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1.
Biosens Bioelectron ; 166: 112431, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32862842

RESUMO

Last few decades, viruses are a real menace to human safety. Therefore, the rapid identification of viruses should be one of the best ways to prevent an outbreak and important implications for medical healthcare. The recent outbreak of coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus which belongs to the single-stranded, positive-strand RNA viruses. The pandemic dimension spread of COVID-19 poses a severe threat to the health and lives of seven billion people worldwide. There is a growing urgency worldwide to establish a point-of-care device for the rapid detection of COVID-19 to prevent subsequent secondary spread. Therefore, the need for sensitive, selective, and rapid diagnostic devices plays a vital role in selecting appropriate treatments and to prevent the epidemics. During the last decade, electrochemical biosensors have emerged as reliable analytical devices and represent a new promising tool for the detection of different pathogenic viruses. This review summarizes the state of the art of different virus detection with currently available electrochemical detection methods. Moreover, this review discusses different fabrication techniques, detection principles, and applications of various virus biosensors. Future research also looks at the use of electrochemical biosensors regarding a potential detection kit for the rapid identification of the COVID-19.


Assuntos
Betacoronavirus , Técnicas Biossensoriais/instrumentação , Técnicas de Laboratório Clínico/instrumentação , Infecções por Coronavirus/diagnóstico , Técnicas Eletroquímicas/instrumentação , Pneumonia Viral/diagnóstico , Vírus/isolamento & purificação , Animais , Betacoronavirus/isolamento & purificação , Betacoronavirus/patogenicidade , Infecções por Coronavirus/virologia , Desenho de Equipamento , Humanos , Nanopartículas Metálicas/química , Nanopartículas Metálicas/ultraestrutura , Microscopia Eletrônica de Varredura , Pandemias , Pneumonia Viral/virologia , Testes Imediatos , Vírus/patogenicidade
2.
Biosens Bioelectron ; 169: 112604, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32980805

RESUMO

Virus severely endangers human life and health, and the detection of viruses is essential for the prevention and treatment of associated diseases. Metal-organic framework (MOF), a novel hybrid porous material which is bridged by the metal clusters and organic linkers, has become a promising biosensor platform for virus detection due to its outstanding properties including high surface area, adjustable pore size, easy modification, etc. However, the MOF-based sensing platforms for virus detection are rarely summarized. This review systematically divided the detection platforms into nucleic acid and immunological (antigen and antibody) detection, and the underlying sensing mechanisms were interpreted. The nucleic acid sensing was discussed based on the properties of MOF (such as metal ion, functional group, geometry structure, size, porosity, stability, etc.), revealing the relationship between the sensing performance and properties of MOF. Moreover, antibodies sensing based on the fluorescence detection and antigens sensing based on molecular imprinting or electrochemical immunoassay were highlighted. Furthermore, the remaining challenges and future development of MOF for virus detection were further discussed and proposed. This review will provide valuable references for the construction of sophisticated sensing platform for the detection of viruses, especially the 2019 coronavirus.


Assuntos
Técnicas Biossensoriais/métodos , Estruturas Metalorgânicas/química , Viroses/virologia , Vírus/isolamento & purificação , Animais , Anticorpos Antivirais/análise , Antígenos Virais/análise , Técnicas Biossensoriais/instrumentação , Técnicas Eletroquímicas/instrumentação , Técnicas Eletroquímicas/métodos , Humanos , Imunoensaio/instrumentação , Imunoensaio/métodos , Modelos Moleculares , Impressão Molecular/instrumentação , Impressão Molecular/métodos , Ácidos Nucleicos/análise , Espectrometria de Fluorescência/instrumentação , Espectrometria de Fluorescência/métodos , Viroses/diagnóstico
3.
Biosens Bioelectron ; 166: 112436, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32750677

RESUMO

Our recent experience of the COVID-19 pandemic has highlighted the importance of easy-to-use, quick, cheap, sensitive and selective detection of virus pathogens for the efficient monitoring and treatment of virus diseases. Early detection of viruses provides essential information about possible efficient and targeted treatments, prolongs the therapeutic window and hence reduces morbidity. Graphene is a lightweight, chemically stable and conductive material that can be successfully utilized for the detection of various virus strains. The sensitivity and selectivity of graphene can be enhanced by its functionalization or combination with other materials. Introducing suitable functional groups and/or counterparts in the hybrid structure enables tuning of the optical and electrical properties, which is particularly attractive for rapid and easy-to-use virus detection. In this review, we cover all the different types of graphene-based sensors available for virus detection, including, e.g., photoluminescence and colorimetric sensors, and surface plasmon resonance biosensors. Various strategies of electrochemical detection of viruses based on, e.g., DNA hybridization or antigen-antibody interactions, are also discussed. We summarize the current state-of-the-art applications of graphene-based systems for sensing a variety of viruses, e.g., SARS-CoV-2, influenza, dengue fever, hepatitis C virus, HIV, rotavirus and Zika virus. General principles, mechanisms of action, advantages and drawbacks are presented to provide useful information for the further development and construction of advanced virus biosensors. We highlight that the unique and tunable physicochemical properties of graphene-based nanomaterials make them ideal candidates for engineering and miniaturization of biosensors.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas Biossensoriais , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Grafite , Pneumonia Viral/diagnóstico , Vírus/isolamento & purificação , Reações Antígeno-Anticorpo , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Técnicas Biossensoriais/instrumentação , Técnicas Biossensoriais/métodos , Técnicas Biossensoriais/tendências , Técnicas de Laboratório Clínico/instrumentação , Técnicas de Laboratório Clínico/métodos , Técnicas de Laboratório Clínico/estatística & dados numéricos , Colorimetria , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , DNA Viral/análise , DNA Viral/genética , Técnicas Eletroquímicas , Desenho de Equipamento , Grafite/química , Humanos , Luminescência , Nanoestruturas/química , Hibridização de Ácido Nucleico , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Pontos Quânticos/química , Análise Espectral Raman , Ressonância de Plasmônio de Superfície , Virologia/métodos , Vírus/genética , Vírus/patogenicidade
4.
Biosens Bioelectron ; 166: 112471, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32777726

RESUMO

The infection and spread of pathogens (e.g., COVID-19) pose an enormous threat to the safety of human beings and animals all over the world. The rapid and accurate monitoring and determination of pathogens are of great significance to clinical diagnosis, food safety and environmental evaluation. In recent years, with the evolution of nanotechnology, nano-sized graphene and graphene derivatives have been frequently introduced into the construction of biosensors due to their unique physicochemical properties and biocompatibility. The combination of biomolecules with specific recognition capabilities and graphene materials provides a promising strategy to construct more stable and sensitive biosensors for the detection of pathogens. This review tracks the development of graphene biosensors for the detection of bacterial and viral pathogens, mainly including the preparation of graphene biosensors and their working mechanism. The challenges involved in this field have been discussed, and the perspective for further development has been put forward, aiming to promote the development of pathogens sensing and the contribution to epidemic prevention.


Assuntos
Bactérias/isolamento & purificação , Betacoronavirus/isolamento & purificação , Técnicas Biossensoriais/métodos , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Grafite , Pandemias , Pneumonia Viral/diagnóstico , Vírus/isolamento & purificação , Animais , Bactérias/genética , Bactérias/patogenicidade , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Grafite/química , Humanos , Técnicas de Diagnóstico Molecular , Nanotecnologia , Vírus/genética , Vírus/patogenicidade
5.
J Appl Lab Med ; 5(5): 897-907, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32674131

RESUMO

BACKGROUND: Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management. METHODS: We evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test. RESULTS: Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results. CONCLUSIONS: Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.


Assuntos
Vírus da Influenza A , Vírus da Influenza B , Influenza Humana , Técnicas de Amplificação de Ácido Nucleico/métodos , Infecções por Vírus de RNA , Infecções Respiratórias , Diagnóstico Diferencial , Humanos , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Vírus da Influenza B/genética , Vírus da Influenza B/isolamento & purificação , Influenza Humana/diagnóstico , Influenza Humana/virologia , Reação em Cadeia da Polimerase Multiplex/métodos , Utilização de Procedimentos e Técnicas , Infecções por Vírus de RNA/diagnóstico , Infecções por Vírus de RNA/virologia , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Vírus/classificação , Vírus/isolamento & purificação
6.
Emerg Microbes Infect ; 9(1): 1671-1681, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32623963

RESUMO

Infectious diseases still remain one of the biggest challenges for human health. Accurate and early detection of infectious pathogens are crucial for transmission control, clinical diagnosis, and therapy. For a traditional reason, most immunological and microbiological laboratories are equipped with instruments designated for antibody-based assays in detection of infectious pathogens or clinical diagnosis. Emerging aptamer-based technologies have pushed a shift from antibody-based to aptamer-based assays due to equal specificity, even better sensitivity, lower manufacturing cost and more flexibility in amending for chemiluminescent, electrochemical or fluorescent detection in a multifaceted and high throughput fashion in comparison of aptamer-based to antibody-based assays. The nature of aptamer-based technologies is particularly suitable for point-of-care testing in remote areas at warm or hot atmosphere, and mass screening for potential infection in pandemic of emerging infectious agents, such as SARS-CoV or SARS-CoV-2 in an epicentre or other regions. This review intends to summarize currently available aptamer-based technologies in detection of bacterial, viral, and protozoan pathogens for research and clinical application. It is anticipated that potential technologies will be further optimized and validated for clinical translation in meeting increasing demands for prompt, precise, and reliable detection of specific pathogens in various atmospheric conditions.


Assuntos
Técnicas Microbiológicas/métodos , Técnica de Seleção de Aptâmeros/métodos , Animais , Bactérias/isolamento & purificação , Humanos , Parasitos/isolamento & purificação , Vírus/isolamento & purificação
7.
Forensic Sci Med Pathol ; 16(3): 457-462, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32578131

RESUMO

Death due to respiratory infection is commonly encountered at autopsy. With only one opportunity to obtain samples for identification of a causative agent, it is important to ensure that sampling regimes are optimized to provide the greatest detection, without the expense and redundancy that can arise from over-sampling. This study was performed retrospectively using data from Coronial autopsies over the period 2012-2019 from which swabs from the nasopharyngeal region, trachea and lung parenchyma, in addition to samples of lung tissue, had been submitted for multiplex PCR detection of respiratory pathogens. From 97 cases with all four samples, there were 24 with at least one positive result for viral infection. Some cases had multiple positive results and a total of 27 respiratory tract viruses were identified, of which rhinovirus, influenza A virus and respiratory syncytial virus were the most common. Seventeen of the 27 viral infections (63%) were identified in all four samples. However, in nearly all cases (96%) the nasopharyngeal swab detected the infective agent when the multiplex PCR panel had detected infection in any of the four sample types. A nasopharyngeal swab is considered to be an optimal sample for detection of respiratory tract viral infection. As the samples analyzed were acquired before the appearance of the COVID-19 virus, the applicability of this finding for COVID-19 screening is not established.


Assuntos
DNA Viral/isolamento & purificação , Pulmão/virologia , Reação em Cadeia da Polimerase Multiplex , Nasofaringe/virologia , Infecções Respiratórias/diagnóstico , Manejo de Espécimes , Virologia , Viroses/diagnóstico , Vírus/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Autopsia , Causas de Morte , DNA Viral/classificação , DNA Viral/genética , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Reprodutibilidade dos Testes , Infecções Respiratórias/virologia , Estudos Retrospectivos , Viroses/virologia , Vírus/classificação , Vírus/genética
8.
Nat Commun ; 11(1): 2533, 2020 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-32439860

RESUMO

Gastroenteritis accounts for nearly 500,000 deaths in children younger than 5 years annually. Although probiotics have been touted as having the potential to expedite diarrhea resolution, recent clinical trials question their effectiveness. A potential explanation is a shift in pathogens following the introduction of a rotavirus vaccine. Here, we report the results of a multi-center, double-blind trial of 816 children with acute gastroenteritis who completed follow-up and provided multiple stool specimens. Participants were randomized to receive a probiotic containing Lactobacillus rhamnosus and Lactobacillus helveticus or placebo. We report no virus-specific beneficial effects attributable to the probiotic, either in reducing clinical symptoms or viral nucleic acid clearance from stool specimens collected up to 28 days following enrollment. We provide pathophysiological and microbiologic evidence to support the clinical findings and conclude that our data do not support routine probiotic administration to children with acute gastroenteritis, regardless of the infecting virus.


Assuntos
Gastroenterite/terapia , Gastroenterite/virologia , Probióticos/uso terapêutico , Doença Aguda , Pré-Escolar , Diarreia/terapia , Diarreia/virologia , Método Duplo-Cego , Fezes/virologia , Feminino , Humanos , Lactente , Lactobacillus helveticus , Lactobacillus rhamnosus , Masculino , Resultado do Tratamento , Carga Viral , Vírus/classificação , Vírus/isolamento & purificação
9.
Nature ; 581(7809): 470-474, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32461640

RESUMO

The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, which-in some cases-leads to gastrointestinal disorders1-4. Here we show that the assembly of the viral community in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium or early stool samples shows few or no particles, but by one month of life particle numbers increase to 109 per gram, and these numbers seem to persist throughout life5-7. We investigated the origin of these viral populations using shotgun metagenomic sequencing of virus-enriched preparations and whole microbial communities, followed by targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut and by one month prophages induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies who were exclusively fed on formula milk compared with those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections8-10. Bacteriophage populations also differed depending on whether or not the infant was breastfed. We show that the colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells; this second phase is modulated by breastfeeding.


Assuntos
Aleitamento Materno , Trato Gastrointestinal/virologia , Vírus/isolamento & purificação , Adulto , Bacteriólise , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Fezes/virologia , Feminino , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Humanos , Lactente , Recém-Nascido , Lisogenia , Masculino , Mecônio/virologia , Prófagos/genética , Prófagos/isolamento & purificação , Vírus/genética
10.
PLoS One ; 15(5): e0233557, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32442222

RESUMO

Intestinal bacterial dysbiosis is evident in children with cystic fibrosis (CF) and intestinal viruses may be contributory, given their influence on bacterial species diversity and biochemical cycles. We performed a prospective, case-control study on children with CF and age and gender matched healthy controls (HC), to investigate the composition and function of intestinal viral communities. Stool samples were enriched for viral DNA and RNA by viral extraction, random amplification and purification before sequencing (Illumina MiSeq). Taxonomic assignment of viruses was performed using Vipie. Functional annotation was performed using Virsorter. Inflammation was measured by calprotectin and M2-pyruvate kinase (M2-PK). Eight CF and eight HC subjects were included (50% male, mean age 6.9 ± 3.0 and 6.4 ± 5.3 years, respectively, p = 0.8). All CF subjects were pancreatic insufficient. Regarding the intestinal virome, no difference in Shannon index between CF and HC was identified. Taxonomy-based beta-diversity (presence-absence Bray-Curtis dissimilarity) was significantly different between CF and HC (R2 = 0.12, p = 0.001). Myoviridae, Faecalibacterium phage FP Taranis and unclassified Gokushovirinae were significantly decreased in CF compared with HC (q<0.05). In children with CF (compared to HC), the relative abundance of genes annotated to (i) a peptidoglycan-binding domain of the peptidoglycan hydrolases (COG3409) was significantly increased (q<0.05) and (ii) capsid protein (F protein) (PF02305.16) was significantly decreased (q<0.05). Picornavirales, Picornaviridae, and Enterovirus were found to positively correlate with weight and BMI (r = 0.84, q = 0.01). Single-stranded DNA viruses negatively correlated with M2-PK (r = -0.86, q = 0.048). Children with CF have an altered intestinal virome compared to well-matched HC, with both taxonomic and predicted functional changes. Further exploration of Faecalibacterium phages, Gokushovirinae and phage lysins are warranted. Intestinal viruses and their functions may have important clinical implications for intestinal inflammation and growth in children with CF, potentially providing novel therapeutic targets.


Assuntos
Fibrose Cística/virologia , Disbiose/virologia , Insuficiência Pancreática Exócrina/virologia , Inflamação/virologia , Intestinos/virologia , Estudos de Casos e Controles , Criança , Pré-Escolar , Fezes/virologia , Feminino , Humanos , Masculino , Estudos Prospectivos , Vírus/classificação , Vírus/isolamento & purificação
11.
Nucleic Acids Res ; 48(W1): W366-W371, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32442274

RESUMO

Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis of infection, guiding individual patient management and treatment strategies, and informing infection prevention and control practices. However, publicly available, streamlined, and reproducible pipelines for analyzing Nanopore metagenomic sequencing data are still lacking. Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. NanoSPC can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. The pipeline can also detect single nucleotide variants and assemble high quality complete consensus genome sequences, permitting high-resolution inference of transmission. We implement NanoSPC using Nextflow manager within Docker images to allow reproducibility and portability of the analysis. Moreover, we deploy NanoSPC to our scalable pathogen pipeline platform, enabling elastic computing for high throughput Nanopore data on HPC cluster as well as multiple cloud platforms, such as Google Cloud, Amazon Elastic Computing Cloud, Microsoft Azure and OpenStack. Users could either access our web interface (https://nanospc.mmmoxford.uk) to run cloud-based analysis, monitor process, and visualize results, as well as download Docker images and run command line to analyse data locally.


Assuntos
Genoma Viral , Metagenômica/métodos , Sequenciamento por Nanoporos/métodos , Software , Vírus/genética , Bactérias/genética , Bactérias/isolamento & purificação , Computação em Nuvem , Vírus/isolamento & purificação
12.
Biosens Bioelectron ; 159: 112214, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32364936

RESUMO

Recent advances in electrochemical biosensors for pathogen detection are reviewed. Electrochemical biosensors for pathogen detection are broadly reviewed in terms of transduction elements, biorecognition elements, electrochemical techniques, and biosensor performance. Transduction elements are discussed in terms of electrode material and form factor. Biorecognition elements for pathogen detection, including antibodies, aptamers, and imprinted polymers, are discussed in terms of availability, production, and immobilization approach. Emerging areas of electrochemical biosensor design are reviewed, including electrode modification and transducer integration. Measurement formats for pathogen detection are classified in terms of sample preparation and secondary binding steps. Applications of electrochemical biosensors for the detection of pathogens in food and water safety, medical diagnostics, environmental monitoring, and bio-threat applications are highlighted. Future directions and challenges of electrochemical biosensors for pathogen detection are discussed, including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, reusable biosensors for process monitoring applications, and low-cost, disposable biosensors.


Assuntos
Bactérias/isolamento & purificação , Técnicas Biossensoriais/instrumentação , Técnicas Eletroquímicas , Eucariotos/isolamento & purificação , Técnicas Microbiológicas/instrumentação , Vírus/isolamento & purificação , Animais , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Eletrodos , Humanos , Técnicas Microbiológicas/normas , Técnicas Microbiológicas/tendências , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia
13.
Int J Infect Dis ; 95: 133-141, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32278934

RESUMO

BACKGROUND: Studies on the etiology of respiratory infections among children in Qatar and surrounding countries are limited. OBJECTIVES: To describe the prevalence and seasonality of RSV, influenza, and other respiratory pathogens among children in Qatar. METHODS: We retrospectively collected and analyzed data of 33,404 children (<15 years) presented with influenza-like illness from 2012 to 2017. RESULTS: At least one respiratory pathogen was detected in 26,138 (78%) of patients. Together, human rhinoviruses (HRV), respiratory syncytial virus (RSV), and influenza viruses comprised nearly two-thirds of all cases, affecting 24%, 19.7%, and 18.5%, respectively. A prevalence of 5-10% was recorded for adenovirus, parainfluenza viruses (PIVs), human bocavirus (HboV), and human coronaviruses (HCoVs). Human metapneumovirus (HMPV), enteroviruses, M. pneumonia, and parechovirus had prevalences below 5%. While RSV, influenza, and HMPV exhibited strong seasonal activity in the winter, HRV was active during low RSV and influenza circulation. The burden of RSV exceeds that of influenza among young age groups, whereas influenza correlated positively with age. Further, HRV, adenovirus, influenza, and RSV infection rates varied significantly between male and females. CONCLUSION: This comprehensive multi-year study provides insights into the etiology of ILI among children in Qatar, which represents the Gulf region. Our results reinforce the significance of active surveillance of respiratory pathogens to improve infection prevention and control strategies, particularly among children.


Assuntos
Influenza Humana/epidemiologia , Infecções por Vírus Respiratório Sincicial/epidemiologia , Infecções Respiratórias/epidemiologia , Viroses/epidemiologia , Adolescente , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Influenza Humana/virologia , Masculino , Orthomyxoviridae/isolamento & purificação , Prevalência , Catar/epidemiologia , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/isolamento & purificação , Infecções Respiratórias/virologia , Estudos Retrospectivos , Rhinovirus/isolamento & purificação , Estações do Ano , Viroses/virologia , Vírus/genética , Vírus/isolamento & purificação
14.
Nat Biotechnol ; 38(5): 563-572, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32341561

RESUMO

Recombinant protein therapeutics, vaccines, and plasma products have a long record of safety. However, the use of cell culture to produce recombinant proteins is still susceptible to contamination with viruses. These contaminations cost millions of dollars to recover from, can lead to patients not receiving therapies, and are very rare, which makes learning from past events difficult. A consortium of biotech companies, together with the Massachusetts Institute of Technology, has convened to collect data on these events. This industry-wide study provides insights into the most common viral contaminants, the source of those contaminants, the cell lines affected, corrective actions, as well as the impact of such events. These results have implications for the safe and effective production of not just current products, but also emerging cell and gene therapies which have shown much therapeutic promise.


Assuntos
Produtos Biológicos/normas , Coleta de Dados/métodos , Contaminação de Medicamentos/prevenção & controle , Vírus/isolamento & purificação , Técnicas de Cultura de Células , Indústria Farmacêutica , Humanos , Disseminação de Informação , Massachusetts
15.
Respir Res ; 21(1): 77, 2020 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-32228581

RESUMO

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by frequent exacerbation phenotypes independent of disease stage. Increasing evidence shows that the microbiota plays a role in disease progression and severity, but long-term and international multicenter assessment of the variations in viral and bacterial communities as drivers of exacerbations are lacking. METHODS: Two-hundred severe COPD patients from Europe and North America were followed longitudinally for 3 years. We performed nucleic acid detection for 20 respiratory viruses and 16S ribosomal RNA gene sequencing to evaluate the bacterial microbiota in 1179 sputum samples collected at stable, acute exacerbation and follow-up visits. RESULTS: Similar viral and bacterial taxa were found in patients from the USA compared to Bulgaria and Czech Republic but their microbiome diversity was significantly different (P < 0.001) and did not impact exacerbation rates. Virus infection was strongly associated with exacerbation events (P < 5E-20). Human rhinovirus (13.1%), coronavirus (5.1%) and influenza virus (3.6%) constitute the top viral pathogens in triggering exacerbation. Moraxella and Haemophilus were 5-fold and 1.6-fold more likely to be the dominating microbiota during an exacerbation event. Presence of Proteobacteria such as Pseudomonas or Staphylococcus amongst others, were associated with exacerbation events (OR > 0.17; P < 0.02) but more strongly associated with exacerbation frequency (OR > 0.39; P < 4E-10), as confirmed by longitudinal variations and biotyping of the bacterial microbiota, and suggesting a role of the microbiota in sensitizing the lung. CONCLUSIONS: This study highlights bacterial taxa in lung sensitization and viral triggers in COPD exacerbations. It provides a global overview of the diverse targets for drug development and explores new microbiome analysis methods to guide future patient management applications.


Assuntos
Bactérias/isolamento & purificação , Pulmão/microbiologia , Pulmão/virologia , Doença Pulmonar Obstrutiva Crônica/microbiologia , Doença Pulmonar Obstrutiva Crônica/virologia , Vírus/isolamento & purificação , Idoso , Idoso de 80 Anos ou mais , Bactérias/genética , Carga Bacteriana , Progressão da Doença , Europa (Continente)/epidemiologia , Feminino , Humanos , Incidência , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Doença Pulmonar Obstrutiva Crônica/diagnóstico , Doença Pulmonar Obstrutiva Crônica/epidemiologia , Estudos Retrospectivos , Fatores de Risco , Escarro/microbiologia , Escarro/virologia , Fatores de Tempo , Estados Unidos/epidemiologia , Carga Viral , Vírus/genética
17.
J Med Microbiol ; 69(3): 427-435, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32118531

RESUMO

Introduction. Diagnosis of acute respiratory infections (ARIs) can be facilitated by the Panther Fusion (PF) automatic, random access PCR system for the detection of influenzavirus A (Flu A) and B (Flu B), parainfluenzavirus (Paraflu), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinovirus (RV) and human adenovirus (AdV) in nasopharyngeal swabs.Aim. To evaluate the performance of PF in comparison with established methods, including subsets of (1) lower respiratory tract (LRT) specimens and (2) upper respiratory tract (URT) hygiene screening specimens of patients without ARI symptoms.Methodology. The performance characteristics of PF were compared with bioMérieux R-Gene and laboratory-developed PCR tests (LDTs). Overall, 1544 specimens with 6658 individual diagnostic requests were analysed.Results. The overall concordances of PF and LDTs for Flu A, Flu B and AdV were 98.4, 99.9 and 96.1%, respectively; by re-testing of discrepant specimens concordances increased to 99.4, 99.9 and 98.0%, respectively. Initial concordances of PF and R-Gene assays for RSV, Paraflu, hMPV and RV were 98.4, 96.3, 99.3 and 96.0%, respectively, and retest concordances were 99.7, 97.9, 99.9 and 98.9%, respectively. No differences to the overall performance were found for the subgroups of LRT and hygiene screening specimens. PCR cycle threshold (Ct) values correlated very well between methods, indicating that a semi-quantitative diagnostic approach using Ct values (e.g. highly vs. weakly positive) could augment the diagnostic information.Conclusion. PF performed similar to R-Gene and LDTs not only for its intended use but also for LRT and hygiene screening specimens with shorter hands-on and turnaround times.


Assuntos
Reação em Cadeia da Polimerase em Tempo Real/métodos , Infecções Respiratórias/diagnóstico , Vírus/isolamento & purificação , Doença Aguda , Humanos , Higiene , Nasofaringe/virologia , Estudos Prospectivos , Infecções Respiratórias/virologia , Vírus/genética
18.
Vet J ; 256: 105425, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32113583

RESUMO

Bovine respiratory disease complex is the most common disease requiring the use of antimicrobials in industrial calf production worldwide. Pathogenic bacteria (Mannheimia haemolytica (Mh), Pasteurella multocida (Pm), Histophilus somni (Hs), and Mycoplasma bovis) and a range of viruses (bovine respiratory syncytial virus, bovine coronavirus, bovine parainfluenza virus type 3, bovine viral diarrhea virus and bovine herpesvirus type 1) are associated with this complex. As most of these pathogens can be present in healthy and diseased calves, simple detection of their presence in diseased calves carries low predictive value. In other multi-agent diseases of livestock, quantification of pathogens has added substantially to the predictive value of microbiological diagnosis. The aim of this study was to evaluate the ability of two recently developed quantitative PCR (qPCR) kits (Pneumo4B and Pneumo4V) to detect and quantify these bacterial and viral pathogens, respectively. Test efficiencies of the qPCR assays, based on nucleic acid dilution series of target bacteria and viruses, were 93-106% and 91-104%, respectively, with assay detection limits of 10-50 copies of nucleic acids. All 44 strains of target bacteria were correctly identified, with no false positive reactions in 135strains of non-target bacterial species. Based on standard curves of log10 CFU versus cycle threshold (Ct) values, quantification was possible over a 5-log range of bacteria. In 92 tracheal aspirate samples, the kappa values for agreement between Pneumo4B and bacterial culture were 0.64-0.84 for Mh, Pm and Hs. In an additional 84 tracheal aspirates, agreement between Pneumo4B or Pneumo 4V and certified diagnostic qPCR assays was moderate (0.57) for M. bovis and high (0.71-0.90) for viral pathogens. Thus Pneumo4 kits specifically detected and quantified the relevant pathogens.


Assuntos
Bactérias/isolamento & purificação , Complexo Respiratório Bovino/microbiologia , Complexo Respiratório Bovino/virologia , Reação em Cadeia da Polimerase Multiplex/veterinária , Vírus/isolamento & purificação , Animais , Bactérias/genética , Complexo Respiratório Bovino/diagnóstico , Bovinos , Reação em Cadeia da Polimerase Multiplex/métodos , Sensibilidade e Especificidade , Vírus/genética
19.
J Clin Microbiol ; 58(5)2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32132186

RESUMO

The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae This multicenter evaluation provides data obtained from 1,994 prospectively collected and 310 retrospectively collected (archived) NPS specimens with performance compared to that of the BioFire FilmArray Respiratory Panel, version 1.7. The overall percent agreement between QIAstat-Dx RP and the comparator testing was 99.5%. In the prospective cohort, the QIAstat-Dx RP demonstrated a positive percent agreement of 94.0% or greater for the detection of all but four analytes: coronaviruses 229E, NL63, and OC43 and rhinovirus/enterovirus. The test also demonstrated a negative percent agreement of ≥97.9% for all analytes. The QIAstat-Dx RP is a robust and accurate assay for rapid, comprehensive testing for respiratory pathogens.


Assuntos
Bactérias/isolamento & purificação , Técnicas de Diagnóstico Molecular/métodos , Reação em Cadeia da Polimerase Multiplex/métodos , Nasofaringe/microbiologia , Nasofaringe/virologia , Vírus/isolamento & purificação , Infecções Bacterianas/diagnóstico , Infecções Bacterianas/microbiologia , Humanos , Técnicas de Diagnóstico Molecular/instrumentação , Reação em Cadeia da Polimerase Multiplex/instrumentação , Estudos Prospectivos , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Estudos Retrospectivos , Viroses/diagnóstico , Viroses/microbiologia
20.
Phys Chem Chem Phys ; 22(8): 4574-4580, 2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32048659

RESUMO

The organization of multiple subcellular compartments is controlled by liquid-liquid phase separation. Phase separation of this type occurs with the emergence of interfacial tension. Aqueous two-phase systems formed by two non-ionic polymers can be used to separate and analyze biological macromolecules, cells and viruses. Phase separation in these systems may serve as the simple model of phase separation in cells also occurring in aqueous media. To better understand liquid-liquid phase separation mechanisms, interfacial tension was measured in aqueous two-phase systems formed by dextran and polyethylene glycol and by polyethylene glycol and sodium sulfate in the presence of different additives. Interfacial tension values depend on differences between the solvent properties of the coexisting phases, estimated experimentally by parameters representing dipole-dipole, ion-dipole, ion-ion, and hydrogen bonding interactions. Based on both current and literature data, we propose a mechanism for phase separation in aqueous two-phase systems. This mechanism is based on the fundamental role of intermolecular forces. Although it remains to be confirmed, it is possible that these may underlie all liquid-liquid phase separation processes in biology.


Assuntos
Biotecnologia/métodos , Extração Líquido-Líquido , Água/química , Separação Celular , Dextranos/química , Complexos Multiproteicos/química , Complexos Multiproteicos/isolamento & purificação , Polietilenoglicóis/química , Sulfatos/química , Tensão Superficial , Vírus/isolamento & purificação
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