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1.
Nat Commun ; 12(1): 1744, 2021 03 19.
Artículo en Inglés | MEDLINE | ID: mdl-33741998

RESUMEN

Interferometric scattering microscopy is increasingly employed in biomedical research owing to its extraordinary capability of detecting nano-objects individually through their intrinsic elastic scattering. To significantly improve the signal-to-noise ratio without increasing illumination intensity, we developed photonic resonator interferometric scattering microscopy (PRISM) in which a dielectric photonic crystal (PC) resonator is utilized as the sample substrate. The scattered light is amplified by the PC through resonant near-field enhancement, which then interferes with the <1% transmitted light to create a large intensity contrast. Importantly, the scattered photons assume the wavevectors delineated by PC's photonic band structure, resulting in the ability to utilize a non-immersion objective without significant loss at illumination density as low as 25 W cm-2. An analytical model of the scattering process is discussed, followed by demonstration of virus and protein detection. The results showcase the promise of nanophotonic surfaces in the development of resonance-enhanced interferometric microscopies.


Asunto(s)
Microscopía de Interferencia/instrumentación , Microscopía de Interferencia/métodos , Óptica y Fotónica/instrumentación , Óptica y Fotónica/métodos , Cristalización , Diseño de Equipo , Oro , Procesamiento de Imagen Asistido por Computador , Nanopartículas del Metal , Nanoestructuras , Fotones , Proteínas/aislamiento & purificación , Virión/aislamiento & purificación , Virus/aislamiento & purificación
2.
BMC Infect Dis ; 21(1): 230, 2021 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-33639884

RESUMEN

BACKGROUND: Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children. METHODS: Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated. RESULTS: A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0-2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3-5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6-14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05). CONCLUSIONS: This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.


Asunto(s)
Técnicas Microbiológicas/métodos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones del Sistema Respiratorio/diagnóstico , Virología/métodos , Adolescente , Edad de Inicio , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Preescolar , Diagnóstico Diferencial , Femenino , Humanos , Lactante , Recién Nacido , Unidades de Cuidado Intensivo Pediátrico , Masculino , Nasofaringe/microbiología , Nasofaringe/virología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Valor Predictivo de las Pruebas , Reproducibilidad de los Resultados , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Virus/genética , Virus/aislamiento & purificación
3.
Viruses ; 13(2)2021 02 06.
Artículo en Inglés | MEDLINE | ID: mdl-33562073

RESUMEN

The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.


Asunto(s)
Quirópteros/virología , Virus/aislamiento & purificación , Zoonosis/virología , Animales , Reservorios de Enfermedades/veterinaria , Reservorios de Enfermedades/virología , Heces/virología , Genoma Viral/genética , Humanos , Aprendizaje Automático , Metagenómica , Filogenia , Virus de la Rabia/clasificación , Virus de la Rabia/genética , Virus de la Rabia/aislamiento & purificación , Saliva/virología , Virus/clasificación , Virus/genética
4.
BMC Infect Dis ; 21(1): 152, 2021 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-33546631

RESUMEN

BACKGROUND: Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms. METHODS: BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified. RESULTS: The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P = 0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4% of the cases co-detection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens. CONCLUSION: Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.


Asunto(s)
Líquido del Lavado Bronquioalveolar/microbiología , Líquido del Lavado Bronquioalveolar/virología , Infecciones del Sistema Respiratorio/diagnóstico , Adolescente , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Niño Hospitalizado , Preescolar , Coinfección/diagnóstico , Coinfección/microbiología , Coinfección/virología , Pruebas Diagnósticas de Rutina , Femenino , Humanos , Lactante , Masculino , Reacción en Cadena de la Polimerasa , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación
5.
Microbiome ; 9(1): 51, 2021 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-33610182

RESUMEN

BACKGROUND: The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS: A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS: The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS: The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.


Asunto(s)
/aislamiento & purificación , Virus/aislamiento & purificación , Zoonosis/diagnóstico , Animales , ADN Viral/genética , Genoma Viral , Humanos , ARN Viral/genética , Virus/clasificación
6.
Viruses ; 13(2)2021 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-33562285

RESUMEN

Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several solutions exist, such as applying a very high depth of sequencing, or performing a relative enrichment of viral genomes associated with capsids. At the end, the quantity of total nucleic acids is often below the concentrations recommended by the manufacturers of library kits, which necessitates to random amplify nucleic acids. Using a pool of 26 viruses representative of viral diversity, we observed a deep impact of the nature of sample (total nucleic acids versus RNA only), the reverse transcription, the random amplification and library construction method on virus recovery. We further optimized the two most promising methods and assessed their performance with fully characterized reference virus stocks. Good genome coverage and limit of detection lower than 100 or 1000 genome copies per mL of plasma, depending on the genome viral type, were obtained from a three million reads dataset. Our study reveals that optimized random amplification is a technique of choice when insufficient amounts of nucleic acid are available for direct libraries constructions.


Asunto(s)
Genoma Viral/genética , Metagenómica/métodos , Técnicas de Amplificación de Ácido Nucleico/métodos , Virus/aislamiento & purificación , Biblioteca Genómica , Humanos , Límite de Detección , Virus/genética
7.
Viruses ; 13(2)2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33572209

RESUMEN

Porcine circovirus 3 (PCV-3) has been widely detected in healthy and diseased pigs; among different pathologic conditions, the strongest evidence of association comes from reproductive disease cases. However, simple viral detection does not imply the causality of the clinical conditions. Detection of PCV-3 within lesions may provide stronger evidence of causality. Thus, this study aimed to assess the frequency of PCV-3 detection in tissues from fetuses/stillborn piglets in cases of reproductive problems in domestic swine, as well as the histopathologic assessment of fetal tissues. Fetuses or stillborn piglets from 53 cases of reproductive failure were collected and analyzed by PCV-3 qPCR. The presence of porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV-2), and porcine parvovirus 1 (PPV1) was also checked. PCV-3 qPCR positive samples with a high viral load were tested by PCV-3 in situ hybridization (ISH), sequenced, and phylogenetically analyzed. PCV-3 DNA was detected in 18/53 (33.9%) reproductive failure cases and in 16 of them PCV-3 was the only pathogen found. PCV-2 DNA was found in 5/53 (9.4%), PRRSV RNA in 4/53 (7.5%) and PPV1 was not detected. Four out of the six PCV-3 qPCR-positive cases with Ct value <30 were positive when tested by ISH. In these samples, PCV-3 was detected within mild histopathologic lesions, such as arteritis and periarteritis in multiple tissues. The present work emphasizes the need to include PCV-3 as a potential causative agent of reproductive failure in swine.


Asunto(s)
Aborto Veterinario/virología , Infecciones por Circoviridae/veterinaria , Circovirus/aislamiento & purificación , Enfermedades de los Porcinos/virología , Feto Abortado/patología , Feto Abortado/virología , Aborto Veterinario/patología , Animales , Animales Domésticos , Infecciones por Circoviridae/patología , Infecciones por Circoviridae/virología , Circovirus/clasificación , Circovirus/genética , ADN Viral/genética , Femenino , Genoma Viral/genética , Filogenia , Embarazo , Mortinato/veterinaria , Porcinos , Enfermedades de los Porcinos/patología , Carga Viral , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación
8.
Viruses ; 13(2)2021 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-33573340

RESUMEN

BACKGROUND: Viral gastroenteritis remains a major cause of hospitalisation in young children. This study aimed to determine the distribution and diversity of enteric viruses in children ≤5 years, hospitalised with gastroenteritis at Kalafong Provincial Tertiary Hospital, Pretoria, South Africa, between July 2016 and December 2017. METHODS: Stool specimens (n = 205) were screened for norovirus GI and GII, rotavirus, sapovirus, astrovirus and adenovirus by multiplex RT-PCR. HIV exposure and FUT2 secretor status were evaluated. Secretor status was determined by FUT2 genotyping. RESULTS: At least one gastroenteritis virus was detected in 47% (96/205) of children. Rotavirus predominated (46/205), followed by norovirus (32/205), adenovirus (15/205), sapovirus (9/205) and astrovirus (3/205). Norovirus genotypes GI.3, GII.2, GII.3, GII.4, GII.7, GII.12, GII.21, and rotavirus strains G1P[8], G2P[4], G2P[6], G3P[4], G3P[8], G8P[4], G8P[6], G9P[6], G9P[8] and sapovirus genotypes GI.1, GI.2, GII.1, GII.4, GII.8 were detected; norovirus GII.4[P31] and rotavirus G3P[4] predominated. Asymptomatic norovirus infection (GI.3, GI.7, GII.4, GII.6, GII.13) was detected in 22% of 46 six-week follow up stools. HIV exposure (30%) was not associated with more frequent or severe viral gastroenteritis hospitalisations compared to unexposed children. Rotavirus preferentially infected secretor children (p = 0.143) and norovirus infected 78% secretors and 22% non-secretors. CONCLUSION: Rotavirus was still the leading cause of gastroenteritis hospitalisations, but norovirus caused more severe symptoms.


Asunto(s)
Gastroenteritis/virología , Virus/aislamiento & purificación , Biodiversidad , Preescolar , Heces/virología , Femenino , Gastroenteritis/terapia , Hospitalización , Humanos , Lactante , Masculino , Sudáfrica , Virus/clasificación , Virus/genética
9.
Trop Anim Health Prod ; 53(1): 79, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33409702

RESUMEN

The aim of this study was to evaluate the compatibility among virus isolation (VI), ELISA, and PCR for diagnosis of the major viral agents (BPIV-3, BRSV, BVDV, and BoHV-1) responsible for BRD in the field samples. For that purpose, a total of 193 samples (133 nasal swabs and 60 lung tissue samples) from cattle with respiratory signs in northwestern Turkey were examined. For VI, all the samples were inoculated at least 3 blind passages onto MDBK cell culture. In addition, the samples were tested by hemadsorption assay and RT-PCR for BPIV-3; nested RT-PCR for BRSV; immunoperoxidase monolayer assay, antigen-ELISA, and RT-PCR for BVDV; and antigen-ELISA and PCR for BoHV-1. The detected 1 (0.52%) BPIV-3 isolate was found to be in the genotype BPIV-3c. No BRSV isolate could be obtained, while 5 (2.59%) samples were evaluated positive in nested-RT PCR. The presence of BVDV antigen in 10 (5.18%) samples and the BVDV genome in 5 (2.59%) samples were detected, while non-cytopathogenic BVDV isolates were obtained only in 2 (1.04%) samples. The detected BVDV strains fell into the genetic clusters of BVDV-1a, -1f, and -1l. For detection of BoHV-1, although viral isolation and Ag-ELISA results were negative, presence of BoHV-1.1 genome was detected in 2 (1.04%) samples. By the results of VI, ELISA, and PCRs, 10.88% (21/193) of samples were found positive for the evaluated viruses. Depending on the obtained data, combined uses of the diagnostic methods were evaluated to be more reliable for routine diagnosis of bovine respiratory viruses.


Asunto(s)
Complejo Respiratorio Bovino/diagnóstico , Pruebas Diagnósticas de Rutina/veterinaria , Ensayo de Inmunoadsorción Enzimática/veterinaria , Pulmón/virología , Nariz/virología , Reacción en Cadena de la Polimerasa/veterinaria , Animales , Complejo Respiratorio Bovino/virología , Pruebas Diagnósticas de Rutina/instrumentación , Pruebas Diagnósticas de Rutina/métodos , Ensayo de Inmunoadsorción Enzimática/métodos , Reacción en Cadena de la Polimerasa/métodos , Virus Sincitial Respiratorio Bovino/aislamiento & purificación , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de ADN/veterinaria , Análisis de Secuencia de ARN/métodos , Análisis de Secuencia de ARN/veterinaria , Turquia , Virus/aislamiento & purificación
10.
Viruses ; 13(1)2021 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-33451082

RESUMEN

Viruses are highly abundant, diverse, and active components of marine environments. Flow cytometry has helped to increase the understanding of their impact on shaping microbial communities and biogeochemical cycles in the pelagic zone. However, to date, flow cytometric quantification of sediment viruses is still hindered by interference from the sediment matrix. Here, we developed a protocol for the enumeration of marine sediment viruses by flow cytometry based on separation of viruses from sediment particles using a Nycodenz density gradient. Results indicated that there was sufficient removal of background interference to allow for flow cytometric quantification. Applying this new protocol to deep-sea and tidal-flat samples, viral abundances enumerated by flow cytometry correlated well (R2 = 0.899) with counts assessed by epifluorescence microscopy over several orders of magnitude from marine sediments of various compositions. Further optimization may be needed for sediments with low biomass or high organic content. Overall, the new protocol enables fast and accurate quantification of marine sediment viruses, and opens up the options for virus sorting, targeted viromics, and single-virus sequencing.


Asunto(s)
Citometría de Flujo/métodos , Sedimentos Geológicos/virología , Agua de Mar , Virus , Microbiología del Agua , Fraccionamiento Químico , Dermoscopía , Carga Viral , Virus/aislamiento & purificación
12.
BMC Infect Dis ; 21(1): 43, 2021 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-33422002

RESUMEN

BACKGROUND: Acute respiratory infections (ARIs) are a worldwide public health problem. It is estimated that up to 80% of cases of ARIs are caused by viruses. In Central America, however, we identified few epidemiologic studies on the main ARI-related viruses in hospitalized children. METHODS: This study retrospectively analyzed the clinical charts of patients ages 29 days to 14 years admitted with diagnoses of ARIs in a pediatric reference hospital in central Panama during 2016. The variables analyzed were age, sex, signs, symptoms, and diagnosis at admission. Samples of patients to whom a viral panel was indicated were analyzed via quantitative polymerase chain reaction, qPCR. RESULTS: The most common virus was respiratory syncytial virus (RSV; 25.9%), followed by influenza A virus (10.6%), rhinovirus (10.6%), parainfluenza type 3 (PIV-3; 8.2%) and adenovirus (5.9%). However, virus detection varied with patient age and season. RSV and Influenza virus were respectively identified mainly during July-November and May-July. All cases of viral co-infection occurred in children < 5-years-old. Both influenza A (H1N1) pdm09 and rhinovirus were detected in all pediatric ages analyzed in this study, unlike RSV and PIV-3, which were only present in children < 5-years-old. CONCLUSIONS: This study analyzed the epidemiological patterns of different respiratory viruses in pediatric patients with ARI from central Panama and found that the prevalence of the specific respiratory viruses identified varied with season and age. The most common viruses were RSV, influenza A, and rhinovirus. There were no reports of human metapneumovirus associated with ARI, which may be explained by the time and geographic location of the study. Knowledge of the local epidemiology of respiratory viruses in tropical countries is helpful in forecasting the peaks of hospitalizations due to ARIs and may help improve prevention efforts aiming at respiratory disease control in these settings.


Asunto(s)
Infecciones del Sistema Respiratorio/virología , Virosis/virología , Virus/aislamiento & purificación , Adolescente , Niño , Preescolar , Coinfección/epidemiología , Coinfección/virología , Femenino , Hospitalización , Hospitales/estadística & datos numéricos , Humanos , Lactante , Masculino , Metapneumovirus/genética , Panamá/epidemiología , Pediatría , Reacción en Cadena en Tiempo Real de la Polimerasa , Infecciones del Sistema Respiratorio/epidemiología , Estudios Retrospectivos , Estaciones del Año , Virosis/epidemiología , Virus/clasificación , Virus/genética
13.
Pediatr Infect Dis J ; 40(1): e12-e17, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33165274

RESUMEN

BACKGROUND: Human coronaviruses (HCoVs) are a significant cause of acute respiratory illness (ARI) in children; however, the role of HCoVs in ARI among hospitalized children in the Middle East is not well defined. METHODS: Children under 2 years admitted with fever and/or respiratory symptoms were enrolled from 2010 to 2013 in Amman, Jordan. Nasal/throat swabs were collected and stored for testing. Demographic and clinical characteristics were collected through parent/guardian interviews and medical chart abstractions. Prior stored specimens were tested for HCoVs (HKU1, OC43, 229E and NL63) by qRT-PCR. RESULTS: Of the 3168 children enrolled, 6.7% were HCoVs-positive. Among HCoV-positive children, the median age was 3.8 (1.9-8.4) months, 59% were male, 14% were premature, 11% had underlying medical conditions and 76% had viral-codetection. The most common presenting symptoms were cough, fever, wheezing and shortness of breath. HCoVs were detected year-round, peaking in winter-spring months. Overall, 56%, 22%, 13% and 6% were OC43, NL63, HKU1 and 229E, respectively. There was no difference in disease severity between the species, except higher intensive care unit admission frequency in NL63-positive subjects. CONCLUSIONS: HCoVs were detected in around 7% of children enrolled in our study. Despite HCoV detection in children with ARI with highest peaks in respiratory seasons, the actual burden and pathogenic role of HCoVs in ARI merits further evaluation given the high frequency of viral codetection.


Asunto(s)
Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Coronavirus/aislamiento & purificación , Enfermedad Aguda , Coinfección/epidemiología , Coinfección/patología , Coinfección/virología , Coronavirus/clasificación , Coronavirus/genética , Infecciones por Coronavirus/patología , Femenino , Hospitalización , Humanos , Lactante , Jordania/epidemiología , Masculino , Vigilancia de la Población , Estudios Prospectivos , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/patología , Infecciones del Sistema Respiratorio/virología , Factores de Riesgo , Estaciones del Año , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación
14.
Methods Mol Biol ; 2178: 251-284, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33128755

RESUMEN

Nowadays, monolithic stationary phases, because of their special morphology and enormous permeability, are widely used for the development and realization of fast dynamic and static processes based on the mass transition between liquid and solid phases. These are liquid chromatography, solid-phase synthesis, microarrays, flow-through enzyme reactors, etc. High-performance liquid chromatography on monoliths, including the bioaffinity mode, represents unique technique appropriate for fast and efficient separation of biological (macro)molecules of different sizes and shapes (proteins, nucleic acids, peptides), as well as such supramolecular systems as viruses.In the edited chapter, the examples of the application of commercially available macroporous monoliths for modern affinity processing are presented. In particular, the original methods developed for efficient isolation and fractionation of monospecific antibodies from rabbit blood sera, the possibility of simultaneous affinity separation of protein G and serum albumin from human serum, the isolation of recombinant products, such as protein G and tissue plasminogen activator, respectively, are described in detail. The suggested and realized multifunctional fractionation of polyclonal pools of antibodies by the combination of several short monolithic columns (disks) with different affinity functionalities stacked in the same cartridge represents the original and practically valuable method that can be used in biotechnology. In addition, macroporous monoliths were adapted to the immobilization of such different enzymes as polynucleotide phosphorylase, ribonuclease A, α-chymotrypsin, chitinolytic biocatalysts, ß-xylosidase, and ß-xylanase. The possibility of use of immobilized enzyme reactors based on monoliths for different purposes is demonstrated.


Asunto(s)
Anticuerpos , Ácidos Nucleicos , Péptidos , Virus , Anticuerpos/química , Anticuerpos/aislamiento & purificación , Cromatografía Líquida de Alta Presión , Ácidos Nucleicos/química , Ácidos Nucleicos/aislamiento & purificación , Péptidos/química , Péptidos/aislamiento & purificación , Virus/química , Virus/aislamiento & purificación
15.
Int J Mol Sci ; 21(24)2020 Dec 17.
Artículo en Inglés | MEDLINE | ID: mdl-33348900

RESUMEN

Cell-cell fusion between eukaryotic cells is a general process involved in many physiological and pathological conditions, including infections by bacteria, parasites, and viruses. As obligate intracellular pathogens, viruses use intracellular machineries and pathways for efficient replication in their host target cells. Interestingly, certain viruses, and, more especially, enveloped viruses belonging to different viral families and including human pathogens, can mediate cell-cell fusion between infected cells and neighboring non-infected cells. Depending of the cellular environment and tissue organization, this virus-mediated cell-cell fusion leads to the merge of membrane and cytoplasm contents and formation of multinucleated cells, also called syncytia, that can express high amount of viral antigens in tissues and organs of infected hosts. This ability of some viruses to trigger cell-cell fusion between infected cells as virus-donor cells and surrounding non-infected target cells is mainly related to virus-encoded fusion proteins, known as viral fusogens displaying high fusogenic properties, and expressed at the cell surface of the virus-donor cells. Virus-induced cell-cell fusion is then mediated by interactions of these viral fusion proteins with surface molecules or receptors involved in virus entry and expressed on neighboring non-infected cells. Thus, the goal of this review is to give an overview of the different animal virus families, with a more special focus on human pathogens, that can trigger cell-cell fusion.


Asunto(s)
Fusión Celular , Membrana Celular/metabolismo , Fusión de Membrana , Proteínas Virales de Fusión/metabolismo , Internalización del Virus , Virus/metabolismo , Animales , Humanos , Virus/aislamiento & purificación
16.
Arch Virol ; 165(12): 2847-2856, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33034764

RESUMEN

Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we detected a novel polyomavirus (RabPyV), and phylogenetic analysis based on the large T antigen, VP1 and VP2 regions indicated that the novel strain might have undergone a recombination event. Recombination analysis based on related genomes confirmed that RabPyV is a multiple recombinant between rodent-like and avian-like polyomaviruses. In fecal samples, three partial or complete genome sequences of viruses belonging to the families Picobirnaviridae, Parvoviridae, Microviridae and Coronaviridae were characterized, and phylogenetic trees were constructed based on the predicted amino acid sequences of viral proteins. This study increases the amount of genetic information on viruses present in laboratory rabbits.


Asunto(s)
Metagenoma , Poliomavirus/aislamiento & purificación , Conejos/virología , Proteínas Virales/genética , Virus/clasificación , Animales , Animales de Laboratorio/virología , Sangre/virología , Heces/virología , Genoma Viral , Boca/virología , Filogenia , Piel/virología , Virus/aislamiento & purificación , Secuenciación Completa del Genoma
17.
Biosens Bioelectron ; 169: 112604, 2020 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-32980805

RESUMEN

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.


Asunto(s)
Técnicas Biosensibles/métodos , Estructuras Metalorgánicas/química , Virosis/virología , Virus/aislamiento & purificación , Animales , Anticuerpos Antivirales/análisis , Antígenos Virales/análisis , Técnicas Biosensibles/instrumentación , Técnicas Electroquímicas/instrumentación , Técnicas Electroquímicas/métodos , Humanos , Inmunoensayo/instrumentación , Inmunoensayo/métodos , Modelos Moleculares , Impresión Molecular/instrumentación , Impresión Molecular/métodos , Ácidos Nucleicos/análisis , Espectrometría de Fluorescencia/instrumentación , Espectrometría de Fluorescencia/métodos , Virosis/diagnóstico
18.
Biosens Bioelectron ; 166: 112431, 2020 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-32862842

RESUMEN

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.


Asunto(s)
Betacoronavirus , Técnicas Biosensibles/instrumentación , Técnicas de Laboratorio Clínico/instrumentación , Infecciones por Coronavirus/diagnóstico , Técnicas Electroquímicas/instrumentación , Neumonía Viral/diagnóstico , Virus/aislamiento & purificación , Animales , Betacoronavirus/aislamiento & purificación , Betacoronavirus/patogenicidad , Infecciones por Coronavirus/virología , Diseño de Equipo , Humanos , Nanopartículas del Metal/química , Nanopartículas del Metal/ultraestructura , Microscopía Electrónica de Rastreo , Pandemias , Neumonía Viral/virología , Pruebas en el Punto de Atención , Virus/patogenicidad
19.
Biosens Bioelectron ; 166: 112436, 2020 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-32750677

RESUMEN

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.


Asunto(s)
Betacoronavirus/aislamiento & purificación , Técnicas Biosensibles , Técnicas de Laboratorio Clínico , Infecciones por Coronavirus/diagnóstico , Grafito , Neumonía Viral/diagnóstico , Virus/aislamiento & purificación , Reacciones Antígeno-Anticuerpo , Betacoronavirus/genética , Betacoronavirus/patogenicidad , Técnicas Biosensibles/instrumentación , Técnicas Biosensibles/métodos , Técnicas Biosensibles/tendencias , Técnicas de Laboratorio Clínico/instrumentación , Técnicas de Laboratorio Clínico/métodos , Técnicas de Laboratorio Clínico/estadística & datos numéricos , Colorimetría , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , ADN Viral/análisis , ADN Viral/genética , Técnicas Electroquímicas , Diseño de Equipo , Grafito/química , Humanos , Luminiscencia , Nanoestructuras/química , Hibridación de Ácido Nucleico , Pandemias , Neumonía Viral/epidemiología , Neumonía Viral/virología , Puntos Cuánticos/química , Espectrometría Raman , Resonancia por Plasmón de Superficie , Virología/métodos , Virus/genética , Virus/patogenicidad
20.
Arch Virol ; 165(11): 2737-2748, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-32816125

RESUMEN

This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.


Asunto(s)
Clasificación/métodos , Virus/clasificación , Terminología como Asunto , Virología/organización & administración , Virus/aislamiento & purificación
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