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  1 / 3954 MEDLINE  
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[PMID]:29179736
[Au] Autor:Erives AJ
[Ad] Endereço:Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA. albert-erives@uiowa.edu.
[Ti] Título:Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance.
[So] Source:Epigenetics Chromatin;10(1):55, 2017 11 28.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like "doublets" in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. RESULTS: Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. CONCLUSIONS: The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases.
[Mh] Termos MeSH primário: DNA Topoisomerases Tipo II/genética
Vírus de DNA/genética
Histonas/genética
Filogenia
[Mh] Termos MeSH secundário: Vírus de DNA/classificação
Genes Virais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Histones); EC 5.99.1.3 (DNA Topoisomerases, Type II)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0162-0


  2 / 3954 MEDLINE  
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[PMID]:29324229
[Au] Autor:Jones MK; Karst SM
[Ad] Endereço:Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
[Ti] Título:Enteric Viruses Hitch a Ride on the Evolutionary Highway.
[So] Source:Cell Host Microbe;23(1):5-6, 2018 01 10.
[Is] ISSN:1934-6069
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:RNA viruses can recombine their genetic material during co-infection. However, the in vivo frequency of co-infections is unclear. In this issue of Cell Host & Microbe, Erickson et al. (2018) demonstrate that an enteric RNA virus concentrates itself through multi-virion binding to bacteria, thus increasing genetic recombination and virus adaptability.
[Mh] Termos MeSH primário: Evolução Biológica
Vírus de RNA/genética
[Mh] Termos MeSH secundário: Coinfecção
Vírus de DNA
Vírus
[Pt] Tipo de publicação:JOURNAL ARTICLE; COMMENT
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180223
[Lr] Data última revisão:
180223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE


  3 / 3954 MEDLINE  
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[PMID]:28464391
[Au] Autor:Lawrence SA; Floge SA; Davy JE; Davy SK; Wilson WH
[Ad] Endereço:School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
[Ti] Título:Exploratory analysis of Symbiodinium transcriptomes reveals potential latent infection by large dsDNA viruses.
[So] Source:Environ Microbiol;19(10):3909-3919, 2017 Oct.
[Is] ISSN:1462-2920
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Coral reefs are in decline worldwide. Much of this decline is attributable to mass coral bleaching events and disease outbreaks, both of which are linked to anthropogenic climate change. Despite increased research effort, much remains unknown about these phenomena, especially the causative agents of many coral diseases. In particular, coral-associated viruses have received little attention, and their potential roles in coral diseases are largely unknown. Previous microscopy studies have produced evidence of viral infections in Symbiodinium, the endosymbiotic algae critical for coral survival, and more recently molecular evidence of Symbiodinium-infecting viruses has emerged from metagenomic studies of corals. Here, we took an exploratory whole-transcriptome approach to virus gene discovery in three different Symbiodinium cultures. An array of virus-like genes was found in each of the transcriptomes, with the majority apparently belonging to the nucleocytoplasmic large DNA viruses. Upregulation of virus-like gene expression following stress experiments indicated that Symbiodinium cells may host latent or persistent viral infections that are induced via stress. This was supported by analysis of host gene expression, which showed changes consistent with viral infection after exposure to stress. If these results can be replicated in Symbiodinium cells in hospite, they could help to explain the breakdown of the coral-Symbiodinium symbiosis, and possibly some of the numerous coral diseases that have yet to be assigned a causative agent.
[Mh] Termos MeSH primário: Vírus de DNA/genética
Dinoflagelados/genética
Dinoflagelados/virologia
Transcriptoma/genética
[Mh] Termos MeSH secundário: Animais
Antozoários/fisiologia
Mudança Climática
Recifes de Corais
Simbiose/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.1111/1462-2920.13782


  4 / 3954 MEDLINE  
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[PMID]:29247338
[Au] Autor:Kemenesi G; Kurucz K; Zana B; Földes F; Urbán P; Vlaschenko A; Kravchenko K; Budinski I; Szodoray-Parádi F; Bücs S; Jére C; Csosz I; Szodoray-Parádi A; Estók P; Görföl T; Boldogh S; Jakab F
[Ad] Endereço:Virological Research Group, János Szentágothai Research Centre, University of Pécs, Pécs, Hungary. kemenesi.gabor@gmail.com.
[Ti] Título:Diverse replication-associated protein encoding circular DNA viruses in guano samples of Central-Eastern European bats.
[So] Source:Arch Virol;163(3):671-678, 2018 Mar.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Circular replication-associated protein encoding single-stranded DNA (CRESS DNA) viruses are increasingly recognized worldwide in a variety of samples. Representative members include well-described veterinary pathogens with worldwide distribution, such as porcine circoviruses or beak and feather disease virus. In addition, numerous novel viruses belonging to the family Circoviridae with unverified pathogenic roles have been discovered in different human samples. Viruses of the family Genomoviridae have also been described as being highly abundant in different faecal and environmental samples, with case reports showing them to be suspected pathogens in human infections. In order to investigate the genetic diversity of these viruses in European bat populations, we tested guano samples from Georgia, Hungary, Romania, Serbia and Ukraine. This resulted in the detection of six novel members of the family Circoviridae and two novel members of the family Genomoviridae. Interestingly, a gemini-like virus, namely niminivirus, which was originally found in raw sewage samples in Nigeria, was also detected in our samples. We analyzed the nucleotide composition of members of the family Circoviridae to determine the possible host origins of these viruses. This study provides the first dataset on CRESS DNA viruses of European bats, and members of several novel viral species were discovered.
[Mh] Termos MeSH primário: Quirópteros/virologia
Circoviridae/genética
Infecções por Vírus de DNA/epidemiologia
Vírus de DNA/genética
DNA de Cadeia Simples/genética
DNA Viral/genética
Genoma Viral
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Circoviridae/classificação
Circoviridae/isolamento & purificação
Infecções por Vírus de DNA/transmissão
Infecções por Vírus de DNA/virologia
Vírus de DNA/classificação
Vírus de DNA/isolamento & purificação
Europa Oriental/epidemiologia
Fezes/virologia
Georgia/epidemiologia
Seres Humanos
Filogenia
Replicação Viral
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (DNA, Viral)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171217
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3678-5


  5 / 3954 MEDLINE  
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[PMID]:29172646
[Au] Autor:Yin XQ; Schneller SW
[Ad] Endereço:Department of Chemistry and Biochemistry, Molette Laboratory for Drug Discovery, Auburn University, Auburn, USA.
[Ti] Título:3,7-Dideazaneplanocin: Synthesis and antiviral analysis.
[So] Source:Antivir Chem Chemother;25(3):90-93, 2017 Dec.
[Is] ISSN:2040-2066
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Objective To synthesize 3,7-dideazaneplanocin and evaluate its antiviral potential. Methods The target 3,7-dideazaneplanocin has been prepared in five steps from a readily available cyclopentenol. A thorough in vitro antiviral analysis was conducted versus both DNA and RNA viruses. Results A rational synthesis of 3,7-dideazaneplanocin was conceived and successfully pursued in such a way that it can be adapted to various analogs of 3,7-dideazaneplanocin. Using standard antiviral assays, no activity for 3,7-dideazaneplanocn was found. Conclusion Two structural features are necessary for adenine-based carbocyclic nucleosides (like neplanocin) for potential antiviral properties: (i) inhibition of S-adenosylhomocysteine hydrolase and/or (ii) C-5' activation via the mono-nucleotide. These two requisite adenine structural features to fit these criteria are not present in in the target 3,7-dideazaneplanocin: (i) an N-7 is necessary for inhibition of the hydrolase and the N-3 is claimed to be essential for phosphorylation at C-5'. Thus, it is not surprising that 3,7-dideazaneplaoncin lacked antiviral properties.
[Mh] Termos MeSH primário: Antivirais/farmacologia
Vírus de DNA/efeitos dos fármacos
Inibidores Enzimáticos/farmacologia
Piridonas/farmacologia
Vírus de RNA/efeitos dos fármacos
[Mh] Termos MeSH secundário: Antivirais/síntese química
Antivirais/química
Inibidores Enzimáticos/síntese química
Inibidores Enzimáticos/química
Hidrolases/antagonistas & inibidores
Hidrolases/metabolismo
Testes de Sensibilidade Microbiana
Conformação Molecular
Piridonas/síntese química
Piridonas/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (3,7-dideazaxanthine); 0 (Antiviral Agents); 0 (Enzyme Inhibitors); 0 (Pyridones); EC 3.- (Hydrolases)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171206
[Lr] Data última revisão:
171206
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1177/2040206617742561


  6 / 3954 MEDLINE  
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[PMID]:28792686
[Au] Autor:Dixon SB; Lane A; O'Brien MM; Burns KC; Mangino JL; Breese EH; Absalon MJ; Perentesis JP; Phillips CL
[Ad] Endereço:Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, Tennessee.
[Ti] Título:Viral surveillance using PCR during treatment of AML and ALL.
[So] Source:Pediatr Blood Cancer;65(1), 2018 Jan.
[Is] ISSN:1545-5017
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: While viral surveillance of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and adenovirus using PCR is routine in patients undergoing hematopoetic stem cell transplant and solid organ transplant, the utility in the nontransplant pediatric leukemia population is unknown. Our institution screens patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) for viral DNAemia by PCR as part of clinical care. PROCEDURE: This retrospective chart review included patients treated for newly diagnosed or relapsed AML or ALL between April 2010 and September 2014. We retrieved data for viral PCR screening, detection and quantification, duration of positivity, and prophylaxis or treatment. RESULTS: One hundred eleven patients were included in analyses. Forty (36.0%) had at least one blood PCR positive for EBV, CMV, or adenovirus. Patients with ALL had significantly higher rates of persistent viral detection and treatment than those with AML (P < 0.02, P < 0.01, respectively). International patients had significantly higher rates of viral detection (P < 0.01), persistence (P < 0.01), any treatment (P < 0.03), and antiviral treatment (P < 0.01); 16.9% of patients who received intravenous immunoglobulin (IVIG) prophylactically had viral detection compared to 63% of patients who did not receive prophylactic IVIG (P = 0.0008). CONCLUSIONS: Patients with ALL were more susceptible than those with AML to viral reactivation that was persistent or resulted in treatment. Patients with relapsed ALL, refractory ALL, or infantile ALL are most likely to benefit from asymptomatic screening for CMV and adenovirus. International patients are at higher risk for reactivation and may merit screening. EBV reactivation was not significant and does not warrant screening.
[Mh] Termos MeSH primário: Infecções por Vírus de DNA/sangue
Vírus de DNA
DNA Viral/sangue
Leucemia Mieloide Aguda
Reação em Cadeia da Polimerase/métodos
[Mh] Termos MeSH secundário: Adolescente
Adulto
Criança
Pré-Escolar
Infecções por Vírus de DNA/prevenção & controle
Feminino
Seres Humanos
Imunoglobulinas Intravenosas/administração & dosagem
Lactente
Recém-Nascido
Leucemia Mieloide Aguda/sangue
Leucemia Mieloide Aguda/virologia
Masculino
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Viral); 0 (Immunoglobulins, Intravenous)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171129
[Lr] Data última revisão:
171129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170810
[St] Status:MEDLINE
[do] DOI:10.1002/pbc.26752


  7 / 3954 MEDLINE  
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[PMID]:28866775
[Au] Autor:Sobhy H
[Ad] Endereço:Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden. haithamsobhy@gmail.com.
[Ti] Título:A comparative review of viral entry and attachment during large and giant dsDNA virus infections.
[So] Source:Arch Virol;162(12):3567-3585, 2017 Dec.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Viruses enter host cells via several mechanisms, including endocytosis, macropinocytosis, and phagocytosis. They can also fuse at the plasma membrane and can spread within the host via cell-to-cell fusion or syncytia. The mechanism used by a given viral strain depends on its external topology and proteome and the type of cell being entered. This comparative review discusses the cellular attachment receptors and entry pathways of dsDNA viruses belonging to the families Adenoviridae, Baculoviridae, Herpesviridae and nucleocytoplasmic large DNA viruses (NCLDVs) belonging to the families Ascoviridae, Asfarviridae, Iridoviridae, Phycodnaviridae, and Poxviridae, and giant viruses belonging to the families Mimiviridae and Marseilleviridae as well as the proposed families Pandoraviridae and Pithoviridae. Although these viruses have several common features (e.g., topology, replication and protein sequence similarities) they utilize different entry pathways to infect wide-range of hosts, including humans, other mammals, invertebrates, fish, protozoa and algae. Similarities and differences between the entry methods used by these virus families are highlighted, with particular emphasis on viral topology and proteins that mediate viral attachment and entry. Cell types that are frequently used to study viral entry are also reviewed, along with other factors that affect virus-host cell interactions.
[Mh] Termos MeSH primário: Infecções por Vírus de DNA/virologia
Vírus de DNA/fisiologia
Ligação Viral
Internalização do Vírus
[Mh] Termos MeSH secundário: Animais
Seres Humanos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171119
[Lr] Data última revisão:
171119
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170904
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3497-8


  8 / 3954 MEDLINE  
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[PMID]:28783452
[Au] Autor:Tzannou I; Papadopoulou A; Naik S; Leung K; Martinez CA; Ramos CA; Carrum G; Sasa G; Lulla P; Watanabe A; Kuvalekar M; Gee AP; Wu MF; Liu H; Grilley BJ; Krance RA; Gottschalk S; Brenner MK; Rooney CM; Heslop HE; Leen AM; Omer B
[Ad] Endereço:Ifigeneia Tzannou, Anastasia Papadopoulou, Swati Naik, Kathryn Leung, Caridad A. Martinez, Carlos A. Ramos, George Carrum, Ghadir Sasa, Premal Lulla, Ayumi Watanabe, Manik Kuvalekar, Adrian P. Gee, Bambi J. Grilley, Robert A. Krance, Stephen Gottschalk, Malcolm K. Brenner, Cliona M. Rooney, Helen E.
[Ti] Título:Off-the-Shelf Virus-Specific T Cells to Treat BK Virus, Human Herpesvirus 6, Cytomegalovirus, Epstein-Barr Virus, and Adenovirus Infections After Allogeneic Hematopoietic Stem-Cell Transplantation.
[So] Source:J Clin Oncol;35(31):3547-3557, 2017 Nov 01.
[Is] ISSN:1527-7755
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Purpose Improvement of cure rates for patients treated with allogeneic hematopoietic stem-cell transplantation (HSCT) will require efforts to decrease treatment-related mortality from severe viral infections. Adoptively transferred virus-specific T cells (VSTs) generated from eligible, third-party donors could provide broad antiviral protection to recipients of HSCT as an immediately available off-the-shelf product. Patient and Methods We generated a bank of VSTs that recognized five common viral pathogens: Epstein-Barr virus (EBV), adenovirus (AdV), cytomegalovirus (CMV), BK virus (BKV), and human herpesvirus 6 (HHV-6). The VSTs were administered to 38 patients with 45 infections in a phase II clinical trial. Results A single infusion produced a cumulative complete or partial response rate of 92% (95% CI, 78.1% to 98.3%) overall and the following rates by virus: 100% for BKV (n = 16), 94% for CMV (n = 17), 71% for AdV (n = 7), 100% for EBV (n = 2), and 67% for HHV-6 (n = 3). Clinical benefit was achieved in 31 patients treated for one infection and in seven patients treated for multiple coincident infections. Thirteen of 14 patients treated for BKV-associated hemorrhagic cystitis experienced complete resolution of gross hematuria by week 6. Infusions were safe, and only two occurrences of de novo graft-versus host disease (grade 1) were observed. VST tracking by epitope profiling revealed persistence of functional VSTs of third-party origin for up to 12 weeks. Conclusion The use of banked VSTs is a feasible, safe, and effective approach to treat severe and drug-refractory infections after HSCT, including infections from two viruses (BKV and HHV-6) that had never been targeted previously with an off-the-shelf product. Furthermore, the multispecificity of the VSTs ensures extensive antiviral coverage, which facilitates the treatment of patients with multiple infections.
[Mh] Termos MeSH primário: Infecções por Vírus de DNA/terapia
Vírus de DNA/imunologia
Transplante de Células-Tronco Hematopoéticas/efeitos adversos
Transplante de Células-Tronco Hematopoéticas/métodos
Imunoterapia Adotiva/métodos
Linfócitos T/imunologia
Linfócitos T/transplante
[Mh] Termos MeSH secundário: Adenovírus Humanos/imunologia
Adulto
Vírus BK/imunologia
Infecções por Vírus de DNA/etiologia
Infecções por Vírus de DNA/virologia
Feminino
Herpesvirus Humano 4/imunologia
Herpesvirus Humano 6/imunologia
Seres Humanos
Masculino
Transplante Homólogo
Resultado do Tratamento
[Pt] Tipo de publicação:CLINICAL TRIAL, PHASE II; JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171117
[Lr] Data última revisão:
171117
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170808
[St] Status:MEDLINE
[do] DOI:10.1200/JCO.2017.73.0655


  9 / 3954 MEDLINE  
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[PMID]:28715975
[Au] Autor:Shulman LM; Davidson I
[Ad] Endereço:Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel; email: lester.shulman@bezeqint.net.
[Ti] Título:Viruses with Circular Single-Stranded DNA Genomes Are Everywhere!
[So] Source:Annu Rev Virol;4(1):159-180, 2017 Sep 29.
[Is] ISSN:2327-0578
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Circular single-stranded DNA viruses infect archaea, bacteria, and eukaryotic organisms. The relatively recent emergence of single-stranded DNA viruses, such as chicken anemia virus (CAV) and porcine circovirus 2 (PCV2), as serious pathogens of eukaryotes is due more to growing awareness than to the appearance of new pathogens or alteration of existing pathogens. In the case of the ubiquitous human circular single-stranded DNA virus family Anelloviridae, there is still no convincing direct causal relation to any specific disease. However, infections may play a role in autoimmunity by changing the homeostatic balance of proinflammatory cytokines and the human immune system, indirectly affecting the severity of diseases caused by other pathogens. Infections with CAV (family Anelloviridae, genus Gyrovirus) and PCV2 (family Circoviridae, genus Circovirus) are presented here because they are immunosuppressive and affect health in domesticated animals. CAV shares genomic organization, genomic orientation, and common features of major proteins with human anelloviruses, and PCV2 DNA may be present in human food and vaccines.
[Mh] Termos MeSH primário: Infecções por Circoviridae/veterinária
Infecções por Vírus de DNA/virologia
Vírus de DNA/genética
DNA Circular
DNA de Cadeia Simples/genética
Genoma Viral
[Mh] Termos MeSH secundário: Anelloviridae/genética
Anelloviridae/isolamento & purificação
Animais
Animais Domésticos/virologia
Archaea/virologia
Autoimunidade
Bactérias/virologia
Vírus da Anemia da Galinha/genética
Vírus da Anemia da Galinha/isolamento & purificação
Infecções por Circoviridae/imunologia
Infecções por Circoviridae/virologia
Circovirus/genética
Circovirus/isolamento & purificação
Infecções por Vírus de DNA/imunologia
Vírus de DNA/isolamento & purificação
Vírus de DNA/fisiologia
DNA Viral
Seres Humanos
Suínos/virologia
Doenças dos Suínos/virologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, Circular); 0 (DNA, Single-Stranded); 0 (DNA, Viral)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171027
[Lr] Data última revisão:
171027
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170719
[St] Status:MEDLINE
[do] DOI:10.1146/annurev-virology-101416-041953


  10 / 3954 MEDLINE  
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[PMID]:28538739
[Au] Autor:Quick J; Grubaugh ND; Pullan ST; Claro IM; Smith AD; Gangavarapu K; Oliveira G; Robles-Sikisaka R; Rogers TF; Beutler NA; Burton DR; Lewis-Ximenez LL; de Jesus JG; Giovanetti M; Hill SC; Black A; Bedford T; Carroll MW; Nunes M; Alcantara LC; Sabino EC; Baylis SA; Faria NR; Loose M; Simpson JT; Pybus OG; Andersen KG; Loman NJ
[Ad] Endereço:Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.
[Ti] Título:Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
[So] Source:Nat Protoc;12(6):1261-1276, 2017 Jun.
[Is] ISSN:1750-2799
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
[Mh] Termos MeSH primário: Vírus de DNA/genética
Genoma Viral
Reação em Cadeia da Polimerase Multiplex/métodos
Vírus de RNA/genética
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Epidemiologia Molecular/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170713
[Lr] Data última revisão:
170713
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170525
[St] Status:MEDLINE
[do] DOI:10.1038/nprot.2017.066



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