in treatment naïve and immunocompromised (CD4 count < 200) people with HIV (PWH). However, the effect of ART on virome composition in PWH on ART with preserved CD4 counts is poorly understood.

Objectives

We aimed to assess the alterations in plasma virome in PWH on ART in comparison to HIV-negative uninfected controls and to further investigate possible associations of plasma viruses with inflammation and immune dysfunction, namely, immunosenescence and immune exhaustion.

Methods

Plasma viral DNA from PWH on ART and controls was used for sequencing on the Illumina Nextseq500 platform, followed by the identification of viral sequences using an automated pipeline, VIROMATCH. Multiplex cytokine assay was performed to measure the concentrations of various cytokines in plasma. Immunophenotyping was performed on PBMCs to identify T cell markers of immunosenescence and immune exhaustion.

Results

In our observational, cross-sectional pilot study, chronically infected PWH on ART had significantly different viral species compositions compared to controls. The plasma virome of PWH showed a significantly high relative abundance of species Human gammaherpesvirus 4, also known as Epstein-Barr virus (EBV). Moreover, EBV emerged as a significant viral taxon differentially enriched in PWH on ART, which further correlated positively with the exhaustion phenotype of T cells and significantly increased TNF-α in PWH on ART. Additionally, a significantly increased proportion of senescent T cells and IL-8 cytokine was detected in PWH on ART.

Conclusion

Altered plasma virome influenced the inflammatory response and T-cell phenotype in PWH on ART.

Anelloviruses versus human immunity: how do we control these viruses?

One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.

Torque Teno Virus in Nasopharyngeal Aspirate of Children With Viral Respiratory Infections

BACKGROUND

Torque teno virus (TTV) is a ubiquitous anellovirus responsible for persistent infections and is considered a marker of immune function. The role of TTV as a facilitator of respiratory infections (RIs) is unknown.

OBJECTIVES

Our aim was to estimate, in a prospective study, the prevalence of TTV in the nasopharyngeal aspirate (NPA) of hospitalized children <5 years old, with RIs and correlate them with outcomes and immune response.

PATIENTS AND METHODS

NPA was taken for testing of 16 respiratory viruses by reverse transcription-polymerase chain reaction (PCR), TTV PCR, and immunologic study.

RESULTS

Sixty hospitalized children with an RI were included. A total of 51/60 patients had positive common respiratory viral (CRV) identification. A total of 23/60 (38.3%) children were TTV+ in NPA. TTV+ patients had other CRVs in 100% of cases versus 78.3% in TTV- ( P = 0.029). The TTV+ patients tended to be older, have fever, and to need pediatric intensive care unit admission more often than TTV- patients. Abnormal chest radiograph was more frequent in the TTV+ patients, odds ratios 2.6 (95% CI: 1.3-5.2). The genetic expression of filaggrin (involved in epithelial barrier integrity) was lower in TTV+ patients; however, the levels of filaggrin in the NPA were increased.

CONCLUSIONS

TTV infection is common in children with RI and could be associated with abnormal imaging in radiograph, greater severity and an alteration in filaggrin gene expression and protein release.

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome

Viruses are the most abundant components of the human gut microbiome with a significant impact on health and disease. The effects of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analysed. Several studies suggested that integrase strand transfers inhibitors (INSTIs) are associated with a healthier gut. Thus, the objective of this work was to evaluate the effects of HIV infection and INSTIs on gut virome composition. 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and their gut virome composition was analysed using shotgun sequencing. Bacteriophages were the most abundant and diverse viruses present in gut. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment. β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group. Differential abundant analysis showed an increase in phages belonging to Caudoviricetes class in the naive group and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group. Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages. Our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis at the viral level, which opens several opportunities for new studies focused on microbiota-based therapies.

Association of post-transplantation anellovirus viral load with kidney transplant rejection in children

BACKGROUND

Post-transplantation immunosuppressive therapy reduces the risk of graft rejection but raises the risk of infection and malignancy. A biomarker of the level of immunosuppression can be helpful in monitoring immunosuppressive therapy. Inverse correlation between Torque teno virus (TTV) from the Anelloviridae (AV) family load and immune competence was described in previous studies. The aim of this study was to analyze the association between AV family viruses' kinetics and the risk for graft rejection in the first year after kidney transplantation in children.

METHODS

The titers of three genera (TTV, TTMDV, and TTMV) from the AV family were monitored by real-time PCR in consecutive samples from children before and after kidney transplantation.

RESULTS

Twenty-one children who underwent kidney transplantation were enrolled. Five out of 21 patients experienced acute graft rejection within a year from transplantation. We found that in patients who experienced graft rejection, the median titers of TTV and total AV titers at 5-6 months post-transplantation were lower than in those who did not. Using a threshold determined by ROC analysis, significant differences in TTV and total AV load were found between patients who had or did not have graft rejection (p = 0.002 and 0.004, respectively). No association was found between the dominance of any AV genus titer and the likelihood of rejection.

CONCLUSION

This pilot study suggests that children after kidney transplantation with low TTV and total AV titers 5-6 months post-transplantation are at increased risk for graft rejection within a year after transplantation. A higher resolution version of the Graphical abstract is available as Supplementary information.

Torque Teno Virus Primary Infection Kinetics in Early Childhood

Human torque teno viruses (TTVs) are a diverse group of small nonenveloped viruses with circular, single-stranded DNA genomes. These elusive anelloviruses are harbored in the blood stream of most humans and have thus been considered part of the normal flora. Whether the primary infection as a rule take(s) place before or after birth has been debated. The aim of our study was to determine the time of TTV primary infection and the viral load and strain variations during infancy and follow-up for up to 7 years. TTV DNAs were quantified in serial serum samples from 102 children by a pan-TTV quantitative PCR, and the amplicons from representative time points were cloned and sequenced to disclose the TTV strain diversity. We detected an unequivocal rise in TTV-DNA prevalence, from 39% at 4 months of age to 93% at 2 years; all children but one, 99%, became TTV-DNA positive before age 4 years. The TTV-DNA quantities ranged from 5 × 10¹ to 4 × 10⁷ copies/mL, both within and between the children. In conclusion, TTV primary infections occur mainly after birth, and increase during the first two years with high intra- and interindividual variation in both DNA quantities and virus strains.

Role of Microbiota in Viral Infections and Pathological Progression

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.

The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications

The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.

Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population

Torque teno virus (TTV) is one of the most common human viruses and can infect an individual with multiple genotypes chronically and persistently. TTV group 6 is a recently discovered phylogenetic group first isolated from eastern Taiwan indigenes, but whether the TTV group 6 was also prevalent in the general population still unknown. One hundred and three randomly collected blood samples from general population and 66 TTV positive DNA samples extracted from Taiwan indigenes were included. A group-6-specific PCR was developed for re-screen over TTV positive samples. Two TTV group 6 positive samples from general population were cloned and sequenced for identifying mix-infected TTVs and confirming their classification by maximum-likelihood and Bayesian inference phylogeny. TTV group 6 can be detected in 4.5% (4/89) and 7.6% (5/66) of TTV positive samples from Taiwanese general population and eastern Taiwan indigenes, respectively. Sample VC09 was mix-infected with TTV groups 3 and 6. Sample VC99 was mix-infected with TTV groups 3, 4 and 6. A highly diverse triple overlapping region was observed, which may represent a unique phenomenon of TTV. The group-6-specific PCR can successfully detect TTV group 6. TTV group 6 may be prevalent worldwide regardless of the geographic region and/or ethnic groups.

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

Torque Teno virus (TTV) is a ubiquitous virus that causes chronic infection in humans with unknown clinical consequences. Here, we investigated the influence of TTV infection on HCV direct-acting antiviral (DAA) efficacy in HIV/HCV coinfected and HCV monoinfected patients as controls. Of 92 study patients, 79.3% were TTV DNA positive; untreated patients exhibited a significantly higher proportion of TTV DNA-positivity vs. sustained virological response (SVR) patients (100.0% vs. 65.2%, p < 0.001), while TTV positivity was not significant in DAA failure patients vs. SVR patients despite HIV/HCV coinfection. TTV DNA viral load was higher among HCV monoinfected patients vs. HIV/HCV coinfected, although marginally significant (p = 0.074) and no significant viral load difference was detected between DAA failures and SVR patients, while untreated vs. SVR patients had a significantly higher viral load (19,884, IQR 5977–333,534, vs. 469, IQR 10–4124, p = 0.004). Alpha-genogroup 3 TTV was the most prevalent genetic group, and no specific strain or genogroup was observed in relapser patients. Among HIV/HCV patients with HCV RNA detectable at end of treatment (EOT), TTV DNA was detected in 9/17 treatment responder patients and 3/5 relapser patients, thus, TTV infection does not appear to influence the control HCV viremia after EOT. Levels of IL-6 IL-4, and CD14 were not significantly different between TTV PCR-positive and -negative patients. These results suggest no association between TTV DNA positivity or viral load and HCV DAA failure whether patients were HIV/HCV coinfected or HCV monoinfected.

Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression

Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10-13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6-2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10-4; q = 0.004, OR, 3.99; 95% CI, 1.74-10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6-40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.

Torque Teno Virus plasma level as novel biomarker of retained immunocompetence in HIV-infected patients

PURPOSE

To predict the course of immune recovery (IR) in HIV-1-infected patients after initiation of combined antiretroviral therapy (cART) by determination of the plasma concentration of Torque Teno Virus (TTV). TTV has been identified as marker for risk assessment in immunosuppressed patients after transplantation procedures. Here, TTV was analyzed in HIV-1-infected therapy-naïve patients to evaluate its use as predictor of the course of IR for guidance of individualized treatment.

METHODS

TTV DNA was quantified in plasma samples of 301 therapy-naïve HIV-1-infected patients and correlated to CD4⁺ cell count, HIV viral load, presence of the herpes viruses CMV, EBV and HHV-8, age and sex. Patients were classified according to their initial CD4⁺ cell count and to the extent of CD4⁺ T-cell increase within the first year of cART.

RESULTS

TTV DNA was detectable in 96% of the patients' plasma samples with a median TTV plasma concentration of 5.37 log₁₀ cop/ml. The baseline CD4⁺ cell count was negatively correlated with TTV plasma concentration (p = 0.003). In patients with a CD4⁺ cell recovery < 50 cells/µl, the median TTV plasma concentration was significantly higher compared to patients with a CD4⁺ cell recovery of > 200 CD4⁺ cells/µl (5.68 log₁₀ cop/ml versus 4.99 log₁₀ cop/ml; p = 0.011). TTV plasma concentration in combination with baseline CD4⁺ cell count were significantly correlated to CD4⁺ cell recovery (p = 0.004). For all other parameters considered, no significant correlation for CD4⁺ cell recovery was found.

CONCLUSION

Within the cohort, the significantly elevated TTV plasma concentration in patients with diminished CD4⁺ cell recovery indicates a more profound immune defect. Baseline TTV plasma concentrations and CD4⁺ cell count are predictive for the course of immune recovery in HIV-1-infected patients with severe immunodeficiency.

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

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.

A Summary of the Fourth Annual Virology Education HIV Microbiome Workshop

Each year, a growing international collection of researchers meets at the NIH to share and discuss developments in the microbiome HIV story. This past year has seen continued progress toward a detailed understanding of host-microbe interactions both within and outside the field of HIV. Commensal microbes are being linked to an ever-growing list of maladies and physiologic states, including major depressive disorder, chronic kidney disease, and Parkinson disease. PubMed citations for "microbiome" are growing at an exponential rate with over 11,000 in 2018. Various microbial taxa have been associated with HIV infection, and some of these taxa associated with HIV infection have also been associated with systemic markers of inflammation in HIV infected individuals. Causality remains unclear however as environmental and behavioral factors may drive HIV risk, inflammation, and gut enterotype. Much of the work currently being done addresses potential mechanisms by which gut microbes influence immune and inflammatory pathways. No portion of the microbiome landscape has grown as rapidly as study of the interplay between gut microbes and response to cancer immunotherapy. As Dr. Wargo discussed in her keynote address, this area has opened the door to better understanding on how commensal microbes interact with the human immune system.

Detection of Torque Teno Virus (TTV) and TTV-Like Minivirus in patients with presumed infectious endophthalmitis in India

Human anelloviruses (Torque Teno Virus (TTV) and TTV Like Mini Virus (TLMV)) are now being reported at a high prevalence across the world, with a controversial disease-inducing potential. The aim of this study was to investigate the role of these anellovirus in vitreous of patients with presumed infectious endophthalmitis. After informed consent, vitreous fluid from patients with endophthalmitis (n = 103) and non-infectious pathologies (n = 102) were analyzed for the presence of TTV and TLMV DNA by qPCR with the limit of quantification defined as 100 copies per reaction. Among the patients clinically diagnosed with endophthalmitis, 29 of the 40 culture proven samples (72.5%) and 42 out of 63 (66.6%) of culture-negative samples were positive for presence of TTV/TLMV. Interestingly, 51 of the 102 (50%) samples in the control group were also positive for TTV/TLMV. Comparing the clinical outcome among patients diagnosed with endophthalmitis, we observed no significant association in the final visual acuity of patients who were positive for presence of TTV/TLMV, however, these patients had significantly higher repeat antibiotic injections (p = 0.03). Further evidence is however needed to correlate TTV / TLMV with a particular pathology or group of pathologies in the eye.

Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis

BACKGROUND

Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC).

METHODS

We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome.

RESULTS

Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence.

CONCLUSION

Presence of virus in stool was not associated with the onset of pediatric UC.

Torque teno virus viremia in patients with chronic arthritis: Influence of biologic therapies

OBJECTIVE

Torque teno virus (TTV) is a highly prevalent non-pathogenic anellovirus whose plasma levels may be a biomarker of immunosuppression. The aim of this study was to assess whether specific immune-targeting with different biologic drugs may differentially modulate TTV viremia in arthritis patients.

METHODS

TTV DNA load was quantified by PCR in a cross-sectional sample of 79 patients with chronic arthritis on biologic therapy (abatacept, infliximab, rituximab or tocilizumab), 31 patients treated with conventional DMARDs (methotrexate and/or leflunomide), and 54 healthy individuals. Longitudinal changes in TTV load were analysed in a second group of 59 patients at baseline and 4-months after biologic therapy. Correlations between clinical or biological characteristics of recruited patients and TTV viremia were also analysed.

RESULTS

In the cross-sectional study, TTV load was significantly higher in patients who received abatacept, infliximab or tocilizumab compared to healthy individuals. Patients treated with rituximab or conventional DMARDs showed TTV loads similar to healthy controls. In the longitudinal study, an increase in the TTV load was observed after anti-TNF, tocilizumab, abatacept and rituximab, but not after secukinumab therapy. Correlations between TTV load and clinical variables such as disease duration, concomitant glucocorticoid or DMARDs therapy, lymphocytes or previous infections were not found. A non-significant trend towards higher TTV load was observed in therapy responders.

CONCLUSION

Patients with chronic arthritis on biologic but not on conventional DMARD or anti-IL17 therapy have increased TTV viremia. This observation provides a basis to prospectively explore the potential value of TTV load as a potential pharmacodynamic biomarker.

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

Background

Strain-level RNA virus characterization is essential for developing prevention and treatment strategies. Viral metagenomic data, which can contain sequences of both known and novel viruses, provide new opportunities for characterizing RNA viruses. Although there are a number of pipelines for analyzing viruses in metagenomic data, they have different limitations. First, viruses that lack closely related reference genomes cannot be detected with high sensitivity. Second, strain-level analysis is usually missing.

Results

In this study, we developed a hybrid pipeline named TAR-VIR that reconstructs viral strains without relying on complete or high-quality reference genomes. It is optimized for identifying RNA viruses from metagenomic data by combining an effective read classification method and our in-house strain-level de novo assembly tool. TAR-VIR was tested on both simulated and real viral metagenomic data sets. The results demonstrated that TAR-VIR competes favorably with other tested tools.

Conclusion

TAR-VIR can be used standalone for viral strain reconstruction from metagenomic data. Or, its read recruiting stage can be used with other de novo assembly tools for superior viral functional and taxonomic analyses. The source code and the documentation of TAR-VIR are available at https://github.com/chjiao/TAR-VIR.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2878-2) contains supplementary material, which is available to authorized users.

Early Post-Transplant Torquetenovirus Viremia Predicts Cytomegalovirus Reactivations In Solid Organ Transplant Recipients

Monitoring the human virome has been recently suggested as a promising and novel area of research for identifying new biomarkers which would help physicians in the management of transplant patients. Imbalance of the immune system in transplant recipients has a significant impact on replication of Torquetenovirus (TTV), the most representative and abundant virus of human virome. TTV kinetic was studied by real-time PCR in 280 liver or kidney transplant recipients who underwent different drug regimens to maintain immunosuppression. During one-year post-transplant follow-up, TTV viremia fluctuated irrespective of transplanted organ type but consistent with the immunosuppression regimen. TTV kinetic in patients who manifested cytomegalovirus (CMV) reactivation within the first four months post-transplant differed from that observed in patients who did not experience CMV complications. Importantly, plasma TTV load measured between day 0 and 10 post-transplant was significantly higher in CMV DNA positive than in CMV DNA negative patients. TTV viremia above 3.45 log DNA copies/ml within the first 10 days post-transplant correlates with higher propensity to CMV reactivation following transplantation. This study provides further evidence for using early post-transplant TTV viremia to predict CMV reactivation in liver or kidney transplant recipients.

Anellovirus loads are associated with outcomes in pediatric lung transplantation

Anelloviruses are DNA viruses ubiquitously present in human blood. Due to their elevated levels in immunosuppressed patients, anellovirus levels have been proposed as a marker of immune status. We hypothesized that low anellovirus levels, reflecting relative immunocompetence, would be associated with adverse outcomes in pediatric lung transplantation. We assayed blood samples from 57 patients in a multicenter study for alpha- and betatorquevirus, two anellovirus genera. The primary short-term outcome of interest was acute rejection, and longer-term outcomes were analyzed individually and as "composite" (death, chronic rejection, or retransplant within 2 years). Patients with low alphatorquevirus levels at 2 weeks post-transplantation were more likely to develop acute rejection within 3 months after transplant (P = .013). Low betatorquevirus levels at 6 weeks and 6 months after transplant were associated with death (P = .047) and the composite outcome (P = .017), respectively. There was an association between low anellovirus levels and adverse outcomes in pediatric lung transplantation. Alphatorquevirus levels were associated with short-term outcomes (ie, acute rejection), while betatorquevirus levels were associated with longer-term outcomes (ie, death, or composite outcome within 2 years). These observations suggest that anelloviruses may serve as useful biomarkers of immune status and predictors of adverse outcomes.

Inside Out: HIV, the Gut Microbiome, and the Mucosal Immune System

The components of the human gut microbiome have been found to influence a broad array of pathologic conditions ranging from heart disease to diabetes and even to cancer. HIV infection upsets the delicate balance in the normal host-microbe interaction both through alterations in the taxonomic composition of gut microbial communities as well as through disruption of the normal host response mechanisms. In this article we review the current methods of gut microbiome analysis and the resulting data regarding how HIV infection might change the balance of commensal bacteria in the gut. Additionally, we cover the various effects gut microbes have on host immune homeostasis and the preliminary but intriguing data on how HIV disrupts those mechanisms. Finally, we briefly describe some of the important biomolecules produced by gut microbiota and the role that they may play in maintaining host immune homeostasis with and without HIV infection.

Torquetenovirus: the human virome from bench to bedside

Torquetenovirus (TTV) is the most abundant component of human virome. Virologists have long ignored this orphan and highly divergent virus, in part because TTV cannot be cultured and because it lacks serology reagents and animal models. Nevertheless, it is almost endemic worldwide and is insensitive to current antiviral drugs, so its monitoring is useful in various conditions. To date, TTV as a marker has proved useful in at least two circumstances: to identify anthropogenic pollution and to assess functional immune competence in immunosuppressed individuals. This review summarizes recent findings about TTV and discusses the main hurdles in translating them into clinical diagnostics.