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1.
In Vivo ; 34(3 Suppl): 1633-1636, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32503822

RESUMO

In a previous study, we identified a 117 base severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence in the human genome with 94.6% identity. The sequence was in chromosome 1p within an intronic region of the netrin G1 (NTNG1) gene. The sequence matched a sequence in the SARS-CoV-2 Orf1b gene in non-structural protein 14 (NSP14), which is an exonuclease and NSP15, an endoribonuclease. In the current study we compared the human genome with other viral genomes to determine some of the characteristics of human sequences found in the latter. Most of the viruses had human sequences, but they were short. Hepatitis A and St Louis encephalitis had human sequences that were longer than the 117 base SARS-Cov-2 sequence, but they were in non-coding regions of the human genome. The SARS-Cov-2 sequence was the only long sequence found in a human gene (NTNG1). The related coronaviruses SARS-Cov had a 41 BP human sequence on chromosome 3 that was not part of a human gene, and MERS had no human sequence. The 117 base SARS-CoV-2 human sequence is relatively close to the viral spike sequence, separated only by NSP16, a 904 base sequence. The mechanism for SARS-CoV-2 infection is the binding of the virus spike protein to the membrane-bound form of angiotensin-converting enzyme 2 (ACE2) and internalization of the complex by the host cell. We have no explanation for the NSP14 and NSP15 SARS-Cov-2 sequences we observed here or how they might relate to infectiousness. Further studies are warranted.


Assuntos
Betacoronavirus/genética , Exorribonucleases/genética , Genoma Viral , Vírus da SARS/genética , Proteínas não Estruturais Virais/genética , Cromossomos Humanos Par 1/genética , Cromossomos Humanos Par 3/genética , Vírus de DNA/genética , Proteínas Ligadas por GPI/genética , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , Netrinas/genética , Alinhamento de Sequência , Homologia de Sequência do Ácido Nucleico , Especificidade da Espécie , Proteínas Virais/genética
2.
Arch Virol ; 165(8): 1843-1847, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32448993

RESUMO

Cocal virus (COCV) is one of the causative agents of vesicular stomatitis, presenting clinical signs indistinguishable from those caused by foot-and-mouth disease virus (FMDV). Therefore, the differentiation of these two viruses via laboratory diagnosis is essential. The objective of this study was to develop and validate a real-time quantitative PCR (RT-qPCR) protocol for the diagnosis of COCV directly from epithelial samples. The method developed had 97% accuracy at 3950 pfu and a repeatability error of 1.29%. RT-qPCR was able to distinguish COCV from other viruses that cause vesicular diseases, an important factor because seroneutralization may produce cross-reactivity between COCV and vesicular stomatitis Alagoas virus (VSAV). No epithelial sample originating from vesicular disease outbreaks between 2014 and 2018 in Brazil was positive for COCV.


Assuntos
Estomatite Vesicular/diagnóstico , Estomatite Vesicular/virologia , Vesiculovirus/genética , Animais , Brasil , Vírus de DNA/genética , Febre Aftosa/diagnóstico , Febre Aftosa/virologia , Vírus da Febre Aftosa/genética , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos
3.
Arch Virol ; 165(8): 1849-1853, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32462285

RESUMO

To characterize their virome, double stranded RNAs extracted from scrapings of two Iranian grapevine varieties held in the Vassal-Montpellier Grapevine Biological Resources Center were analysed by high-throughput sequencing. In addition to several well-known grapevine viruses, divergent isolates of the newly described grapevine Kizil Sapak virus were identified in both accessions. Four complete genome sequences were determined, as well as two additional partial sequences (1,580 and 3,849 nucleotides long). These genomic sequences highlight the molecular diversity of this poorly known virus. In view of the absence of amplification of the GKSV isolates characterized here using the published primer pair, novel degenerate, polyvalent primers were designed, providing a more robust diagnosis.


Assuntos
Vírus/genética , Vitis/virologia , Vírus de DNA/genética , Genoma Viral/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Irã (Geográfico) , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , RNA de Cadeia Dupla/genética , Sequenciamento Completo do Genoma
4.
Arch Virol ; 165(5): 1225-1229, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32146505

RESUMO

Using a high-throughput sequencing approach, we identified four genomoviruses (family Genomoviridae) associated with a sweet orange (Citrus sinensis) plant collected in Tunisia. The ssDNA genomes of these genomoviruses, which were amplified, cloned and Sanger sequenced, range in size from 2156 to 2191 nt. Three of these viruses share > 99% full-genome pairwise sequence identity and are referred to as citrus Tunisia genomovirus 1 (CTNGmV-1). The CTNGmV-1 isolates share < 62% genome-wide pairwise nucleotide sequence identity with other genomoviruses and belong to the genus Gemykolovirus. The genome of the fourth virus, which was called CTNGmV-2, shares < 68% nucleotide sequence identity with other genomoviruses and belongs to the genus Gemycircularvirus. Based on the species demarcation criteria for members of the family Genomoviridae, CTNGmV-1 and -2 would each represent a new species. Although found associated with Citrus sp. plants, it is likely that these viruses infect fungi or other organisms associated with the plants.


Assuntos
Citrus/virologia , Vírus de DNA/classificação , Vírus de DNA/isolamento & purificação , Micovírus/classificação , Micovírus/isolamento & purificação , Análise de Sequência de DNA , Vírus de DNA/genética , Micovírus/genética , Filogenia , Vírus de Plantas/classificação , Vírus de Plantas/genética , Vírus de Plantas/isolamento & purificação , Homologia de Sequência do Ácido Nucleico , Tunísia
5.
Arch Virol ; 165(3): 771-774, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31960157

RESUMO

Long-distance migratory insects carry microorganisms that can potentially play a crucial role in the life cycles of their hosts. Here, we used Illumina and Sanger sequencing to determine the complete genome sequence of a novel circular Rep-encoding single-stranded (ss) DNA virus from an important migratory pest, Agrotis ipsilon (Hufnagel). The full genome of this new virus is about 2, 242 nt in length and shares 55-75% genome-wide pairwise sequence identity with members of the family Genomoviridae but 91% nucleotide sequence identity with finch-associated genomovirus 3 isolate S30P_D, which is tentatively abbreviated "FaGmV-3". Viral infection rates in A. ipsilon from Yantai, Langfang and Xinxiang were 4.5% (n = 88), 11.8% (n = 85) and 0% (n = 35), respectively. Phylogenetic analysis based on the deduced amino acid sequence of Rep indicated that the Agrotis ipsilon-associated virus is closely related to members of the genus Gemykibivirus, and we propose it to be a new member of this genus. Hence, it is tentatively named "Agrotis ipsilon-associated genomovirus" (AiGmV).


Assuntos
Vírus de DNA , Vírus de Insetos/classificação , Vírus de Insetos/genética , Mariposas/virologia , Sequência de Aminoácidos , Animais , Sequência de Bases , China , Vírus de DNA/classificação , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , DNA de Cadeia Simples/genética , Vírus de Insetos/isolamento & purificação , Análise de Sequência de DNA
6.
Viruses ; 12(2)2020 Jan 26.
Artigo em Inglês | MEDLINE | ID: mdl-31991902

RESUMO

The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.


Assuntos
Vírus de DNA/isolamento & purificação , Fezes/virologia , Tartarugas/virologia , Animais , Arizona , Vírus de DNA/classificação , Vírus de DNA/genética , DNA Circular , DNA de Cadeia Simples/genética , Genoma Viral , Microviridae/classificação , Microviridae/genética , Microviridae/isolamento & purificação , Microvirus/classificação , Microvirus/genética , Microvirus/isolamento & purificação , Filogenia , Recombinação Genética , Proteínas Virais/genética
7.
Nature ; 578(7795): 432-436, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31968354

RESUMO

Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.


Assuntos
Biodiversidade , Vírus de DNA/classificação , Vírus de DNA/genética , Células Eucarióticas/metabolismo , Células Eucarióticas/virologia , Interações entre Hospedeiro e Microrganismos/genética , Metagenômica , Animais , Proteínas do Capsídeo/genética , Transferência Genética Horizontal , Genoma Viral/genética , Vírus Gigantes/classificação , Vírus Gigantes/genética , Filogenia
8.
Arch Virol ; 165(2): 403-406, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31797130

RESUMO

BACKGROUND: In May 2018, a 8 year old thoroughbred mare died at an equestrian club in Changji, Xinjiang, China. The horse had been imported from the United States in 2013. She became pregnant in December 2016 but, after foaling, gradually lost weight and died in May 2018. This study aim to identify the pathogen, who cause of horse death, using virome. RESULTS: We have identified an Equ1-like virus from the fecal virome of a dead thoroughbred mare in China. Full genomic sequencing and phylogenetic analysis of the virus, tentatively named "kirkovirus Cj-7-7", showed that it was closely related to kirkovirus Equ1 and clustered together with po-circo-like viruses 21, 22, 41, and 51, suggesting that it should be assigned to the proposed family "Kirkoviridae". An epidemiological investigation showed that kirkovirus Cj-7-7 circulates in horses of northern Xinjiang and may specifically infect intestinal cells. CONCLUSIONS: Our findings demonstrate the genetic diversity and geographic distribution of Kirkoviruses, and the prevalence of Kirkovirus Cj-7-7 in Xinjiang, China.


Assuntos
Infecções por Vírus de DNA/veterinária , Vírus de DNA/classificação , Vírus de DNA/isolamento & purificação , Fezes/virologia , Doenças dos Cavalos/virologia , Animais , China , Análise por Conglomerados , Infecções por Vírus de DNA/patologia , Infecções por Vírus de DNA/virologia , Vírus de DNA/genética , Genoma Viral , Doenças dos Cavalos/patologia , Cavalos , Filogenia , Análise de Sequência de DNA , Homologia de Sequência , Estados Unidos , Sequenciamento Completo do Genoma
9.
Talanta ; 207: 120308, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31594570

RESUMO

Given the threat that ostreid herpesvirus 1 (OsHV-1) poses to shellfish aquaculture, the need for rapid, user-friendly and cost-effective methods to detect this marine pathogen and minimise its impact is evident. In this work, an electrochemical biosensor for the detection of OsHV-1 based on isothermal recombinase polymerase amplification (RPA) was developed. The system was first tested and optimised on maleimide microtitre plates as a proof-of-concept, before being implemented on miniaturised gold electrodes. Amperometric detection of the isothermally amplified product was achieved through a sandwich hybridisation assay with an immobilised thiolated capture probe and a horseradish peroxidase (HRP)-labelled reporter probe. Calibration curves were constructed using PCR-amplified OsHV-1 DNA, achieving a limit of detection of 207 OsHV-1 target copies. The biosensor was applied to the analysis of 16 oyster samples from an infectivity experiment, and results were compared with those obtained by qPCR analysis, showing a strong degree of correlation (r = 0.988). The simplicity, rapidity, cost-effectiveness and potential for in-situ testing with the developed biosensor provide a valuable tool for the detection of OsHV-1 in aquaculture facilities, improving their management.


Assuntos
Técnicas Biossensoriais/métodos , Crassostrea/virologia , Vírus de DNA/genética , DNA Viral/análise , DNA Viral/genética , Miniaturização , Temperatura , Animais , Técnicas Biossensoriais/economia , Calibragem , Calorimetria , Análise Custo-Benefício , Eletroquímica , Eletrodos , Limite de Detecção , Técnicas de Amplificação de Ácido Nucleico , Fatores de Tempo
10.
J Gen Virol ; 101(2): 226-239, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31855134

RESUMO

Diaphorina citri densovirus (DcDV) is an ambisense densovirus with a 5071 nt genome. Phylogenetic analysis places DcDV in an intermediate position between those in the Ambidensovirus and Iteradensovirus genera, a finding that is consistent with the observation that DcDV possesses an Iteradensoviris-like non-structural (NS) protein-gene cassette, but a capsid-protein (VP) gene cassette resembling those of other ambisense densoviruses. DcDV is maternally transmitted to 100 % of the progeny of infected female Diaphorina citri, and the progeny of infected females carry DcDV as a persistent infection without outward phenotypic effects. We were unable to infect naïve individuals by oral inoculation, however low levels of transient viral replication are detected following intrathoracic injection of DcDV virions into uninfected D. citri insects. Transcript mapping indicates that DcDV produces one transcript each from the NS and VP gene cassettes and that these transcripts are polyadenylated at internal sites to produce a ~2.2 kb transcript encoding the NS proteins and a ~2.4 kb transcript encoding the VP proteins. Additionally, we found that transcriptional readthrough leads to the production of longer non-canonical transcripts from both genomic strands.


Assuntos
Densovirus , Genoma Viral , Hemípteros/virologia , Viroses/transmissão , Animais , Proteínas do Capsídeo/genética , Classificação , Vírus de DNA/genética , Densovirus/classificação , Densovirus/genética , Densovirus/isolamento & purificação , Genes Virais , Transmissão Vertical de Doença Infecciosa , Vírus de Insetos/classificação , Parvoviridae/classificação , Filogenia , Proteínas não Estruturais Virais/genética , Proteínas Virais/genética
11.
BMC Genet ; 20(1): 96, 2019 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-31830898

RESUMO

BACKGROUND: Variants of the Ostreid herpesvirus 1 (OsHV-1) cause high losses of Pacific oysters globally, including in Tomales Bay, California, USA. A suite of new variants, the OsHV-1 microvariants (µvars), cause very high mortalities of Pacific oysters in major oyster-growing regions outside of the United States. There are currently no known Pacific oysters in the United States that are resistant to OsHV-1 as resistance has yet to be evaluated in these oysters. As part of an effort to begin genetic selection for resistance to OsHV-1, 71 families from the Molluscan Broodstock Program, a US West Coast Pacific oyster breeding program, were screened for survival after exposure to OsHV-1 in Tomales Bay. They were also tested in a quarantine laboratory in France where they were exposed to a French OsHV-1 microvariant using a plate assay, with survival recorded from three to seven days post-infection. RESULTS: Significant heritability for survival were found for all time points in the plate assay and in the survival phenotype from a single mortality count in Tomales Bay. Genetic correlations between survival against the French OsHV-1 µvar in the plate assay and the Tomales Bay variant in the field trait were weak or non-significant. CONCLUSIONS: Future breeding efforts will seek to validate the potential of genetic improvement for survival to OsHV-1 through selection using the Molluscan Broodstock Program oysters. The lack of a strong correlation in survival between OsHV-1 variants under this study's exposure conditions may require independent selection pressure for survival to each variant in order to make simultaneous genetic gains in resistance.


Assuntos
Crassostrea/crescimento & desenvolvimento , Vírus de DNA/genética , Resistência à Doença , Animais , Cruzamento , California , Crassostrea/genética , Crassostrea/virologia , Vírus de DNA/classificação , França , Variação Genética , Mortalidade , Seleção Genética
12.
Arch Virol ; 164(12): 3035-3043, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31602543

RESUMO

Seasonally recurrent outbreaks of mass mortality in Pacific oysters (Crassostrea gigas) caused by microvariant genotypes of ostreid herpesvirus 1 (OsHV-1) occur in Europe, New Zealand and Australia. The incubation period for OsHV-1 under experimental conditions is 48-72 hours and depends on water temperature, as does the mortality. An in vivo growth curve for OsHV-1 was determined by quantifying OsHV-1 DNA at 10 time points between 2 and 72 hours after exposure to OsHV-1. The peak replication rate was the same at 18 °C and 22 °C; however, there was a longer period of amplification leading to a higher peak concentration at 22 °C (2.34 × 107 copies/mg at 18 hours) compared to 18 °C (1.38 × 105 copies/mg at 12 hours). The peak viral concentration preceded mortality by 72 hours and 20 hours at 18 °C and 22 °C, respectively. Cumulative mortality to day 14 was 45.9% at 22 °C compared to 0.3% at 18 °C. The prevalence of OsHV-1 infection after 14 days at 18 °C was 33.3%. No mortality from OsHV-1 occurred when the water temperature in tanks of oysters challenged at 18 °C was increased to 22 °C for 14 days. The influence of water temperature prior to exposure to OsHV-1 and during the initial virus replication is an important determinant of the outcome of infection in C. gigas.


Assuntos
Crassostrea/fisiologia , Crassostrea/virologia , Vírus de DNA/crescimento & desenvolvimento , Frutos do Mar/virologia , Animais , Crassostrea/crescimento & desenvolvimento , Vírus de DNA/genética , DNA Viral/genética , Temperatura
13.
Proc Natl Acad Sci U S A ; 116(45): 22591-22597, 2019 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-31636205

RESUMO

Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the Sulfolobus polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a T = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.


Assuntos
Vírus de Archaea/fisiologia , Vírus de DNA/fisiologia , DNA Forma A/genética , DNA Viral/genética , Montagem de Vírus , Vírus de Archaea/genética , Vírus de Archaea/ultraestrutura , Capsídeo/metabolismo , Capsídeo/ultraestrutura , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , Microscopia Crioeletrônica , Vírus de DNA/genética , Vírus de DNA/ultraestrutura , DNA Forma A/metabolismo , DNA Viral/metabolismo , Sulfolobus/virologia
14.
Proc Natl Acad Sci U S A ; 116(39): 19585-19592, 2019 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-31506349

RESUMO

Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.


Assuntos
Evolução Biológica , Eucariotos/genética , Vírus Gigantes/genética , Núcleo Celular/genética , Citoplasma/virologia , Vírus de DNA/genética , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Células Eucarióticas/metabolismo , Evolução Molecular , Vírus Gigantes/metabolismo , Filogenia
15.
J Vet Diagn Invest ; 31(5): 719-725, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31423916

RESUMO

Aves polyomavirus 1, psittacine beak and feather disease virus, and psittacid herpesvirus 1 are important pathogens of psittacine birds with the potential to cause substantial morbidity and mortality. Using publically available nucleotide sequences, we developed and validated a triplex real-time PCR (rtPCR) assay to rapidly detect these 3 viruses. The assay had high analytical sensitivity, detecting <6 copies of viral DNA per reaction, and 100% analytical specificity, showing no cross-reactivity with 59 other animal pathogens. Archived formalin-fixed, paraffin-embedded tissues from psittacine birds diagnosed at postmortem as infected with each of the viruses as well as virus-negative birds were used to validate the utility of the assay. Birds were selected for the positive cohort if they showed histologic evidence of infection (i.e., characteristic inclusion bodies in tissues); birds in the negative cohort had final diagnoses unrelated to the pathogens of interest. The triplex rtPCR assay confirmed 98% of histopathology-positive cases, and also identified subclinical infections that were not observed by histologic examination, including coinfections. Birds that tested positive only by rtPCR had significantly higher cycle threshold values compared to those with histologic evidence of infection. Positive, negative, and overall percentage agreements as well as the kappa statistic between the results of the assay and histopathology were high, demonstrating the usefulness of the assay as a tool to confirm disease diagnoses, and to improve detection of subclinical infections.


Assuntos
Doenças das Aves/diagnóstico , Infecções por Vírus de DNA/veterinária , Vírus de DNA/isolamento & purificação , Herpesviridae/isolamento & purificação , Reação em Cadeia da Polimerase Multiplex/veterinária , Psittaciformes/virologia , Alphaherpesvirinae/genética , Alphaherpesvirinae/isolamento & purificação , Animais , Doenças das Aves/virologia , Infecções por Circoviridae/diagnóstico , Infecções por Circoviridae/veterinária , Infecções por Circoviridae/virologia , Circovirus/genética , Circovirus/isolamento & purificação , Infecções por Vírus de DNA/diagnóstico , Infecções por Vírus de DNA/virologia , Vírus de DNA/genética , DNA Viral , Herpesviridae/genética , Papagaios/virologia , Polyomaviridae/genética , Polyomaviridae/isolamento & purificação , Polyomavirus/genética , Polyomavirus/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/veterinária
16.
Emerg Microbes Infect ; 8(1): 1205-1218, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31409221

RESUMO

The in silico analyses of 109 replication-competent genomic DNA sequences isolated from cow milk and its products (97 in the bovine meat and milk factors 2 group - BMMF2, and additional 4 in BMMF1) seems to place these in a specific class of infectious agents spanning between bacterial plasmid and circular ssDNA viruses. Satellite-type small plasmids with partial homology to larger genomes, were also isolated in both groups. A member of the BMMF1 group H1MBS.1 was recovered in a distinctly modified form from colon tissue by laser microdissection. Although the evolutionary origin is unknown, it draws the attention to the existence of a hitherto unrecognized, broad spectrum of potential pathogens. Indirect hints to the origin and structure of our isolates, as well as to their replicative behaviour, result from parallels drawn to the Hepatitis deltavirus genome structure and replication.


Assuntos
Neoplasias do Colo/virologia , Vírus de DNA/isolamento & purificação , Laticínios/virologia , Leite/virologia , Soro/virologia , Vírus não Classificados/isolamento & purificação , Animais , Bovinos , Vírus de DNA/genética , Humanos , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Vírus não Classificados/genética
17.
Environ Microbiol ; 21(12): 4548-4562, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31325353

RESUMO

Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.


Assuntos
Bactérias/isolamento & purificação , Crassostrea/microbiologia , Microbiota , Animais , Bactérias/classificação , Bactérias/genética , Vírus de DNA/classificação , Vírus de DNA/genética , Vírus de DNA/isolamento & purificação , Europa (Continente) , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota/genética , Tipagem Molecular , Filogenia , RNA Bacteriano , RNA Ribossômico 16S , Reação em Cadeia da Polimerase em Tempo Real , Vibrio/genética , Vibrio/isolamento & purificação , Virulência/genética
18.
Annu Rev Virol ; 6(1): 275-296, 2019 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-31283444

RESUMO

Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.


Assuntos
Cromossomos , Replicação do DNA , Vírus de DNA/genética , DNA Viral/genética , Genoma Viral , Interações entre Hospedeiro e Microrganismos/genética , Herpesvirus Humano 4/genética , Herpesvirus Humano 8/genética , Humanos , Papillomaviridae/genética , Replicação Viral/genética
19.
Int J Mol Sci ; 20(13)2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31266227

RESUMO

Although cytomegalovirus (CMV) DNA detection in urine is the standard method for diagnosing congenital cytomegalovirus infection (CCMVI), polymerase chain reaction (PCR) is not comprehensively available. Currently, the efficacy of CMV-specific IgM (CMV-IgM) and CMV-specific IgG (CMV-IgG) detection remains unclear. To determine the sensitivity and specificity of CMV-specific antibodies at birth, we investigated CMV-IgM and CMV-IgG titers in CCMVI cases and non-CCMVI controls, with confirmed diagnoses by urine quantitative real-time PCR within 3 weeks after birth. We included 174 infants with suspected CCMVI in whom serological testing was performed within the first 2 weeks after birth during 2012-2018. We classified the participants into a CCMVI group (n = 32) and non-CCMVI group (n = 142) based on their urine PCR results. The CMV-IgM-positive rate was 27/32 (84.4%) in the CCMVI group, compared with 1/142 (0.7%) in the non-CCMVI group (p < 0.0001). The positive CMV-IgG rates were 32/32 (100%) in the CCMVI group and 141/142 (99.3%) in the non-CCMVI group. The positive predictive value for CMV-IgM was high at 96.4% (27/28). This value may be sufficient for clinical use, especially in settings with limited resources where PCR is unavailable. However, CCMVI screening by CMV-IgM alone appears insufficient because of the considerable number of false-negative cases.


Assuntos
Infecções por Citomegalovirus/congênito , Infecções por Citomegalovirus/diagnóstico , Citomegalovirus/imunologia , Imunoglobulina M/metabolismo , Anticorpos Antivirais/metabolismo , Citomegalovirus/genética , Infecções por Citomegalovirus/imunologia , Vírus de DNA/genética , DNA Viral/análise , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Valor Preditivo dos Testes , Estudos Prospectivos , Urina/virologia
20.
BMC Evol Biol ; 19(1): 149, 2019 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337330

RESUMO

BACKGROUND: Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. RESULTS: We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. CONCLUSIONS: We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.


Assuntos
Antivirais/metabolismo , Vírus de DNA/genética , Moluscos/virologia , Edição de RNA/genética , RNA Viral/genética , Proteínas de Ligação a RNA/metabolismo , Animais , Teorema de Bayes , Vírus de DNA/fisiologia , Regulação da Expressão Gênica , Genoma Viral , Modelos Moleculares , Moluscos/genética , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Domínios Proteicos , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Transcriptoma/genética
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