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1.
ACS Sens ; 6(3): 613-627, 2021 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-33660987

RESUMEN

Viruses have caused significant damage to the world. Effective detection is required to relieve the impact of viral infections. A biomolecule can be used as a template such as deoxyribonucleic acid (DNA), peptide, or protein, for the growth of silver nanoclusters (AgNCs) and for recognizing a virus. Both the AgNCs and the recognition elements are tunable, which is promising for the analysis of new viruses. Considering that a new virus such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently requires a facile sensing strategy, various virus detection strategies based on AgNCs including fluorescence enhancement, color change, quenching, and recovery are summarized. Particular emphasis is placed on the molecular analysis of viruses using DNA stabilized AgNCs (DNA-AgNCs), which detect the virus's genetic material. The more widespread applications of AgNCs for general virus detection are also discussed. Further development of these technologies may address the challenge for facile detection of SARS-CoV-2.


Asunto(s)
Técnicas Biosensibles , ADN Viral/química , Nanopartículas del Metal/química , Plata/química , Virus/genética , Fluorescencia , Humanos
2.
J Vis Exp ; (168)2021 02 18.
Artículo en Inglés | MEDLINE | ID: mdl-33682858

RESUMEN

Parkinson's disease (PD) is a progressive disorder traditionally defined by resting tremor and akinesia, primarily due to loss of dopaminergic neurons in the substantia nigra. Affected brain areas display intraneuronal fibrillar inclusions consisting mainly of alpha-synuclein (asyn) proteins. No animal model thus far has recapitulated all characteristics of this disease. Here, we describe the use of stereotaxic injection to deliver chemicals, proteins, or viral vectors intracranially in order to mimic various aspects of PD. These methods are well-established and widely used throughout the PD field. Stereotaxic injections are incredibly flexible; they can be adjusted in concentration, age of animal used for injection, brain area targeted and in animal species used. Combinations of substances allow for rapid variations to assess treatments or alter severity of the pathology or behavioral deficits. By injecting toxins into the brain, we can mimic inflammation and/or a severe loss of dopaminergic neurons resulting in substantial motor phenotypes. Viral vectors can be used to transduce cells to mimic genetic or mechanistic aspects. Preformed fibrillar asyn injections best recapitulate the progressive phenotype over an extended period of time. Once these methods are established, it can be economical to generate a new model compared to creating a new transgenic line. However, this method is labor intensive as it requires 30 minutes to four hours per animal depending on the model used. Each animal will have a slightly different targeting and therefore create a diverse cohort which on one hand can be challenging to interpret results from; on the other hand, help mimic a more realistic diversity found in patients. Mistargeted animals can be identified using behavioral or imaging readouts, or only after being sacrificed leading to smallercohort size after the study has already been concluded. Overall, this method is a rudimentary but effective way to assess a diverse set of PD aspects.


Asunto(s)
Sistemas de Liberación de Medicamentos , Vectores Genéticos/administración & dosificación , Enfermedad de Parkinson/tratamiento farmacológico , Técnicas Estereotáxicas , Virus/genética , Anestesia , Animales , Encéfalo/patología , Modelos Animales de Enfermedad , Humanos , Masculino , Cuidados Posoperatorios
3.
Cell Rep ; 34(11): 108872, 2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33730572

RESUMEN

Viruses need to hijack the translational machinery of the host cell for a productive infection to happen. However, given the dynamic landscape of tRNA pools among tissues, it is unclear whether different viruses infecting different tissues have adapted their codon usage toward their tropism. Here, we collect the coding sequences of 502 human-infecting viruses and determine that tropism explains changes in codon usage. Using the tRNA abundances across 23 human tissues from The Cancer Genome Atlas (TCGA), we build an in silico model of translational efficiency that validates the correspondence of the viral codon usage with the translational machinery of their tropism. For instance, we detect that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is specifically adapted to the upper respiratory tract and alveoli. Furthermore, this correspondence is specifically defined in early viral proteins. The observed tissue-specific translational efficiency could be useful for the development of antiviral therapies and vaccines.


Asunto(s)
Biosíntesis de Proteínas/genética , Virosis/genética , Virus/genética , Línea Celular , Línea Celular Tumoral , Uso de Codones/genética , Genes Relacionados con las Neoplasias/genética , Células HCT116 , Células HEK293 , Células HeLa , Células Hep G2 , Humanos , Alveolos Pulmonares/virología , ARN de Transferencia/genética , Infecciones del Sistema Respiratorio/virología , Tropismo/genética , Proteínas Virales/genética , Virosis/virología
4.
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
5.
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
6.
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
7.
Nat Commun ; 12(1): 1226, 2021 02 22.
Artículo en Inglés | MEDLINE | ID: mdl-33619257

RESUMEN

The goal of the National Cancer Institute's (NCI's) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive ( https://gdc.cancer.gov/ ).


Asunto(s)
Análisis de Datos , Bases de Datos Genéticas , Genómica , Secuencia de Bases , Variaciones en el Número de Copia de ADN/genética , Metilación de ADN/genética , Regulación de la Expresión Génica , Genoma Humano , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Anotación de Secuencia Molecular , Mutación/genética , National Cancer Institute (U.S.) , RNA-Seq , Reproducibilidad de los Resultados , Estados Unidos , Virus/genética
8.
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
9.
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
10.
Cell Host Microbe ; 29(2): 152-154, 2021 02 10.
Artículo en Inglés | MEDLINE | ID: mdl-33571441

RESUMEN

Nucleocytoplasmic large DNA viruses (NCLDVs) are widespread in the biosphere. This issue of Cell Host & Microbe, Nelson et al., and a recent Nature paper, Moniruzzaman et al., show NCLDVs can integrate into host genomes, highlighting a mechanism of large-scale virus-mediated horizontal gene transfer (vHGT) driving eukaryotic evolution.


Asunto(s)
Virus Gigantes , Microalgas , Virus , Virus ADN/genética , Eucariontes/genética , Transferencia de Gen Horizontal , Virus Gigantes/genética , Virus/genética
11.
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
12.
Methods Mol Biol ; 2243: 107-122, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33606255

RESUMEN

Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.


Asunto(s)
Metagenoma/genética , Microbiota/genética , Archaea/genética , Bacterias/genética , Humanos , Metagenómica/métodos , Análisis de Secuencia de ADN/métodos , Virus/genética
13.
mBio ; 12(1)2021 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-33402534

RESUMEN

The development of safe and effective vaccines against viruses is central to disease control. With advancements in DNA synthesis technology, the production of synthetic viral genomes has fueled many research efforts that aim to generate attenuated viruses by introducing synonymous mutations. Elucidation of the mechanisms underlying virus attenuation through synonymous mutagenesis is revealing interesting new biology that can be exploited for vaccine development. Here, we review recent advancements in this field of synthetic virology and focus on the molecular mechanisms of attenuation by genetic recoding of viruses. We highlight the action of the zinc finger antiviral protein (ZAP) and RNase L, two proteins involved in the inhibition of viruses enriched for CpG and UpA dinucleotides, that are often the products of virus recoding algorithms. Additionally, we discuss current challenges in the field as well as studies that may illuminate how other host functions, such as translation, are potentially involved in the attenuation of recoded viruses.


Asunto(s)
Genoma Viral , Vacunas Atenuadas/genética , Vacunas Virales/genética , Virus/genética , Animales , Virus ADN , Fosfatos de Dinucleósidos , Endorribonucleasas/genética , Humanos , Mutación Silenciosa , Replicación Viral
14.
Sci Total Environ ; 767: 144589, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33422963

RESUMEN

The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.


Asunto(s)
Virus , Aguas Residuales , Biblioteca de Genes , Humanos , Metagenómica , Virus/genética
15.
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
16.
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
17.
Nat Rev Microbiol ; 19(1): 3, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33203987
18.
Methods Mol Biol ; 2225: 93-105, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33108659

RESUMEN

In vivo wound healing models are predictive preclinical tests for therapeutics that enhance skin repair or limit scarring. Large animals, such as swine, heal in a manner similar to humans, but testing is impractical and expensive. Experiments in mice are more economic, but may be less translatable as this species heals primarily through contraction, not by the processes of epithelialization and granulation tissue formation as seen in human wounds. Here, we describe a murine model of thermal burn injury that closely mimics human healing, resulting in a large, hypertrophic-like scar. This practical, reproducible model is ideal for testing promising wound-healing therapies, such as virus-derived growth factors and immune-modulatory proteins.


Asunto(s)
Quemaduras/patología , Cicatriz/prevención & control , Modelos Animales de Enfermedad , Repitelización/genética , Animales , Quemaduras/genética , Quemaduras/terapia , Cicatriz/genética , Cicatriz/patología , Femenino , Expresión Génica , Calor , Humanos , Factores Inmunológicos/biosíntesis , Factores Inmunológicos/genética , Factores Inmunológicos/farmacología , Péptidos y Proteínas de Señalización Intercelular/biosíntesis , Péptidos y Proteínas de Señalización Intercelular/genética , Péptidos y Proteínas de Señalización Intercelular/farmacología , Ratones , Ratones Endogámicos C57BL , Repitelización/efectos de los fármacos , Piel/efectos de los fármacos , Piel/lesiones , Transgenes , Virus/genética
19.
PLoS Biol ; 18(12): e3001045, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33370271

RESUMEN

Host-pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these "molecular scars" as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.


Asunto(s)
Interacciones Huésped-Patógeno/genética , Mitocondrias/genética , Estrés Fisiológico/genética , Animales , Proteínas del Complejo de Cadena de Transporte de Electrón/genética , Proteínas del Complejo de Cadena de Transporte de Electrón/metabolismo , Complejo IV de Transporte de Electrones/genética , Complejo IV de Transporte de Electrones/metabolismo , Evolución Molecular , Redes Reguladoras de Genes/genética , Interacciones Huésped-Patógeno/fisiología , Humanos , MicroARNs/genética , Mitocondrias/metabolismo , Filogenia , Estrés Fisiológico/fisiología , Virus/genética
20.
Viruses ; 12(12)2020 12 10.
Artículo en Inglés | MEDLINE | ID: mdl-33322070

RESUMEN

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.


Asunto(s)
Biología Computacional , Bases de Datos Genéticas , Metagenómica/métodos , Virus/genética , Biología Computacional/métodos , Variación Genética , Genoma Viral , Interacciones Huésped-Patógeno , Humanos , Interfaz Usuario-Computador , Proteínas Virales/genética , Proteínas Virales/metabolismo , Virus/metabolismo , Navegador Web
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