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1.
mBio ; 12(4): e0177721, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34399607

RESUMO

Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR. We found that COVID-19 patients had upper respiratory microbiome dysbiosis and greater change over time than critically ill patients without COVID-19. Oropharyngeal microbiome diversity at the first time point correlated inversely with disease severity during hospitalization. Microbiome composition was also associated with systemic immune parameters in blood, as measured by lymphocyte/neutrophil ratios and immune profiling of peripheral blood mononuclear cells. Intubated patients showed patient-specific lung microbiome communities that were frequently highly dynamic, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Thus, the respiratory tract microbiome and commensal viruses are disturbed in COVID-19 and correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, its possible use as biomarkers, and the role of bacterial and viral taxa identified here in COVID-19 pathogenesis. IMPORTANCE COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.


Assuntos
Bactérias/classificação , Disbiose/microbiologia , Pulmão/microbiologia , Nasofaringe/microbiologia , Orofaringe/microbiologia , SARS-CoV-2/imunologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Anelloviridae/classificação , Anelloviridae/genética , Anelloviridae/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , COVID-19/patologia , Feminino , Humanos , Contagem de Linfócitos , Masculino , Microbiota , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Índice de Gravidade de Doença
2.
Arch Virol ; 166(10): 2943-2953, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34383165

RESUMO

Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.


Assuntos
Anelloviridae/classificação , Mamíferos/virologia , Anelloviridae/genética , Animais , Sequência de Bases , DNA Viral/genética , Bases de Dados Genéticas , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Terminologia como Assunto
3.
Arch Virol ; 166(10): 2937-2942, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34347169

RESUMO

The genus Gyrovirus was assigned to the family Anelloviridae in 2017 with only one recognized species, Chicken anemia virus. Over the last decade, many diverse viruses related to chicken anemia virus have been identified but not classified. Here, we provide a framework for the classification of new species in the genus Gyrovirus and communicate the establishment of nine new species. We adopted the 'Genus + freeform epithet' binomial system for the naming of these species.


Assuntos
Gyrovirus/classificação , Terminologia como Assunto , Anelloviridae/classificação , Anelloviridae/genética , Animais , Proteínas do Capsídeo/genética , Vírus da Anemia da Galinha/classificação , Vírus da Anemia da Galinha/genética , DNA Viral/genética , Bases de Dados Genéticas , Genoma Viral/genética , Gyrovirus/genética , Humanos , Filogenia , Análise de Sequência de DNA
4.
Arch Virol ; 166(9): 2623-2625, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34244860

RESUMO

Here, using viral metagenomics combined with conventional PCR, the complete genome sequence of a novel anellovirus (named anel-ch-zj and GenBank no. MT157223) from nasopharynx secretion specimens from hospitalized neonates was determined, and the deduced amino acid sequence of its ODF1 protein was found to be only 33.19%-39.33% identical to those of related anelloviruses with sequences available in the GenBank database, suggesting that it represents a putative new genus within the family Anelloviridae. PCR screening of 135 samples (including 45 nasopharynx secretion, 45 blood, and 45 fecal specimens collected from 45 individual hospitalized neonates) indicated that two nasopharynx secretion, two blood, and four fecal samples were positive for anel-ch-zj. Further PCR screening of 50 blood samples, 115 fecal samples, and 396 nasopharynx secretions collected from hospitalized children 1-5 years old did not yield any positive results. Whether this novel anellovirus detected in neonates is associated with specific diseases needs future investigation.


Assuntos
Anelloviridae/classificação , Anelloviridae/isolamento & purificação , Criança Hospitalizada , Filogenia , Anelloviridae/genética , DNA Viral/genética , Fezes/virologia , Humanos , Recém-Nascido , Metagenômica , Nasofaringe/virologia , Reação em Cadeia da Polimerase , Sequenciamento Completo do Genoma
5.
Sci Rep ; 11(1): 6921, 2021 03 25.
Artigo em Inglês | MEDLINE | ID: mdl-33767340

RESUMO

Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.


Assuntos
Anelloviridae/isolamento & purificação , Sangue/virologia , Viroma , Voluntários Saudáveis , Humanos , Metagenômica
6.
Res Vet Sci ; 134: 171-180, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33387757

RESUMO

Emerging viral diseases include pathogens that can threaten the health of the Canadian swineherd. Anelloviruses and Circoviruses comprise of pathogens with veterinary significance. The aim of this study was to determine the genomic organization and phylogenetic relationships of Torque teno sus virus (TTsusV) and Porcine circovirus (PCV) from Canadian pig samples. Fecal and tissue specimens were collected during the winter, spring and summer of 2018. We utilized either virus- or genus-specific PCR assays to characterize the occurrence and genetic diversity of TTsusV and PCV in Canadian pigs. Pairwise comparison of all partial sequences and identity calculation was performed using MAFFT algorithm implemented in Sequence Demarcation Tool (SDT). The obtained full-length sequences were aligned using ClustalW, and phylogeny was inferred using a Maximum likelihood (ML) method by Geneious software. The PCR detection results revealed that the overall positive rate of TTsusV type-1 and type-2 was 45.6% and 32.6%, respectively. The TTsusV isolate MK990454 from Canada clustered in the subtype TTsusV1b, while the TTsusV isolate MK872392 fell in the subtype TTsusV2c, and all showed similarity to known American and Chinese isolates. In addition, our screening PCR showed that 2.7% of stool samples were positive for PCV1. Phylogenetic analysis using the full-length sequence demonstrated that PCV1 (MK872393) isolated from Quebec clustered with other Chinese PCV1 strains. Despite the far geographical distance between Canada and China, the close similarity between Canadian and Chinese TTsusV1 and 2, and PCV1 sequences may be explained by a considerable amount of pig trade between these two nations.


Assuntos
Circovirus/genética , Biologia Computacional , Suínos/virologia , Torque teno virus/genética , Anelloviridae/genética , Animais , Canadá , China , Genômica , Filogenia , Reação em Cadeia da Polimerase/veterinária
7.
Arch Virol ; 166(2): 461-474, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33392821

RESUMO

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.


Assuntos
Anelloviridae/genética , Uso do Códon/genética , Códon/genética , Genoma Viral/genética , Proteínas/genética , Aminoácidos/genética , Biologia Computacional/métodos , Evolução Molecular , Mutação/genética , Seleção Genética/genética
8.
J Vet Diagn Invest ; 33(2): 279-282, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33084531

RESUMO

We used unbiased next-generation sequencing (NGS) to detect unknown viruses in cats. Serum or plasma samples were obtained from clinically ill cats with suspected acute viral infections. Nucleic acid was extracted from serum or plasma samples to construct a complementary DNA library for NGS. Comprehensive nucleotide sequencing analyses enabled detection of the genomes of various viruses, including the severe fever with thrombocytopenia syndrome virus, feline immunodeficiency virus, feline morbillivirus, parvovirus, and Torque teno felis virus. Our findings indicate that comprehensive nucleotide analyses of serum or plasma samples can be used to detect infections with unknown viruses in cats.


Assuntos
Doenças do Gato/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Phlebovirus/isolamento & purificação , Febre Grave com Síndrome de Trombocitopenia/veterinária , Anelloviridae/isolamento & purificação , Animais , Doenças do Gato/virologia , Gatos , Vírus da Panleucopenia Felina/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Vírus da Imunodeficiência Felina/isolamento & purificação , Morbillivirus/isolamento & purificação , Febre Grave com Síndrome de Trombocitopenia/diagnóstico , Febre Grave com Síndrome de Trombocitopenia/virologia
9.
J Med Virol ; 93(6): 4038-4041, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33058155

RESUMO

Here, using viral metagenomics, a novel anellovirus with strain name HuAV-zj-ad1 was detected in blood sample from a child with atopic dermatitis. The complete genome sequence of HuAV-zj-ad1 was determined and fully characterized. The circular genome of HuAV-zj-ad1 is 2841 nt in length and includes four polyprotein ORFs. Phylogenetic analysis and pairwise sequence comparisons based on the amino acid sequences of ORF1, ORF2, ORF3, ORF4 indicated that HuAV-zj-ad1 belonged to a novel species within the genus Betatorquevirus. Polymerase chain reaction screening results showed this anellovirus was not present 50 blood samples from normal children. Whether this novel species of anellovirus has association with a certain disease needs further study.


Assuntos
Anelloviridae/genética , Dermatite Atópica/virologia , Genoma Viral , Metagenômica/métodos , Viroses/sangue , Anelloviridae/classificação , Pré-Escolar , Dermatite Atópica/complicações , Humanos , Lactente , Filogenia , RNA Viral/genética , Análise de Sequência de DNA , Viroses/virologia
10.
J Transl Med ; 18(1): 485, 2020 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-33317538

RESUMO

Chronic fatigue often starts with an acute viral infection-as witnessed in the case of SARS-CoV-2-but indirect consequences of these infections are presumably the actual cause of the condition. As recently reviewed in this journal, the culprit could be a virus already present in the patient. The review covers several types of viruses, but concludes that the question is still open. The focus is on well known, pathogenic viruses for which there are ample diagnostic tools. I argue that there is one lesser-known group of viruses, the related anello- and circoviruses, which ought to be investigated. More or less everyone harbours at least one strain of these viruses in the blood, while not in the spinal fluid. They normally replicate at a low level, but their activity increases in an immune suppressed host; and there are cases where they do reach the brain. The initial infection could facilitate their access to the brain.


Assuntos
Anelloviridae , COVID-19 , Circoviridae , Síndrome de Fadiga Crônica , Viroses , Vírus , Humanos , SARS-CoV-2
11.
J Clin Virol ; 133: 104687, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33176237

RESUMO

BACKGROUND: Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host. OBJECTIVE: To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases. STUDY DESIGN: Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses. RESULTS: TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region. CONCLUSIONS: These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.


Assuntos
Anelloviridae , Infecções por Vírus de DNA , MicroRNAs , Torque teno virus , Anelloviridae/genética , Infecções por Vírus de DNA/líquido cefalorraquidiano , Infecções por Vírus de DNA/diagnóstico , DNA Viral/genética , Humanos , MicroRNAs/líquido cefalorraquidiano , Reação em Cadeia da Polimerase em Tempo Real , Torque teno virus/genética
12.
J Clin Virol ; 132: 104643, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32961430

RESUMO

BACKGROUND: An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients. METHODS: A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones. RESULTS: Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples. CONCLUSIONS: Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.


Assuntos
Anelloviridae , Vírus , Adulto , Idoso , Anelloviridae/genética , Medula Óssea , Criança , Feminino , Humanos , Masculino , Metagenômica , Pessoa de Meia-Idade , Filogenia
13.
Viruses ; 12(8)2020 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-32718049

RESUMO

An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.


Assuntos
Linfonodos/patologia , Linfonodos/virologia , Leões-Marinhos/virologia , Serosite/patologia , Serosite/veterinária , Esteatite/patologia , Viroma , Anelloviridae/classificação , Anelloviridae/isolamento & purificação , Animais , Animais Selvagens , California , Feminino , Inflamação , Metagenômica , Parvovirus/classificação , Parvovirus/isolamento & purificação , Polyomavirus/classificação , Polyomavirus/isolamento & purificação , Serosite/virologia , Esteatite/virologia
14.
BMC Oral Health ; 20(1): 196, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32646510

RESUMO

BACKGROUND: Herpesviruses and bacteria and their interplay have long been believed to play important roles in the pathogenesis of periodontitis, but other microbial entities in the oral environment might also be involved. Anelloviruses are commonly detected in human, including in oral samples. The aim of the present study was to explore the occurrence and co-occurrence of human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), and human anelloviruses (HTTVs) in gingival tissue samples collected from participants recruited in Shanghai, China. METHODS: Gingival tissues were collected from 159 participants (57 with aggressive periodontitis (AP), 59 with chronic periodontitis (CP) and 43 with healthy periodontal status). The presence of HCMV, EBV, torque teno virus (TTV), torque teno mini virus (TTMV) and torque teno midi virus (TTMDV) DNA was detected by nested-PCR. The virus loads were quantified by real-time PCR. RESULTS: The detection rates of EBV, TTV, TTMV and TTMDV were significantly higher in the AP and CP groups compared to the healthy group (all P < 0.01). A statistically significant association was found between EBV, TTV and TTMV virus load and periodontitis (all P < 0.05). Participants infected with EBV showed significantly higher infection rates and higher virus loads of TTV and TTMV than the EBV-negative group (all P < 0.05). The coexistence rates of EBV and anelloviruses and the coexistence of three HTTVs were significantly higher in AP and CP groups (all P < 0.01). CONCLUSIONS: Collectively, results obtained in this study suggest that HTTVs and the coexistence of EBV and HTTVs in particular, may be associated with periodontitis. Possible mechanisms of the interaction between herpesviruses and anelloviruses in the context of periodontitis require further investigation.


Assuntos
Anelloviridae , Grupo com Ancestrais do Continente Asiático , Herpesviridae , China/epidemiologia , Feminino , Herpesvirus Humano 4 , Humanos , Masculino
15.
Infect Genet Evol ; 85: 104421, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32580027

RESUMO

Crab-eating (Cerdocyon thous) and Pampas foxes (Lycalopex gymnocercus) are wild canids distributed in South America. Domestic dogs (Canis lupus familiaris) and wild canids may share viral pathogens, including rabies virus (RABV), canine distemper virus (CDV), and canine parvovirus 2 (CPV-2). To characterize the virome of these wild canid species, the present work evaluated the spleen and mesenteric lymph node virome of 17 crab-eating and five Pampas foxes using high-throughput sequencing (HTS). Organ samples were pooled and sequenced using an Illumina MiSeq platform. Additional PCR analyses were performed to identify the frequencies and host origin for each virus detected by HTS. Sequences more closely related to the Paramyxoviridae, Parvoviridae and Anelloviridae families were detected, as well as circular Rep-encoding single-stranded (CRESS) DNA viruses. CDV was found only in crab-eating foxes, whereas CPV-2 was found in both canid species; both viruses were closely related to sequences reported in domestic dogs from southern Brazil. Moreover, the present work reported the detection of canine bocavirus (CBoV) strains that were genetically divergent from CBoV-1 and 2 lineages. Finally, we also characterized CRESS DNA viruses and anelloviruses with marked diversity. The results of this study contribute to the body of knowledge regarding wild canid viruses that can potentially be shared with domestic canids or other species.


Assuntos
Cães/virologia , Raposas/virologia , Viroma , Vírus/classificação , Vírus/genética , Anelloviridae/classificação , Anelloviridae/genética , Animais , Bocavirus/classificação , Bocavirus/genética , Brasil , Vírus de DNA/classificação , Vírus de DNA/genética , DNA Viral , Vírus da Cinomose Canina/classificação , Vírus da Cinomose Canina/genética , Sequenciamento de Nucleotídeos em Larga Escala , Linfonodos/virologia , Metagenômica , Paramyxoviridae/classificação , Paramyxoviridae/genética , Parvoviridae/classificação , Parvoviridae/genética , Parvovirus Canino/classificação , Parvovirus Canino/genética , Filogenia , RNA Viral , Baço/virologia , Uruguai , Viroses/veterinária , Viroses/virologia , Vírus/isolamento & purificação
16.
J Crohns Colitis ; 14(11): 1600-1610, 2020 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-32406906

RESUMO

BACKGROUND AND AIMS: Dysbiosis of the gut microbiota is a well-known correlate of the pathogenesis of inflammatory bowel disease [IBD]. However, few studies have examined the microbiome in very early-onset [VEO] IBD, which is defined as onset of IBD before 6 years of age. Here we focus on the viral portion of the microbiome-the virome-to assess possible viral associations with disease processes, reasoning that any viruses potentially associated with IBD might grow more robustly in younger subjects, and so be more detectable. METHODS: Virus-like particles [VLPs] were purified from stool samples collected from patients with VEO-IBD [n = 54] and healthy controls [n = 23], and characterized by DNA and RNA sequencing and VLP particle counts. RESULTS: The total number of VLPs was not significantly different between VEO-IBD and healthy controls. For bacterial viruses, the VEO-IBD subjects were found to have a higher ratio of Caudovirales vs to Microviridae compared to healthy controls. An increase in Caudovirales was also associated with immunosuppressive therapy. For viruses infecting human cells, Anelloviridae showed higher prevalence in VEO-IBD compared to healthy controls. Within the VEO-IBD group, higher levels of Anelloviridae DNA were also positively associated with immunosuppressive treatment. To search for new viruses, short sequences enriched in VEO-IBD samples were identified, and some could be validated in an independent cohort, although none was clearly viral; this provides sequence tags to interrogate in future studies. CONCLUSIONS: These data thus document perturbations to normal viral populations associated with VEO-IBD, and provide a biomarker-Anelloviridae DNA levels-potentially useful for reporting the effectiveness of immunosuppression.


Assuntos
Anelloviridae/isolamento & purificação , Fezes/virologia , Imunossupressores/uso terapêutico , Doenças Inflamatórias Intestinais , Viroma/fisiologia , Idade de Início , Biomarcadores Farmacológicos/análise , Pré-Escolar , Correlação de Dados , Feminino , Microbioma Gastrointestinal/fisiologia , Humanos , Doenças Inflamatórias Intestinais/epidemiologia , Doenças Inflamatórias Intestinais/fisiopatologia , Doenças Inflamatórias Intestinais/virologia , Masculino , Metagenoma/imunologia , Fatores de Risco , Estados Unidos/epidemiologia , Vírus/classificação , Vírus/isolamento & purificação
17.
Viruses ; 12(3)2020 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-32244962

RESUMO

Viruses are ubiquitous in nature; however, very few have been identified in the Leporid species. In the fall of 2018, an outbreak of myxomatosis in Iberian hares (Lepus granatensis) was reported in Spain and a novel recombinant myxoma virus strain (MYXV-Tol) was identified. To investigate variability within the recombinant region of the MYXV-Tol and identify any potential viral coinfections, samples (ear, eyelid or vaginal) of Iberian hares were collected from Spain and analyzed. The presence of the recombinant region of the MYXV-Tol was confirmed in six out of eleven samples analyzed. Additionally, a polyomavirus (family Polyomaviridae), representing a putative new species, and anelloviruses (family Anelloviridae) belonging to two putative species were identified, some as coinfection with the recombinant MYXV-Tol. The two polyomavirus genomes were identified in two hares and share >99% genome-wide identity. Based on the analysis of their large T-antigen, the new polyomavirus clusters in a distant clade from other mammals sharing <64% amino acid identity. A total of 14 anelloviruses were identified, which share 63-99% genome-wide identity. Overall, our results show a coinfection of different DNA viruses in the studied samples and raise awareness regarding the extensive unsampled diversity of viruses in hares.


Assuntos
Anelloviridae , Doenças dos Animais/epidemiologia , Doenças dos Animais/virologia , Coinfecção/veterinária , Lebres/virologia , Myxoma virus , Polyomavirus , Anelloviridae/genética , Animais , Genoma Viral , Myxoma virus/genética , Filogenia , Polyomavirus/genética , Recombinação Genética , Espanha/epidemiologia
18.
AIDS ; 34(6): 827-832, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32271249

RESUMO

OBJECTIVES: Improving immune status of people living with HIV through antiretroviral therapy (ART) may also reduce shedding of other viruses in semen. We characterized the seminal fluid virome of men with HIV and tested potential associations between viruses present and CD4 T-cell count, HIV viremia, and antiretroviral therapy (ART) status. DESIGN AND METHODS: Metagenomics was used to enrich and sequence viral nucleic acids from the seminal fluid of 55 semen samples from 42 men living with HIV from San Francisco with a median age of 33 (IQR, 28.7-45) and median CD4 T-cell counts of 837 cells/µl (IQR, 258-1571 cells/µl). All samples were collected between 2005 and 2015, and ART status was ascertained from medical records. RESULTS: Anelloviruses, cytomegalovirus (CMV), and multiple genotypes of human papillomaviruses were detected. Participants shed from 0 to 4 distinct human viruses. Longitudinally collected seminal fluid samples showed changes in the viruses shed. Viruses were more frequently shed by individuals with detectable HIV viremia (43.7 vs. 15.4%, P = 0.042). A trend was seen for increased shedding by individuals who were not on ART (42.8 vs. 17.8%, P = 0.082) or with CD4 T-cell count less than 350 cells/µl (35.3 vs. 20%, P = 0.27). CONCLUSION: Seminal fluid from men with HIV from San Francisco contains nucleic acids from three different DNA viral families. A greater number of viruses, particularly CMV, were shed by participants with detectable HIV viremia (18.9 vs. 0%, P = 0.022). Control of viremia through ART may lower shedding of other viruses in semen in addition to HIV.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Infecções por HIV/tratamento farmacológico , Infecções por HIV/virologia , HIV-1/isolamento & purificação , Sêmen/virologia , Viroma , Anelloviridae/isolamento & purificação , Terapia Antirretroviral de Alta Atividade , Sangue/virologia , Contagem de Linfócito CD4 , Citomegalovirus/isolamento & purificação , DNA Viral/genética , DNA Viral/isolamento & purificação , Genótipo , Infecções por HIV/diagnóstico , HIV-1/genética , Humanos , Masculino , Metagenômica , RNA Viral , São Francisco , Eliminação de Partículas Virais
19.
FEMS Microbiol Rev ; 44(3): 305-313, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32188999

RESUMO

Anelloviruses are small, single stranded circular DNA viruses. They are extremely diverse and have not been associated with any disease so far. Strikingly, these small entities infect most probably the complete human population, and there are no convincing examples demonstrating viral clearance from infected individuals. The main transmission could be via fecal-oral or airway route, as infections occur at an early age. However, due to the lack of an appropriate culture system, the virus-host interactions remain enigmatic. Anelloviruses are obviously mysterious viruses, and their impact on human life is not yet known, but, with no evidence of a disease association, a potential beneficial effect on human health should also be investigated.


Assuntos
Anelloviridae/classificação , Anelloviridae/fisiologia , Interações entre Hospedeiro e Microrganismos , Humanos
20.
PLoS One ; 15(3): e0230714, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32214388

RESUMO

A study was conducted to investigate the serum virome of sows with and without stillbirths after farrowing. Sera from sows with at least one stillbirth or with normal litters were collected immediately after farrowing. Viral DNA was extracted from serum pools and submitted to high throughput sequencing. No differences in the proportion of virus-related reads were found in both groups (p > 0.05). A variety of viral DNA genomes were identified, mostly representative of three viral families: Anelloviridae, Circoviridae and Smacoviridae. Besides, a number of novel unclassified circular Rep-encoding single stranded DNA (CRESS DNA) viruses were also identified. These findings suggest that the presence of such viral genomes in sows' sera bears no correlation with stillbirths' occurrence; it seems likely that these constitute part of the normal serum microbiome of sows at farrowing.


Assuntos
DNA Viral/sangue , DNA Viral/genética , Genoma Viral/genética , Natimorto/veterinária , Anelloviridae/genética , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Suínos
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