RESUMEN

Freshwater mussels (order: Unionida) are highly imperiled globally and are increasingly the focus of captive propagation efforts to protect and restore wild populations. The Upper Tennessee River Basin (UTRB) in Virginia is a freshwater biodiversity hotspot hosting at least 45 of North America's ~300 species of freshwater mussels, including 21 threatened and endangered species listed under the U.S. Endangered Species Act. Recent studies have documented that viruses and other microbes have contributed to freshwater mussel population declines in the UTRB. We conducted a multi-year longitudinal study of captive-reared hatchery mussels released to restoration sites throughout the UTRB to evaluate their viromes and compare them to captive hatchery environments. We documented 681 viruses from 27 families. The hatchery mussels had significantly less viruses than those deployed to wild sites, with only 20 viruses unique to the hatchery mussels. After the hatchery mussels were released into the wild, their number of viruses initially spiked and then increased steadily over time, with 451 viruses in total unique to the mussels in the wild. We found Clinch densovirus 1 (CDNV-1), a virus previously associated with mass mortality events in the Clinch River, in all samples, but the wild site mussels consistently had significantly higher CDNV-1 levels than those held in the hatchery. Our data document substantial differences between the viruses in the mussels in the hatchery and wild environments and rapid virome shifts after the mussels are released to the wild sites. These findings indicate that mussel release programs might benefit from acclimatization periods or other measures to mitigate the potential negative effects of rapid exposure to infectious agents found in natural environments.

RESUMEN

A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.

Asunto(s)

Genoma Viral , Sistemas de Lectura Abierta , Parvovirus , Filogenia , Lobos , Animales , Lobos/virología , Parvovirus/genética , Parvovirus/clasificación , Parvovirus/aislamiento & purificación , Proteínas de la Cápside/genética , Infecciones por Parvoviridae/virología , Infecciones por Parvoviridae/veterinaria , Composición de Base , China , ADN Viral/genética

RESUMEN

Fusarium head blight (FHB) continues to be a major problem in wheat production and is considered a disease complex caused by several fungal pathogens including Fusarium culmorum, F. graminearum and F. equiseti. With the objective of investigating diversity of mycoviruses in FHB-associated pathogens, we isolated Fusarium spp. from six wheat (Triticum aestivum) cultivars. In total, 56 Fusarium isolates (29 F. culmorum, 24 F. graminearum, one F. equiseti) were screened for mycoviruses by extracting and sequencing double-stranded RNA. We found that a large proportion of Fusarium isolates (46 %) were infected with mycoviruses. F. culmorum, previously described to harbor only one mycovirus, tended to host more viruses than F. graminearum, with a few isolates harboring seven mycoviruses simultaneously. Based on the RNA-dependent RNA polymerase domain analysis, ten were positive-sense single-stranded RNA viruses (related to viruses from families Mitoviridae, Botourmiaviridae, Narnaviridae, Tymoviridae, Gammaflexiviridae, as well as proposed Ambiguiviridae and ormycovirus viral group), one was double-stranded RNA virus (Partitiviridae), and five were negative-sense single-stranded RNA viruses (related to members in the families of Yueviridae, Phenuiviridae, Mymonaviridae, as well as proposed Mycoaspiviridae). Five mycoviruses were shared between F. graminearum and F. culmorum. These results increase our general understanding of mycovirology. To our knowledge, this is the first in-depth report of the mycovirome in F. culmorum and the first report on the diversity of mycoviruses from Danish isolates of FHB-causing fungi in general.

Asunto(s)

Virus Fúngicos , Fusarium , Filogenia , Enfermedades de las Plantas , Virus ARN , ARN Viral , Triticum , Fusarium/virología , Virus Fúngicos/clasificación , Virus Fúngicos/genética , Virus Fúngicos/aislamiento & purificación , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Triticum/microbiología , Triticum/virología , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , ARN Viral/genética , Genoma Viral

RESUMEN

The role of gut microbiota in health and disease is being thoroughly examined in various contexts, with a specific focus on the bacterial fraction due to its significant abundance. However, despite their lower abundance, viruses within the gut microbiota are gaining recognition for their crucial role in shaping the structure and function of the intestinal microbiota, with significant effects on the host as a whole, particularly the immune system. Similarly, environmental factors such as stress are key in modulating the host immune system, which in turn influences the composition of the gut virome and neurological functions through the bidirectional communication of the gut-brain axis. In this context, alterations in the host immune system due to stress and/or dysbiosis of the gut virome are critical factors in the development of both infectious and noninfectious diseases. The molecular mechanisms and correlation patterns between microbial species are not yet fully understood. This literature review seeks to explore the interconnected relationship between stress and the gut virome, with a focus on how this interaction is influenced by the host's immune system. We also discuss how disturbances in this finely balanced system can lead to the onset and/or progression of diseases.

Asunto(s)

Disbiosis , Microbioma Gastrointestinal , Estrés Fisiológico , Viroma , Humanos , Microbioma Gastrointestinal/fisiología , Enfermedades Transmisibles/virología , Enfermedades Transmisibles/microbiología , Animales , Virus/clasificación

RESUMEN

When a virus crosses from one host species to another, the consequences can be devastating. However, animal models to empirically evaluate cross-species transmission can fail to recapitulate natural transmission routes, physiologically relevant doses of pathogens, and population structures of naturally circulating viruses. Here, we present a new model of cross-species transmission where deer mice (Peromyscus maniculatus) are exposed to the natural virome of pet store mice (Mus musculus). Using RNA sequencing, we tracked viral transmission via fecal-oral routes and found the evidence of transmission of murine astroviruses, coronaviruses, and picornaviruses. Deep sequencing of murine kobuvirus revealed tight bottlenecks during transmission and purifying selection that leaves limited diversity present after transmission from Mus to Peromyscus. This work provides a structure for studying viral bottlenecks across species while keeping natural variation of viral populations intact and a high resolution look at within-host dynamics that occur during the initial stages of cross-species viral transmission.IMPORTANCEViral spillover events can have devastating public health consequences. Tracking cross-species transmission in real-time and evaluating viral evolution during the initial spillover event are useful for understanding how viruses adapt to new hosts. Using our new animal model and next generation sequencing, we develop a framework for understanding intrahost viral evolution and bottleneck events, which are very difficult to study in natural transmission settings.

RESUMEN

In this study, meta-transcriptome sequencing was conducted on a total of 18 sugarbeet (Beta vulgaris L. subsp. vulgaris) sample libraries to profile the virome of field-grown sugarbeet to identify the occurrence and distribution of known and potentially new viruses from five different states in the United States. Sugarbeet roots with symptoms resembling rhizomania caused by beet necrotic yellow vein virus (BNYVV), or leaves exhibiting leaf-curling, yellowing to browning, or green mosaic were collected from the sugarbeet growing areas of California, Colorado, Idaho, Minnesota, and North Dakota. In silico analysis of de novo assembled contigs revealed the presence of nearly full-length genomes of BNYVV, beet soil-borne virus (BSBV), and beet soil-borne mosaic virus (BSBMV), which represent known sugarbeet-infecting viruses. Among those, BNYVV was widespread across the locations, whereas BSBV was prevalent in Minnesota and Idaho, and BSBMV was only detected in Minnesota. In addition, two recently reported Beta vulgaris satellite virus isoforms (BvSatV-1A and BvSatV-1B) were detected in new locations, indicating the geographical expansion of this known virus. Besides these known sugarbeet-infecting viruses, the bioinformatic analysis identified the widespread occurrence of a new uncharacterized Erysiphe necator-associated abispo virus (En_abispoV), a fungus-related virus that was identified in all 14 libraries. En_abispoV contains two RNA components, and nearly complete sequences of both RNA1 and RNA2 were obtained from RNASeq and were further confirmed by primer-walking RT-PCR and Sanger sequencing. Phylogenetic comparison of En_abispoV isolates obtained in this study showed varying levels of genetic diversity within RNA1 and RNA2 compared to previously reported isolates. The undertaken meta-transcriptomic approach revealed the widespread nature of coexisting viruses associated with field-grown sugarbeet exhibiting virus disease-like symptoms in the United States.

RESUMEN

In advanced wastewater treatment plants on pig farms, meticulous design aims to eliminate intrinsic pollutants such as organic matter, heavy metals, and biological contaminants. In our field survey across Southern China, a notable disparity in wastewater treatment procedures among various farming facilities lies in the utilization of terminal chemical oxidation post-sedimentation tank. However, recent focus in wastewater surveillance has predominantly centered on antibiotic resistance genes, leaving the efficacy of virus removal in different effluent systems largely unexplored. To profile virus composition at the effluent, assess the virus elimination efficiency of chemical oxidation at the effluent end, and the potential environmental driver of virus abundance, we deployed a meta-transcriptomics approach to first determine the total virome in effluent specimens of terminal clean water tank system (CWT) and terminal chemical oxidation system (TCO) in Southern China pig farms, respectively. From these data, 172 viruses were identified, with a median reads per million (RPM) of 27,789 in CWT and 19,982 in TCO. Through the integration of analyses encompassing the co-occurrence patterns within viral communities, the ecology of viral diversity, and a comparative assessment of average variation degrees, we have empirically demonstrated that the procedure of TCO may perturb viral communities and diminish their abundance, particularly impacting RNA viral communities. However, despite the diminished abundance, pathogenic viruses such as PEDV and PRRSV persisted in the effluent following chemical deoxidation at a moderate RPM value, indicating a substantial in situ presence at effluent. Our environmental driver modeling, employing GLM and mantel tests, substantiated the intricate nature of virus community variation within the effluent, influenced heterogeneously by diverse factors. Notably, pond temperature emerged as the foremost determinant, while fishing farming exhibited a positive correlation with virus diversity (p < 0.05). This revelation of the cryptic persistence of virus communities in wastewater effluent expands our understanding of the varied responses of different virus categories to oxidation. Such insights transcend mere virus characterization, offering valuable implications for enhancing biosafety measures in farming practices and informing wastewater-based epidemiological surveillance.

RESUMEN

Paddy fields include two interconnected ecosystems-soil and floodwater. Microbes and viruses are an integral component of these ecosystems, yet the viral communities have not been extensively studied. We present an analysis of the viromes of paddy floodwater collected during the two cropping seasons in India, the kharif and rabi seasons respectively. The overall taxonomic and functional characteristics appeared to be similar in both seasons, suggesting stability of the viral community. Taxonomically, the families of tailed bacteriophages dominated. The predominance of functional roles related to lytic phages further confirmed this. We reconstructed two complete and several partial viral genomes from the assembled data. The genomes did not align with any known sequences, thus representing novel viruses of the floodwater ecosystem. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-024-01292-9.

RESUMEN

Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.

RESUMEN

BACKGROUND: The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments. METHODS: We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV. RESULTS: The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections. CONCLUSIONS: The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.

Asunto(s)

COVID-19 , Coinfección , Infecciones por Papillomavirus , SARS-CoV-2 , Humanos , Sierra Leona/epidemiología , Estudios Retrospectivos , COVID-19/virología , COVID-19/epidemiología , Infecciones por Papillomavirus/virología , Infecciones por Papillomavirus/epidemiología , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/clasificación , Coinfección/virología , Coinfección/epidemiología , Femenino , Adulto , Masculino , Persona de Mediana Edad , Adulto Joven , Nasofaringe/virología , Adolescente , Metagenómica , Filogenia , Papillomaviridae/genética , Papillomaviridae/clasificación , Papillomaviridae/aislamiento & purificación , Anciano , Niño

RESUMEN

Immune-mediated gastrointestinal (GI) diseases, including achalasia, celiac disease, and inflammatory bowel diseases, pose significant challenges in diagnosis and management due to their complex etiology and diverse clinical manifestations. While genetic predispositions and environmental factors have been extensively studied in the context of these conditions, the role of viral infections and virome dysbiosis remains a subject of growing interest. This review aims to elucidate the involvement of viral infections in the pathogenesis of immune-mediated GI diseases, focusing on achalasia and celiac disease, as well as the virome dysbiosis in IBD. Recent evidence suggests that viral pathogens, ranging from common respiratory viruses to enteroviruses and herpesviruses, may trigger or exacerbate achalasia and celiac disease by disrupting immune homeostasis in the GI tract. Furthermore, alterations in the microbiota and, specifically, in the virome composition and viral-host interactions have been implicated in perpetuating chronic intestinal inflammation in IBD. By synthesizing current knowledge on viral contributions to immune-mediated GI diseases, this review aims to provide insights into the complex interplay between viral infections, host genetics, and virome dysbiosis, shedding light on novel therapeutic strategies aimed at mitigating the burden of these debilitating conditions on patients' health and quality of life.

Asunto(s)

Disbiosis , Virosis , Humanos , Disbiosis/inmunología , Virosis/inmunología , Virosis/complicaciones , Virosis/virología , Enfermedades Gastrointestinales/virología , Enfermedades Gastrointestinales/inmunología , Enfermedades Gastrointestinales/etiología , Enfermedades Inflamatorias del Intestino/inmunología , Enfermedades Inflamatorias del Intestino/virología , Animales , Microbioma Gastrointestinal/inmunología , Virus/inmunología , Virus/patogenicidad , Enfermedad Celíaca/virología , Enfermedad Celíaca/inmunología , Viroma

RESUMEN

The mass rearing of animals in close quarters can be highly conducive to microbe transmission, including pathogens. This has been shown multiple times in the case of important industrial insects such as crickets, silkworms, and honeybees. One industrial insect of increasing importance is the black soldier fly (Diptera: Hermetia illucens), as it can convert organic waste into high-quality protein and fatty acids. Along with this, they take up far less space than traditional protein sources, as millions of black soldier flies can be reared in a relatively small facility. Because of this, there is a growing interest in the pathogens that could impact black soldier fly-rearing efforts. So far, only three black soldier fly-associated viruses have been identified. We used metatranscriptomic sequencing to survey black soldier fly guts, frass, and diet for viruses. We detected sequences from two novel viruses. One, which we name Hermetia illucens sigma-like virus 1, is phylogenetically related to viruses of the genus Sigmavirus, which have been highly studied in Drosophila. The other novel virus, which we name Hermetia illucens inse-like virus 1, is the second double-stranded RNA virus of the order Ghabrivirales described in the black soldier fly, and groups within a new family of insect viruses called the Inseviridae. We also detected two black soldier fly-associated viruses previously identified by our group: BSF nairo-like virus 1 and BSF uncharacterized bunyavirus-like 1. Consistent with our previous study, these two viruses are found primarily in frass samples and occur together more often than expected at random. When analyzing host transcription, we found significant differences in gene expression for eight candidate antiviral genes in the black soldier fly when comparing samples with and without viral sequences. Our results suggest that black soldier fly-virus interactions are ongoing, and they could be of interest to black soldier fly producers.

Asunto(s)

Dípteros , Filogenia , Animales , Dípteros/virología , Virus de Insectos/genética , Virus de Insectos/clasificación , Virus de Insectos/fisiología , Interacciones Huésped-Patógeno/genética

RESUMEN

Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.

Asunto(s)

Cacao , Fermentación , Viroma , Cacao/virología , Cacao/microbiología , Virus/genética , Virus/clasificación , Virus/aislamiento & purificación , Hongos/virología , Hongos/genética , Hongos/clasificación , Filogenia , Bacteriófagos/genética , Bacteriófagos/clasificación , Bacteriófagos/aislamiento & purificación , Costa Rica , Bacterias/genética , Bacterias/clasificación , Bacterias/virología , Metagenómica , Genoma Viral

RESUMEN

Studies on animal virome have mainly concentrated on chordates and medically significant invertebrates, often overlooking sylvatic mosquitoes, constituting a major part of mosquito species diversity. Despite their potential role in arbovirus transmission, the viromes of sylvatic mosquitoes remain largely unexplored. These mosquitoes may also harbor insect-specific viruses (ISVs), affecting arboviral transmission dynamics. The Cerrado biome, known for rapid deforestation and its status as a biodiversity hotspot, offers an ideal setting for investigating mosquito viromes due to potential zoonotic spillover risks from land use changes. This study aimed to characterize the viromes of sylvatic mosquitoes collected from various locations within Minas Gerais state, Brazil. The total RNA was extracted from mosquito pools of Psorophora albipes, Sabethes albiprivus, Sa. chloropterus, Psorophora ferox, and Coquillettidia venezuelensis species, followed by high-throughput sequencing (HTS). Bioinformatic analysis included quality control, contig assembly, and viral detection. Sequencing data analysis revealed 11 near-complete viral genomes (new viruses are indicated with asterisks) across seven viral families and one unassigned genus. These included: Xinmoviridae (Ferox mosquito mononega-like virus* and Albipes mosquito Gordis-like virus*), Phasmaviridae (Sabethes albiprivus phasmavirus*), Lispiviridae (Pedras lispivirus variant MG), Iflaviridae (Sabethes albiprivus iflavivirus*), Virgaviridae (Buriti virga-like virus variant MG and Sabethes albiprivus virgavirus 1*), Flaviviridae (Psorophora ferox flavivirus*), Mesoniviridae (Alphamesonivirus cavallyense variant MG), and the genus Negevirus (Biggie virus variant MG virus and Coquillettidia venezuelensis negevirus*). Moreover, the presence of ISVs and potential novel arboviruses underscores the need for ongoing surveillance and control strategies to mitigate the risk of emerging infectious diseases.

Asunto(s)

Infecciones por Arbovirus , Arbovirus , Culicidae , Mosquitos Vectores , Filogenia , Viroma , Animales , Brasil , Arbovirus/genética , Arbovirus/clasificación , Arbovirus/aislamiento & purificación , Viroma/genética , Culicidae/virología , Infecciones por Arbovirus/transmisión , Infecciones por Arbovirus/virología , Mosquitos Vectores/virología , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Virus de Insectos/genética , Virus de Insectos/clasificación , Virus de Insectos/aislamiento & purificación

RESUMEN

Fecal filtrate transfer (FFT) is emerging as a safer alternative to traditional fecal microbiota transplantation (FMT) - particularly in the context of necrotizing enterocolitis (NEC), a severe gastrointestinal condition affecting preterm infants. Using a preterm piglet model, FFT has demonstrated superiority over FMT in safety and NEC prevention. Since FFT is virtually devoid of bacteria, prokaryotic viruses (bacteriophages) are assumed to mediate the beneficial effects. However, this assumption remains unproven. To address this gap, we separated virus-like particles (30 kDa to 0.45 µm) of donor feces from the residual postbiotic fluid. We then compared clinical and gut microbiota responses to these fractions with the parent FFT solution after transferring them to NEC-susceptible preterm piglets. Virome transfer was equally effective as FFT in reducing the severity of NEC-like pathology. The bacterial compositional data corroborated clinical findings as virome transfer reduced the relative abundance of several NEC-associated pathogens e.g. Klebsiella pneumoniae and Clostridium perfringens. Virome transfer diversified gut viral communities with concomitant constraining effects on the bacterial composition. Unexpectedly, virome transfer, but not residual postbiotic fluid, led to earlier diarrhea. While diarrhea may be a minor concern in human infants, future work should identify ways of eliminating this side effect without losing treatment efficacy.

Asunto(s)

Enterocolitis Necrotizante , Trasplante de Microbiota Fecal , Heces , Microbioma Gastrointestinal , Enterocolitis Necrotizante/prevención & control , Enterocolitis Necrotizante/terapia , Animales , Heces/virología , Heces/microbiología , Trasplante de Microbiota Fecal/métodos , Porcinos , Humanos , Bacterias/clasificación , Bacterias/aislamiento & purificación , Bacterias/genética , Animales Recién Nacidos , Modelos Animales de Enfermedad , Viroma , Clostridium perfringens , Bacteriófagos/genética , Bacteriófagos/fisiología , Diarrea/terapia , Diarrea/virología , Diarrea/prevención & control , Diarrea/microbiología

RESUMEN

BACKGROUND: Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce. METHODS: We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia. RESULTS: Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing. CONCLUSIONS: This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.

Asunto(s)

Líquido del Lavado Bronquioalveolar , Secuenciación de Nucleótidos de Alto Rendimiento , Nasofaringe , Viroma , Virus , Humanos , Preescolar , Nasofaringe/virología , Nasofaringe/microbiología , Líquido del Lavado Bronquioalveolar/virología , Líquido del Lavado Bronquioalveolar/microbiología , Masculino , Femenino , Lactante , Virus/aislamiento & purificación , Virus/genética , Virus/clasificación , Niño , Orofaringe/virología , Orofaringe/microbiología , Neumonía/microbiología , Neumonía/virología , Neumonía/diagnóstico , Metagenómica/métodos

RESUMEN

While the viromes and immune systems of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores (order Eulipotyphla) despite their wide geographic distribution. Anthropogenic land use and outdoor recreational activities, as well as changes in the range of shrews, may lead to an expansion of the human-shrew interface with the risk of spillover infections, as reported for Borna disease virus 1. We investigated the virome of 45 individuals of 4 white-toothed shrew species present in Europe, using metagenomic RNA sequencing of tissue and intestine pools. Moderate to high abundances of sequences related to the families Paramyxoviridae, Nairoviridae, Hepeviridae and Bornaviridae were detected. Whole genomes were determined for novel orthoparamyxoviruses (n=3), orthonairoviruses (n=2) and an orthohepevirus. The novel paramyxovirus, tentatively named Hasua virus, was phylogenetically related to the zoonotic Langya virus and Mòjiang virus. The novel orthonairoviruses, along with the potentially zoonotic Erve virus, fall within the shrew-borne Thiafora virus genogroup. The highest viral RNA loads of orthoparamyxoviruses were detected in the kidneys, in well-perfused organs for orthonairoviruses and in the liver and intestine for orthohepevirus, indicating potential transmission routes. Notably, several shrews were found to be coinfected with viruses from different families. Our study highlights the virus diversity present in shrews, not only in biodiversity-rich regions but also in areas influenced by human activity. This study warrants further research to characterize and assess the clinical implications and risk of these viruses and the importance of shrews as reservoirs in European ecosystems.

Asunto(s)

Filogenia , Musarañas , Animales , Musarañas/virología , Genoma Viral , Europa (Continente) , Paramyxoviridae/genética , Paramyxoviridae/aislamiento & purificación , Paramyxoviridae/clasificación , Metagenómica , Viroma/genética , ARN Viral/genética , Humanos

RESUMEN

Despite advancements in medical interventions, the disease burden caused by viral pathogens remains large and highly diverse. This burden includes the wide range of signs and symptoms associated with active viral replication as well as a variety of clinical sequelae of infection. Moreover, there is growing evidence supporting the existence of sex- and ethnicity-based health disparities linked to viral infections and their associated diseases. Despite several well-documented disparities in viral infection rates, our current understanding of virus-associated health disparities remains incomplete. This knowledge gap can be attributed, in part, to limitations of the most commonly used viral detection methodologies, which lack the breadth needed to characterize exposures across the entire virome. Additionally, virus-related health disparities are dynamic and often differ considerably through space and time. In this study, we utilize PepSeq, an approach for highly multiplexed serology, to broadly assess an individual's history of viral exposures, and we demonstrate the effectiveness of this approach for detecting infection disparities through a pilot study of 400 adults aged 30-60 in Phoenix, AZ. Using a human virome PepSeq library, we observed expected seroprevalence rates for several common viruses and detected both expected and previously undocumented differences in inferred rates of infection between our male/female and Hispanic/non-Hispanic White individuals. IMPORTANCE: Our understanding of population-level virus infection rates and associated health disparities is incomplete. In part, this is because of the high diversity of human-infecting viruses and the limited breadth and sensitivity of traditional approaches for detecting infection events. Here, we demonstrate the potential for modern, highly multiplexed antibody detection methods to greatly increase our understanding of disparities in rates of infection across subpopulations (e.g., different sexes or ethnic groups). The use of antibodies as biomarkers allows us to detect evidence of past infections over an extended period, and our approach for highly multiplexed serology (PepSeq) allows us to measure antibody responses against hundreds of viruses in an efficient and cost-effective manner.

RESUMEN

Amphibians are an essential class in the maintenance of global ecosystem equilibrium, but they face serious extinction risks driven by climate change and infectious diseases. Unfortunately, the virus diversity harbored by these creatures has been rarely investigated. By profiling the virus flora residing in different tissues of 100 farmed black-spotted frogs (Rana nigromaculata) using a combination of DNA and RNA viromic methods, we captured 28 high-quality viral sequences covering at least 11 viral families. Most of these sequences were remarkably divergent, adding at least 10 new species and 4 new genera within the families Orthomyxoviridae, Adenoviridae, Nodaviridae, Phenuiviridae, and Picornaviridae. We recovered five orthomyxovirus segments, with three distantly neighboring two Chinese fish-related viruses. The recombination event of frog virus 3 occurred among the frog and turtle strains. The relative abundance and molecular detection revealed different tissue tropisms of these viruses, with the orthomyxovirus and adenoviruses being enteric and probably also neurotropic, but the new astrovirus and picornavirus being hepatophilic. These results expand the spectrum of viruses harbored by anurans, highlighting the necessity to continuously monitor these viruses and to investigate the virus diversity in a broader area with more diverse amphibian species.