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Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases.

The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory … ID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathway …

Profiling of RNA Viruses in Biting Midges (Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis.

Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 7 … idges identified. Others included Chironomidae and Cecidomyiidae. Our findings reveal a diverse RNA virome among Kenyan midges that includes previously unknown viruses. Further, metabarcoding analysis based on COI (cytochrome c oxidase subunit 1 mitochondrial gene) barcodes reveal a diverse array of midge species among the insects used in the study. Succ …

HERQ-9 Is a New Multiplex PCR for Differentiation and Quantification of All Nine Human Herpesviruses.

Infections with the nine human herpesviruses (HHVs) are globally prevalent and characterized by lifelong persistence. Reactivations can pote … effects of herpesvirus coinfections. Furthermore, its high sensitivity enables studies on the human virome, often dealing with minute quantities of persisting HHVs.IMPORTANCE By adulthood, almost all humans become infected by at least one herpesvirus (HHV). The maladies inflicted by these microbes extend beyond the initial infection, as they remain insid …

ViroFind: A novel target-enrichment deep-sequencing platform reveals a complex JC virus population in the brain of PML patients.

Deep nucleotide sequencing enables the unbiased, broad-spectrum detection of viruses in clinical samples without requiring an a priori hypot … that has been previously underappreciated. ViroFind can be used to investigate the structure of the virome with unprecedented depth in health and disease state.

Pseudomonas aeruginosa Virulence Bacteriophage Isolated From Inflammatory Mouse Feces Exhibits Bactericidal Activity in Infected Wounds of a Mouse Model.

BACKGROUND: Recently, bacteriophages have risen as a potent therapy for superbug infections. The mammal gut demonstrates an interesting sour … a proof of concept that the irritated gut acts as a source of bacteriophages. CONCLUSIONS: The gut virome was a promising and interesting source of antimicrobial and immunomodulating bacteriophage.

The genomic diversity of arthropod-specific viruses reinforces the continental distribution pattern of Aedes aegypti.

BACKGROUND: Aedes aegypti is the primary vector of arboviruses worldwide, including dengue, Zika, chikungunya, and yellow fever. It is believed to have originated in Africa and migrated to the Americas during the sixteenth and seventeenth centuries, subsequently spreading to Asia and Oceania between the nineteenth and twentieth centuries. These mosquitoes harbor insect-specific viruses (ISVs), which represent the majority of their core virome. Phasivirus phasiense (PCLV), cell-fusing agent virus (CFAV), and Aedes anphevirus (AeAV) stand out for their global distribution in vectors. Within this…

Torque Teno Virus Loads as a Marker of Immunosuppression in Pediatric Kidney Transplant Recipients.

BACKGROUND: Long-term renal function and survival after kidney transplantation rely on appropriate immunosuppressive treatment to prevent th … t been linked with any specific human illness, but which constitutes a major component of the human virome. Host antiviral responses allow TTV levels to be controlled; however, viral persistence remains, explaining the high prevalence in human populations, including healthy individuals. Important confounders of TTV load include time since transplantation …

Viral metagenomics reveals two novel anelloviruses in feces of experimental rats.

BACKGROUND: Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral … or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique. METHODS: Fecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq pla …

The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease.

BACKGROUND: Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only ~50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. METHODS: The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing…

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.

BACKGROUND: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead … duration treatment protocol thus appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD. Improvements in GI symptoms, ASD symptoms, and the microbiome all persisted for at least 8 weeks after treatment ended, suggesting a long-term impact. TRIAL REGISTRATION: This trial was registered on t …

Respiratory microbiota as a good predictor of outcome in humoral immunodeficiency. Methodological and conceptual difficulties in comprehensive microbiome analysis.

UNLABELLED: The microbiome as a broad term defines the most dynamic ecological system in which, apart from the biocenosis, there is unique n … with humoral immunodeficiencies, apart from the capsular cocci and H. influenzae. Research on human virome, including CMV, is also focused on the cellular immunity, but in many situations in the clinic the humoral compartment are the exclusive, still effective, barrier against viral replication. AIM: The aim of study was to perform an integrated microbi …

Wastewater genomic surveillance to track infectious disease-causing pathogens in low-income countries: Advantages, limitations, and perspectives.

The emergence of infectious diseases, particularly those caused by respiratory pathogens like COVID-19 and influenza viruses, poses a signif … A, B and RSV virus infections during the third wave of COVID-19 caused by the Omicron variant. The virome was concentrated from wastewater collected from two sewersheds of two cities, Agadir and Inezgane, using the the polyethylene glycol (PEG)/NaCl method. All 26 samples from both cities exhibited positive results for SARS-CoV-2, indicating varying vir …

Metagenomic Discovery of 83 New Human Papillomavirus Types in Patients with Immunodeficiency.

Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samples from 48 patients with rare genetic immunodeficiencies, including patients with warts, hypogammaglobulinem

Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.

Parvoviridae (small, nonenveloped ssDNA viruses) currently includes 281 species in two vertebrate- and four invertebrate-infecting subfamilies. While parvovirus-derived sequences are frequently identified in viromes, their taxonomy and host affiliation can be challenging due to high host and genetic diversity. We investigated the faecal parvovirome of 46 bats (7 insectivorous and 1 frugivorous species) from Eswatini and identified 28 novel viral species in 29 individuals (63.0%). The majority of these (22/28, 78.6%) belonged to nine genera (including two that are previously undescribed) within…

High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments.

Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported. Here we utilized published whole-transcriptome RNA sequencing (RNA-seq) data sets from seven different PTCL studies and new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across PTCL subtypes. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma…

Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications.

Increasing data indicate that insects serve as major reservoirs and vectors of viruses, which account for the continuously increasing ecolog … mprehensive insight into the origin, spread, and evolution of RNA viruses. Of course, a large-scale virome project involving more organisms would provide more-detailed information about the virus infections in insects.

Two Waves of Specific B Cell Memory Immunoreconstruction Observed in Anti-HHV1-3 IgG Kinetics after Hematopoietic Stem Cell Transplantation.

BACKGROUND: Humoral memory and specific antibody levels depend on the kind of antigen and individual immunofactors. The presence of IgM antibodies or a fourfold rise in specific IgG levels are generally accepted as diagnostic factors in the serology of acute viral infections. This basic model is not adequate for the herpes virome, especially after hematopoietic stem cell transplantation (HSCT), due to continuous, usually multifocal antigenic stimulation, various donor serostatuses, immunosuppression, and individual immunoreconstitution. METHODS: A case-control study was conducted to identify …

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.

Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the … ney bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been de …

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

The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interac

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… The blood and CSF virome have also been explored in the context of HSCT. A group obtained plasma samples from 40 1-month post-transplant allogenic HSCT patients to study the plasma virome. … Overall, much remains to be understood about the viromes of the different human microbiotas. …

Oral health's inextricable connection to systemic health: Special populations bring to bear multimodal relationships and factors connecting periodontal disease to systemic diseases and conditions.

The landscape in dentistry is changing as emerging studies continue to reveal that periodontal health impacts systemic health, and vice vers … f the oral microbial dysbiosis, including putative bacterial periodontopathogens and shifts in oral virome composition during disease. Multiple laboratory and clinical studies have illustrated that both eukaryotic and prokaryotic viruses within subgingival plaque and periodontal tissues affect periodontal inflammation, putative periodontopathogens, and t …