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1.
Arch Virol ; 164(11): 2829-2836, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31486908

RESUMO

The complete sequence of the medium (M) and small (S) RNA genome segments were determined for twelve isolates of impatiens necrotic spot virus from eight plant species. The M- and S-RNAs of these isolates shared 97-99% and 93-98% nucleotide sequence identity, respectively, with the corresponding full-length sequences available in public databases. Phylogenetic analysis based on the M- or S-RNA sequences showed incongruence in the phylogenetic position of some isolates, suggesting intraspecies segment reassortment. The lack of phylogenetic discordance in individual and concatenated sequences of individual genes encoded by M- or S-RNAs suggests that segment reassortment rather than recombination is driving evolution of these INSV isolates.


Assuntos
RNA Viral/genética , Vírus Reordenados/genética , Tospovirus/genética , Sequência de Bases , Genoma Viral/genética , Plantas/virologia , Análise de Sequência de RNA , Tospovirus/isolamento & purificação
2.
Arch Virol ; 164(11): 2849-2852, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31502078

RESUMO

Arracacha virus B type (AVB-T) and oca (AVB-O) strains from arracacha (Arracacia xanthorrhiza) and oca (Oxalis tuberosa) samples collected in 1975 and two additional isolates obtained from arracacha (AVB-PX) and potato (AVB-6A) in Peru in 1976 and 1978, respectively, were studied. In its host responses and serological properties, AVB-PX most resembled AVB-T, whereas AVB-6A most resembled AVB-O. Complete genomic sequences of the RNA-1 and RNA-2 of each isolate were obtained following high-throughput sequencing of RNA extracts from isolates preserved for 38 (AVB-PX) or 32 (the other 3 isolates) years, and compared with a genomic sequence of AVB-O obtained previously (PV-0082). RNA-2 was unexpectedly divergent compared to RNA-1, with the nucleotide (nt) sequence identity of different AVB isolates varying by up to 76% (RNA-2) and 89% (RNA-1). The coat protein amino acid sequences were the most divergent, with AVB-O and AVB-6A having only 68% identity to AVB-T and AVB-PX. Since the RNA2 sequence differences between the two isolate groupings also coincided with host range, symptom, and serological differences, AVB demonstrates considerable intraspecific divergence.


Assuntos
Genoma Viral/genética , RNA Viral/genética , Secoviridae/genética , Sequência de Aminoácidos , Sequência de Bases , Proteínas do Capsídeo/genética , Sequenciamento de Nucleotídeos em Larga Escala , Magnoliopsida/virologia , Oxalidaceae/virologia , Peru , Doenças das Plantas/virologia , Secoviridae/isolamento & purificação , Solanum tuberosum/virologia
3.
Arch Virol ; 164(11): 2747-2759, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31502079

RESUMO

RNA silencing is a major antiviral mechanism in plants, which is counteracted by virus-encoded proteins with silencing suppression activity. ORFs encoding putative silencing suppressor proteins that share no structural or sequence homology have been identified in the genomes of four criniviruses. In this study, we investigated the RNA silencing suppression activity of several proteins encoded by the RNA1 (RdRp, p22) and RNA2 (CP, CPm and p26) of cucurbit chlorotic yellows virus (CCYV) using co-agroinfiltration assays on Nicotiana benthamiana plants. Our results indicate that p22 is a suppressor of local RNA silencing that does not interfere with cell-to-cell movement of the RNA silencing signal or with systemic silencing. Furthermore, comparisons of the suppression activity of CCYV p22 with that of two other well-known crinivirus suppressors (CYSDV p25 and ToCV p22) revealed that CCYV p22 is a weaker suppressor of local RNA silencing than the other two proteins. Finally, a comparative sequence analysis of the p22 genes of seven Greek CCYV isolates was performed, revealing a high level of conservation. Taken together, our research advances our knowledge about plant-virus interactions of criniviruses, an emergent group of pathogens that threatens global agriculture.


Assuntos
Crinivirus/genética , Interferência de RNA/fisiologia , RNA Viral/genética , Tabaco/virologia , Proteínas do Core Viral/genética , Genoma Viral/genética , Interações Hospedeiro-Patógeno/genética , Doenças das Plantas/virologia
4.
Arch Virol ; 164(11): 2891-2894, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31506787

RESUMO

Contigs with sequence similarity to potato virus P (PVP), which belongs to the genus Carlavirus, were identified by high-throughput sequencing analysis in potato tubers collected from a farmer's potato production field in Surazhevka, Artyom, Primorskiy Krai (Russia) in 2018. The complete genome sequence of this virus consisted of 8,394 nucleotides, excluding the poly(A) tail. This is the first report of PVP being detected outside South America. The isolate had high sequence similarity to PVP isolates from Argentina and Brazil, but low sequence similarity was observed in the genes encoding the RNA-dependent RNA polymerase (69% nucleotide sequence identity and 80% amino acid sequence identity) and coat protein (78% nucleotide sequence identity and 89% amino acid sequence identity). Phylogenetic analysis revealed that this PVP-like virus clustered with known PVP isolates but was distinct from them. Comparison of the sequences using the classification criteria of the ICTV indicated that this PVP-like virus is a strain of PVP.


Assuntos
Carlavirus/genética , Genoma Viral/genética , Doenças das Plantas/virologia , Solanum tuberosum/virologia , Sequência de Aminoácidos , Proteínas do Capsídeo/genética , Carlavirus/classificação , Carlavirus/isolamento & purificação , RNA Polimerases Dirigidas por DNA/genética , Sequenciamento de Nucleotídeos em Larga Escala , RNA Viral/genética , Federação Russa , Sequenciamento Completo do Genoma
5.
J Agric Food Chem ; 67(33): 9241-9253, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31369258

RESUMO

Antiviral compounds targeting viral replicative processes have been studied as an alternative for the control of begomoviruses. Previously, we have reported that the peptide AmPep1 has strong affinity binding to the replication origin sequence of tomato yellow leaf curl virus (TYLCV). In this study, we describe the mechanism of action of this peptide as a novel alternative for control of plant-infecting DNA viruses. When AmPep1 was applied exogenously to tomato and Nicotiana benthamiana plants infected with TYLCV, a decrease in the synthesis of the two viral DNA strands (CS and VS) was observed, with a consequent delay in the development of disease progress in treated plants. The chemical mechanism of action of AmPep1 was deduced using Raman spectroscopy and molecular modeling showing the formation of chemical interactions such as H bonds and electrostatic interactions and the formation of π-π interactions between both biomolecules contributing to tampering with the viral replication.


Assuntos
Amaranthus/química , Antivirais/química , Antivirais/farmacologia , Begomovirus/efeitos dos fármacos , Peptídeos/química , Peptídeos/farmacologia , RNA Viral/química , Replicação Viral/efeitos dos fármacos , Begomovirus/química , Begomovirus/genética , Begomovirus/fisiologia , Sequências Repetidas Invertidas/efeitos dos fármacos , Lycopersicon esculentum/virologia , Doenças das Plantas/virologia , Proteínas de Plantas/química , RNA Viral/genética , Tabaco/virologia
6.
Mem Inst Oswaldo Cruz ; 114: e190074, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31460570

RESUMO

BACKGROUND: Hepatitis delta virus (HDV) infections in hepatitis B virus (HBV) carriers are the most severe form of viral hepatitis. HDV prevalence is high in the Brazilian Amazon, but studies in other regions of the country are still scarce and often underestimated its prevalence by including a small numbers of individuals. OBJECTIVE: This study aimed to determine the serological prevalence of hepatitis D, the genotypes circulating and to evaluate the associated risk factors for acquisition of HDV in Minas Gerais state, Brazil. METHODS: We screened plasma samples (n = 498) from HBV chronic carriers for anti-HD antibodies using a commercial enzyme-linked immunosorbent assay (ELISA) kit. For those samples that were positive for anti-HD antibodies, we performed a reverse transcriptase (RT) nested-polymerase chain reaction (nested-PCR) in order to detect the viral genome and identify the viral genotypes circulating in the state. FINDINGS: The prevalence was 6.22% (31/498). Blood transfusion was the only risk factor associated with HDV infection [risk ratio: 3.73; 95% confidence interval (CI): 1.44 to 9.65]. For 26 anti-HD positive patients, HDAg gene sequences were determined and in all patients HDV genotype 1 was found. CONCLUSIONS: This study confirmed the circulation of HDV in Minas Gerais, an area previously considered non-endemic for hepatitis D in Brazil. The prevalence found in this study is much higher when compared to other studies performed in Brazil, probably because the population in our study was selected with minimal bias. Furthermore, in 26 anti-HD positive plasma samples, we were also able to detect the viral genome, indicating that these patients were experienced an active infection at the time of sample collection. These findings emphasise the importance of anti-HD testing in HBV infected individuals, which may contribute to this disease control in Brazil.


Assuntos
Anticorpos Anti-Hepatite/sangue , Hepatite B Crônica/epidemiologia , Hepatite D/epidemiologia , Vírus Delta da Hepatite , RNA Viral/genética , Adolescente , Adulto , Brasil/epidemiologia , Criança , Pré-Escolar , Estudos Transversais , Ensaio de Imunoadsorção Enzimática , Feminino , Genótipo , Hepatite B Crônica/complicações , Hepatite D/complicações , Hepatite D/diagnóstico , Vírus Delta da Hepatite/genética , Vírus Delta da Hepatite/imunologia , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular , Filogenia , Prevalência , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Risco , Adulto Jovem
7.
Dokl Biochem Biophys ; 486(1): 201-205, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31367821

RESUMO

Infection of mice with influenza A viruses led to the formation of clones of lymphocytes that specifically recognizes viral domains in the central zone of the NSP protein (amino acid positions 83-119). Computer analysis of the primary structure of the NSP protein showed the presence of T-cell epitopes in the central part of the NSP molecule. The findings indicate that the viral NSP gene is expressed in the infected animals and verify the concept of the bipolar strategy (ambisense strategy) of the influenza A virus genome.


Assuntos
Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H1N1/fisiologia , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/fisiologia , Leucócitos/imunologia , RNA Viral/genética , Proteínas Virais/genética , Sequência de Aminoácidos , Animais , Leucócitos/virologia , Camundongos , Camundongos Endogâmicos BALB C , Domínios Proteicos , Proteínas Virais/química , Proteínas Virais/metabolismo
8.
Arch Virol ; 164(11): 2853-2857, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31377887

RESUMO

A double-stranded RNA (dsRNA) segment was extracted from the ectomycorrhizal fungus Geopora sumneriana (Cooke) M. Torre, and its full-length cDNA sequence, comprising 3146 nucleotides, was determined. Sequence analysis revealed the presence of a large open reading frame (ORF) on the positive strand of this dsRNA segment when the mold mitochondrial genetic code was applied. The ORF encodes a putative RNA-dependent RNA polymerase (RdRp), which shares the highest degree of similarity with Tuber excavatum mitovirus, with 37.52% identity. This dsRNA segment represents the genome replication intermediate of a novel mitovirus that was tentatively designated as "Geopora sumneriana mitovirus 1" (GsMV1). Phylogenetic analysis further suggested that GsMV1 is a member of the family Narnaviridae. This is the first study reporting on a mitovirus genome sequence in the ectomycorrhizal fungus G. sumneriana.


Assuntos
Colletotrichum/virologia , Micovírus/classificação , Micovírus/genética , Genoma Viral/genética , Sequência de Aminoácidos , Sequência de Bases , Micovírus/isolamento & purificação , Fases de Leitura Aberta/genética , RNA Replicase/genética , RNA Viral/genética , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
9.
Arch Virol ; 164(11): 2859-2863, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31385115

RESUMO

In this study, we report the molecular characterization of a novel mycovirus in a phytopathogenic fungus of the species Colletotrichum gloeosporioides, which we named "Colletotrichum gloeosporioides RNA virus 1" (CgRV1). The virus has a dsRNA genome of 2,975 bp and possesses two non-overlapping open reading frames (ORFs 1 and 2). The smaller ORF1 encodes a protein of unknown function, and the larger ORF2 encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis based on the RdRp sequence showed that CgRV1 clustered with and is closely related to unclassified mycoviruses that are distinct from members of the family Partitiviridae.


Assuntos
Colletotrichum/virologia , Micovírus/genética , Genoma Viral/genética , Vírus não Classificados/genética , Sequência de Aminoácidos , Micovírus/isolamento & purificação , Fases de Leitura Aberta/genética , Doenças das Plantas/microbiologia , RNA Viral/genética , Vírus não Classificados/isolamento & purificação
10.
Arch Virol ; 164(11): 2789-2792, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31414286

RESUMO

Replication of the dengue virus (DENV) genome occurs in a vesicle in the endoplasmic reticulum by a complex of host and viral proteins. Two host proteins, STT3A and STT3B, as members of the oligosaccharyl transferase complex, have been implicated in playing structural roles in the vesicle in mammalian cells, and the absence of these proteins has been shown to decrease DENV replication. Aedes aegypti is the main vector of the virus and has been used previously as a model organism to study mosquito-virus interactions. In this study, we found that genes of the oligosaccharyl transferase complex have no effect on replication of DENV in mosquito cells.


Assuntos
Aedes/virologia , Vírus da Dengue/crescimento & desenvolvimento , Vírus da Dengue/genética , Hexosiltransferases/genética , Proteínas de Membrana/genética , Replicação Viral/genética , Animais , Benzamidas/farmacologia , Linhagem Celular , Cercopithecus aethiops , Dengue/virologia , Retículo Endoplasmático/virologia , Genoma Viral/genética , Glicosilação , Hexosiltransferases/antagonistas & inibidores , Interações Hospedeiro-Patógeno , Proteínas de Membrana/antagonistas & inibidores , RNA Viral/genética , Sulfonamidas/farmacologia , Células Vero
11.
Arch Virol ; 164(11): 2683-2690, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31428915

RESUMO

Current antiviral therapies against hepatitis B virus (HBV) infections, such as treatment with nucleos(t)ide analogs (NAs) and interferon alpha, can significantly lower HBV DNA titers, eventually to undetectable levels. However, it is still difficult to completely eliminate the stable template of HBV, the covalently closed circular DNA (cccDNA), and this contributes to viral rebound when treatment is discontinued. HBV pregenomic RNA (pgRNA), which was recently found to be present in the enveloped mature HBV viral particle in blood, is tentatively regarded, with still accumulating clinical evidence, as a novel bona fide virological marker reflecting the amount and status of cccDNA when serum HBV DNA becomes undetectable. HBV pgRNA and DNA share almost identical sequences, and it is therefore difficult to differentiate pgRNA from viral DNA using normal PCR methods. To exclude interference from viral DNA, methods for measuring pgRNA usually require a selective DNA degradation step, which is complicated and time-consuming and also compromises the accuracy of detection. In this study, we developed a simplified quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay with improved accuracy achieved by probing the polyA tail of pgRNA. Using clinical serum samples, we observed that not all patients share the same 3' sequence, suggesting slight differences between HBV strains in the way they end transcription. We then designed and evaluated a universal primer and probe set for distinguishing HBV pgRNA from HBV DNA. Our results demonstrated that a one-step qRT-PCR assay could selectively amplify HBV pgRNA from a mixture of HBV RNA and DNA, which is valuable for clinical applications.


Assuntos
Vírus da Hepatite B/genética , Técnicas de Amplificação de Ácido Nucleico/métodos , RNA/sangue , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , DNA Viral/análise , DNA Viral/genética , Hepatite B/virologia , Humanos , RNA Viral/análise , RNA Viral/genética
12.
Arch Virol ; 164(11): 2805-2810, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31451963

RESUMO

Physalis peruviana is a perennial solanaceous plant that has recently been established as a commercial crop in Brazil. This work reports the near-complete genome sequence, particle morphology, and plant host responses to a putative new sobemovirus, named "physalis rugose mosaic virus". The virus, characterized by isometric particles of ca. 30 nm in diameter, causes foliar symptoms of mosaic, malformation and blistering, accompanied by stunting. The near-complete genome sequence comprises 4175 nucleotides and contains five open reading frames that are similar to those of other sobemoviruses. In addition to P. peruviana, the new virus systemically infected Capsicum annuum, Nicotiana tabacum and Solanum lycopersicum by mechanical inoculation. Thus, this virus may cause disease in these crops in the field.


Assuntos
Genoma Viral/genética , Vírus do Mosaico/classificação , Vírus do Mosaico/crescimento & desenvolvimento , Physalis/virologia , Doenças das Plantas/virologia , Vírus de Plantas/classificação , Vírus de Plantas/genética , Brasil , Capsicum/virologia , Lycopersicon esculentum/virologia , Vírus do Mosaico/genética , Vírus de Plantas/crescimento & desenvolvimento , RNA Viral/genética , Tabaco/virologia
13.
Arch Virol ; 164(11): 2725-2733, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31468140

RESUMO

Porcine reproductive and respiratory syndrome (PRRS) is one of the most highly infectious diseases in the pig industry, resulting in enormous economic losses worldwide. In this study, a PRRS virus (PRRSV) strain was isolated from primary porcine alveolar macrophage cells in Xinjiang in northwest China. This new strain was sequenced and designated as XJzx1-2015, and its sequence was then compared to those of other representative PRRSV strains from around the world. Complete genomic characterisation showed that the full-length nucleotide sequence of XJzx1-2015 exhibited low-level similarity to NB/04 (91.6%), JXA1 (90.5%), CH-1a (90.2%), VR-2332 (86.9%), QYYZ (85.7%), and JL580 (82.2%), with the highest similarity to HK13 (91.7%) sequence identity. Nonstructural protein 2 (NSP2) and glycosylated protein (GP) 2 of XJzx1-2015 had deletions of five and two amino acids, respectively, corresponding to strain VR-2332 positions 475-479 and 173-174. Phylogenetic analysis based on complete genome sequences showed that XJzx1-2015 and four other strains from China formed a new subgenotype closely related to other sublineage 8.7 (JXA1-like) strains belonging to the North American genotype. However, phylogenetic analysis based on NSP2 and GP5 showed that XJzx1-2015 clustered with sublineage 8.7 (JXA1-like, CH-1a-like) and lineage 3 (QYYZ-like) strains, respectively. Recombination analysis indicated that XJzx1-2015 is an intersubgenotype recombinant of CH-1a-like and QYYZ-like strains. Overall, our findings demonstrate that XJzx1-2015 is a novel PRRSV strain with a significantly high frequency of mutation and a recombinant between lineage 3 and sublineage 8.7 identified in northwest China. These results provide important insights into PRRSV evolution.


Assuntos
Genoma Viral/genética , Síndrome Respiratória e Reprodutiva Suína/epidemiologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/genética , Doenças dos Suínos/epidemiologia , Sequência de Aminoácidos , Animais , China/epidemiologia , Macrófagos Alveolares/virologia , Filogenia , Síndrome Respiratória e Reprodutiva Suína/virologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/classificação , Vírus da Síndrome Respiratória e Reprodutiva Suína/isolamento & purificação , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Alinhamento de Sequência , Suínos , Doenças dos Suínos/virologia
14.
Mem Inst Oswaldo Cruz ; 114: e190160, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31411312

RESUMO

Human enteroviruses (EVs) are associated with a wide spectrum of human diseases. Here we report the complete genome sequences of one EV-C99 strain and one E29 strain obtained from children suffering from acute gastroenteritis, without symptoms of enteroviral syndromes. This is the first report of EV-C99 in South America, and the second E29 genome described worldwide. Continuous surveillance on EVs is vital to provide further understanding of the circulation of new or rare EV serotypes in the country. The present study also highlights the capacity of EVs to remain in silent circulation in populations.


Assuntos
Enterovirus Humano B/genética , Enterovirus Humano C/genética , Infecções por Enterovirus/virologia , Idoso , Brasil , Pré-Escolar , Enterovirus Humano B/isolamento & purificação , Enterovirus Humano C/isolamento & purificação , Fezes/virologia , Humanos , Masculino , Filogenia , RNA Viral/genética
15.
Arch Virol ; 164(10): 2641-2644, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31375908

RESUMO

We report the complete genome sequence of a novel nucleorhabdovirus, apple rootstock virus A (ApRVA), isolated from Malus spp. in South Korea. ApRVA has a 14,043-nt single-stranded negative-sense RNA genome. In the antigenome sense, it contains seven open reading frames, encoding the putative nucleocapsid protein, phosphoprotein, cell-to-cell movement protein, matrix protein, glycoprotein, RNA-dependent RNA polymerase, and an additional hypothetical protein, the gene for which is located between the genes for the matrix protein and glycoprotein. The complete genome sequence of ApRVA showed 47.45% nucleotide sequence identity to that of black currant-associated rhabdovirus 1. The genome organization, phylogenetic relationships, and sequence similarities to other nucleorhabdoviruses suggest that ApRVA is a new member of the genus Nucleorhabdovirus.


Assuntos
Genoma Viral , Malus/virologia , Raízes de Plantas/virologia , Rhabdoviridae/classificação , Rhabdoviridae/genética , Análise de Sequência de DNA , Ordem dos Genes , Fases de Leitura Aberta , Filogenia , RNA Viral/genética , República da Coreia , Rhabdoviridae/isolamento & purificação , Homologia de Sequência do Ácido Nucleico , Proteínas Virais/genética
16.
Arch Virol ; 164(10): 2585-2592, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31377889

RESUMO

Marbled eel reovirus (MERV) is an aquareovirus (AQRV) isolated from diseased marbled eels (Anguilla marmorata) with petechial skin hemorrhage. In this study, we propagated MERV in a cell line derived from the brain of Aequidens rivulatus and purified viral particles by using a discontinuous cesium chloride gradient. Genomic RNA sequences were obtained through next-generation sequencing. MERV, similar to most other AQRVs, showed the presence of 11 double-stranded RNA segments encoding 12 proteins; however, the genome sequence displayed very little similarity to known AQRV sequences. Furthermore, the structural proteins of MERV were most closely related to American grass carp reovirus with sequence identity values of no more than 64.89%. Phylogenetic analysis based on the sequences of structural proteins indicated that MERV shows an evolutionary history between AQRV-B and -G, which belong to the saline and freshwater environment subgroups, respectively. We also observed that MERV showed a closer relationship to orthoreoviruses based on the protein sequences of NS38 and NS73. In summary, MERV is a novel AQRV that could be classified as a member of the new proposed AQRV species "Aquareovirus H". The taxonomic assignments and evolution of AQRVs thus warrant further investigation.


Assuntos
Anguilla/virologia , Doenças dos Peixes/virologia , Infecções por Reoviridae/veterinária , Reoviridae/isolamento & purificação , Animais , Encéfalo/virologia , Linhagem Celular , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Microscopia Eletrônica de Transmissão , Filogenia , RNA de Cadeia Dupla/genética , RNA Viral/genética , Reoviridae/classificação , Reoviridae/genética , Infecções por Reoviridae/virologia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Coloração e Rotulagem , Proteínas Virais/genética , Vírion/ultraestrutura , Cultura de Vírus
17.
BMC Bioinformatics ; 20(1): 409, 2019 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-31362694

RESUMO

BACKGROUND: Internal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5' cap-dependent translation initiation mechanism. IRES usually function when 5' cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool. RESULTS: This paper systematically examines the features that can distinguish IRES from non-IRES sequences. Sequence features such as kmer words, structural features such as QMFE, and sequence/structure hybrid features are evaluated as possible discriminators. They are incorporated into an IRES classifier based on XGBoost. The XGBoost model performs better than previous classifiers, with higher accuracy and much shorter computational time. The number of features in the model has been greatly reduced, compared to previous predictors, by including global kmer and structural features. The contributions of model features are well explained by LIME and SHapley Additive exPlanations. The trained XGBoost model has been implemented as a bioinformatics tool for IRES prediction, IRESpy (https://irespy.shinyapps.io/IRESpy/), which has been applied to scan the human 5' UTR and find novel IRES segments. CONCLUSIONS: IRESpy is a fast, reliable, high-throughput IRES online prediction tool. It provides a publicly available tool for all IRES researchers, and can be used in other genomics applications such as gene annotation and analysis of differential gene expression.


Assuntos
Biologia Computacional/métodos , Sítios Internos de Entrada Ribossomal/genética , Software , Regiões 5' não Traduzidas/genética , Algoritmos , Sequência de Bases , Humanos , Modelos Teóricos , Probabilidade , RNA Viral/genética
18.
Rev Inst Med Trop Sao Paulo ; 61: e34, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31269110

RESUMO

After the introduction of the rotavirus vaccine, the number of rotavirus-associated deaths and the predicted annual rotavirus detection rate had slightly declined worldwide. Taking in account that in Colombia, Rotarix vaccine was introduced in 2009, the purpose of this study was to evaluate the presence of rotavirus A in children under five years who were treated for acute diarrhoea in Bucaramanga, Colombia and, moreover, to determine the genotypes of rotavirus present in those children. We performed an analytical cross-sectional study of rotavirus A in faecal samples from children up to five years of age. Stool samples were screened for rotavirus A using a lateral-flow immunochromatographic assay and confirmed using a VP6 sandwich ELISA. Genotyping of rotavirus A-positive samples was performed by PCR and sequencing of VP7 and VP4 genes. The overall prevalence of rotavirus was 30.53% (95% confidence interval [CI] 21.2 - 39.7). Most of the children with rotavirus (86.2%) had received two doses of the rotavirus vaccine. G3 strains accounted for the vast majority of cases (82.8%), followed by G12 strains (13.8%) and G3/G9 coinfections (3.4%). Among the P genotypes, P[8] was the most prevalent (69%), followed by P[9] (31%). The most common G[P] genotype combination was G3P[8], followed by G3P[9]. The main finding in this study was that rotavirus, in a Colombian region, is still an important pathogen in children under five years old, previously vaccinated. The results showed that different factors, such as kindergarten attendance, could explain the epidemiology and transmission of rotavirus in Bucaramanga.


Assuntos
Diarreia/epidemiologia , Infecções por Rotavirus/epidemiologia , Rotavirus/genética , Doença Aguda , Pré-Escolar , Colômbia/epidemiologia , Estudos Transversais , Diarreia/virologia , Ensaio de Imunoadsorção Enzimática , Fezes/virologia , Feminino , Genótipo , Humanos , Lactente , Recém-Nascido , Tipagem Molecular , Filogenia , Reação em Cadeia da Polimerase , Prevalência , RNA Viral/genética , Rotavirus/classificação , Infecções por Rotavirus/virologia
19.
Virol J ; 16(1): 89, 2019 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-31277670

RESUMO

A tenuivirus, referred to here as JKI 29327, was isolated from a black medic (Medicago lupulina) plant collected in Austria. The virus was mechanically transmitted to Nicotiana benthamiana, M. lupulina, M. sativa, Pisum sativum and Vicia faba. The complete genome was determined by high throughput sequencing. The genome of JKI 29327 consists of eight RNA segments closely related to those of melon chlorotic spot virus (MeCSV) isolate E11-018 from France. Since segments RNA 7 and 8 of JKI 29327 are shorter, its genome is slightly smaller (by 247 nts) than that of E11-018. Pairwise comparisons between the predicted virus proteins of JKI 29327 and their homologues in E11-018 showed aa identities ranging from 80.6 to 97.2%. Plants infected with E11-081 gave intermediate DAS-ELISA reactions with polyclonal antibodies to JKI 29327. Since JKI 29327 and E11-018 appear to be closely related both serologically and genetically, we propose to regard JKI 29327 as the black medic strain of MeCSV. To our knowledge, JKI 29327 represents the second tenuivirus identified from a dicotyledonous plant. Serological and molecular diagnostic methods were developed for future detection.


Assuntos
Cucurbitaceae/virologia , Doenças das Plantas/virologia , Tenuivirus/genética , Tenuivirus/isolamento & purificação , Áustria , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Ervilhas/virologia , Filogenia , RNA Viral/genética , Tabaco/virologia , Vicia faba/virologia , Proteínas Virais/genética
20.
BMC Infect Dis ; 19(1): 601, 2019 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-31291899

RESUMO

BACKGROUND: Despite effective antiretroviral therapy developed over the last decade, HIV infection remains a major worldwide public health problem. Recently, a promising preventive treatment has been made available for HIV prophylaxis, PrEP for pre-ExPosure Prophylaxis. Indeed, it was shown to significantly reduce the risk of HIV infection in patients exposed to high risk of infection such as men having sex with men (MSM), heterosexuals and people who inject drugs. Several issues pertaining to PrEP remain uncertain including short and long-term adverse events, drug resistance, risk compensation and resurgence of other sexually transmitted infections. CASE PRESENTATION: We report a case of a 52-year-old MSM eligible for PrEP as he was exposed to a high risk of HIV infection, presented no clinical symptoms of HIV primary infection and was seronegative for HIV. PrEP therapy was then initiated with fixed association of emtricitabine-tenofovir disoproxil. One month later, HIV tests using two different assays were positive, despite perfect compliance reported by the patient and confirmed by plasma drug level. A retrospective search for plasma viral RNA in the blood sample before PrEP initiation turned out positive. Genotyping and treatment sensitivity performed on sample after one month of PrEP showed a virus resistance to lamivudine and emtricitabine. Similar cases in the literature and pivotal studies have reported HIV infections in patients initiating or undergoing PrEP. These patients where either infected but still seronegative, displaying no clinical symptoms upon enrollment, or became infected during PrEP. Reasons are mainly poor compliance to treatment, resistance to PrEP, and lack of diagnosis before PrEP. Guidelines advocate safe sex behavior before initiation, search for clinical signs of HIV primary infection and two different serologic tests performed with one-month interval. DISCUSSION AND CONCLUSIONS: Our patient newly HIV infected received PrEP as he was still seronegative. Current recommendations fail to screen recently HIV infected, but still seronegative patients who are initiating PrEP. This issue raises strong concerns regarding the lack of adequate selection for eligibility to PrEP and may contribute to exposing partners to HIV infection and select viral mutations. Infection risk could be minimized by search for plasma viral HIV RNA at pre-inclusion, at least for patients suspected of unsafe behaviors such as non-respect of the non-exposure period before PrEP initiation.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Infecções por HIV/prevenção & controle , Guias de Prática Clínica como Assunto/normas , Profilaxia Pré-Exposição/normas , Fármacos Anti-HIV/efeitos adversos , Fármacos Anti-HIV/farmacologia , Farmacorresistência Viral/efeitos dos fármacos , Farmacorresistência Viral/genética , Infecções por HIV/sangue , Infecções por HIV/diagnóstico , Homossexualidade Masculina , Humanos , Masculino , Pessoa de Meia-Idade , RNA Viral/sangue , RNA Viral/genética
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