Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 16.629
Filtrar
2.
Infectio ; 25(4): 270-275, oct.-dic. 2021. tab, graf
Artigo em Espanhol | LILACS, COLNAL | ID: biblio-1286721

RESUMO

Resumen Objetivo: Comparar la expresión de mRNA y proteínas de SFRP1, PTPRN, CDO1, EDNRB, CDX2, EPB41L3 y HAND1 en pacientes con lesión intra-epitelial cervical de bajo y alto grado, con posterior progresión o regresión. Material y Método: Se realizó análisis de expresión de genes mediante RT-PCR y análisis de expresión de proteínas por inmunohistoquímica. El análisis estadís tico fue realizado con las pruebas: Wilcoxon, coeficiente de correlación de Spearman e índice de concordancia. Las muestras fueron pareadas en momento 1 y momento 2. Resultados: SFRP1 mostró tendencia de mayor expresión de mRNA en lesión intra-epitelial de bajo grado (momento 2) Vs. alto grado (momento 1). La expresión de proteínas por inmunohistoquímica de SFRP1 en casos de progresión (83,3 %) mostró disminución en su graduación (p = 0,0313*); los demás genes en estudio no tuvieron cambios estadísticamente significativos. Discusión: SFRP1 mostró comportamiento ajustado a resultados de estudios previos donde se encontró hipermetilado en lesiones intra-epiteliales de alto grado; su subexpresión por hipermetilación se reportó en otros canceres, proceso que colabora con su silenciamiento y transición epitelial-mesenquimatosa del cáncer de cuello uterino. Conclusiones. SFRP1 es potencial biomarcador en lesiones preneoplásicas del cuello uterino asociadas al virus de papiloma humano.


Abstract Objective. The aim of this work was to compare the expression of mRNA and proteins of SFRP1, PTPRN, CDO1, EDNRB, CDX2, EPB41L3 and HAND1 in patients with low and high grade cervical intraepithelial lesion, with subsequent progression or regression. Material and Methods: Gene expression analysis was conducted through RT-PCR and protein expression analysis was performed by immunohistochemistry. The statistics analysis were Wilcoxon test, Spearman's correlation coefficient and concordance index. The samples were paired during moment 1 (initial patient diag nosis) and moment 2 (follow-up histological diagnosis). Results: SFRP1 showed a trend of higher mRNA expression in low-grade intra-epithelial lesions (moment 2) Vs. high-grade (moment 1). The expression of proteins by immunohistochemistry of SFRP1 in progression cases (83.3%) showed a decrease in its graduation (p = 0.0313*); the other genes under study had no statistically significant. Discussion: SFRP1 showed a biological behavior adjusted to the results of previous studies where hypermethylation was found in high-grade intra-epithelial lesions; its subexpression by hypermethylation has been reported in other cancers, a process that collaborates with its silencing and epithelial-mesenchymal tran sition of cervical. Conclusions. SFRP1 is a potential biomarker in preneoplastic lesions of the cervix associated with human papillomavirus.


Assuntos
Humanos , Feminino , Adulto , Papiloma , Sondas de DNA de HPV , Vírus , Proteínas , Neoplasias do Colo do Útero , Progressão da Doença , Alphapapillomavirus
3.
Infectio ; 25(4): 296-299, oct.-dic. 2021. tab, graf
Artigo em Espanhol | LILACS, COLNAL | ID: biblio-1286726

RESUMO

Resumen La identificación del nuevo Coronavirus tipo 2 en marzo de 2020 en Colombia ha generado paradigmas e incógnitas en la epidemiología nacional con respecto a la llegada aproximada del virus y sus mecanismos de diseminación local en los departamentos y ciudades principales. Presentamos el caso de un paciente con COVID-19 que tuvo su inicio de síntomas dos semanas antes de la declaración del primer caso en Colombia, lo que sugiere circulación del virus y transmisión local en Colombia previo a la declaración de la epidemia.


Abstract The identification of Coronavirus type 2 in March 2020 in Colombia has generated paradigms and unknows in the national epidemiology regarding the approxi mate arrival of the virus and its mechanisms of local dissemination in the main departments and cities. We present the case of a patient with COVID-19 that had its onset of symptoms two weeks before the declaration of the first case in Colombia, wich moves the circulation of the virus and local transmission in Colombia prior the declaration of the epidemic.


Assuntos
Humanos , Masculino , Adulto , Coronavirus , COVID-19 , Pneumonia , Vírus , Epidemiologia , Colômbia , Epidemias , Infecções
4.
Infectio ; 25(4): 289-292, oct.-dic. 2021. tab, graf
Artigo em Espanhol | LILACS, COLNAL | ID: biblio-1286724

RESUMO

Resumen La trombosis de senos venosos cerebrales es un evento infrecuente en la población pediátrica y sus manifestaciones clínicas pueden variar dependiendo de la localización y extensión de la lesión, etiología o grupo etario (1); así mismo, la asociación de esta patología con virus es poco común, sin embargo, se han repor tado casos de trombosis de senos venosos en pacientes adultos con SARS-CoV-2 en relación con los mecanismos de lesión endotelial y respuesta inflamatoria que desencadena mecanismos procoagulantes. A continuación se presenta el primer caso reportado en Colombia de un caso de trombosis venosa cerebral en un lactante previamente sano, que debuta con un cuadro infeccioso gastrointestinal que resuelve y una semana después se presenta con cefalea y paralisis del VI par craneal derecho. Se documentó por angioto mografía trombosis del seno venoso sagital con extensión a senos transversos; los laboratorios fueron negativos para otras causas sistémicas y con prueba de anticuerpos para coronavirus positiva.


Abstract Cerebral venous sinus thrombosis is infrequent in the pediatric population and its clinical manifestations may vary depending on the anatomical location and the extent of the lesion, etiology or age group(1). The association of this pathology with viruses is uncommon, however, cases in adults with SARS-Cov2 have been reported triggered by procoagulant mechanisms due to endothelial injury and inflammatory response. The following article is the first reported case in Colombia of cerebral venous thrombosis in a previously healthy child, who debuted with gastrointestinal infectious disease and a week later with headache and sixth right cranial nerve palsy . The diagnosis of sagittal venous sinus thrombosis with extension to transverse sinuses was documented in a computed tomography angiography; laboratories for systemic diseases were negative and antibodies for coronavirus were positive.


Assuntos
Humanos , Masculino , Lactente , Trombose dos Seios Intracranianos , SARS-CoV-2 , COVID-19 , Trombose , Vírus , Coronavirus , Trombose Venosa , Doenças dos Nervos Cranianos , Seios Transversos , Cefaleia
5.
BMC Infect Dis ; 21(1): 997, 2021 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-34556046

RESUMO

BACKGROUND: Nonrandom multiple respiratory virus (RV) detection provides evidence for viral interference among respiratory viruses. However, little is known as to whether it occurs randomly. METHODS: The prevalence of dual RV detection (DRVD) in patients with acute respiratory illnesses (ARIs) at 4 academic medical centers was investigated; data about the prevalence of 8 RVs were collected from the Korean national RV surveillance dataset. Linear regression analysis was performed to assess the correlation between observed and estimated prevalence of each type of DRVD. RESULTS: In total, 108 patients with ARIs showing DRVD were included in this study between 2011 and 2017. In several types of regression analysis, a strong correlation was observed between the observed and estimated prevalence of each type of DRVD. Excluding three DRVD types (influenza/picornavirus, influenza/human metapneumovirus, and adenovirus/respiratory syncytial virus), the slope of the regression line was higher than that of the line of random occurrence (1.231 > 1.000) and the 95% confidence interval of the regression line was located above the line of random occurrence. CONCLUSIONS: Contrary to the results of previous epidemiologic studies, most types of DRVD occur more frequently than expected from the prevalence rates of individual RV, except for three underrepresented pairs above.


Assuntos
Influenza Humana , Metapneumovirus , Vírus Sincicial Respiratório Humano , Infecções Respiratórias , Viroses , Vírus , Adulto , Humanos , Infecções Respiratórias/epidemiologia , Viroses/epidemiologia
6.
Artigo em Inglês | MEDLINE | ID: mdl-34574450

RESUMO

Different preventive public health measures were adopted globally to limit the spread of SARS-CoV-2, such as hand hygiene and the use of masks, travel restrictions, social distance actions such as the closure of schools and workplaces, case and contact tracing, quarantine and lockdown. These measures, in particular physical distancing and the use of masks, might have contributed to containing the spread of other respiratory viruses that occurs principally by contact and droplet routes. The aim of this study was to evaluate the prevalence of different respiratory viruses (influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, 3 and 4, rhinovirus, adenovirus, metapneumovirus and human coronaviruses) after one year of the pandemic. Furthermore, another aim was to evaluate the possible impact of these non-pharmaceutical measures on the circulation of seasonal respiratory viruses. This single center study was conducted between January 2017-February 2020 (pre-pandemic period) and March 2020-May 2021 (pandemic period). All adults >18 years with respiratory symptoms and tested for respiratory pathogens were included in the study. Nucleic acid detection of all respiratory viruses was performed by multiplex real time PCR. Our results show that the test positivity for influenza A and B, metapneumovirus, parainfluenza virus, respiratory syncytial virus and human coronaviruses decreased with statistical significance during the pandemic. Contrary to this, for adenovirus the decrease was not statistically significant. Conversely, a statistically significant increase was detected for rhinovirus. Coinfections between different respiratory viruses were observed during the pre-pandemic period, while the only coinfection detected during pandemic was between SARS-CoV-2 and rhinovirus. To understand how the preventive strategies against SARS-CoV-2 might alter the transmission dynamics and epidemic patterns of respiratory viruses is fundamental to guide future preventive recommendations.


Assuntos
COVID-19 , Coinfecção , Infecções Respiratórias , Vírus , Adulto , Coinfecção/epidemiologia , Controle de Doenças Transmissíveis , Humanos , Itália/epidemiologia , Pandemias , Infecções Respiratórias/epidemiologia , Estudos Retrospectivos , SARS-CoV-2
7.
Artigo em Inglês | MEDLINE | ID: mdl-34574472

RESUMO

BACKGROUND: Social distancing measures are used to reduce the spreading of COVID-19. The aim of this study was to assess the impact of local restrictions on the transmission of respiratory virus infections. METHODS: we retrospectively analyzed the nasopharyngeal samples of all patients (0-18 years old) admitted with respiratory symptoms in a large Italian tertiary hospital during the last three seasons from 2018 to 2021. RESULTS: A strong reduction in all viral respiratory infections was observed in the last season (2020-2021) compared to the two previous seasons (-79.69% and -80.66%, respectively). In particular, we found that during the epidemic period 2018-2019 and 2019-2020, the total number of Respiratory Syncytial Virus (RSV) cases was, respectively 726 and 689, while in the last season a total of five cases was detected. In the first months of 2018-2019 and 2019-2020, the total flu infections were 240 and 354, respectively, while in the last season we did not detect any influenza virus. As other viruses, the presence of Rhinovirus declined, but to a lesser extent: a total of 488 cases were assessed compared to the 1030 and 1165 cases of the two previous respective epidemic seasons. CONCLUSIONS: Public health interventions and distancing (including continuous use of face masks) settled to counter the pandemic spread of COVID-19 had a macroscopic impact on all respiratory virus transmission and related diseases, with a partial exception of Rhinovirus. The absence of viruses' circulation could result in a lack of immunity and increased susceptibility to serious infections in the next seasons.


Assuntos
COVID-19 , Influenza Humana , Infecções por Vírus Respiratório Sincicial , Infecções Respiratórias , Vírus , Adolescente , Criança , Pré-Escolar , Humanos , Lactente , Recém-Nascido , Influenza Humana/epidemiologia , Pandemias , Infecções por Vírus Respiratório Sincicial/epidemiologia , Infecções Respiratórias/epidemiologia , Estudos Retrospectivos , SARS-CoV-2 , Estações do Ano
8.
Mater Sci Eng C Mater Biol Appl ; 129: 112356, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34579878

RESUMO

Recent COVID-19 pandemic has claimed millions of lives due to lack of a rapid diagnostic tool. Global scientific community is now making joint efforts on developing rapid and accurate diagnostic tools for early detection of viral infections to preventing future outbreaks. Conventional diagnostic methods for virus detection are expensive and time consuming. There is an immediate requirement for a sensitive, reliable, rapid and easy-to-use Point-of-Care (PoC) diagnostic technology. Electrochemical biosensors have the potential to fulfill these requirements, but they are less sensitive for sensing viruses/viral infections. However, sensitivity and performance of these electrochemical platforms can be improved by integrating carbon nanostructure, such as graphene and carbon nanotubes (CNTs). These nanostructures offer excellent electrical property, biocompatibility, chemical stability, mechanical strength and, large surface area that are most desired in developing PoC diagnostic tools for detecting viral infections with speed, sensitivity, and cost-effectiveness. This review summarizes recent advancements made toward integrating graphene/CNTs nanostructures and their surface modifications useful for developing new generation of electrochemical nanobiosensors for detecting viral infections. The review also provides prospects and considerations for extending the graphene/CNTs based electrochemical transducers into portable and wearable PoC tools that can be useful in preventing future outbreaks and pandemics.


Assuntos
Técnicas Biossensoriais , COVID-19 , Grafite , Nanotubos de Carbono , Vírus , Humanos , Pandemias , SARS-CoV-2
9.
Anal Chem ; 93(38): 12938-12943, 2021 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-34520175

RESUMO

We use the Φ6 bacteriophage previously exploited as a BSL-1 surrogate of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS) coronavirus to obtain the first high-resolution gas phase mobility spectra of an enveloped virus. The relative full width at half-maximum found for the viral mobility distribution (FWHMZ < 3.7%) is substantially narrower than that reported by prior mobility or microscopy studies with other enveloped viruses. It is nevertheless not as narrow as that recently found for several non-enveloped viruses (FWHMZ ≈ 2%), presumably due to particle to particle variability of enveloped viruses. This 3.7% is an upper bound to the actual width. Nevertheless, the well-defined mobility peaks obtained indicate that gas phase mobility analysis is a more discriminating methodology than that previously demonstrated for physically based non-genetic viral diagnostic of enveloped viruses. These results are obtained by analysis of the original cell culture medium containing the virus, purified only by passage through a 0.22 µm filter and by dialysis into a 10 mM aqueous ammonium acetate buffer. We confirmed that this buffer exchange preserves infectivity. Therefore, the 63.7 nm mobility diameter found, although smaller than the 75 nm previously inferred by microscopy, corresponds to the full particle including the envelope.


Assuntos
Bacteriófagos , Coronavírus da Síndrome Respiratória do Oriente Médio , Vírus , Diálise Renal
10.
Biomed Res Int ; 2021: 5313832, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34485513

RESUMO

Background: Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. Methods: We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies. Results: Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively. Conclusion: The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.


Assuntos
COVID-19/epidemiologia , Coinfecção/epidemiologia , Coinfecção/virologia , Humanos , Pandemias/prevenção & controle , Prevalência , SARS-CoV-2/patogenicidade , Viroses/epidemiologia , Viroses/virologia , Vírus/patogenicidade
11.
Theranostics ; 11(18): 9133-9161, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34522231

RESUMO

During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.


Assuntos
Aptâmeros de Nucleotídeos , Bactérias/genética , Doenças Transmissíveis/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Vírus/genética , Aptâmeros de Nucleotídeos/farmacologia , Técnicas Biossensoriais , Teste para COVID-19/métodos , Controle de Doenças Transmissíveis , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/virologia , Ensaio de Imunoadsorção Enzimática/métodos , Interações Hospedeiro-Patógeno/imunologia , Humanos , Técnica de Seleção de Aptâmeros , Internalização do Vírus
12.
Mol Cell ; 81(17): 3447-3448, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34478653

RESUMO

Valencia-Sánchez et al. (2021) and Liu et al. (2021) provide structural and biological insights about the existence and importance of a nucleosome-like particle in a family of giant viruses.


Assuntos
Vírus Gigantes , Vírus , Genoma , Vírus Gigantes/genética , Nucleossomos/genética
13.
Philos Trans R Soc Lond B Biol Sci ; 376(1837): 20200358, 2021 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-34538140

RESUMO

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.


Assuntos
Reservatórios de Doenças/virologia , Saúde Global , Pandemias/prevenção & controle , Zoonoses/prevenção & controle , Zoonoses/virologia , Animais , Animais Selvagens , COVID-19/prevenção & controle , COVID-19/veterinária , Ecologia , Humanos , Laboratórios , Aprendizado de Máquina , Fatores de Risco , SARS-CoV-2 , Vírus , Zoonoses/epidemiologia
14.
ACS Sens ; 6(9): 3445-3450, 2021 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-34505501

RESUMO

Accurate single virus detection is critical for disease diagnosis and early prevention, especially in view of current pandemics. Numerous detection methods have been proposed with the single virus sensitivity, including the optical approaches and immunoassays. However, few of them hitherto have the capability of both trapping and detection of single viruses in the microchannel. Here, we report an optofluidic potential well array to trap nanoparticles stably in the flow stream. The nanoparticle is bound with single viruses and fluorescence quantum dots through an immunolabeling protocol. Single viruses can be swiftly captured in the microchannel by optical forces and imaged by a camera. The number of viruses in solution and on each particle can be quantified via image processing. Our method can trap and detect single viruses in the 1 mL serum or water in 2 h, paving an avenue for the advanced, fast, and accurate clinical diagnosis, as well as the study of virus infectivity, mutation, drug inhibition, etc.


Assuntos
Vírus , Vírus/genética
15.
Cells ; 10(9)2021 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-34571822

RESUMO

As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.


Assuntos
Esfingolipídeos/metabolismo , Viroses , Transporte Biológico , Membrana Celular/química , Ceramidas/metabolismo , Sistemas de Liberação de Medicamentos , HIV/crescimento & desenvolvimento , Interações entre Hospedeiro e Microrganismos , Membranas Intracelulares/química , SARS-CoV-2/crescimento & desenvolvimento , Vírion , Replicação Viral , Vírus/crescimento & desenvolvimento
16.
Commun Biol ; 4(1): 1086, 2021 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-34526645
17.
Biocontrol Sci ; 26(3): 177-180, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34556620

RESUMO

Ethanol is an effective disinfectant against the novel coronavirus SARS-CoV-2. However, its effective concentration has not been shown, and we therefore analyzed the effects of different concentrations of ethanol on SARS-CoV-2. When SARS-CoV-2 was treated with varying ethanol concentrations and examined for changes in infectivity, the ethanol concentration at which 99% of the infectious titers were reduced was 24.1% (w/w) [29.3% (v/v)]. For reference, ethanol susceptibility was also examined with other envelope viruses, including influenza virus, vesicular stomatitis virus in the family Rhabdoviridae, and Newcastle disease virus in the family Paramyxoviridae, and the 99% inhibitory concentrations were found to be 28.8%(w/w) [34.8% (v/v)], 24.0% (w/w) [29.2% (v/v)], and 13.3% (w/w) [16.4% (v/v)], respectively. Some differences from SARS-CoV-2 were observed, but the differences were not significant. It was concluded that ethanol at a concentration of 30%(w/w) [36.2% (v/v)] almost completely inactivates SARS-CoV-2.


Assuntos
Desinfetantes/farmacologia , Etanol/farmacologia , SARS-CoV-2/efeitos dos fármacos , COVID-19/virologia , Desinfetantes/análise , Etanol/análise , Humanos , SARS-CoV-2/crescimento & desenvolvimento , SARS-CoV-2/fisiologia , Inativação de Vírus/efeitos dos fármacos , Vírus/efeitos dos fármacos , Vírus/crescimento & desenvolvimento
18.
BMC Bioinformatics ; 22(1): 438, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34525942

RESUMO

BACKGROUND: The field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery. However, functional annotation of the increasing number of viral genomes is lagging behind. This is highlighted by the degree of annotation of the protein clusters in the prokaryotic Virus Orthologous Groups (pVOGs) database, with 83% of its current 9518 pVOGs having an unknown function. RESULTS: In this study we describe a machine learning approach to explore potential functional associations between pVOGs. We measure seven genomic features and use them as input to a Random Forest classifier to predict protein-protein interactions between pairs of pVOGs. After systematic evaluation of the model's performance on 10 different datasets, we obtained a predictor with a mean accuracy of 0.77 and Area Under Receiving Operation Characteristic (AUROC) score of 0.83. Its application to a set of 2,133,027 pVOG-pVOG interactions allowed us to predict 267,265 putative interactions with a reported probability greater than 0.65. At an expected false discovery rate of 0.27, we placed 95.6% of the previously unannotated pVOGs in a functional context, by predicting their interaction with a pVOG that is functionally annotated. CONCLUSIONS: We believe that this proof-of-concept methodology, wrapped in a reproducible and automated workflow, can represent a significant step towards obtaining a more complete picture of bacteriophage biology.


Assuntos
Vírus , Genoma Viral/genética , Genômica , Metagenômica , Células Procarióticas , Vírus/genética
19.
Euro Surveill ; 26(38)2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34558405

RESUMO

BackgroundSeasonal influenza-like illness (ILI) affects millions of people yearly. Severe acute respiratory infections (SARI), mainly influenza, are a leading cause of hospitalisation and mortality. Increasing evidence indicates that non-influenza respiratory viruses (NIRV) also contribute to the burden of SARI. In Belgium, SARI surveillance by a network of sentinel hospitals has been ongoing since 2011.AimWe report the results of using in-house multiplex qPCR for the detection of a flexible panel of viruses in respiratory ILI and SARI samples and the estimated incidence rates of SARI associated with each virus.MethodsWe defined ILI as an illness with onset of fever and cough or dyspnoea. SARI was defined as an illness requiring hospitalisation with onset of fever and cough or dyspnoea within the previous 10 days. Samples were collected in four winter seasons and tested by multiplex qPCR for influenza virus and NIRV. Using catchment population estimates, we calculated incidence rates of SARI associated with each virus.ResultsOne third of the SARI cases were positive for NIRV, reaching 49.4% among children younger than 15 years. In children younger than 5 years, incidence rates of NIRV-associated SARI were twice that of influenza (103.5 vs 57.6/100,000 person-months); co-infections with several NIRV, respiratory syncytial viruses, human metapneumoviruses and picornaviruses contributed most (33.1, 13.6, 15.8 and 18.2/100,000 person-months, respectively).ConclusionEarly testing for NIRV could be beneficial to clinical management of SARI patients, especially in children younger than 5 years, for whom the burden of NIRV-associated disease exceeds that of influenza.


Assuntos
Influenza Humana , Orthomyxoviridae , Infecções Respiratórias , Vírus , Bélgica/epidemiologia , Criança , Humanos , Lactente , Influenza Humana/diagnóstico , Influenza Humana/epidemiologia , Saúde Pública , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/epidemiologia , Vigilância de Evento Sentinela , Vírus/genética
20.
Nat Commun ; 12(1): 5523, 2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34535646

RESUMO

RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.


Assuntos
RNA Polimerases Dirigidas por DNA/antagonistas & inibidores , RNA Polimerases Dirigidas por DNA/química , Vírus/metabolismo , Regulação Alostérica , Sequência de Aminoácidos , Proteínas Arqueais/metabolismo , Microscopia Crioeletrônica , DNA/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , Modelos Moleculares , Ligação Proteica , Estrutura Secundária de Proteína , Fatores de Tempo , Proteínas Virais/metabolismo , Viroides/metabolismo
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...