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Clinical relevance of plasma virome dynamics in liver transplant recipients.

BACKGROUND: The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients. METHODS: Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were…

Virome analysis of tick-borne viruses in Heilongjiang Province, China.

Ticks are implicated in the transmission of various human and livestock pathogens worldwide. This study aimed to understand the geographical distribution of tick species, along with tick-associated viruses, in Heilongjiang Province, northeast China. Molecular methods were used to classify tick species, with next-generation sequencing and polymerase chain reaction-based analyses used to assess the viromes of ticks from four representative sampling locations in the Greater Khingan Mountains. Five species of ixodid ticks were identified, including Ixodes persulcatus, Dermacentor nuttalli, Dermace…

First insight into the virome composition of the vulnerable Naemorhedus griseus.

The Chinese goral (Naemorhedus griseus) is identified as a vulnerable species on the Red List of China's Biodiversity and listed as a national second-class key protected wild animal in China. Despite its widespread distribution in China, there has been scant research into the pathogens harbored by this species, and our understanding of the virus diversity remains limited. In the present study, we performed the whole virome profiling of a rescue-failed Naemorhedus griseus, which identified a diverse viral community across multiple organ tissues of the animal. Specifically, abundant bacteriophag…

Non-Sexual Transmission of Papillomavirus: Is It Part of Our Virome?

BACKGROUND: Human papillomavirus (HPV) has traditionally been considered a sexually transmitted infection, yet accumulating evidence demonst … nfants, and children, and evaluate metagenomic evidence positioning HPV as a component of the human virome across multiple body sites. RESULTS: Published studies report that vertical transmission occurs in approximately 18.2% of HPV-positive mothers, with neonatal HPV positivity of 3.4% at birth and 100% genotype concordance in transmission pairs. Trans …

Divergent coronaviruses discovered in the virome of lamprey with reddening syndrome.

UNLABELLED: Lamprey reddening syndrome (LRS) is an emerging disease affecting pouched lamprey (Geotria australis; kanakana/piharau), a culturally and ecologically significant species in Aotearoa, New Zealand. Characterized by skin hemorrhaging and elevated mortality, the etiology of LRS has remained unresolved despite previous investigations. We used a metatranscriptomic approach to characterize viral communities in 28 lamprey from New Zealand and Tasmania, Australia, comparing diseased and presumably healthy individuals. This analysis revealed eight fish-infecting RNA viruses, seven of which

Metagenomic Analysis of Viromes of Aedes Mosquitoes across India.

Metagenomic analysis of Aedes aegypti and Ae. albopictus mosquitoes from diverse geographical regions of India revealed the presence of several insect viruses of human interest. Most abundant reads found in Ae. aegypti mosquitoes were of Phasi Charoen-like virus (PCLV), Choristoneura fumiferana granulovirus (CfGV), Cell fusing agent virus (CFAV), and Wenzhou sobemo-like virus 4 (WSLV4), whereas WSLV4 and CfGV constituted the highest percentage of reads in Ae. albopictus viromes. Other reads that were of low percentage included Hubei mosquito virus 2 (HMV2), Porcine astrovirus 4 (PAstV4), and W…

Viromes of 15 Pepper (Capsicum annuum L.) Cultivars.

Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in fiv…

Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases.

More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses an…

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/…

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.

Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds …

Temporal response of the human virome to immunosuppression and antiviral therapy.

There are few substantive methods to measure the health of the immune system, and the connection between immune strength and the viral component of the microbiome is poorly understood. Organ transplant recipients are treated with posttransplant therapies that combine immunosuppressive and antiviral drugs, offering a window into the effects of immune modulation on the virome. We used sequencing of cell-free DNA in plasma to investigate drug-virome interactions in a cohort of organ transplant recipients (656 samples, 96 patients) and find that antivirals and immunosuppressants strongly affect th…

Plant virome analysis by high-throughput sequencing: concepts and approaches.

The metagenomic approach based on high-throughput sequencing is becoming increasingly prevalent for the detection of viral infections in pla … ntation and analytical capacity improving. This review summarizes key approaches to analyzing plant virome using high-throughput sequencing. The analysis process, from sample collection to bioinformatic data processing, validation and interpretation, is described in detail. The features of sequencing platforms and the factors affecting sequencing quality …

Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.

Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever

Dahlia Virome Analysis Reveals Multiple Novel Viruses in Mixed Infections.

Dahlia is an economically important ornamental crop in the United States and worldwide. Dahlia is primarily propagated vegetatively through bulbs, which can result in vertical transmission of and constant accumulation of viruses. In this study, mosaic and yellowing symptoms were observed in Dahlia plants in a residential garden in California. Dahlia samples were collected and sequenced using high-throughput sequencing (HTS). HTS analysis was used to explore the Dahlia virome in the symptomatic plants, which revealed the presence of several contigs with homology to known Dahlia-infecting viruse…

Brain virome dysbiosis in Parkinson's disease and multiple system atrophy.

Viral elements have been reported in human brain tissue, yet their presence in the putamen-a region critically affected in Parkinson's disease (PD) and multiple system atrophy (MSA)has not been characterized. We analyzed whole-genome sequencing data from 32 post-mortem putamen samples (PD: n = 10; MSA: n = 10; healthy controls: n = 12) available under NCBI BioProjects PRJNA756274, PRJNA563007, PRJNA321439, PRJNA555211, and PRJNA555099. Using MetaPhlAn4 for virome profiling, LEfSe for biomarker discovery, and Wilcoxon and ROC analyses for validation, we found that neurodegenerative samples exhi…

Interaction between gut virome and microbiota on inflammatory bowel disease.

Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, is a chronic condition marked by recurring gastrointestinal inflammation. While immune, genetic, and environmental factors are well-studied, the gut virome has received less attention. This editorial highlights the work which investigates the gut virome's role in IBD and its interactions with the bacterial microbiome and host immune system. The gut virome consists of bacteriophages, eukaryotic viruses, and endogenous retroviruses. Among these, Caudovirales bacteriophages are predominant and influence bacteri…

Virome capture sequencing for comprehensive HPV genotyping in cervical samples.

ObjectiveThis study aims to explore HPV genotyping in the cervical specimen using VirCapSeq by comparing the results with the reverse blot hybridization assay (REBA).MethodsA secondary cross-sectional data of HPV genotypes in 35 cervical specimens was obtained from VirCapSeq and REBA methods. The .FASTQ files were downloaded from the NCBI Sequence Read Archive (SRA) (accession number PRJNA766412) and HPV genotyping was bioinformatically analyzed by mapping the sequences to the PaVE database. HPV genotypes detected by REBA and NGS were compared. All specimens were stratified by histology into c

Виром ДНК связан с аутоиммунными заболеваниями и COVID-19.

Аберрантная иммунная реакция на вирусные патогены способствует патогенезу, но наше понимание патологических иммунных реакций, вызванных вирусами в вироме человека, особенно в масштабе населения, остается ограниченным. Мы проанализировали наборы данных о последовательности целых генов 6,321 Японцы, включая пациентов с аутоиммунными заболеваниями (псориаз вульгарис, ревматоидный артрит (RA), системный волшебный эритематос (SLE), легочный альвеолярный протеиноз (PAP) или множественный склероз) и коронавирусное заболевание 2019 (В тыс.COVID-19) или здоровый контроль. Систематическая количественная

Совпадение в аннотации оригинала
Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, including patients with autoimmune diseases (psoriasis vulgari…

Plasma virome dynamics in chronic hepatitis B virus infected patients.

The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome w…

Виром мозга в нейродегенеративных расстройствах: Отчёты от анализа транскриптомных данных.

Нейродегенеративные расстройства (ND) представляют собой хронические заболевания центральной нервной системы, которые постепенно ухудшают структуру и функции нейронов. Этиология НУ включает генетические факторы, старение, инфекции, голод, травмы мозга и травмы спинного мозга. Вместе с тем неясно, влияют ли вирусные инфекции на прогнозы НУ или способствуют их развитию. Поэтому мы изучили распространенность нейротропических вирусов в образцах головного мозга с помощью транскриптомных данных. В общей сложности для изучения распространенности 18 различных вирусов по 129 наборам данных по здоровым

Совпадение в аннотации оригинала
Neurodegenerative disorders (NDs) are chronic ailments of the central nervous system that gradually deteriorate the structures and functions … rom healthy and ND subjects. Our findings support the evidence pointing to the existence of a brain virome where certain viruses co-occur. We further hypothesize that distinct virome profiles are linked to different forms of NDs.