Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients

The Role of Microbiome and Virome in Idiopathic Pulmonary Fibrosis

The interest in the lung microbiome and virome and their contribution to the pathogenesis, perpetuation and progression of idiopathic pulmonary fibrosis (IPF) has been increasing during the last decade. The utilization of high-throughput sequencing to detect microbial and/or viral genetic material in bronchoalveolar lavage fluid or lung tissue samples has amplified the ability to identify and quantify specific microbial and viral populations. In stable IPF, higher microbial burden is associated with worse prognosis but no specific microbe has been identified to contribute to this. Additionally, no causative relation has been established. Regarding viral infections, although in the past they have been associated with IPF, causation has not been proved. Although in the past the diagnosis of acute exacerbation of IPF (AE-IPF) was not considered in patients with overt infection, this was amended in the last few years and infection is considered a cause for exacerbation. Besides this, a higher microbial burden has been found in the lungs of patients with AE-IPF and an association with higher morbidity and mortality has been confirmed. In contrast, an association of AE-IPF with viral infection has not been established. Despite the progress during the last decade, a comprehensive knowledge of the microbiome and virome in IPF and their role in disease pathogenesis are yet elusive. Although association with disease severity, risk for progression and mortality has been established, causation has not been proven and the potential use as a biomarker or the benefits of antimicrobial therapeutic strategies are yet to be determined.

The gut virome of healthy children during the first year of life is diverse and dynamic

In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation

There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.

Breast Milk Virome and Bacterial Microbiome Resilience in Kenyan Women Living with HIV

Breast milk is nutritionally and immunologically beneficial in early life but is also a potential source of infection. Little is known about breast milk microbiota of women living with HIV (WLHIV), the impact of severe immunosuppression, and the contribution to mortality of HIV-exposed infants. Here, we performed metagenomic sequencing to characterize the bacterial microbiome and DNA virome of breast milk samples at 1 month postpartum from Kenyan WLHIV who were not receiving combination antiretroviral therapy (cART), 23 women with CD4 counts of <250 and 30 women with CD4 of >500; and additionally, 19 WLHIV with infants that lived and 26 WLHIV with infants that died during the first 2 years of life were included. We found that breast milk bacterial microbiomes in this study population were highly diverse but shared a core community composed of the Streptococcaceae, Staphylococcaceae, Moraxellaceae, and Eubacteriaceae families. The breast milk virome was dominated by human cytomegalovirus (CMV) and included the bacteriophage families Myoviridae, Siphoviridae, and Podoviridae. Bacterial microbiome and virome profiles and diversity were not significantly altered by HIV immunosuppression, as defined by a CD4 of <250. CMV viral load was not associated with maternal CD4 counts or infant mortality. In conclusion, we show that the core bacterial and viral communities are resilient in breast milk despite immunosuppression in WLHIV.

IMPORTANCE Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk. We performed the first breast milk virome study of an HIV population. In this study cohort of Kenyan women living with HIV from the pre-antiretroviral therapy era, we found that breast milk harbors a core bacterial microbiome and a virome dominated by human cytomegalovirus. The virome and bacterial microbiome were not substantially altered by immunosuppression or associated with infant mortality. Together, these findings indicate resilience of the microbial community in breast milk compartmentalization. These findings advance out fundamental understanding of the breast milk core microbiome and virome interactions in the context of HIV disease.

VirionFinder: Identification of Complete and Partial Prokaryote Virus Virion Protein From Virome Data Using the Sequence and Biochemical Properties of Amino Acids

Viruses are some of the most abundant biological entities on Earth, and prokaryote virus are the dominant members of the viral community. Because of the diversity of prokaryote virus, functional annotation cannot be performed on a large number of genes from newly discovered prokaryote virus by searching the current database; therefore, the development of an alignment-free algorithm for functional annotation of prokaryote virus proteins is important to understand the viral community. The identification of prokaryote virus proteins (PVVPs) is a critical step for many viral analyses, such as species classification, phylogenetic analysis and the exploration of how prokaryote virus interact with their hosts. Although a series of PVVP prediction tools have been developed, the performance of these tools is still not satisfactory. Moreover, viral metagenomic data contains fragmented sequences, leading to the existence of some incomplete genes. Therefore, a tool that can identify partial prokaryote virus proteins is also needed. In this work, we present a novel algorithm, called VirionFinder, to identify the complete and partial PVVPs from non-prokaryote virus virion proteins (non-PVVPs). VirionFinder uses the sequence and biochemical properties of 20 amino acids as the mathematical model to encode the protein sequences and uses a deep learning technique to identify whether a given protein is a PVVP. Compared with the state-of-the-art tools using artificial benchmark datasets, the results show that under the same specificity (Sp), the sensitivity (Sn) of VirionFinder is approximately 10-34% much higher than the Sn of these tools on both complete and partial proteins. When evaluating related tools using real virome data, the recognition rate of PVVP-like sequences of VirionFinder is also much higher than that of the other tools. We expect that VirionFinder will be a powerful tool for identifying novel virion proteins from both complete prokaryote virus genomes and viral metagenomic data. VirionFinder is freely available at https://github.com/zhenchengfang/VirionFinder.

A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing

AIMS

Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS.

METHODS AND RESULTS

We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.

CONCLUSION

NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.

Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

BACKGROUND

Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment.

METHODS

To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis.

RESULTS

Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups.

CONCLUSION

Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

Torque teno viral load reflects immunosuppression in paediatric kidney-transplanted patients-a pilot study

BACKGROUND

Chronic deterioration of kidney graft function is related to inadequate immunosuppression (IS). A novel tool to assess the individual net state of IS in transplanted patients might be the monitoring of Torque teno virus (TTV) viral load. TTV is a non-pathogen virus detectable in almost all individuals. TTV level in the peripheral blood has been linked to the immune-competence of its host and should thus reflect IS after solid organ transplantation.

METHODS

TTV plasma load was quantified monthly by RT-PCR for a period of 1 year in 45 kidney-transplanted children. Post-transplant time was at least 3 months. The relation of the virus DNA levels to IS and transplant-specific clinical and laboratory parameters was analysed longitudinally.

RESULTS

TTV DNA was detectable in 94.5% of the plasma samples. There was a significant association with the post-transplant follow-up time as well as with the type of IS regimen, with lower virus loads in patients after longer post-transplant time and mTOR inhibitor-based IS. Furthermore, a significant positive correlation with the dose of prednisolone and mycophenolate mofetil was found.

CONCLUSIONS

TTV levels show an association/correlation with the strength of IS. Further studies are needed in order to evaluate TTV measurement as a tool for IS monitoring for hard clinical outcomes such as presence of donor-specific antibodies, rejections or infections-common consequences of insufficient or too intense IS.

The human virome: assembly, composition and host interactions

The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 10³¹ particles on Earth. The human virome is similarly vast and complex, consisting of approximately 10¹³ particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.

The Interplay Between Respiratory Microbiota and Innate Immunity in Flavor E-Cigarette Vaping Induced Lung Dysfunction

Global usage of electronic nicotine delivery systems (ENDS) has been increasing in the last decade. ENDS are non-combustible tobacco products that heat and aerosolize a liquid containing humectants, with added flavorings and often nicotine. Though ENDS are promoted as a less harmful alternative to smoking, current evidence links their use to a wide range of deleterious health effects including acute and chronic lung damage. ENDS can elicit an inflammatory response and impair the innate immune response in the lungs. Exposure to ENDS flavorings results in abnormal activation of the lung epithelial cells and β-defensins, dysfunction of the macrophage phagocytic activity, increased levels of mucin (MUC5AC) and abnormal activation of the neutrophilic response (NETosis). ENDS menthol flavorings disrupt innate immunity and might be associated with allergies and asthma through activation of transient receptor potential ankyrin 1 (TRAP1). Recent studies have expanded our understanding of the relationship between the homeostasis of lung innate immunity and the immunomodulatory effect of the host-microbiota interaction. Alterations of the normal respiratory microbiota have been associated with chronic obstructive pulmonary disease (COPD), asthma, atopy and cystic fibrosis complications which are strongly associated with smoking and potentially with ENDS use. Little is known about the short-and long-term effects of ENDS on the respiratory microbiota, their impact on the innate immune response and their link to pulmonary health and disease. Here we review the interaction between the innate immune system and the respiratory microbiota in the pathogenesis of ENDS-induced pulmonary dysfunction and identify future areas of research.

Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease

BACKGROUND AND AIMS

Dysbiosis of the gut microbiota is a well-known correlate of the pathogenesis of inflammatory bowel disease [IBD]. However, few studies have examined the microbiome in very early-onset [VEO] IBD, which is defined as onset of IBD before 6 years of age. Here we focus on the viral portion of the microbiome-the virome-to assess possible viral associations with disease processes, reasoning that any viruses potentially associated with IBD might grow more robustly in younger subjects, and so be more detectable.

METHODS

Virus-like particles [VLPs] were purified from stool samples collected from patients with VEO-IBD [n = 54] and healthy controls [n = 23], and characterized by DNA and RNA sequencing and VLP particle counts.

RESULTS

The total number of VLPs was not significantly different between VEO-IBD and healthy controls. For bacterial viruses, the VEO-IBD subjects were found to have a higher ratio of Caudovirales vs to Microviridae compared to healthy controls. An increase in Caudovirales was also associated with immunosuppressive therapy. For viruses infecting human cells, Anelloviridae showed higher prevalence in VEO-IBD compared to healthy controls. Within the VEO-IBD group, higher levels of Anelloviridae DNA were also positively associated with immunosuppressive treatment. To search for new viruses, short sequences enriched in VEO-IBD samples were identified, and some could be validated in an independent cohort, although none was clearly viral; this provides sequence tags to interrogate in future studies.

CONCLUSIONS

These data thus document perturbations to normal viral populations associated with VEO-IBD, and provide a biomarker-Anelloviridae DNA levels-potentially useful for reporting the effectiveness of immunosuppression.

Role of pulmonary microorganisms in the development of chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a chronic obstructive respiratory disease characterized by irreversible airway limitation and persistent respiratory symptoms. The main clinical symptoms of COPD are dyspnoea, chronic cough, and sputum. COPD is often accompanied by other respiratory diseases, which can cause worsening of the disease. COPD patients with dyspnoea and aggravation of cough and sputum symptoms represent acute exacerbations of COPD (AECOPD). There is mounting evidence suggesting that dysbiosis of pulmonary microbiota participates in the disease. However, investigations of dysbiosis of pulmonary microbiota and the disease are still in initial phases. To screen, diagnose, and treat this respiratory disease, integrating data from different studies can improve our understanding of the occurrence and development of COPD and AECOPD. In this review, COPD epidemiology and the primary triggering mechanism are explored. Emerging knowledge regarding the association of inflammation, caused by pulmonary microbiome imbalance, and changes in lung microbiome flora species involved in the development of the disease are also highlighted. These data will further our understanding of the pathogenesis of COPD and AECOPD and may yield novel strategies for the use of pulmonary microbiota as a potential therapeutic intervention.

Viral metagenomics reveals diverse anelloviruses in bone marrow specimens from hematologic patients

BACKGROUND

An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients.

METHODS

A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones.

RESULTS

Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples.

CONCLUSIONS

Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.

Links Between Inflammatory Bowel Disease and Chronic Obstructive Pulmonary Disease

Inflammatory bowel disease (IBD) and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the gastrointestinal and respiratory tracts, respectively. These mucosal tissues bear commonalities in embryology, structure and physiology. Inherent similarities in immune responses at the two sites, as well as overlapping environmental risk factors, help to explain the increase in prevalence of IBD amongst COPD patients. Over the past decade, a tremendous amount of research has been conducted to define the microbiological makeup of the intestine, known as the intestinal microbiota, and determine its contribution to health and disease. Intestinal microbial dysbiosis is now known to be associated with IBD where it impacts upon intestinal epithelial barrier integrity and leads to augmented immune responses and the perpetuation of chronic inflammation. While much less is known about the lung microbiota, like the intestine, it has its own distinct, diverse microflora, with dysbiosis being reported in respiratory disease settings such as COPD. Recent research has begun to delineate the interaction or crosstalk between the lung and the intestine and how this may influence, or be influenced by, the microbiota. It is now known that microbial products and metabolites can be transferred from the intestine to the lung via the bloodstream, providing a mechanism for communication. While recent studies indicate that intestinal microbiota can influence respiratory health, intestinal dysbiosis in COPD has not yet been described although it is anticipated since factors that lead to dysbiosis are similarly associated with COPD. This review will focus on the gut-lung axis in the context of IBD and COPD, highlighting the role of environmental and genetic factors and the impact of microbial dysbiosis on chronic inflammation in the intestinal tract and lung.

Bronchoalveolar lavage as a diagnostic procedure: a review of known cellular and molecular findings in various lung diseases

Bronchoalveolar lavage (BAL) is a commonly used procedure in the evaluation of lung disease as it allows for sampling of the lower respiratory tract. In many circumstances, BAL differential cell counts have been reported to be typical of specific lung disorders. In addition, more specific diagnostic tests including molecular assays such as polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay, special cytopathologic stains, or particular microscopic findings have been described as part of BAL fluid analysis. This review focuses on common cellular and molecular findings of BAL in a wide range of lung diseases. Since the performance of the first lung irrigation in 1927, BAL has become a common and important diagnostic tool. While some pulmonary disorders have a highly characteristic signature of BAL findings, BAL results alone often lack specificity and require interpretation along with other clinical and radiographic details. Development of new diagnostic assays is certain to reinforce the utility of BAL in the future. Our review of the BAL literature is intended to serve as a resource to assist clinicians in the care of patients with lung disorders.

Metagenomic Virome Sequencing in Living Donor and Recipient Kidney Transplant Pairs Revealed JC Polyomavirus Transmission

Background

Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living-donor kidney transplantation.

Methods

Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4–6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random polymerase chain reaction (PCR), and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR.

Results

We analyzed a total of 30 living kidney donor and recipient pairs, with a follow-up of at least 1 year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in the urine of 7 donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in 6 cases, suggesting transmission from the transplant donor to the recipient, despite recipient seropositivity for JCPyV at the time of transplantation.

Conclusions

Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor’s virome for transplant outcomes.

Advanced "lab-on-a-chip" to detect viruses - Current challenges and future perspectives

Massive viral outbreaks draw attention to viruses that have not been thoroughly studied or understood. In recent decades, microfluidic chips, known as "lab-on-a-chip", appears as a promising tool for the detection of viruses. Here, we review the development of microfluidic chips that could be used in response to viral detection, specifically for viruses involved in more recent outbreaks. The advantages as well as the disadvantages of microfluidic systems are discussed and analyzed. We also propose ideas for future development of these microfluidic chips and we expect this advanced technology to be used in the future for viral outbreaks.

The virome in hematology-Stem cell transplantation and beyond

The virome has been recently studied in hematology and mostly in the setting of allogeneic hematopoietic stem cell transplantation. However, in hematology (as in the setting of nonhematological disorders) the study of the microbiome (that indeed includes the virome) is a growing field. The overall field is moving beyond species catalogue to the understanding of the complex ecological relationship that microbes have with each other and with their host. Here we review the existing literature on the virome in transplant recipients and in other settings, and discuss potential applications of the virome study in hematology.

Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam

Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012-2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology.

Semen virome of men with HIV on or off antiretroviral treatment

OBJECTIVES

Improving immune status of people living with HIV through antiretroviral therapy (ART) may also reduce shedding of other viruses in semen. We characterized the seminal fluid virome of men with HIV and tested potential associations between viruses present and CD4 T-cell count, HIV viremia, and antiretroviral therapy (ART) status.

DESIGN AND METHODS

Metagenomics was used to enrich and sequence viral nucleic acids from the seminal fluid of 55 semen samples from 42 men living with HIV from San Francisco with a median age of 33 (IQR, 28.7-45) and median CD4 T-cell counts of 837 cells/μl (IQR, 258-1571 cells/μl). All samples were collected between 2005 and 2015, and ART status was ascertained from medical records.

RESULTS

Anelloviruses, cytomegalovirus (CMV), and multiple genotypes of human papillomaviruses were detected. Participants shed from 0 to 4 distinct human viruses. Longitudinally collected seminal fluid samples showed changes in the viruses shed. Viruses were more frequently shed by individuals with detectable HIV viremia (43.7 vs. 15.4%, P = 0.042). A trend was seen for increased shedding by individuals who were not on ART (42.8 vs. 17.8%, P = 0.082) or with CD4 T-cell count less than 350 cells/μl (35.3 vs. 20%, P = 0.27).

CONCLUSION

Seminal fluid from men with HIV from San Francisco contains nucleic acids from three different DNA viral families. A greater number of viruses, particularly CMV, were shed by participants with detectable HIV viremia (18.9 vs. 0%, P = 0.022). Control of viremia through ART may lower shedding of other viruses in semen in addition to HIV.

Impact of the microbiota on solid organ transplant rejection

PURPOSE OF REVIEW

The microbiota in mammalian hosts can affect maturation and function of the immune system and has been associated with health and disease. We will review new findings on how this dynamic environmental factor impacts alloimmunity and therapy in transplant hosts.

RECENT FINDINGS

The microbiota changes after transplantation and immunosuppressive therapy. New data indicate that different microbial community structures have distinct impact on graft outcome, from promoting, to inhibiting or being neutral to transplant survival. In addition, we will address reciprocal interactions between the microbiota and immunosuppressive drugs, as well as the suitability of the microbiota as a predictive biomarker and its utility as adjunct therapy in transplantation.

SUMMARY

Advances in microbiome sequencing and wider availability of gnotobiotic facilities are enabling mechanistic investigations into the commensal communities and pathways that modulate allograft outcome, responsiveness to immunosuppression and side effects of drugs. A better understanding of the functions of the microbiota may help mitigate drug toxicity, predict drug dosage and dampen alloimmunity in transplant patients.

Torque teno virus in liver diseases: On the way towards unity of view

The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology, diagnostic methods, possible replication sites, and pathogenicity factors are described. TTV is a virus that is frequently detectable in patients with different viral hepatitides, in cases of hepatitis without an obvious viral agent, as well as in a healthy population. There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection. There are sufficient histological signs of liver damage, which confirm that the virus can undergo a replicative cycle in hepatocytes. Along with this, cytological hybridization in TTV-infected cells has shown no substantial cytopathic (cell-damaging) effects that are characteristic of pathogenic hepatotropic viruses. Studying TTV has led to the evolution of views on its role in the development of human pathology. The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses, including the viruses of the known types of hepatitides. The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a non-pathogenic virus. It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status. The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses. Fortunately, the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties. The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.

The Role of Lung and Gut Microbiota in the Pathology of Asthma

Asthma is a common chronic respiratory disease affecting more than 300 million people worldwide. Clinical features of asthma and its immunological and molecular etiology vary significantly among patients. An understanding of the complexities of asthma has evolved to the point where precision medicine approaches, including microbiome analysis, are being increasingly recognized as an important part of disease management. Lung and gut microbiota play several important roles in the development, regulation, and maintenance of healthy immune responses. Dysbiosis and subsequent dysregulation of microbiota-related immunological processes affect the onset of the disease, its clinical characteristics, and responses to treatment. Bacteria and viruses are the most extensively studied microorganisms relating to asthma pathogenesis, but other microbes, including fungi and even archaea, can potently influence airway inflammation. This review focuses on recently discovered connections between lung and gut microbiota, including bacteria, fungi, viruses, and archaea, and their influence on asthma.

Probiotics and prebiotics potential for the care of skin, female urogenital tract, and respiratory tract

The prebiotics and probiotics market is constantly growing due to the positive effects of its consumption on human health, which extends beyond the digestive system. In addition, the synbiotic products market is also expanding due to the synergistic effects between pre- and probiotics that provide additional benefits to consumers. Pre- and probiotics are being evaluated for their effectiveness to treat and prevent infectious diseases in other parts of the human body where microbial communities exist. This review examines the scientific data related to the effects of pre- and probiotics on the treatment of diseases occurring in the skin, female urogenital tract, and respiratory tract. The evidence suggests that probiotics consumption can decrease the presence of eczema in children when their mothers have consumed probiotics during pregnancy and lactation. In women, probiotics consumption can effectively prevent recurrent urinary tract infections. The consumption of synbiotic products can reduce respiratory tract infections and their duration and severity. However, the outcomes of the meta-analyses are still limited and not sufficiently conclusive to support the use of probiotics to treat infectious diseases. This is largely a result of the limited number of studies, lack of standardization of the studies, and inconsistencies between the reported results. Therefore, it is advisable that future studies consider these shortcomings and include the evaluation of the combined use of pre- and probiotics.

Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes

BACKGROUND

Microbial exposures in utero and early life shape the infant microbiome, which can profoundly impact on health. Compared to the bacterial microbiome, very little is known about the virome. We set out to characterize longitudinal changes in the gut virome of healthy infants born to mothers with or without type 1 diabetes using comprehensive virome capture sequencing.

METHODS

Healthy infants were selected from Environmental Determinants of Islet Autoimmunity (ENDIA), a prospective cohort of Australian children with a first-degree relative with type 1 diabetes, followed from pregnancy. Fecal specimens were collected three-monthly in the first year of life.

RESULTS

Among 25 infants (44% born to mothers with type 1 diabetes) at least one virus was detected in 65% (65/100) of samples and 96% (24/25) of infants during the first year of life. In total, 26 genera of viruses were identified and >150 viruses were differentially abundant between the gut of infants with a mother with type 1 diabetes vs without. Positivity for any virus was associated with maternal type 1 diabetes and older infant age. Enterovirus was associated with older infant age and maternal smoking.

CONCLUSIONS

We demonstrate a distinct gut virome profile in infants of mothers with type 1 diabetes, which may influence health outcomes later in life. Higher prevalence and greater number of viruses observed compared to previous studies suggests significant underrepresentation in existing virome datasets, arising most likely from less sensitive techniques used in data acquisition.

Anellovirus Dynamics Are Associated With Primary Graft Dysfunction in Lung Transplantation

Primary graft dysfunction (PGD) is the leading cause of early death in lung transplant. Anelloviruses are small circular DNA viruses that have been noted to be present at elevated levels in immunosuppressed patients. They have been associated with both short- and long-term outcomes in lung transplant, and we hypothesized that anellovirus dynamics might be associated with the development of PGD.

Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness

The global virome is largely uncharacterized but is now being unveiled by metagenomic DNA sequencing. Exploring the human respiratory virome, in particular, can provide insights into oro-respiratory diseases. Here, we use metagenomics to identify a family of small circular DNA viruses-named Redondoviridae-associated with human diseases. We first identified two redondovirus genomes from bronchoalveolar lavage samples from human lung donors. We then queried thousands of metagenomic samples and recovered 17 additional complete redondovirus genomes. Detections were exclusively in human samples and mostly from respiratory tract and oro-pharyngeal sites, where Redondoviridae was the second most prevalent eukaryotic DNA virus family. Redondovirus sequences were associated with periodontal disease, and abundances decreased with treatment. Some critically ill patients in a medical intensive care unit were found to harbor high levels of redondoviruses in respiratory samples. These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.

High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques (Macaca fascicularis)

Cynomolgus macaques are common across South East Asian countries including Thailand. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) captures wild-borne cynomolgus macaque for research use. Limited information is available on the enteric viruses and possible zoonotic infections into or from cynomolgus macaques. We characterized and compare the fecal virome of two populations; healthy wild-originated captive cynomolgus macaques (n = 43) reared in NPRCT-CU and healthy wild cynomolgus macaques (n = 35). Over 90% of recognized viral sequence reads amplified from feces were from bacterial viruses. Viruses from seven families of mammalian viruses were also detected (Parvoviridae, Anelloviridae, Picornaviridae, Adenoviridae, Papillomaviridae, Herpesviridae, and Caliciviridae). The genomes of a member of a new picornavirus genus we named Mafapivirus, a primate chapparvovirus, and a circular Rep-encoding single-strand (CRESS) DNA virus were also characterized. Higher abundance of CRESS DNA viruses of unknown tropism and invertebrate-tropic ambidensovirus were detected in wild versus captive macaques likely reflecting dietary differences. Short term rearing in captivity did not have a pronounced effect on the diversity of mammalian viruses of wild cynomolgus macaques. This study is the first report of the fecal virome of cynomolgus macaques, non-human primates frequently used in biomedical research and vaccination studies.

Functional effects of the microbiota in chronic respiratory disease

The composition of the lung microbiome is increasingly well characterised, with changes in microbial diversity or abundance observed in association with several chronic respiratory diseases such as asthma, cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease. However, the precise effects of the microbiome on pulmonary health and the functional mechanisms by which it regulates host immunity are only now beginning to be elucidated. Bacteria, viruses, and fungi from both the upper and lower respiratory tract produce structural ligands and metabolites that interact with the host and alter the development and progression of chronic respiratory diseases. Here, we review recent advances in our understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases. We also describe the present understanding of how respiratory microbiota can influence the efficacy of common therapies for chronic respiratory disease, and the potential of manipulation of the microbiome as a therapeutic strategy. Finally, we highlight some of the limitations in the field and propose how these could be addressed in future research.

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.

Community-Acquired Respiratory Viruses in Transplant Patients: Diversity, Impact, Unmet Clinical Needs

Patients undergoing solid-organ transplantation (SOT) or allogeneic hematopoietic cell transplantation (HCT) are at increased risk for infectious complications. Community-acquired respiratory viruses (CARVs) pose a particular challenge due to the frequent exposure pre-, peri-, and posttransplantation. Although influenza A and B viruses have a top priority regarding prevention and treatment, recent molecular diagnostic tests detecting an array of other CARVs in real time have dramatically expanded our knowledge about the epidemiology, diversity, and impact of CARV infections in the general population and in allogeneic HCT and SOT patients. These data have demonstrated that non-influenza CARVs independently contribute to morbidity and mortality of transplant patients. However, effective vaccination and antiviral treatment is only emerging for non-influenza CARVs, placing emphasis on infection control and supportive measures. Here, we review the current knowledge about CARVs in SOT and allogeneic HCT patients to better define the magnitude of this unmet clinical need and to discuss some of the lessons learned from human influenza virus, respiratory syncytial virus, parainfluenzavirus, rhinovirus, coronavirus, adenovirus, and bocavirus regarding diagnosis, prevention, and treatment.

Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.

Effect of Geographic Isolation on the Nasal Virome of Indigenous Children

The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses.IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health

BACKGROUND

The virome is a network of viruses normally inhabiting humans. It forms a conspicuous portion of the so-called microbiome, once generically referred to as resident flora. Indeed, viruses infecting humans without leading to clinical disease are increasingly recognized as part of the microbiome and have an impact on the development of our immune system. In addition, they activate inflammasomes, multiprotein complexes that assemble in cells and that are responsible for the downstream effects of sensing pathogens.

OBJECTIVE

This review aims at summarizing the evidence on the role of the virome in modulating inflammation and emphasizes evidence for Anelloviruses as useful molecular markers to monitor inflammatory processes and immune system competence.

METHOD

We carried out a review of the literature published in the last 5 years and summarized older literature to take into account ground-breaking discoveries concerning inflammasome assembly and virome.

RESULTS

A massive amount of data recently emerging demonstrate that the microbiome closely reflects what we eat, and many other unexpected variables. Composition, location, and amount of the microbiome have an impact on innate and adaptive immune defences. Viruses making up the virome contribute to shaping the immune system. Anelloviruses, the best known of such viruses, are present in most human beings, persistently without causing apparent disease. Depending on their interplay with such viruses, inflammasomes instruct host defences to tolerate or forfeit a specific microorganism.

CONCLUSION

The virome plays an important role in shaping human immune defences and contributes to inflammatory processes by quenching or increasing them.

Introduction to Techniques and Methodologies for Characterizing the Human Respiratory Virome

There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.

Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples

RATIONALE

The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers.

OBJECTIVES

We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA sequencing. Because DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination.

METHODS

We analyzed specimens from subjects with sarcoidosis (n = 93), control subjects without sarcoidosis (n = 72), and various environmental controls (n = 150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, BAL, Kveim reagent, and fresh granulomatous spleen from a patient with sarcoidosis. All specimens were analyzed by bacterial 16S and fungal internal transcribed spacer ribosomal RNA gene sequencing. In addition, BAL was analyzed by shotgun sequencing of fractions enriched for viral particles, and Kveim and spleen were subjected to whole-genome shotgun sequencing.

MEASUREMENTS AND MAIN RESULTS

In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared with nonsarcoidosis tissues; in the other tissue set, we detected enrichment of several bacterial lineages in sarcoidosis but not Cladosporiaceae. BAL showed limited enrichment of Aspergillus fungi. Several microbial lineages were detected in Kveim and spleen, including Cladosporium. No microbial lineage was enriched in more than one sample type after correction for multiple comparisons.

CONCLUSIONS

Metagenomic sequencing revealed enrichment of microbes in single types of sarcoidosis samples but limited concordance across sample types. Statistical analysis accounting for environmental contamination was essential to avoiding false positives.

Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation

Solid organ transplantation (SOT) recipients receive immunosuppressive therapy to avoid rejection of the transplanted organ. Immunosuppressive therapy increases the risk of infections. However, no existing marker reliably reveals the status of the immune function in SOT recipients. Torque-Teno virus or Transfusion-transmitted virus (TTV) has gained attention as a possible endogenous marker of the immune function. TTV is a non-enveloped, circular single strand DNA virus, and it may be considered a part of the human virome. In a bidirectional relationship, the immune system detects TTV and TTV may also modulate the activity of immune system. These characteristics have made the virus a possible candidate indicator of immune function. In this systematic review, we describe the role and potential function of TTV viral load as an endogenous marker of the immune function and consequently the level of immune suppression in SOT recipients.

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.

Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders

Posttransplant lymphoproliferative disorders (PTLDs), 50%-80% of which are strongly associated with Epstein-Barr virus (EBV), carry a high morbidity and mortality. Most clinical/epidemiological/tumor characteristics do not consistently associate with worse patient survival, so our aim was to identify if other viral genomic characteristics associated better with survival. We extracted DNA from stored paraffin-embedded PTLD tissues at our center, identified viral sequences by metagenomic shotgun sequencing (MSS), and analyzed the data in relation to clinical outcomes. Our study population comprised 69 PTLD tissue samples collected between 1991 and 2015 from 60 subjects. Nucleotide sequences from at least one virus were detected by MSS in 86% (59/69) of the tissues (EBV in 61%, anelloviruses 52%, gammapapillomaviruses 14%, CMV 7%, and HSV in 3%). No viruses were present in higher proportion in EBV-negative PTLD (compared to EBV-positive PTLD). In univariable analysis, death within 5 years of PTLD diagnosis was associated with anellovirus (P = 0.037) and gammapapillomavirus (P = 0.036) detection by MSS, higher tissue qPCR levels of the predominant human anellovirus species torque teno virus (TTV; P = 0.016), T cell type PTLD, liver, brain or bone marrow location. In multivariable analyses, T cell PTLD (P = 0.006) and TTV PCR level (P = 0.012) remained significant. In EBV-positive PTLD, EBNA-LP, EBNA1 and EBNA3C had significantly higher levels of nonsynonymous gene variants compared to the other EBV genes. Multiple viruses are detectable in PTLD tissues by MSS. Anellovirus positivity, not EBV positivity,was associated with worse patient survival in our series. Confirmation and extension of this work in larger multicenter studies is desirable.

Infectious Disease Transmission in Solid Organ Transplantation: Donor Evaluation, Recipient Risk, and Outcomes of Transmission

In 2016, the Transplantation Society of Australia and New Zealand, with the support of the Australian Government Organ and Tissue authority, commissioned a literature review on the topic of infectious disease transmission from deceased donors to recipients of solid organ transplants. The purpose of this review was to synthesize evidence on transmission risks, diagnostic test characteristics, and recipient management to inform best-practice clinical guidelines. The final review, presented as a special supplement in Transplantation Direct, collates case reports of transmission events and other peer-reviewed literature, and summarizes current (as of June 2017) international guidelines on donor screening and recipient management. Of particular interest at the time of writing was how to maximize utilization of donors at increased risk for transmission of human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, given the recent developments, including the availability of direct-acting antivirals for hepatitis C virus and improvements in donor screening technologies. The review also covers emerging risks associated with recent epidemics (eg, Zika virus) and the risk of transmission of nonendemic pathogens related to donor travel history or country of origin. Lastly, the implications for recipient consent of expanded utilization of donors at increased risk of blood-borne viral disease transmission are considered.

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.

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.

Lower Airway Virology in Health and Disease-From Invaders to Symbionts

Studies of human airway virome are relatively recent and still very limited. Culture-independent microbial techniques showed growing evidence of numerous viral communities in the respiratory microbial ecosystem. The significance of different acute respiratory viruses is already known in the pathogenesis of chronic conditions, such as asthma, cystic fibrosis (CF), or chronic obstructive lung disease (COPD), and their exacerbations. Viral pathogens, such as influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, or rhinovirus, have been associated with impaired immune response, acute exacerbations, and decrease in lung function in chronic lung diseases. However, more data have attributed a role to Herpes family viruses or the newly identified Anelloviridae family of viruses in chronic diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), or CF. Impaired antiviral immunity, bacterial colonization, or used medication, such as glucocorticoids or antibiotics, contribute to the imbalance of airway microbiome and may shape the local viral ecosystem. A specific part of virome, bacteriophages, frames lung microbial communities through direct contact with its host, the specific bacteria known as Pseudomonas aeruginosa or their biofilm formation. Moreover, antibiotic resistance is induced through phages via horizontal transfer and leads to more severe exacerbations of chronic airway conditions. Morbidity and mortality of asthma, COPD, CF, and IPF remains high, despite an increased understanding and knowledge about the impact of respiratory virome in the pathogenesis of these conditions. Thus, more studies focus on new prophylactic methods or therapeutic agents directed toward viral⁻host interaction, microbial metabolic function, or lung microbial composition rearrangement.

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome

BACKGROUND

The role of commensal viruses in humans is poorly understood, and the impact of the virome on lung health and smoking-related disease is particularly understudied.

METHODS

Genetic material from acellular bronchoalveolar lavage fluid was sequenced to identify and quantify viral members of the lower respiratory tract which were compared against concurrent bronchoalveolar lavage bacterial, metabolite, cytokine and cellular profiles, and clinical data. Twenty smoker and 10 nonsmoker participants with no significant comorbidities were studied.

RESULTS

Viruses that infect bacteria (phages) represented the vast majority of viruses in the lung. Though bacterial communities were statistically indistinguishable across smokers and nonsmokers as observed in previous studies, lung viromes and metabolic profiles were significantly different between groups. Statistical analyses revealed that changes in viral communities correlate most with changes in levels of arachidonic acid and IL-8, both potentially relevant for chronic obstructive pulmonary disease (COPD) pathogenesis based on prior studies.

CONCLUSIONS

Our assessment of human lung DNA viral communities reveals that commensal viruses are present in the lower respiratory tract and differ between smokers and nonsmokers. The associations between viral populations and local immune and metabolic tone suggest a significant role for virome-host interaction in smoking related lung disease.

Temporal dynamics of the lung and plasma viromes in lung transplant recipients

The human virome plays an important role for the clinical outcome of lung transplant recipients (LTRs). While pathogenic viruses may cause severe infections, non-pathogenic viruses may serve as potential markers for the level of immunosuppression. However, neither the complexity of the virome in different compartments nor the dynamics of the virus populations posttransplantation are yet understood. Therefore, in this study the virome was analyzed by metagenomic sequencing in simultaneously withdrawn bronchoalveolar lavage (BAL) and plasma samples of 15 LTRs. In seven patients, also follow-up samples were investigated for abundance and dynamics of virus populations posttransplantation. Five eukaryotic and two prokaryotic virus families were identified in BAL, and nine eukaryotic and two prokaryotic families in plasma. Anelloviruses were the most abundant in both compartments, followed by Herpes- and Coronaviruses. Virus abundance was significantly higher in LTRs than in healthy controls (Kruskal-Wallis test, p<0.001). Up to 48 different anellovirus strains were identified within a single LTR. Analyses in the follow-up patients revealed for the first time a highly complex and unique dynamics of individual anellovirus strains in the posttransplantation period. The abundance of anelloviruses in plasma was inversely correlated with that of other eukaryotic viruses (Pearson correlation coefficient r = -0.605; p<0.05). A broad spectrum of virus strains co-exists in BAL and plasma of LTRs. Especially for the anelloviruses, a high degree of co-infections and a highly individual and complex dynamics after transplantation was observed. The biological impact of these findings and their relation to clinical variables remain to be elucidated by future analyses.

Role of the lung microbiome in HIV pathogenesis

PURPOSE OF REVIEW

The purpose of this review is to summarize recent findings on the lung microbiome in HIV-infected patients and associated pulmonary diseases, and the relationship of airway microbial communities to metabolic and immune signatures within this patient population.

RECENT FINDINGS

The lung microbiome in HIV infection is a relatively new and rapidly developing field; early studies in the field produced inconclusive evidence as to whether HIV-infection changes the lower airway microbiome. More recent microbiome investigations have addressed these inconsistencies by incorporating systems biology approaches and laboratory models. Several investigations have now identified enrichment of Prevotella, Veillonella, and Streptococcus in the lower airways as consistent correlates of advanced HIV-infection and HIV-associated pulmonary diseases. These bacteria are associated with specific metabolic and immune profiles within the lung and circulation, providing the first indication that the lung microbiome may play a functional role in the pathogenesis of HIV-infection and HIV-associated pulmonary disease.

SUMMARY

This review summarizes knowledge to date on the lung microbiome in HIV infection, as well as challenges and accomplishments in the field within the last 2 years. Although the lung microbiome in HIV infection is still an emerging field, recent studies have formed a framework for future functional analysis of microbes in HIV pathogenesis.

The respiratory virome in chronic obstructive pulmonary disease

Aim: To characterize the respiratory virome in moderate/severe chronic obstructive pulmonary disease (COPD) patients using metagenomics, with healthy subjects as the reference. Patients & Methods: Sputum COPD samples were collected during stability and exacerbations with negative usual-care microbiologic analysis. Results: Eukaryotic viruses from the Anelloviridae, Herpesviridae and Retroviridae families and phages from the Shiphoviridae family were commonly found in COPD, and the respiratory virome in stability and noninfectious exacerbations showed a substantial similarity. DNA viruses with the highest relative abundance in COPD are Anelloviridae. Conclusion: These results support a colonizing role for eukaryotic viruses in COPD and highlight the importance of analyzing both DNA and RNA viruses when focusing on the respiratory virome.

Development of a standardized real time PCR for Torque teno viruses (TTV) viral load detection and quantification: A new tool for immune monitoring

BACKGROUND

Torque teno viruses (TTV) are small DNA viruses whose replication is closely linked to immune status. A growing number of publications underlined the potential of TTV viral load as an indicator of immunosuppression.

OBJECTIVES

To demonstrate the analytical performance of the first standardized RUO (Research Use Only) assay to detect and quantify human TTV DNA in whole blood and plasma.

STUDY DESIGN

We established analytical performances for TTV load measurement in various populations. The TTV kinetics were followed in kidney recipients. TTV viral load was analyzed on whole blood samples from 42 kidney recipients follow-up, 53 kidney deceased donors and 31 healthy volunteers.

RESULTS

The qPCR TTV assay detects the most prevalent human TTV genotypes and does not cross react with other viruses. Limit of detection was 2.2 log₁₀ copies/mL in whole blood and plasma, linearity and precision were demonstrated over the range 1.61 to 10.61 log₁₀ copies/mL in whole blood. Prevalence of TTV DNA in blood differed significantly among groups: 45% in healthy volunteers, 74% in donors and 83% in kidney recipients. In kidney recipients, early TTV kinetics were comparable to those previously observed with in-house assays in other transplant settings: viral load increased from an average of 4.3 log₁₀ to 7.9 log₁₀ copies/mL within the first 75 days post transplantation.

CONCLUSION

This TTV assay showed high analytical sensitivity, specificity, linearity and precision. It is a useful standardized tool to further evaluate TTV load as a biomarker of immune status that could improve individual treatment strategy.