RESUMO
Human immunodeficiency virus-1 (HIV-1) infection disrupts the homeostatic equilibrium between the host and commensal microbes. However, the dynamic changes of plasma commensal viruses and their role in HIV/simian immunodeficiency virus (SIV) pathogenesis are rarely reported. Here, we investigated the longitudinal changes of plasma virome, inflammation levels, and disease markers using an SIV-infected Macaca leonina model. Large expansions of plasma Anelloviridae, Parvoviridae, Circoviridae and other commensal viruses, and elevated levels of inflammation and D-dimer were observed since the chronic phase of SIV infection. Anelloviridae abundance appears to correlate positively with the CD4+ T cell count but negatively with SIV load especially at the acute phase, whereas other commensal viruses' abundances show opposite correlations with the two disease markers. Antiretroviral therapy slightly reduces but does not substantially reverse the expansion of commensal viruses. Furthermore, 1387 primate anellovirus open reading frame 1 sequences of more than 1500 nucleotides were annotated. The data reveal different roles of commensal viruses in SIV pathogenesis.
Assuntos
Síndrome de Imunodeficiência Adquirida dos Símios , Vírus da Imunodeficiência Símia , Animais , Síndrome de Imunodeficiência Adquirida dos Símios/virologia , Síndrome de Imunodeficiência Adquirida dos Símios/sangue , Carga Viral , Viroma/genética , Macaca , Contagem de Linfócito CD4RESUMO
The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.
Assuntos
Microbioma Gastrointestinal , Metagenômica , Viroma , Animais , Bovinos , Microbioma Gastrointestinal/genética , Viroma/genética , Tibet , MetagenomaRESUMO
Advances in sequencing technologies and bioinformatics have led to breakthroughs in the study of virus biodiversity. Millipedes (Diplopoda, Myriapoda, Arthropoda) include more than 12,000 extant species, yet data on virus diversity in Diplopoda are scarce. This study aimed to explore the virome of the millipedes collected in the Dong Nai Biosphere Reserve in Vietnam. We studied 14 species of millipedes and managed to assemble and annotate the complete coding genomes of 16 novel viruses, the partial coding genomes of 10 more viruses, and several fragmented viral sequences, which may indicate the presence of about 54 more viruses in the studied samples. Among the complete and partial genomes, 27% were putative members of the order Picornavirales. Most of the discovered viruses were very distant from the viruses currently present in the relevant databases. At least eight viruses meet the criteria to be recognized as a new species by the International Committee on Taxonomy of Viruses, and, for two of them, a higher taxonomic status (genus and even family) can be suggested.
Assuntos
Artrópodes , Biodiversidade , Genoma Viral , Filogenia , Vírus , Vírus/classificação , Vírus/genética , Vírus/isolamento & purificação , Animais , Vietnã , Artrópodes/virologia , Artrópodes/classificação , Viroma/genética , Variação GenéticaRESUMO
South Africa has a small but growing olive industry. Until now, no virological research has been carried out on this crop locally. Seventeen samples were collected from various olive cultivars from a single producer in the Stellenbosch growing area of South Africa. RNAseq was performed on total RNA, and the compositions of the metaviromes were determined. Olive leaf yellowing-associated virus was detected for the first time in South Africa, as well as four novel viruses from the family Closteroviridae and one each from the families Tymoviridae and Solemoviridae.
Assuntos
Genoma Viral , Olea , Filogenia , Doenças das Plantas , África do Sul , Olea/virologia , Genoma Viral/genética , Doenças das Plantas/virologia , RNA Viral/genética , Closteroviridae/genética , Closteroviridae/isolamento & purificação , Closteroviridae/classificação , Vírus de Plantas/genética , Vírus de Plantas/classificação , Vírus de Plantas/isolamento & purificação , Tymoviridae/genética , Tymoviridae/isolamento & purificação , Tymoviridae/classificação , Genômica , Viroma/genéticaRESUMO
After plants transitioned from water to land around 450 million years ago, they faced novel pathogenic microbes. Their colonization of diverse habitats was driven by anatomical innovations like roots, stomata, and vascular tissue, which became central to plant-microbe interactions. However, the impact of these innovations on plant immunity and pathogen infection strategies remains poorly understood. Here, we explore plant-virus interactions in the bryophyte Marchantia polymorpha to gain insights into the evolution of these relationships. Virome analysis reveals that Marchantia is predominantly associated with RNA viruses. Comparative studies with tobacco mosaic virus (TMV) show that Marchantia shares core defense responses with vascular plants but also exhibits unique features, such as a sustained wound response preventing viral spread. Additionally, general defense responses in Marchantia are equivalent to those restricted to vascular tissues in Nicotiana, suggesting that evolutionary acquisition of developmental innovations results in re-routing of defense responses in vascular plants.
Assuntos
Marchantia , Nicotiana , Doenças das Plantas , Vírus do Mosaico do Tabaco , Marchantia/genética , Marchantia/virologia , Doenças das Plantas/virologia , Vírus do Mosaico do Tabaco/fisiologia , Nicotiana/virologia , Imunidade Vegetal/genética , Interações Hospedeiro-Patógeno/imunologia , Regulação da Expressão Gênica de Plantas , Viroma/genética , Vírus de Plantas/fisiologia , Vírus de Plantas/genéticaRESUMO
Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.
Assuntos
Bactérias , Bacteriófagos , Microbioma Gastrointestinal , Transferência Genética Horizontal , Bacteriófagos/genética , Humanos , Microbioma Gastrointestinal/genética , Bactérias/virologia , Bactérias/genética , Metagenômica/métodos , Variação Genética , Viroma/genética , Genoma Viral , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
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.
Assuntos
Viroses , Humanos , Masculino , Feminino , Viroses/epidemiologia , Viroses/diagnóstico , Pessoa de Meia-Idade , Adulto , Disparidades nos Níveis de Saúde , Estudos Soroepidemiológicos , Projetos Piloto , Vírus/genética , Vírus/classificação , Vírus/isolamento & purificação , Testes Sorológicos/métodos , Viroma/genéticaRESUMO
Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.
Assuntos
Bacteriófagos , Fígado Gorduroso , Microbioma Gastrointestinal , Americanos Mexicanos , Viroma , Humanos , Masculino , Feminino , Microbioma Gastrointestinal/genética , Bacteriófagos/genética , Pessoa de Meia-Idade , Viroma/genética , Fígado Gorduroso/genética , Estudos Transversais , Adulto , Diabetes Mellitus , Fezes/microbiologia , Fezes/virologia , IdosoRESUMO
Barramundi aquaculture is at risk of severe disease outbreaks and massive production losses. Here we used bioinformatics to screen 84 farmed barramundi transcriptomes to identify novel viruses that could threaten barramundi aquaculture and to establish a barramundi aquaculture virome. We discovered five novel viruses: latid herpesvirus 1 (LatHV-1) from the Alloherpesviridae family, barramundi parvovirus 1 (BParV1) from the Parvoviridae family, barramundi calicivirus 1 (BCaV1) from the Caliciviridae family, and barramundi associated picorna-like virus 1 and 2 (BPicV1 and BPicV2) from the Picornaviridae family. LatHV-1, BCaV1, and BParV1 are closely related to pathogenic viruses found in other fish species that can cause mass mortality in farms. To aid in future viral surveillance, we also designed and successfully tested an RT-PCR assay for the detection of BCaV1. Overall, we discovered a range of pathogenic viruses in barramundi aquaculture, paving the way for developing effective detection methods to assist early outbreak management.
Assuntos
Aquicultura , Doenças dos Peixes , Animais , Doenças dos Peixes/virologia , Doenças dos Peixes/epidemiologia , Austrália/epidemiologia , Ásia/epidemiologia , Filogenia , Perciformes/virologia , Viroma/genética , Vírus/genética , Vírus/classificação , Vírus/isolamento & purificação , Transcriptoma , Viroses/veterinária , Viroses/virologia , Viroses/epidemiologia , Picornaviridae/genética , Picornaviridae/isolamento & purificação , Picornaviridae/classificaçãoRESUMO
Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species ( ≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.
Assuntos
Bactérias , Água Subterrânea , Metagenômica , Viroma , Vírus , Água Subterrânea/microbiologia , Água Subterrânea/virologia , Vírus/genética , Vírus/classificação , Vírus/isolamento & purificação , Viroma/genética , Bactérias/genética , Bactérias/virologia , Bactérias/metabolismo , Bactérias/classificação , China , Archaea/virologia , Archaea/genética , Archaea/metabolismo , Filogenia , Microbiologia da Água , Metagenoma , Genoma Viral/genéticaRESUMO
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.
Assuntos
Filogenia , Musaranhos , Animais , Musaranhos/virologia , Genoma Viral , Europa (Continente) , Paramyxoviridae/genética , Paramyxoviridae/isolamento & purificação , Paramyxoviridae/classificação , Metagenômica , Viroma/genética , RNA Viral/genética , HumanosRESUMO
Shrews being insectivores, serve as natural reservoirs for a wide array of zoonotic viruses, including the recently discovered Langya henipavirus (LayV) in China in 2018. It is crucial to understand the shrew-associated virome, viral diversity, and new viruses. In the current study, we conducted high-throughput sequencing on lung samples obtained from 398 shrews captured along the eastern coast of China, and characterized the high-depth virome of 6 common shrew species (Anourosorex squamipes, Crocidura lasiura, Crocidura shantungensis, Crocidura tanakae, Sorex caecutiens, and Suncus murinus). Our analysis revealed numerous shrew-associated viruses comprising 54 known viruses and 72 new viruses that significantly enhance our understanding of mammalian viruses. Notably, 34 identified viruses possess spillover-risk potential and six were human pathogenic viruses: LayV, influenza A virus (H5N6), rotavirus A, rabies virus, avian paramyxovirus 1, and rat hepatitis E virus. Moreover, ten previously unreported viruses in China were discovered, six among them have spillover-risk potential. Additionally, all 54 known viruses and 12 new viruses had the ability to cross species boundaries. Our data underscore the diversity of shrew-associated viruses and provide a foundation for further studies into tracing and predicting emerging infectious diseases originated from shrews.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Pulmão , Musaranhos , Viroma , Animais , Musaranhos/virologia , China , Pulmão/virologia , Viroma/genética , Filogenia , Vírus de RNA/genética , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificação , RNA Viral/genética , Vírus da Influenza A/genética , Vírus da Influenza A/classificação , Vírus da Influenza A/isolamento & purificação , Vírus da Raiva/genética , Vírus da Raiva/classificação , Vírus da Raiva/isolamento & purificação , Reservatórios de Doenças/virologiaRESUMO
The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.
Assuntos
Microbioma Gastrointestinal , Genoma Viral , Metagenômica , Viroma , Vírus , Animais , Suínos , Viroma/genética , Metagenômica/métodos , Vírus/genética , Vírus/classificação , Vírus/isolamento & purificação , Mineração de Dados , Metagenoma , FilogeniaRESUMO
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.
Assuntos
Infecções por Arbovirus , Arbovírus , Culicidae , Mosquitos Vetores , Filogenia , Viroma , Animais , Brasil , Arbovírus/genética , Arbovírus/classificação , Arbovírus/isolamento & purificação , Viroma/genética , Culicidae/virologia , Infecções por Arbovirus/transmissão , Infecções por Arbovirus/virologia , Mosquitos Vetores/virologia , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Vírus de Insetos/genética , Vírus de Insetos/classificação , Vírus de Insetos/isolamento & purificaçãoRESUMO
Viral communities exist in a variety of ecosystems and play significant roles in mediating biogeochemical processes, whereas viruses inhabiting strongly alkaline geochemical systems remain underexplored. In this study, the viral diversity, potential functionalities, and virus-host interactions in a strongly alkaline environment (pH = 10.4-12.4) exposed to the leachates derived from the serpentinization-like reactions of smelting slags were investigated. The viral populations (e.g., Herelleviridae, Queuovirinae, and Inoviridae) were closely associated with the dominating prokaryotic hosts (e.g., Meiothermus, Trueperaceae, and Serpentinomonas) in this ultrabasic environment. Auxiliary metabolic genes (AMGs) suggested that viruses may enhance hosts' fitness by facilitating cofactor biosynthesis, hydrogen metabolism, and carbon cycling. To evaluate the activity of synthesis of essential cofactor vitamin B9 by the viruses, a viral folA (vfolA) gene encoding dihydrofolate reductase (DHFR) was introduced into a thymidine-auxotrophic strain Escherichia coli MG1655 ΔfolA mutant, which restored the growth of the latter in the absence of thymidine. Notably, the homologs of the validated vDHFR were globally distributed in the viromes across various ecosystems. The present study sheds new light on the unique viral communities in hyperalkaline ecosystems and their potential beneficial impacts on the coexisting microbial consortia by supplying essential cofactors. IMPORTANCE: This study presents a comprehensive investigation into the diversity, potential functionalities, and virus-microbe interactions in an artificially induced strongly alkaline environment. Functional validation of the detected viral folA genes encoding dihydrofolate reductase substantiated the synthesis of essential cofactors by viruses, which may be ubiquitous, considering the broad distribution of the viral genes associated with folate cycling.
Assuntos
Microbiota , Concentração de Íons de Hidrogênio , Viroma/genética , Vírus/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Tetra-Hidrofolato Desidrogenase/genética , Tetra-Hidrofolato Desidrogenase/metabolismo , Bactérias/genética , Bactérias/metabolismo , Bactérias/classificaçãoRESUMO
Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.
Assuntos
Aedes , Anopheles , Culex , Genoma Viral , Filogenia , Viroma , Animais , Brasil , Feminino , Anopheles/virologia , Viroma/genética , Aedes/virologia , Culex/virologia , Mosquitos Vetores/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Vírus de Insetos/genética , Vírus de Insetos/classificação , Vírus de Insetos/isolamento & purificaçãoRESUMO
Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE: Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.
Assuntos
Pradaria , Vírus de RNA , Microbiologia do Solo , Vírus de RNA/genética , RNA Viral/genética , Solo/química , Viroma/genéticaRESUMO
Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments. IMPORTANCE: Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.
Assuntos
Culicidae , Filogenia , Viroma , Animais , Brasil , Viroma/genética , Culicidae/virologia , Mosquitos Vetores/virologia , Genoma Viral , RNA Viral/genética , Vírus de Insetos/genética , Vírus de Insetos/classificação , Vírus de Insetos/isolamento & purificação , Vírus de RNA/genética , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificaçãoRESUMO
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.
Assuntos
Antozoários , Bactérias , Bacteriófagos , Genoma Viral , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Bacteriófagos/classificação , Antozoários/virologia , Antozoários/microbiologia , Animais , Bactérias/virologia , Bactérias/genética , Bactérias/classificação , Metagenoma , Simbiose , Recifes de Corais , Viroma/genética , Prófagos/genéticaRESUMO
The viromes of freshwater bodies are underexplored. The Picornavirales order, with 371 acknowledged species, is one of the most expansive and diverse groups of eukaryotic RNA viruses. In this study, we add 513 picorna-like viruses to the assemblage of more than 2000 unassigned picorna-like viruses. Our set of the aquatic Picornavirales virome of the Teltow Canal in Berlin, Germany, consists of 239 complete and 274 partial genomes. This urban freshwater body is characterized by the predominance of marna-like viruses (30.8%) and dicistro-like viruses (19.1%), whereas picornaviruses, iflaviruses, solinvi-like viruses, polycipi-like viruses, and nora-like viruses are considerably less prevalent. Caliciviruses and secoviruses were absent in our sample. Although presenting characteristic domains of Picornavirales, more than 100 viruses (20.8%) could not be assigned to any of the 9 Picornavirales families. Thirty-three viruses of the Marnaviridae-mostly locarna-like viruses-exhibit a monocistronic genome layout. Besides a wealth of novel virus sequences, viruses with peculiar features are reported. Among these is a clade of untypeable marna-like viruses with dicistronic genomes, but with the capsid protein-encoding open reading frame located at the 5' part of their RNA. A virus with a similar genome layout but clustering with dicistroviruses was also observed. We further detected monocistronic viruses with a polymerase gene related to aparaviruses. The detection of Aichi virus and five novel posa-like viruses indicates a slight burden in municipal wastewater.