RESUMO
Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.
Assuntos
Vírus da Febre Aftosa/genética , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Quase-Espécies , Animais , Vírus da Febre Aftosa/classificação , Genes ViraisRESUMO
CRISPR-mediated transcriptional activation, also known as CRISPR-on, has proven efficient for activation of individual or multiple endogenous gene expression in cultured cells from several species. However, the potential of CRISPR-on technology in preimplantation mammalian embryos remains to be explored. Here, we report for the first time the successful modulation of endogenous gene expression in bovine embryos by using the CRISPR-on system. As a proof of principle, we targeted the promoter region of either SMARCA4 or TFAP2C genes, transcription factors implicated in trophoblast lineage commitment during embryo development. We demonstrate that CRISPR-on provides temporal control of endogenous gene expression in bovine embryos, by simple cytoplasmic injection of CRISPR RNA components into one cell embryos. dCas9VP160 activator was efficiently delivered and accurately translated into protein, being detected in the nucleus of all microinjected blastomeres. Our approach resulted in the activation of SMARCA expression shortly after microinjection, with a consequent effect on downstream differentiation promoting factors, such as TFAP2C and CDX2. Although targeting of TFAP2C gene did not result in a significant increase in TFAP2C expression, there was a profound induction in CDX2 expression on day 2 of development. Finally, we demonstrate that CRISPR-on system is suitable for gene expression modulation during the preimplantation period, since no detrimental effect was observed on microinjected embryo development. This study constitutes a first step toward the application of the CRISPR-on system for the study of early embryo cell fate decisions in cattle and other mammalian embryos, as well as to design novel strategies that may lead to an improved trophectoderm development.
Assuntos
DNA Helicases/metabolismo , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/genética , Proteínas Nucleares/metabolismo , Fator de Transcrição AP-2/metabolismo , Fatores de Transcrição/metabolismo , Animais , Bovinos , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , DNA Helicases/genética , Fertilização in vitro/veterinária , Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Técnicas de Maturação in Vitro de Oócitos/veterinária , Proteínas Nucleares/genética , Regiões Promotoras Genéticas , Fator de Transcrição AP-2/genética , Fatores de Transcrição/genéticaRESUMO
Bacteremia due to Staphylococcus aureus is defined as the isolation of this microorganism in at least one blood culture. A metastatic infection is caused by the hematogenous dissemination and subsequent location of the microorganism in a site other than the one where the infection started. The prevalence of these secondary sources of infection is low in the pediatric population, which is a diagnostic challenge. Here we describe the case of a pediatric patient with facial cellulitis due to Staphylococcus aureus, with metastatic infection and torpid course.
La bacteriemia por Staphylococcus aureus se define como el aislamiento de dicho germen en al menos un cultivo de sangre. Las metástasis infecciosas se originan por diseminación hematógena y su poste- rior localización en un sitio distinto al órgano en donde se originó el proceso infeccioso. La prevalencia en la presentación de estos focos infecciosos secundarios es baja en la edad pediátrica, por lo que re- presenta un desafío diagnóstico. Se presenta el caso de un paciente pediátrico con una celulitis facial por Staphylococcus aureus, con metástasis infecciosas y evolución tórpida.
Assuntos
Bacteriemia , Infecções Estafilocócicas , Humanos , Criança , Celulite (Flegmão)/diagnóstico , Celulite (Flegmão)/etiologia , Staphylococcus aureus , Infecções Estafilocócicas/epidemiologia , Bacteriemia/epidemiologiaRESUMO
INTRODUCTION: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. MATERIAL AND METHODS: We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. RESULTS: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. DISCUSSION: Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.
Assuntos
COVID-19 , Coinfecção , Humanos , SARS-CoV-2/genética , Filogenia , Genoma Viral , Biologia Computacional , Sequência ConsensoRESUMO
The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/epidemiologia , Argentina/epidemiologia , Pandemias , FilogeniaRESUMO
The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.
Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Argentina/epidemiologia , SARS-CoV-2/genética , Filogenia , COVID-19/epidemiologia , MutaçãoRESUMO
The epidemiological surveillance of SARS-CoV-2 by means of whole-genome sequencing has revealed the emergence and co-existence of multiple viral lineages or subtypes throughout the world. Moreover, it has been shown that several subtypes of this virus display particular phenotypes, such as increased transmissibility or reduced susceptibility to neutralizing antibodies, leading to the denomination of Variants of Interest (VOI) or Variants of Concern (VOC). Thus, subtyping of SARS-CoV-2 is a crucial step for the surveillance of this pathogen. Here, we present Covidex, an open-source, alignment-free machine learning subtyping tool. It is a shiny web app that allows an ultra-fast and accurate classification of SARS-CoV-2 genome sequences into the three most used nomenclature systems (GISAID, Nextstrain, Pango lineages). It also categorizes input sequences as VOI or VOC, according to current definitions. The program is cross-platform compatible and it is available via Source-Forge https://sourceforge.net/projects/covidex or via the web application http://covidex.unlu.edu.ar.
Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Humanos , Mutação , Filogenia , SARS-CoV-2/genética , Sequenciamento Completo do GenomaRESUMO
Plant interactions with endophytic bacteria produce mutual benefits and contribute to environmental sustainability. Handroanthus impetiginosus (Mart. ex DC.) Mattos 'pink lapacho' (syn. Tabebuia impetiginosa, Bignoniaceae) is a medicinal, ornamental and forestal native tree from South and Mesoamerica. Plant growth promoting bacteria (PGPB) isolated from pink lapacho are scarcely described. The aim of this work was to isolate and characterize native endophytic bacteria from pink lapacho. Ten bacterial strains were isolated from leaves and six from roots of naturally growing trees in Luján (Central-Eastern region of Argentina). Endophytes were identified as Bacillus, Paenibacillus, Pseudomonas, Rhizobium, Rummeliibacillus and Methylobacterium genera, according to 16S rRNA gene sequencing and phylogenetic analysis. In the present study, a strain of the Rummelibacillus genus (L14) has been first ever reported as endophyte. This strain was capable of growing in Nfb medium and exhibited zinc solubilization ability. A high percentage of strains showed PGPB traits; namely 88% fixed nitrogen, 63% solubilized zinc, 69% solubilized phosphate and 63% produced indole compounds such as IAA. Most strains were salt tolerant that confer them a potential competitive advantage to survive in saline conditions. To the best of our knowledge, this is the first study reporting an approach to assess the diversity of cultivable endophytic bacteria of H. impetiginosus tree and its plant growth promoting capacity. The knowledge about this kind of associations could contribute to environmental sustainability by developing effective biofertilizers that minimize the use of chemical fertilizers and pesticides.
Assuntos
Tabebuia , Bactérias , Endófitos/genética , Filogenia , Raízes de Plantas/microbiologia , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/efeitos da radiação , Tabebuia/efeitos dos fármacos , Tabebuia/fisiologiaRESUMO
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
Assuntos
Biologia Computacional , Pesquisadores , Vírus , Europa (Continente) , Feminino , Humanos , Pesquisadores/estatística & dados numéricos , Vírus/genéticaRESUMO
RNA interference (RNAi) is a well-conserved mechanism in eukaryotic cells that directs post-transcriptional gene silencing through small RNA molecules. RNAi has been proposed as an alternative approach for rapid and specific control of viruses including foot-and-mouth disease virus (FMDV), the causative agent of a devastating animal disease with high economic impact. The aim of this work was to assess the antiviral activity of different small RNA shuttles targeting the FMDV RNA-dependent RNA polymerase coding sequence (3D). Three target sequences were predicted within 3D considering RNA accessibility as a major criterion. The silencing efficacy of short-hairpin RNAs (shRNAs) and artificial microRNAs (amiRNAs) targeting the selected sequences was confirmed in fluorescent reporter assays. Furthermore, BHK-21 cells transiently expressing shRNAs or amiRNAs proved 70 to >95% inhibition of FMDV growth. Interestingly, dual expression of amiRNAs did not improve FMDV silencing. Lastly, stable cell lines constitutively expressing amiRNAs were established and characterized in terms of antiviral activity against FMDV. As expected, viral replication in these cell lines was delayed. These results show that the target RNA-accessibility-guided approach for RNAi design rendered efficient amiRNAs that constrain FMDV replication. The application of amiRNAs to complement FMDV vaccination in specific epidemiological scenarios shall be explored further.
RESUMO
SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.
RESUMO
Apoptosis involvement in liver damage related to hepatitis C virus (HCV) chronic infection has been suggested. Although liver biopsy represents the gold standard for evaluating disease severity, non-invasive tests are a growing medical need. The aim of this study was to detect apoptosis markers in liver and serum from pediatric HCV-infected patients and to assess its utility to predict liver damage progression. Twenty-three patients were included. Liver biopsies were used for histological analysis as well as for immunodetection of a viral protein (NS3) and apoptosis markers (activated caspase-3 [casp-3a], caspase-generated CK-18 fragment [M30] and TUNEL). M30 was quantified in paired serum and biopsy samples. NS3 correlated both with casp-3a (r = 0.83, P < 0.0001) and TUNEL (r = 0.61, P < 0.0017). Casp-3a and TUNEL also displayed a correlation (r = 0.56, P = 0.005). Both NS3 and casp-3a were associated with fibrosis stage (P = 0.03). Serum M30 [median: 122.15 UL-1 (86.68-794.58)] was higher in patients than in controls [median: 81.44 UL-1 (41.17-129.30)], (P < 0.0001). M30 showed a correlation with steatosis, and indeed it was linked to severe grade (P = 0.004). In children, HCV would be involved in liver damage through apoptosis induction. The apoptosis markers detected reflect liver injury. Serum M30 might be useful as a marker to detect the extent of liver steatosis.
Assuntos
Apoptose , Necrose Gordurosa/diagnóstico , Hepatite C Crônica/complicações , Hepatite C Crônica/patologia , Fígado/patologia , Fígado/virologia , Adolescente , Biomarcadores , Biópsia , Caspase 3/análise , Criança , Pré-Escolar , Necrose Gordurosa/patologia , Feminino , Hepatite C Crônica/diagnóstico , Histocitoquímica , Humanos , Imuno-Histoquímica , Marcação In Situ das Extremidades Cortadas , Lactente , Queratina-18/análise , Masculino , Proteínas não Estruturais Virais/análiseRESUMO
Foot-and-mouth disease is a viral illness that affects cloven-hoofed animals causing serious economic losses. Inactivated vaccines against its causative agent, foot-and-mouth disease virus (FMDV), require approximately seven days to induce protection. Therefore, antiviral strategies are needed to provide earlier protection and to stop the spread of this highly contagious virus during outbreak situations. In this way, our group has previously demonstrated that the baculovirus (BV) Autographa californica multiple nucleopolyhedrovirus (AcMNPV), an insect virus with immunostimulant effects, induces a nonspecific antiviral status that protects C57BL/6 mice against a lethal challenge with FMDV A/Arg/01 at 3 hours or 3 days post inoculation. In this work, we studied the immunological mechanisms involved in this protection. Firstly, we compared the protection elicited by AcMNPV in wild type mice and in knock-out mice lacking the subunit IFNAR1 of the receptor for type I interferons (IFNs). Our results showed that type I IFNs are key to prevent the death of the animals after the FMDV challenge. On the other hand, we evaluated the role of NK and NKT cells by depleting these cell subsets with anti-NK1.1 monoclonal antibody. These cells proved to be necessary for the induction of IFN-γ by AcMNPV and to prevent the onset of a severe disease after the FMDV challenge. We propose BV as a novel tool for the development of antiviral strategies because of the high levels of IFNs induced and the NK/NKT cells-mediated immune response elicited.
Assuntos
Febre Aftosa/imunologia , Febre Aftosa/prevenção & controle , Interferon Tipo I/imunologia , Células T Matadoras Naturais/imunologia , Nucleopoliedrovírus/imunologia , Vacinas Virais , Animais , Feminino , Vírus da Febre Aftosa/imunologia , Técnicas de Inativação de Genes , Camundongos , Camundongos Endogâmicos C57BL , Células RAW 264.7 , Receptor de Interferon alfa e beta/genética , Células Sf9 , Spodoptera , Vacinação , Vacinas Virais/imunologiaRESUMO
Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user's needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.
RESUMO
La bacteriemia por Staphylococcus aureus se define como el aislamiento de dicho germen en al menos un cultivo de sangre. Las metástasis infecciosas se originan por diseminación hematógena y su posterior localización en un sitio distinto al órgano en donde se originó el proceso infeccioso. La prevalencia en la presentación de estos focos infecciosos secundarios es baja en la edad pediátrica, por lo que representa un desafío diagnóstico. Se presenta el caso de un paciente pediátrico con una celulitis facial por Staphylococcus aureus, con metástasis infecciosas y evolución tórpida.
Bacteremia due to Staphylococcus aureus is defined as the isolation of this microorganism in at least one blood culture. A metastatic infection is caused by the hematogenous dissemination and subsequent location of the microorganism in a site other than the one where the infection started. The prevalence of these secondary sources of infection is low in the pediatric population, which is a diagnostic challenge. Here we describe the case of a pediatric patient with facial cellulitis due to Staphylococcus aureus, with metastatic infection and torpid course.
Assuntos
Humanos , Masculino , Criança , Infecções Estafilocócicas/epidemiologia , Bacteriemia/epidemiologia , Staphylococcus aureus , Celulite (Flegmão)/diagnóstico , Celulite (Flegmão)/etiologiaRESUMO
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3'untranslated regions (3'UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs. However, current knowledge about their targets is limited. Since target prediction algorithms rely on complementarity between 3'UTRs and miRNA sequences, a major limitation is the lack of accurate sequence information of 3'UTR for most species including parasitic helminths. We performed RNA-seq and developed a pipeline that integrates the transcriptomic data with available genomic data of this parasite in order to identify 3'UTRs of Echinococcus canadensis. The high confidence set of 3'UTRs obtained allowed the prediction of miRNA targets in Echinococcus through a bioinformatic approach. We performed for the first time a comparative analysis of miRNA targets in Echinococcus and Taenia. We found that many evolutionarily conserved target sites in Echinococcus and Taenia may be functional and under selective pressure. Signaling pathways such as MAPK and Wnt were among the most represented pathways indicating miRNA roles in parasite growth and development. Genome-wide identification and characterization of miRNA target genes in Echinococcus provide valuable information to guide experimental studies in order to understand miRNA functions in the parasites biology. miRNAs involved in essential functions, especially those being absent in the host or showing sequence divergence with respect to host orthologs, might be considered as novel therapeutic targets for echinococcosis control.
Assuntos
Echinococcus/crescimento & desenvolvimento , Echinococcus/genética , Regulação da Expressão Gênica , MicroRNAs/genética , MicroRNAs/metabolismo , Regiões 3' não Traduzidas , Animais , Perfilação da Expressão Gênica , Genes de Helmintos , Genômica , Análise de Sequência de RNA , Taenia/genética , Taenia/crescimento & desenvolvimentoRESUMO
Adult C57BL/6J mice have been used to study Foot-and-mouth disease virus (FMDV) biology. In this work, two variants of an FMDV A/Arg/01 strain exhibiting differential pathogenicity in adult mice were identified and characterized: a non-lethal virus (A01NL) caused mild signs of disease, whereas a lethal virus (A01L) caused death within 24-48h independently of the dose used. Both viruses caused a systemic infection with pathological changes in the exocrine pancreas. Virus A01L reached higher viral loads in plasma and organs of inoculated mice as well as increased replication in an ovine kidney cell line. Complete consensus sequences revealed 6 non-synonymous changes between A01L and A10NL genomes that might be linked to replication differences, as suggested by in silico prediction studies. Our results highlight the biological significance of discrete genomic variations and reinforce the usefulness of this animal model to study viral determinants of lethality.
Assuntos
Vírus da Febre Aftosa/patogenicidade , Febre Aftosa/patologia , Febre Aftosa/virologia , Interações Hospedeiro-Patógeno , Replicação Viral , Estruturas Animais/virologia , Animais , Linhagem Celular , Modelos Animais de Doenças , Vírus da Febre Aftosa/fisiologia , Camundongos , Camundongos Endogâmicos C57BL , Mutação de Sentido Incorreto , Pâncreas/patologia , Plasma/virologia , Análise de Sequência de DNA , Análise de Sobrevida , Carga ViralRESUMO
RNA interference (RNAi) appears as a promising strategy to control virus replication. While the antiviral power of short-hairpin RNAs or small-interfering RNAs against FMDV has been demonstrated widely, safer RNAi effectors such as artificial microRNAs (amiRs) have not been evaluated extensively. In this work, transgenic monoclonal cell lines constitutively expressing different amiRs targeting FMDV 3D-coding region or 3'UTR were established. Certain cell lines showed an effective, sequence-specific amiR-mediated silencing activity that was accomplished by degradation of the target mRNA, as demonstrated in co-transfection experiments of reporter genes fused to FMDV target sequences. However, FMDV replication in these amiR-expressing cells was affected barely. Experiments aimed at elucidating the cause of RNAi failure demonstrated limited accessibility of the targeted region in the molecular environment of the viral RNA. Since RNAi is mediated by large-dimension silencing complexes containing the siRNA and not simply by a linear oligonucleotide, we propose that target selection should consider not only the local RNA structure but also the global conformation of target RNA.
Assuntos
Antivirais/metabolismo , Vírus da Febre Aftosa/genética , Inativação Gênica , MicroRNAs/metabolismo , Regiões 3' não Traduzidas , Animais , Antígenos Virais/genética , Linhagem Celular , Cricetinae , Vírus da Febre Aftosa/crescimento & desenvolvimento , MicroRNAs/genética , Conformação de Ácido Nucleico , RNA Viral/genética , Proteínas não Estruturais Virais/genéticaRESUMO
A reverse genetics approach was used to identify viral genetic determinants of the differential virulence displayed by two field foot-and-mouth disease virus (FMDV) strains (A/Arg/00 and A/Arg/01) isolated in Argentina during the 2000-2001 epidemics. A molecular clone of A/Arg/01 strain and viral chimeras containing the S-fragment or the internal ribosome entry site (IRES) of A/Arg/00 in the A/Arg/01 backbone were constructed and characterized. The IRES appeared as a determining factor of the lower level of A/Arg/00 replication in cell culture. High-throughput RNA probing revealed structural differences between both IRESs. Translation experiments using either synthetic viral RNAs (in vitro) or bicistronic plasmids (in vivo) showed that these IRESs' activities differ when the viral 3' untranslated region (UTR) is present, suggesting that their function is differentially modulated by this region. This work provides experimental evidence supporting the role of the IRES-3'UTR modulation in determining the level of FMDV replication in field strains.
Assuntos
Regiões 3' não Traduzidas , Doenças dos Bovinos/virologia , Vírus da Febre Aftosa/genética , Vírus da Febre Aftosa/patogenicidade , Febre Aftosa/virologia , RNA Viral/metabolismo , Animais , Argentina/epidemiologia , Sequência de Bases , Bovinos , Doenças dos Bovinos/epidemiologia , Febre Aftosa/epidemiologia , Vírus da Febre Aftosa/classificação , Vírus da Febre Aftosa/fisiologia , Regulação Viral da Expressão Gênica , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Biossíntese de Proteínas , RNA Viral/química , RNA Viral/genética , Ribossomos/genética , Ribossomos/metabolismo , Virulência , Replicação ViralRESUMO
Classic phylogenetic and modern population-based clustering methods were used to analyze hepatitis C virus (HCV) evolution in plasma and to assess viral compartmentalization within peripheral blood mononuclear cells (PBMCs) in 6 children during 3.2-9.6yr of follow-up. Population structure analysis of cloned amplicons encompassing hypervariable region 1 led to the distinction of two evolutionary patterns, one highly divergent and another one genetically homogeneous. Viral adaptability was reflected by co-evolution of viral communities switching rapidly from one to another in the context of divergence and stability associated with highly homogeneous communities which were replaced by new ones after long periods. Additionally, viral compartmentalization of HCV in PBMCs was statistically demonstrated, suggesting their role as a pool of genetic variability. Our results support the idea of a community-based structure of HCV viral populations during chronic infection and highlight a role of the PBMC compartment in the persistence of such structure.