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1.
Sheng Wu Gong Cheng Xue Bao ; 35(12): 2284-2294, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31880136

RESUMO

With the development of liquid biopsy technology, plasma cell-free DNA (cfDNA) becomes one of the research hotspots. Whole-genome bisulfite sequencing of plasma cell-free DNA has shown great potential medical applications such as cancer detection. However, the practical stability evaluation is still lacking. In this study, plasma cell-free DNA samples from two volunteers at different time were collected and prepared for sequencing in multiple laboratories. The library preparation strategies include pre-bisulfite, post-bisulfite and regular whole-genome sequencing. We established a set of quality control references for plasma cell-free DNA sequencing data and evaluated practical stability of blood collection, DNA extraction, and library preparation and sequencing depth. This work provided a technical practice guide for the application of plasma cfDNA methylation sequencing for clinical applications.


Assuntos
Sequenciamento Completo do Genoma , Ácidos Nucleicos Livres , Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Sequência de DNA , Sulfitos
2.
Yi Chuan ; 41(12): 1138-1147, 2019 Dec 20.
Artigo em Chinês | MEDLINE | ID: mdl-31857285

RESUMO

Pathogenic Escherichia coli (E. coli) is the most common pathogen causing urinary tract infection in animals. We investigated the antibiotic resistance and virulence genes of pathogenic E. coli CCHTP derived from urine with occult blood of the giant panda by whole genome sequencing. The flanking sequencing of resistance and virulence genes in genomic islands were also analyzed. Our results demonstrate that E. coli CCHTP contains different families of antibiotic resistance genes, most of which are efflux pump related genes, including multiple drug resistance efflux pump genes mdfA, emrE, and mdtN. A total of 166 virulence factors and 563 virulence genes were identified, and the most virulence factors and related genes are involved in host cell attachment and invasion processes. Furthermore, sequence analysis of 19 genomic islands revealed that antibiotic and virulence genes are associated with mobile genetic elements (transposon and insertion sequence) in GIs011 and GIs017. These structures can mediate horizontal transfer of antibiotic and virulence genes. Our work described the distribution of antibiotic resistance genes and virulence genes in E. coli CCHTP, which may provide an important guidance for treatment and rational drug use of E. coli CCHTP infection in the giant panda.


Assuntos
Farmacorresistência Bacteriana , Proteínas de Escherichia coli , Escherichia coli , Urina , Ursidae , Animais , Farmacorresistência Bacteriana/genética , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Genoma Bacteriano , Urina/microbiologia , Ursidae/microbiologia , Virulência/genética , Fatores de Virulência/genética , Sequenciamento Completo do Genoma
3.
Zhonghua Fu Chan Ke Za Zhi ; 54(12): 808-814, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31874470

RESUMO

Objective: To evaluate the application of combinatorial probe anchor synthesis (cPAS)-based high-throughput low coverage whole genome sequencing in chromosomal aberration detection in spontaneous miscarriage. Methods: From September 2015 to May 2017, spontaneous miscarriage samples were collected from Inner Mongolia Maternal and Child Health Care Hospital. Those samples were further analyzed with two independent methods, fluorescence in situ hybridization (FISH) and low coverage whole genome sequencing on the BGISEQ-500 high-throughput platform. The performance of low coverage whole genome sequencing was assessed by comparing to FISH results. Results: In 595 spontaneous miscarried specimens, low coverage whole genome sequencing revealed 144 cases (24.2%, 144/595) chromosomal abnormalities, of which a subset of 137 cases (23.0%, 137/595) were detected as aneuploidies, 2 cases (0.3%, 2/595) as mosaicisms and 5 cases (0.8%, 5/595) as copy number variation (≥5 Mb). Conclusion: cPAS-based high-throughput low coverage whole genome sequencing is a reliable method in detecting chromosomal aberrations inspontaneous abortion tissues, including chromosome aneuploidies, mosaicisms and copy number variation (≥5 Mb).


Assuntos
Aborto Espontâneo/genética , Aberrações Cromossômicas/estatística & dados numéricos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Criança , China , Aberrações Cromossômicas/embriologia , Cromossomos/genética , DNA/genética , Variações do Número de Cópias de DNA/genética , Feminino , Humanos , Hibridização in Situ Fluorescente , Gravidez , Sequenciamento Completo do Genoma/métodos
4.
Yi Chuan ; 41(11): 979-993, 2019 Nov 20.
Artigo em Chinês | MEDLINE | ID: mdl-31735702

RESUMO

With rapid advances in next-generation sequencing technologies, the genomes of many organisms have been sequenced and widely applied in different settings. Mitochondrial genome data is equally important and the high-throughput whole-genome data typically contain mitochondrial genome (mitogenome) sequences. How to extract and assemble the mitogenome from massive whole-genome sequencing (WGS) data remain a hot area in molecular biology, genetics and medicine. The cataloging and analysis of accumulating mitogenome data promotes the development of assembly strategies and corresponding software applications related to mitochondrial DNA from the WGS data. Mitogenome assembly strategies can be divided into mitogenome-reference strategy and de novo strategy. Each strategy has different advantages and limitations with respect to the difference of bait mitogenome-linked short reads from the WGS data and corresponding assembly strategy. In this review, we summarize and compare current mitogenome assembly strategies and the software applications available. We also provide suggestions related to use different assembly strategies and software applications, and the expected benefits and limitations of methods references in life science.


Assuntos
Genoma Mitocondrial , Software , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
5.
Arch Virol ; 164(12): 3141-3144, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31598844

RESUMO

In this study, we report a novel double-stranded RNA (dsRNA) virus, Beauveria bassiana partitivirus 3 (BbPV-3), derived from the entomogenous fungus Beauveria bassiana isolate RCEF5853 from China. The genome of BbPV-3, whose sequence was determined by metagenomic sequencing, RT-PCR, and RACE cloning, comprises two dsRNA genome segments that are 1,856 and 1,719 bp long. The first segment contains a single ORF (ORF-1) encoding a 584-amino-acid-long protein (66.05 kDa) with a conserved RNA-dependent RNA polymerase (RdRp) motif. The second segment also has a single ORF (ORF-2) encoding a 500-amino-acid-long coat protein (CP) (55.9 kDa). The CP and RdRp sequences showed highest identity of 43.4% and 60.2%, respectively, to those of Colletotrichum eremochloae partitivirus 1. Phylogenetic analysis of the RdRp domain of the polyprotein revealed that BbPV-3 grouped together with the members of the genus Epsilonpartitivirus. Hence, we proposed that Beauveria bassiana partitivirus 3 is a novel member of the proposed genus Epsilonpartitivirus.


Assuntos
Beauveria/virologia , Micovírus/isolamento & purificação , Genoma Viral , Vírus de RNA/isolamento & purificação , Sequência de Bases , China , Micovírus/classificação , Micovírus/genética , Filogenia , RNA Replicase/genética , Vírus de RNA/classificação , Vírus de RNA/genética , RNA Viral/genética , Proteínas Virais/genética , Sequenciamento Completo do Genoma
6.
Arch Virol ; 164(12): 3089-3093, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31595357

RESUMO

The phage vB_BthS-HD29phi infecting Bacillus thuringiensis strain HD29 was isolated and purified. The morphology of the phage showed that it belongs to the family Siphoviridae. The phage genome was 32,181 bp in length, comprised linear double-stranded DNA with an average G + C content of 34.9%, and exhibited low similarity to known phage genomes. Genomic and phylogenetic analysis revealed that vB_BthS-HD29phi is a novel phage. In total, 50 putative ORFs were predicted in the phage genome, and only 18 ORFs encoded proteins with known functions. This article reports the genome sequence of a new tailed phage and increases the known genetic diversity of tailed phages.


Assuntos
Fagos Bacilares/genética , Bacillus thuringiensis/virologia , Genoma Viral , Siphoviridae/genética , Fagos Bacilares/classificação , Fagos Bacilares/isolamento & purificação , Composição de Bases , Sequência de Bases , DNA Viral/genética , Variação Genética , Filogenia , Siphoviridae/classificação , Siphoviridae/isolamento & purificação , Sequenciamento Completo do Genoma
7.
N Engl J Med ; 381(17): 1644-1652, 2019 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-31597037

RESUMO

Genome sequencing is often pivotal in the diagnosis of rare diseases, but many of these conditions lack specific treatments. We describe how molecular diagnosis of a rare, fatal neurodegenerative condition led to the rational design, testing, and manufacture of milasen, a splice-modulating antisense oligonucleotide drug tailored to a particular patient. Proof-of-concept experiments in cell lines from the patient served as the basis for launching an "N-of-1" study of milasen within 1 year after first contact with the patient. There were no serious adverse events, and treatment was associated with objective reduction in seizures (determined by electroencephalography and parental reporting). This study offers a possible template for the rapid development of patient-customized treatments. (Funded by Mila's Miracle Foundation and others.).


Assuntos
Proteínas de Membrana Transportadoras/genética , Mutagênese Insercional , Lipofuscinoses Ceroides Neuronais/tratamento farmacológico , Lipofuscinoses Ceroides Neuronais/genética , Oligonucleotídeos Antissenso/uso terapêutico , Medicina de Precisão , Doenças Raras/tratamento farmacológico , Biópsia , Criança , Desenvolvimento Infantil , Descoberta de Drogas , Drogas em Investigação/uso terapêutico , Eletroencefalografia , Feminino , Humanos , Testes Neuropsicológicos , RNA Mensageiro , Convulsões/diagnóstico , Convulsões/tratamento farmacológico , Pele/patologia , Sequenciamento Completo do Genoma
9.
Arch Virol ; 164(12): 3127-3131, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31559494

RESUMO

A cytorhabdovirus, tentatively named "strawberry-associated virus 1" (SaV1), was identified in strawberry (Fragaria ananassa Duch.), and its complete genome sequence was determined. Its negative-sense single-stranded RNA genome is composed of 14,159 nucleotides and contains eight open reading frames (ORFs) in the canonical order 3'-N-P-P3-M-G-P6-P7-L-5. The ORFs are separated by conserved intergenic sequences, and the genome coding region is flanked by 3' and 5' untranslated regions of 179 and 856 nt, respectively. SaV1 N and L genes shares 32-57% and 38-64% amino acid sequence identity with those of nine reported cytorhabdoviruses, respectively. Phylogenetic analysis showed that SaV1 clustered with high confidence with representative cytorhabdoviruses and is most closely related to tomato yellow mottle-associated virus. There are two additional small genes of unknown function between the G and L genes. We propose that SaV1 should be considered a member of a novel species in the genus Cytorhabdovirus, family Rhabdoviridae.


Assuntos
Fragaria/virologia , Genoma Viral , Doenças das Plantas/virologia , Rhabdoviridae/genética , DNA Intergênico/genética , Fases de Leitura Aberta , Filogenia , Rhabdoviridae/classificação , Rhabdoviridae/isolamento & purificação , Proteínas Virais/genética , Sequenciamento Completo do Genoma
10.
Arch Virol ; 164(11): 2843-2848, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31494777

RESUMO

The Cooper and Los Angeles (LA) strains were the two original respiratory strains of bovine herpesvirus type 1.1 (BoHV-1.1) isolated in the 1950s from cattle with infectious bovine rhinotracheitis. We report the complete genome sequence for the BoHV-1.1 LA strain and compare it to the prototype Cooper strain and six wild-type BoHV-1.1 isolates. A nucleotide sequence divergence of 0.74% was noted across the two complete genomes, caused by 19 single-nucleotide polymorphisms (SNPs) involving 12 genes and insertions/deletions that primarily affected the number of repeats within reiterated repeat regions of the genome. Phylogenetic analysis revealed that Cooper and LA strains are genetically the most ancient strains from which all of the more-recently isolated field strains of BoHV-1.1 evolved.


Assuntos
Genoma Viral/genética , Infecções por Herpesviridae/veterinária , Herpesvirus Bovino 1/genética , Rinotraqueíte Infecciosa Bovina/virologia , Animais , Sequência de Bases , Bovinos , Doenças dos Bovinos/virologia , Genótipo , Herpesvirus Bovino 1/classificação , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
11.
Arch Virol ; 164(12): 3107-3109, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31529221

RESUMO

The lumpy skin disease virus (LSDV) vaccine, Herbivac LS, batch 008, was sequenced and found to differ from the Neethling vaccine strain in the locus encoding a superoxide dismutase (SOD) homolog. The presence of a SOD homolog, be it full-length (as in Herbivac LS) or truncated (as in Neethling) may affect vaccine immunogenicity.


Assuntos
Vírus da Doença Nodular Cutânea/genética , Superóxido Dismutase/genética , Sequenciamento Completo do Genoma/métodos , Animais , Bovinos , Tamanho do Genoma , Vírus da Doença Nodular Cutânea/classificação , Vírus da Doença Nodular Cutânea/enzimologia , Mutação , Proteínas Virais/genética , Vacinas Virais/genética
12.
Arch Virol ; 164(12): 3115-3119, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31535209

RESUMO

A virulent phage, named ST20, infecting Escherichia coli O165:H8 was isolated from wastewater and subjected to genomic sequencing using the Illumina HiSeq system. Genomic analysis revealed that it contains double-stranded DNA, and its complete genome consists of 44,517 nucleotides with an average GC content of 50.81%. Morphological observations showed that phage ST20 belongs to the order Caudovirales and the family Siphoviridae due to its characteristic icosahedral capsid and a long noncontractile tail. This phage was further characterized by one-step growth curve analysis and measurement of its stability at 4 °C. The study has implications for the development of potential biocontrol agents.


Assuntos
Escherichia coli Shiga Toxigênica/virologia , Siphoviridae/classificação , Sequenciamento Completo do Genoma/métodos , Bacteriófagos/classificação , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Bacteriófagos/patogenicidade , Composição de Bases , Tamanho do Genoma , Siphoviridae/genética , Siphoviridae/isolamento & purificação , Siphoviridae/patogenicidade , Virulência , Águas Residuárias/microbiologia
13.
Arch Virol ; 164(12): 3121-3126, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31538253

RESUMO

An epizootic hemorrhagic disease virus (EHDV) strain designated YN09-04 was isolated from sentinel cattle in China. The length of its complete genome was 19,344 bp in total, consisting of 10 segments ranging in size from 810 bp (S10) to 3942 bp (S1). Based on phylogenetic analysis of the S2 sequence, YN09-04 clusters with EHDV serotype 7 (EHDV-7) strains form a distinct, well-supported subgroup, indicating that YN09-04 belongs to EHDV-7. However, the origin of the YN09-04 genome is very complex. The S2 and S6 of YN09-04 cluster with those of Japanese EHDV-7 strains, whereas the S1, S3, S4, S5 and S7 of YN09-04 share high nucleotide sequence identity and a close relationship with those of Japanese Ibaraki viruses, and the S8, S9 and S10 nucleotide sequences of YN09-04 are more similar to those of some Australian EHDV strains than to those of other isolates. These results suggest that the genome of YN09-04 likely originated from a reassortment event between EHDV strains that were similar to the current Japanese and Australian strains and that YN09-04 and some EHDVs from Japan and Australia share the same ancestors. This is the first report of the isolation, identification and complete-genome phylogenetic analysis of an EHDV-7 strain from China.


Assuntos
Doenças dos Bovinos/virologia , Vírus da Doença Hemorrágica Epizoótica/classificação , Infecções por Reoviridae/veterinária , Sequenciamento Completo do Genoma/métodos , Animais , Austrália , Bovinos , China , Genoma Viral , Vírus da Doença Hemorrágica Epizoótica/genética , Vírus da Doença Hemorrágica Epizoótica/isolamento & purificação , Japão , Filogenia , Infecções por Reoviridae/virologia
14.
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
15.
Arch Virol ; 164(12): 3111-3113, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31531744

RESUMO

The complete genome of the novel phage vB_EcoS_PHB17, which infects Shiga-toxin-producing Escherichia coli, was sequenced, revealing a linear double-stranded DNA genome of 48,939 bp with 46% GC content and protruding 150-bp 5' cohesive termini. The genome contained 85 open reading frames, 28 of which were annotated with known functions. No tRNA-encoding genes were detected. Phylogenetic analysis suggested that phage PHB17 is a novel phage of family Siphoviridae.


Assuntos
Escherichia coli Shiga Toxigênica/virologia , Siphoviridae/classificação , Sequenciamento Completo do Genoma/métodos , Composição de Bases , Tamanho do Genoma , Genoma Viral , Fases de Leitura Aberta , Filogenia , Siphoviridae/genética , Siphoviridae/isolamento & purificação
16.
Implement Sci ; 14(1): 79, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409417

RESUMO

BACKGROUND: Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS: In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS: Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS: For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.


Assuntos
Genoma Bacteriano , Genômica/métodos , Prática de Saúde Pública , Humanos , Sequenciamento Completo do Genoma
17.
Nucleic Acids Res ; 47(18): 9666-9684, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31392335

RESUMO

Break induced replication (BIR) is a double strand break repair pathway that can promote genetic instabilities similar to those observed in cancer. Instead of a replication fork, BIR is driven by a migration bubble where asynchronous synthesis between leading and lagging strands leads to accumulation of single-stranded DNA (ssDNA) that promotes mutation. However, the details of the mechanism of mutagenesis, including the identity of the participating proteins, remain unknown. Using yeast as a model, we demonstrate that mutagenic ssDNA is formed at multiple positions along the BIR track and that Pol ζ is responsible for the majority of both spontaneous and damage-induced base substitutions during BIR. We also report that BIR creates a potent substrate for APOBEC3A (A3A) cytidine deaminase that can promote formation of mutation clusters along the entire track of BIR. Finally, we demonstrate that uracil glycosylase initiates the bypass of DNA damage induced by A3A in the context of BIR without formation of base substitutions, but instead this pathway frequently leads to chromosomal rearrangements. Together, the expression of A3A during BIR in yeast recapitulates the main features of APOBEC-induced kataegis in human cancers, suggesting that BIR might represent an important source of these hyper-mutagenic events.


Assuntos
Cromossomos/genética , Citidina Desaminase/genética , Reparo do DNA/genética , Proteínas/genética , Recombinação Genética , Quebras de DNA de Cadeia Dupla , Dano ao DNA/genética , Replicação do DNA/genética , DNA de Cadeia Simples/genética , Humanos , Mutagênese/genética , Mutação , Saccharomyces cerevisiae/genética , Sequenciamento Completo do Genoma
18.
Gene ; 716: 144016, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31377318

RESUMO

Drug resistance of malaria parasites remains a problem affecting antimalarial treatment and control of the disease. We previously synthesized an antimalarial endoperoxide, N-89, having high antimalarial effects in vitro and in vivo. In this study we seek to understand the resistant mechanism against N-89 by establishing a highly N-89-resistant clone, named NRC10H, of the Plasmodium falciparum FCR-3 strain. We describe gene mutations in the parent FCR-3 strain and the NRC10H clone using whole-genome sequencing and subsequently by expression profiling using quantitative real-time PCR. Seven genes related to drug resistance, proteolysis, glycophosphatidylinositol anchor biosynthesis, and phosphatidylethanolamine biosynthesis exhibited a single amino acid substitution in the NRC10H clone. Among these seven genes, the multidrug resistance protein 2 (mdr2) variant A532S was found only in NRC10H. The genetic status of the P. falciparum endoplasmic reticulum-resident calcium binding protein (PfERC), a potential target of N-89, was similar between the NRC10H clone and the parent FCR-3 strain. These findings suggest that the genetic alterations of the identified seven genes, in particular mdr2, in NRC10H could give rise to resistance of the antimalarial endoperoxide N-89.


Assuntos
Antimaláricos/farmacologia , Compostos Heterocíclicos com 2 Anéis/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Compostos de Espiro/farmacologia , Resistência a Medicamentos/genética , Genômica , Plasmodium falciparum/genética , Plasmodium falciparum/metabolismo , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , RNA Mensageiro/metabolismo , Sequenciamento Completo do Genoma
19.
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
20.
Arch Virol ; 164(11): 2881-2885, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31456087

RESUMO

Aquatic birds are known to be a reservoir for the most common influenza A viruses (IAVs). In the annual surveillance program, we collected the feces of migratory birds for the detection of IAVs in South Korea in November 2016. A novel reassorted H3N3 avian influenza virus (AIV) containing genes from viruses of wild and domestic birds was identified and named A/aquatic bird/South Korea/sw006/2016(H3N3). The polymerase basic 2 (PB2) and non-structural (NS) genes of this isolate are most closely related to those of wild-bird-origin AIV, while the polymerase basic 1 (PB1), polymerase acidic (PA), hemagglutinin (HA), nucleoprotein (NP), neuraminidase (NA), and matrix (M) genes are most closely related to those of domestic-bird-origin AIV. A/aquatic bird/South Korea/sw006/2016 contains PA, NP, M, and NS genes were most closely related to those of AIV subtype H4 and PB2, PB1, and HA genes that are most closely related to those of AIV subtype H3N8, while the NA gene was most closely related to those of subtype H10, which was recently detected in humans in China. These results suggest that novel reassortment of AIV strains occurred due to interaction between wild and domestic birds. Hence, we emphasize the need for continued surveillance of avian influenza virus in bird populations.


Assuntos
Genoma Viral/genética , Vírus da Influenza A Subtipo H3N8/genética , Influenza Aviária/virologia , Vírus Reordenados/genética , Animais , Aves/virologia , Vírus da Influenza A Subtipo H3N8/isolamento & purificação , Neuraminidase/genética , Proteínas não Estruturais Virais/genética , Proteínas Virais/genética , Sequenciamento Completo do Genoma
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