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1.
Front Cell Infect Microbiol ; 11: 790422, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34900762

RESUMO

Patients with Coronavirus Disease 2019 (COVID-19), due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection mainly present with respiratory issues and related symptoms, in addition to significantly affected digestive system, especially the intestinal tract. While several studies have shown changes in the intestinal flora of patients with COVID-19, not much information is available on the gut virome of such patients. In this study, we used the viromescan software on the latest gut virome database to analyze the intestinal DNA virome composition of 15 patients with COVID-19 and investigated the characteristic alternations, particularly of the intestinal DNA virome to further explore the influence of COVID-19 on the human gut. The DNA viruses in the gut of patients with COVID-19 were mainly crAss-like phages (35.48%), Myoviridae (20.91%), and Siphoviridae (20.43%) family of viruses. Compared with healthy controls, the gut virome composition of patients with COVID-19 changed significantly, especially the crAss-like phages family, from the first time of hospital admission. A potential correlation is also indicated between the change in virome and bacteriome (like Tectiviridae and Bacteroidaceae). The abundance of the viral and bacterial population was also analyzed through continuous sample collection from the gut of patients hospitalized due to COVID-19. The gut virome is indeed affected by the SARS-CoV-2 infection, and along with gut bacteriome, it may play an important role in the disease progression of COVID-19. These conclusions would be helpful in understanding the gut-related response and contribute to the treatment and prevention strategies of COVID-19.


Assuntos
COVID-19 , Microbioma Gastrointestinal , DNA , Humanos , SARS-CoV-2 , Viroma
2.
Prog Mol Biol Transl Sci ; 183: 355-409, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34656333

RESUMO

Intrinsically disordered proteins and regions (IDPs/IDRs) make up a large part of viral proteomes, but their real prevalence across the global plant virome is still murky, partly because of their massive diversity. Here, we propose an evolutionary quantitative proteomic approach to foray into genomic signatures that are preserved in the amino acid sequences of orthologous IDRs. Markedly, we found that relatively abundant IDP varies substantially in viral species among and within plant virus families, including according to genome size, partition or replication strategies. We also demonstrate that most encoded proteomic modules of the plant virome contain multiple disordered features that are phylogenomically preserved, and can be correlated to genomic, bio-physical and evolutionary strategies. Furthermore, our focused interactome-wide analysis highlights lines of evidence indicating that various IDPs with similar evolutionary signatures modulate viral multifunctionality. Moreover, estimated fractions of IDR in the vicinity of pivotal evolutionary structural domains embedded in interaction modules are strongly enriched with affinity binding functional annotations and relate to vector-borne virus transmission modes. Importantly, molecular recognition features (MoRFs) are abundantly widespread in IDRs of viral hallmark modules and their binding partners. Finally, we propose a coarse-grained conceptual framework in which evolutionary proteome-wide IDP/IDRs patterns can be, rather, reliably exploited to elucidate their foundational fine-tuning role in plant virus transmission mechanisms. While opening unexplored avenues for consistently predicting virus-host functions for many new or uncharacterized viruses based on their proteomic repertoire, other considerations advocating further structural IDP research in Plant Virology are thoroughly discussed in light of viral modular evolution.


Assuntos
Proteínas Intrinsicamente Desordenadas , Vírus , Humanos , Proteoma , Proteômica , Viroma
3.
J Gen Virol ; 102(10)2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34704919

RESUMO

The endosymbiont bacteria of the genus Wolbachia are associated with multiple mutualistic effects on insect biology, including nutritional and antiviral properties. Members of the genus Wolbachia naturally occur in fly species of the genus Drosophila, providing an operational model host for studying how virome composition may be affected by its presence. Drosophila simulans populations can carry a variety of strains of members of the genus Wolbachia, with the wAu strain associated with strong antiviral protection under experimental conditions. We used D. simulans sampled from the Perth Hills, Western Australia, to investigate the potential virus protective effect of the wAu strain of Wolbachia on individual wild-caught flies. Our data revealed no appreciable variation in virus composition and abundance between individuals infected or uninfected with Wolbachia associated with the presence or absence of wAu. However, it remains unclear whether wAu might affect viral infection and host survival by increasing tolerance rather than inducing complete resistance. These data also provide new insights into the natural virome diversity of D. simulans. Despite the small number of individuals sampled, we identified a repertoire of RNA viruses, including nora virus, galbut virus, thika virus and La Jolla virus, that have been identified in other species of the genus Drosophila. Chaq virus-like sequences associated with galbut virus were also detected. In addition, we identified five novel viruses from the families Reoviridae, Tombusviridae, Mitoviridae and Bunyaviridae. Overall, this study highlights the complex interaction between Wolbachia and RNA virus infections and provides a baseline description of the natural virome of D. simulans.


Assuntos
Drosophila simulans/microbiologia , Vírus de RNA/fisiologia , Viroma/fisiologia , Wolbachia/fisiologia , Animais , Drosophila simulans/virologia , Feminino , Filogenia , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação , Simbiose , Viroma/genética , Wolbachia/isolamento & purificação
4.
J Gen Virol ; 102(10)2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34714225

RESUMO

Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.


Assuntos
Doenças dos Bovinos/virologia , Bovinos/virologia , Diarreia/veterinária , Intestinos/virologia , Viroma , Animais , Caliciviridae/classificação , Caliciviridae/genética , Caliciviridae/isolamento & purificação , Vírus de DNA/classificação , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , Indústria de Laticínios , Diarreia/virologia , Fezes/virologia , Genoma Viral , Mamastrovirus/classificação , Mamastrovirus/genética , Mamastrovirus/isolamento & purificação , Metagenômica , Filogenia
5.
DNA Res ; 28(6)2021 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-34586399

RESUMO

The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8 kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥5 kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.


Assuntos
Metagenômica , Viroma , Algoritmos , Biomassa , Quimera , DNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Sequência de DNA
6.
Appl Environ Microbiol ; 87(23): e0144821, 2021 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-34550753

RESUMO

Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.


Assuntos
Vírus de RNA/isolamento & purificação , SARS-CoV-2/isolamento & purificação , Viroma , Águas Residuárias/virologia , Vigilância Epidemiológica Baseada em Águas Residuárias , COVID-19/epidemiologia , California , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Reação em Cadeia da Polimerase , Vírus de RNA/classificação , Vírus de RNA/genética , SARS-CoV-2/classificação , SARS-CoV-2/genética , Análise de Sequência de RNA
7.
Nat Commun ; 12(1): 5398, 2021 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-34518545

RESUMO

As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.


Assuntos
Ciclo do Carbono , Células Procarióticas/virologia , Esgotos/virologia , Viroma/genética , Vírus/genética , Purificação da Água/métodos , Archaea/classificação , Archaea/genética , Archaea/virologia , Bactérias/classificação , Bactérias/genética , Bactérias/virologia , Metabolismo Energético/genética , Genes Virais/genética , Variação Genética , Interações Hospedeiro-Patógeno , Fases de Leitura Aberta/genética , Células Procarióticas/metabolismo , Análise de Sequência de DNA/métodos , Esgotos/microbiologia , Vírus/classificação , Vírus/metabolismo
8.
PLoS Pathog ; 17(8): e1009780, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34407148

RESUMO

Triatomine assassin bugs comprise hematophagous insect vectors of Trypanosoma cruzi, the causative agent of Chagas disease. Although the microbiome of these species has been investigated to some extent, only one virus infecting Triatoma infestans has been identified to date. Here, we describe for the first time seven (+) single-strand RNA viruses (RpV1-7) infecting Rhodnius prolixus, a primary vector of Chagas disease in Central and South America. We show that the RpVs belong to the Iflaviridae, Permutotetraviridae and Solemoviridae and are vertically transmitted from the mothers to the progeny via transovarial transmission. Consistent with this, all the RpVs, except RpV2 that is related to the entomopathogenic Slow bee paralysis virus, established persistent infections in our R. prolixus colony. Furthermore, we show that R. prolixus ovaries express 22-nucleotide viral siRNAs (vsiRNAs), but not viral piRNAs, that originate from the processing of dsRNA intermediates during viral replication of the RpVs. Interestingly, the permutotetraviruses and sobemoviruses display shared pools of vsiRNAs that might provide the basis for a cross-immunity system. The vsiRNAs are maternally deposited in the eggs, where they likely contribute to reduce the viral load and protect the developing embryos. Our results unveil for the first time a complex core virome in R. prolixus and begin to shed light on the RNAi-based antiviral defenses in triatomines.


Assuntos
Doença de Chagas/transmissão , Insetos Vetores/virologia , Vírus de RNA/fisiologia , Rhodnius/virologia , Triatoma/virologia , Trypanosoma cruzi/fisiologia , Viroma , Animais , Feminino , Genoma Viral , Oogênese , Vírus de RNA/classificação , RNA Interferente Pequeno/genética , Coelhos , Transcriptoma
10.
J Clin Invest ; 131(15)2021 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-34338230

RESUMO

The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities. Aberrant populations (dysbiosis) have been demonstrated in many pulmonary diseases not traditionally considered microbial in origin, and potential pathways of microbe-host crosstalk are emerging. The question now is whether and how dysbiotic microbiota contribute to initiation or perpetuation of injury. The fungal microbiome and virome are less well studied. This Review highlights features of the lung microbiome, unique considerations in studying it, examples of dysbiosis in selected disease, emerging concepts in lung microbiome-host interactions, and critical areas for investigation.


Assuntos
Pneumopatias , Pulmão , Micobioma , Viroma , Animais , Humanos , Pulmão/microbiologia , Pulmão/virologia , Pneumopatias/microbiologia , Pneumopatias/virologia
11.
Periodontol 2000 ; 87(1): 282-298, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34463988

RESUMO

Mediators of the initiation, development, and recurrence of periodontitis include the oral microbiome embedded in subgingival plaque and the host immune response to a dysbiosis within this dynamic and complex microbial community. Although mediators have been studied extensively, researchers in the field have been unable to fully ascribe certain clinical presentations of periodontitis to their nature. Emergence of high-throughput sequencing technologies has resulted in better characterization of the microbial oral dysbiosis that extends beyond the extensively studied putative bacterial periodontopathogens to a shift in the oral virome composition during disease conditions. Although the biological dark matter inserted by retroviruses was once believed to be nonfunctional, research has revealed that it encodes historical viral-eukaryotic interactions and influences host development. The objective of this review is to evaluate the proposed association of herpesviruses to the etiology and pathogenesis of periodontal disease and survey the highly abundant prokaryotic viruses to delineate their potential roles in biofilm dynamics, as well as their interactions with putative bacterial periodontopathogens and eukaryotic cells. The findings suggest that potential novel periodontal therapies targeting or utilizing the oral virome can alleviate certain clinical presentations of periodontitis. Perhaps it is time to embrace the viral dark matter within the periodontal environment to fully comprehend the pathogenesis and systemic implications of periodontitis.


Assuntos
Microbiota , Periodontite , Vírus , Disbiose , Humanos , Viroma
12.
Arch Virol ; 166(10): 2751-2762, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34341873

RESUMO

Ticks are important vector arthropods that transmit various pathogens to humans and other animals. Tick-borne viruses are of particular concern to public health as these are major agents of emerging and re-emerging infectious diseases. The Phenuiviridae family of tick-borne viruses is one of the most diverse groups and includes important human pathogenic viruses such as severe fever with thrombocytopenia syndrome virus. Phenuivirus-like sequences were detected during the surveillance of tick-borne viruses using RNA virome analysis from a pooled sample of Haemaphysalis formosensis ticks collected in Ehime, Japan. RT-PCR amplification and Sanger sequencing revealed the nearly complete viral genome sequence of all three segments. Comparisons of the viral amino acid sequences among phenuiviruses indicated that the detected virus shared 46%-70% sequence identity with known members of the Kaisodi group in the genus Uukuvirus. Furthermore, phylogenetic analysis of the viral proteins showed that the virus formed a cluster with the Kaisodi group viruses, suggesting that this was a novel virus, which was designated "Toyo virus" (TOYOV). Further investigation of TOYOV is needed, and it will contribute to understanding the natural history and the etiological importance of the Kaisodi group viruses.


Assuntos
Vírus de RNA de Sentido Negativo/classificação , Carrapatos/virologia , Sequência de Aminoácidos , Animais , Genoma Viral/genética , Humanos , Japão , Vírus de RNA de Sentido Negativo/genética , Vírus de RNA de Sentido Negativo/isolamento & purificação , Filogenia , RNA Viral/genética , Análise de Sequência de DNA , Proteínas Virais/genética , Viroma/genética
13.
Sci Rep ; 11(1): 16584, 2021 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-34400676

RESUMO

Currently, there are increasing concerns about the possibility of a new epidemic due to emerging reports of Mayaro virus (MAYV) fever outbreaks in areas of South and Central America. Haemagogus mosquitoes, the primary sylvan vectors of MAYV are poorly characterized and a better understanding of the mosquito's viral transmission dynamics and interactions with MAYV and other microorganisms would be important in devising effective control strategies. In this study, a metatranscriptomic based approach was utilized to determine the prevalence of RNA viruses in field-caught mosquitoes morphologically identified as Haemagogus janthinomys from twelve (12) forest locations in Trinidad, West Indies. Known insect specific viruses including the Phasi Charoen-like and Humaiata-Tubiacanga virus dominated the virome of the mosquitoes throughout sampling locations while other viruses such as the avian leukosis virus, MAYV and several unclassified viruses had a narrower distribution. Additionally, assembled contigs from the Ecclesville location suggests the presence of a unique uncharacterized picorna-like virus. Mapping of RNA sequencing reads to reference mitochondrial sequences of potential feeding host animals showed hits against avian and rodent sequences, which putatively adds to the growing body of evidence of a potentially wide feeding host-range for the Haemagogus mosquito vector.


Assuntos
Culicidae/virologia , Vírus de RNA/isolamento & purificação , Viroma , Infecções por Alphavirus/epidemiologia , Infecções por Alphavirus/virologia , Animais , Sequência de Bases , Aves , Culicidae/microbiologia , Surtos de Doenças , Reservatórios de Doenças/virologia , Geografia Médica , Especificidade de Hospedeiro , Insetos Vetores/virologia , Filogenia , Proteobactérias/genética , Vírus de RNA/classificação , Vírus de RNA/genética , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , RNA Viral/genética , RNA Viral/isolamento & purificação , Roedores , Togaviridae/genética , Togaviridae/isolamento & purificação , Trinidad e Tobago/epidemiologia , Viroma/genética
14.
Water Res ; 203: 117568, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34450465

RESUMO

The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed >40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and (+)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment.


Assuntos
Vírus , Águas Residuárias , Humanos , Filogenia , Rios , Viroma , Vírus/genética
15.
Viruses ; 13(7)2021 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-34372602

RESUMO

Arthropod-borne infections are a medical and economic threat to humans and livestock. Over the last three decades, several unprecedented viral outbreaks have been recorded in the Western part of the Arabian Peninsula. However, little is known about the circulation and diversity of arthropod-borne viruses in this region. To prepare for new outbreaks of vector-borne diseases, it is important to detect which viruses circulate in each vector population. In this study, we used a metagenomics approach to characterize the RNA virome of ticks infesting dromedary camels (Camelus dromedaries) in Makkah province, Saudi Arabia. Two hundred ticks of species Hyalomma dromedarii (n = 196) and Hyalomma impeltatum (n = 4) were collected from the Alkhurma district in Jeddah and Al-Taif city. Virome analysis showed the presence of several tick-specific viruses and tick-borne viruses associated with severe illness in humans. Some were identified for the first time in the Arabian Peninsula. The human disease-associated viruses detected included Crimean Congo Hemorrhagic fever virus and Tamdy virus (family Nairoviridae), Guertu virus (family Phenuiviridae), and a novel coltivirus that shares similarities with Tarumizu virus, Tai forest reovirus and Kundal virus (family Reoviridae). Furthermore, Alkhurma hemorrhagic virus (Flaviviridae) was detected in two tick pools by specific qPCR. In addition, tick-specific viruses in families Phenuiviridae (phleboviruses), Iflaviridae, Chuviridae, Totiviridae and Flaviviridae (Pestivirus) were detected. The presence of human pathogenetic viruses warrants further efforts in tick surveillance, xenosurveillence, vector control, and sero-epidemiological investigations in human and animal populations to predict, contain and mitigate future outbreaks in the region.


Assuntos
Metagenômica/métodos , RNA Viral/genética , Doenças Transmitidas por Carrapatos/virologia , Carrapatos/virologia , Viroma/genética , Vírus/genética , Animais , Camelus , Humanos , Arábia Saudita , Doenças Transmitidas por Carrapatos/prevenção & controle , Vírus/classificação , Vírus/isolamento & purificação
16.
Nan Fang Yi Ke Da Xue Xue Bao ; 41(6): 862-869, 2021 Jun 20.
Artigo em Chinês | MEDLINE | ID: mdl-34238738

RESUMO

OBJECTIVE: To explore the differences in gut virome and microbiome between patients with stroke and healthy volunteers. OBJECTIVE: Fifteen patients with acute ischemic stroke treated in the Department of Neurology of Nanfang Hospital between February, 2014 and February, 2016 and 15 healthy volunteers matched for age and sex were enrolled in this study. Virome sequencing and 16S rRNA sequencing were performed on stool samples of all the participants, and the composition and structures of the virome and microbiome were compared between the two groups. OBJECTIVE: No significant difference was found in the overall diversity of virome between the stroke patients and the healthy volunteers (alpha diversity: P=0.320; beta diversity: P=0.169, R2=0.037), but virome composition differed significantly between the two groups. The relative abundance of Bacteroides phage B40_8 and Cronobacter phage CS01 increased significantly in patients with stroke. The structures and composition of the microbiome in patients with stroke also differed significantly from those of the healthy volunteers (alpha diversity: P=0.950; beta diversity: P=0.005, R2=0.117). The relative abundance of Megasphaera increased while that of Bifidobacterium decreased in patients with stroke. Correlation analysis showed that in the virome of stroke patients, the relative abundance of the phage preying Streptococcus was positively correlated with that of their hosts (r=0.550, P=0.036), while in the virome of healthy volunteers, the relative abundance of the phage preying Faecalibacterium (r=0.520, P=0.049), Bilophila (r=0.541, P=0.040) and Roseburia (r=0.526, P=0.046) were positively correlated with that of their respective hosts. OBJECTIVE: Stroke patients have similar overall diversity of the virome to healthy volunteers but different virome composition and interaction patterns between the virome and microbiome. The gut microbiome also differs between stroke patients and healthy volunteers. The relative abundance of opportunistic pathogens increases but that of symbiotic bacteria decreases in stroke patients.


Assuntos
Isquemia Encefálica , Microbiota , Acidente Vascular Cerebral , Fezes , Humanos , RNA Ribossômico 16S/genética , Viroma
17.
Ecotoxicol Environ Saf ; 222: 112552, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34325201

RESUMO

Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.


Assuntos
Metagenômica , Purificação da Água , Animais , Antibacterianos , Genes Bacterianos , Suínos , Viroma , Águas Residuárias
18.
Arch Virol ; 166(10): 2743-2749, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34327587

RESUMO

Diversity analysis has been performed routinely on microbiomes, including human viromes. Shared species analysis has been conducted only rarely, but it can be a powerful supplement to diversity analysis. In the present study, we conducted integrated diversity and shared species analyses of human viromes by reanalyzing three published datasets of human viromes with more than 250 samples from healthy vs. diseased individuals and/or rural vs. urban individuals. We found significant differences in the virome diversity measured in the Hill numbers between the healthy and diseased individuals, with diseased individuals exhibiting higher virome diversity than healthy individuals, and rural individual exhibiting higher virome diversity than urban individuals. We applied both "read randomization" and "sample randomization" algorithms to perform shared species analysis. With the more conservative sample randomization algorithm, the observed number of shared species was significantly smaller than the expected shared species in 50% (8 of 16) of the comparisons. These results suggest that integrated diversity and shared species analysis can offer more comprehensive insights in comparing human virome samples than standard diversity analysis alone with potentially powerful applications in differentiating the effects of diseases or other meta-factors.


Assuntos
Biodiversidade , Viroma , Bases de Dados Genéticas , Genoma Viral/genética , Nível de Saúde , Humanos , População Rural , População Urbana , Viroma/genética
19.
Lett Appl Microbiol ; 73(4): 486-494, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34268776

RESUMO

During the period from late 2019 to early 2020, we performed a foodborne virus detection from shellfish collected in Singapore at retail level. Multiple human enteric viruses were included as our targets including human noroviruses (NoVs) GI and GII, hepatitis A virus, hepatitis E virus and rotavirus. Out of the 60 shellfish samples, 23 (38·3%) were detected to be positive by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with human enteric viruses. Six samples were selected to proceed with virome capture sequencing with positive control samples spiked with serially diluted NoV GII clinical samples in oyster extract. As a result, the natural sample with comparable Ct values (34·0-35·0) of the spiked sample as detected by RT-qPCR generated much lower read counts (>7-log2 cumulative sum scaling difference) and genome coverage (406 nt. vs 3715 nt.), suggesting that the RT-qPCR positive signals detected from the shellfish samples collected at the retail market were likely from degraded RNA derived from inactive virus particles.


Assuntos
Norovirus , Ostreidae , Animais , Contaminação de Alimentos/análise , Humanos , Norovirus/genética , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Frutos do Mar , Singapura , Viroma
20.
Sci Rep ; 11(1): 14913, 2021 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-34290346

RESUMO

Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, IgA has been shown to be involved in gut homeostatic regulation by 'recognizing' and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.


Assuntos
Deficiência de IgA/microbiologia , Deficiência de IgA/virologia , Microbiota , Boca/microbiologia , Boca/virologia , Viroma , Adolescente , Adulto , Idoso , Criança , Feminino , Humanos , Imunoglobulina A/fisiologia , Imunoglobulina M/deficiência , Masculino , Metagenômica , Microbiota/genética , Pessoa de Meia-Idade , Saliva/microbiologia , Saliva/virologia , Viroma/genética , Adulto Jovem
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