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1.
Infect Genet Evol ; 66: 9-12, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30201501

RESUMO

Cycloviruses, small ssDNA viruses belonging to the Circoviridae family, have been suggested as possible causes of enteric, respiratory and neurological disorders in human patients. One of these species, cyclovirus-Vietnam (CyCV-VN), initially isolated from cerebrospinal fluid samples of patients with unexplained neurological disorders, has since been reported in serum samples from chronically patients infected with HBV, HCV or HIV, in Italy. On the other hand, CyCV-VN was not detected in serum samples from healthy individuals. Here, we report on a high prevalence of 43.4% (40/92) of CyCV-VN in plasma samples from asymptomatic blood donors from Madagascar. Interestingly, this virus was not detected by metagenomics and PCR in six other African countries, suggesting regional differences in CyCV-VN prevalence across Africa. Phylogenetic analysis based on the complete genomes showed that CyCV-VN sequences isolated from blood were most closely related to sequences previously reported from human stool in Madagascar. Further investigations using larger cohorts are required to determine the global epidemiology, the natural history and the pathological significance, if any, of CyCV-VN infection in humans.


Assuntos
Doadores de Sangue , Infecções por Circoviridae/virologia , Circoviridae , Adolescente , Adulto , Circoviridae/classificação , Circoviridae/genética , Infecções por Circoviridae/sangue , DNA Viral , Feminino , Genoma Viral , Humanos , Madagáscar/epidemiologia , Masculino , Metagenômica/métodos , Pessoa de Meia-Idade , Filogenia , Prevalência , Vigilância em Saúde Pública , Adulto Jovem
2.
Arch Virol ; 163(9): 2569-2573, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29774431

RESUMO

Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.6% genome-wide identity to known cycloviruses and 61.6-65.1% among themselves. Thus, according to the current species demarcation criteria, they represent three novel cycloviruses. Notably, DfCyV-10 has a predicted replication-associated protein (Rep) that is most similar to that of bat associated cyclovirus 2 (BatACyV-2), a cyclovirus discovered in China, with 79.4% amino acid sequence identity, but a putative capsid protein (Cp) most similar to that of BatACyV-10, a cyclovirus discovered in Brazil, with 71.7% amino acid sequence identity. These data are useful for understanding the diversity and evolution of cycloviruses, especially those found in insects.


Assuntos
Proteínas do Capsídeo/genética , Circoviridae/genética , DNA Viral/genética , Genoma Viral , Odonatos/virologia , Filogenia , Sequência de Aminoácidos , Animais , Evolução Biológica , China , Circoviridae/classificação , Circoviridae/isolamento & purificação , Variação Genética , Conformação de Ácido Nucleico , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
3.
Vet J ; 232: 57-64, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29428093

RESUMO

A number of novel viruses have been associated with canine gastroenteritis in recent years, from viral families as diverse as Caliciviridae and Picornaviridae to Parvoviridae and Circoviridae. The ability of many of these viruses to cause disease is uncertain, but epidemiological studies are continually adding to our knowledge of these potential pathogens. This review presents a summary of the latest research and current understanding of novel viruses associated with canine gastroenteritis.


Assuntos
Doenças do Cão/virologia , Gastroenterite/veterinária , Animais , Caliciviridae/isolamento & purificação , Circoviridae/isolamento & purificação , Coronaviridae/isolamento & purificação , Cães , Fezes/virologia , Gastroenterite/epidemiologia , Gastroenterite/virologia , Parvoviridae/isolamento & purificação , Picornaviridae/isolamento & purificação , Rotavirus/isolamento & purificação , Viroses/epidemiologia , Viroses/veterinária , Viroses/virologia
4.
Arch Virol ; 163(3): 671-678, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29247338

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.


Assuntos
Quirópteros/virologia , Circoviridae/genética , Infecções por Vírus de DNA/epidemiologia , Vírus de DNA/genética , DNA de Cadeia Simples/genética , DNA Viral/genética , Genoma Viral , 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 , República da Geórgia/epidemiologia , Humanos , Filogenia , Replicação Viral
5.
Arch Virol ; 162(12): 3925-3929, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28940019

RESUMO

The genome sequence of a novel avian cyclovirus is described in this study. The genome size and orientation of predicted genes was similar to those described in other vertebrate and insect origin cycloviruses. The greatest genome sequence identity was shared with a dragonfly cyclovirus (nt, 60.6%). Phylogenetic analysis showed marginal relatedness with another avian cyclovirus, the chicken associated cyclovirus 1. In contrast, along a short fragment of the replication-associated protein coding gene (rep) (spanning nt 1240-1710) the duck origin cyclovirus was very similar to human origin and honey bee origin rep sequences (human - TN4, 98%; honey bee - hb10, 100%). Related cyclovirus strains existing amongst various animal species living in diverse ecosystems and separated by large geographic distances show the need for additional studies to better understand the ecology and epidemiology of cycloviruses.


Assuntos
Circoviridae/classificação , Circoviridae/genética , Patos/virologia , Genoma Viral , Análise de Sequência de DNA , Animais , Circoviridae/isolamento & purificação , Ordem dos Genes , Genes Virais , Filogenia , Homologia de Sequência
6.
J Gen Virol ; 98(8): 1997-1998, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28786778

RESUMO

The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80 % genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/circoviridae.


Assuntos
Infecções por Circoviridae/virologia , Circoviridae/classificação , Animais , Circoviridae/genética , Circoviridae/isolamento & purificação , Circoviridae/fisiologia , Genoma Viral , Humanos , Fases de Leitura Aberta , Replicação Viral
7.
Proc Natl Acad Sci U S A ; 114(30): E6166-E6175, 2017 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-28696303

RESUMO

Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of autoimmunity in children at risk for type 1 diabetes (T1D). A total of 220 virus-enriched preparations from serially collected fecal samples from 11 children (cases) who developed serum autoantibodies associated with T1D (of whom five developed clinical T1D) were compared with samples from controls. Intestinal viromes of case subjects were less diverse than those of controls. Among eukaryotic viruses, we identified significant enrichment of Circoviridae-related sequences in samples from controls in comparison with cases. Enterovirus, kobuvirus, parechovirus, parvovirus, and rotavirus sequences were frequently detected but were not associated with autoimmunity. For bacteriophages, we found higher Shannon diversity and richness in controls compared with cases and observed that changes in the intestinal virome over time differed between cases and controls. Using Random Forests analysis, we identified disease-associated viral bacteriophage contigs after subtraction of age-associated contigs. These disease-associated contigs were statistically linked to specific components of the bacterial microbiome. Thus, changes in the intestinal virome preceded autoimmunity in this cohort. Specific components of the virome were both directly and inversely associated with the development of human autoimmune disease.


Assuntos
Autoimunidade , Diabetes Mellitus Tipo 1/virologia , Microbioma Gastrointestinal , Intestinos/virologia , Circoviridae/isolamento & purificação , Estudos de Coortes , Diabetes Mellitus Tipo 1/imunologia , Predisposição Genética para Doença , Humanos , Lactente , Recém-Nascido
8.
Zoonoses Public Health ; 64(8): 636-646, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-28371451

RESUMO

Bats are considered as the reservoirs of several emerging infectious disease, and novel viruses are continually found in bats all around the world. Studies conducted in southern China found that bats carried a variety of viruses. However, few studies have been conducted on bats in northern China, which harbours a diversity of endemic insectivorous bats. It is important to understand the prevalence and diversity of viruses circulating in bats in northern China. In this study, a total of 145 insectivorous bats representing six species were collected from northern China and screened with degenerate primers for viruses belonging to six families, including coronaviruses, astroviruses, hantaviruses, paramyxoviruses, adenoviruses and circoviruses. Our study found that four of the viruses screened for were positive and the overall detection rates for astroviruses, coronaviruses, adenoviruses and circoviruses in bats were 21.4%, 15.9%, 20% and 37.2%, respectively. In addition, we found that bats in northern China harboured a diversity of novel viruses. Common Serotine (Eptesicus serotinu), Fringed long-footed Myotis (Myotis fimriatus) and Peking Myotis (Myotis pequinius) were investigated in China for the first time. Our study provided new information on the ecology and phylogeny of bat-borne viruses.


Assuntos
Quirópteros/virologia , Vírus/isolamento & purificação , Adenoviridae/genética , Adenoviridae/isolamento & purificação , Animais , Astroviridae/genética , Astroviridae/isolamento & purificação , China/epidemiologia , Circoviridae/genética , Circoviridae/isolamento & purificação , Coronaviridae/genética , Coronaviridae/isolamento & purificação , Filogenia , Vírus/classificação , Vírus/genética
9.
Arch Virol ; 162(8): 2403-2407, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28447216

RESUMO

Members of the viral family Circoviridae are increasingly recognized worldwide. Bats seem to be natural reservoirs or dietary-related dispensers of these viruses. Here, we report a distantly related member of the genus Cyclovirus detected in the faeces of a great roundleaf bat (Hipposideros armiger). Interestingly, the novel virus lacks a Circoviridae-specific stem-loop structure, although a Geminiviridae-like nonamer sequence was detected in the large intergenic region. Based on these differences and its phylogenetic position, we propose that our new virus represents a distant and highly divergent member of the genus Cyclovirus. However it is lacking several characteristics of members of the genus, which raises a challenge in its taxonomic classification.


Assuntos
Quirópteros/virologia , Infecções por Circoviridae/veterinária , Circoviridae/genética , Circoviridae/isolamento & purificação , Variação Genética , Animais , Circoviridae/classificação , Infecções por Circoviridae/epidemiologia , Infecções por Circoviridae/virologia , DNA Intergênico , Reservatórios de Doenças/virologia , Fezes/virologia , Geminiviridae/genética , Filogenia , Vietnã/epidemiologia
10.
J Clin Virol ; 81: 12-5, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27270127

RESUMO

BACKGROUND: Cyclovirus Vietnam (CyCV-VN) is a CyCV detected in 2013 from cerebrospinal fluid (CSF) samples of patients with neurological disorders. Information on prevalence, pathogenesis and disease association of CyCV-VN is still very patchy. OBJECTIVES AND STUDY DESIGN: In this study, we have used a PCR assay targeting the Rep gene to investigate the prevalence of CyCV-VN infection in blood and CSF samples of 346 Italian subjects. RESULTS: Overall, 7% of blood samples were positive for CyCV-VN while the virus was not detected in any of the CSF samples. The prevalence of CyCV-VN was relatively high in HIV positive patients (21%), modest in patients with HBV or HCV infection (6%), and low in transplant recipient patients (2%). Positive patients showed low levels of CyCV-VN viremia. The virus was not detected in serum samples from healthy individuals. Longitudinal analysis of serum samples obtained from selected patients showed a stable or transient presence of circulating CyCV-VN. CONCLUSIONS: The present study is the first to demonstrate CyCV-VN DNA circulation in Italy and to cast light on some biological aspects of this novel virus of men.


Assuntos
Infecções por Circoviridae/virologia , Circoviridae , DNA Viral/sangue , Infecções por HIV/complicações , Adulto , Idoso , Circoviridae/genética , Circoviridae/isolamento & purificação , Infecções por Circoviridae/sangue , Infecções por Circoviridae/complicações , Estudos de Coortes , Feminino , Hepatite B/complicações , Hepatite C/complicações , Humanos , Hospedeiro Imunocomprometido , Itália , Masculino , Pessoa de Meia-Idade
11.
Virus Genes ; 52(5): 727-31, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27115421

RESUMO

Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.


Assuntos
Infecções por Circoviridae/virologia , Circovirus/genética , Genoma Viral/genética , Paleógnatas/virologia , Animais , Proteínas do Capsídeo/genética , Circoviridae/genética , DNA de Cadeia Simples/genética , DNA Viral/genética , Nova Zelândia , Fases de Leitura Aberta/genética , Filogenia
12.
J Clin Virol ; 68: 76-8, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26071341

RESUMO

BACKGROUND: Cyclovirus (CyCV) Malawi strain VS5700009 has recently been discovered and reported in clinical cerebrospinal fluid (CSF) samples. Further epidemiological and case-control studies are warranted. The availability of a highly sensitive and specific detection assay for this new virus is thus crucial. OBJECTIVES: To evaluate the performance of the first and the only available PCR assay for CyCV-VS5700009. STUDY DESIGN: A total of 100 CSF samples collected during January-December 2010 were selected for PCR detection of CyCV-VS5700009. Positive PCR amplicons were subjected to sequencing confirmation and BLAST analysis. RESULTS: Initial PCR screening for CyCV-VS5700009 identified one sample, showing a PCR band of expected size (380 bp). Sequencing and BLAST analysis, however, indicated that the band was 364 bp in length and showed >99% nucleotide homology to a human gene known as nuclear receptor coactivator 6 (NCOA6). Pairwise sequence alignment confirmed that both the forward and reverse PCR primers used had significant homology (>70%) to NCOA6. None of the CSF samples tested were positive for CyCV-VS5700009. CONCLUSIONS: The original PCR assay for CyCV-VS5700009 detection may have potential cross-reactivity with contaminating human genomic DNA. The assay may be of little diagnostic use on clinical specimens that are rich in host DNA such as biopsy tissues.


Assuntos
Líquido Cefalorraquidiano/virologia , Infecções por Circoviridae/diagnóstico , Circoviridae/isolamento & purificação , Encefalite Viral/diagnóstico , Reações Falso-Positivas , Reação em Cadeia da Polimerase/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Circoviridae/genética , Feminino , Humanos , Lactente , Recém-Nascido , Malaui , Masculino , Pessoa de Meia-Idade , Adulto Jovem
13.
Virus Genes ; 51(1): 148-51, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-26089292

RESUMO

A novel cyclovirus was identified in the intestinal contents of Taiwan squirrels (Callosciurus erythraeus thaiwanensis) collected in Kanagawa prefecture, Japan, by metagenomic analysis, and was named Taiwan squirrel cyclovirus-1 (TsCyV-1). Phylogenetic analysis showed that TsCyV-1 formed a branch separate from other representative cyclovirus strains. TsCyV-1 is considered to be a new species in the genus Cyclovirus because the criteria for demarcation of cyclovirus species is proposed as nucleotide identities <80 %.


Assuntos
Circoviridae/classificação , Circoviridae/isolamento & purificação , DNA Viral/química , DNA Viral/genética , Conteúdo Gastrointestinal/virologia , Genoma Viral , Sciuridae/virologia , Animais , Circoviridae/genética , Análise por Conglomerados , Japão , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Homologia de Sequência
14.
Appl Environ Microbiol ; 81(12): 3934-45, 2015 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-25841004

RESUMO

The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.


Assuntos
Circoviridae/isolamento & purificação , Vírus de DNA/classificação , Vírus de DNA/isolamento & purificação , Microviridae/isolamento & purificação , Microbiologia do Solo , Solo/classificação , Sequência de Bases , Biodiversidade , Proteínas do Capsídeo/genética , Circoviridae/classificação , Circoviridae/genética , Vírus de DNA/genética , DNA de Cadeia Simples/genética , DNA Viral/genética , Genoma Viral , Irlanda , Metagenômica , Microviridae/classificação , Microviridae/genética , Filogenia , Escócia , Análise de Sequência de DNA , Vírion/classificação , Vírion/isolamento & purificação
15.
Virology ; 482: 98-104, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25839169

RESUMO

Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.


Assuntos
Circoviridae/isolamento & purificação , DNA Circular/genética , DNA de Cadeia Simples/genética , Diarreia/virologia , Encefalite/virologia , Genoma Viral , Esgotos/virologia , Adolescente , Adulto , Idoso , Brasil , Líquido Cefalorraquidiano/virologia , Criança , Pré-Escolar , Circoviridae/genética , Análise por Conglomerados , DNA Circular/isolamento & purificação , DNA de Cadeia Simples/isolamento & purificação , Fezes/virologia , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Nicarágua , Filogenia , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Homologia de Sequência , Sri Lanka , Adulto Jovem
16.
PLoS One ; 10(2): e0118070, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25688970

RESUMO

Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.


Assuntos
Quirópteros/virologia , Circoviridae/genética , DNA de Cadeia Simples/genética , Ingestão de Alimentos , Genômica , Insetos , Animais , Brasil , Quirópteros/fisiologia , Circoviridae/classificação , Fezes/virologia , Variação Genética , Filogenia , Reação em Cadeia da Polimerase
17.
Sci Rep ; 4: 7552, 2014 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-25518947

RESUMO

Cycloviruses, small ssDNA viruses of the Circoviridae family, have been identified in the cerebrospinal fluid from symptomatic human patients. One of these species, cyclovirus-Vietnam (CyCV-VN), was shown to be restricted to central and southern Vietnam. Here we report the detection of CyCV-VN species in stool samples from pigs and humans from Africa, far beyond their supposed limited geographic distribution.


Assuntos
Circoviridae/genética , Fezes/virologia , Adolescente , África , Animais , Sequência de Bases , Criança , Pré-Escolar , DNA Viral/genética , Genoma Viral/genética , Humanos , Lactente , Recém-Nascido , Dados de Sequência Molecular , Filogenia , Suínos , Vietnã
18.
Gene ; 552(2): 209-18, 2014 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-25241644

RESUMO

Microsatellites or Simple Sequence Repeats (SSRs) are tandem iterations of one to six base pairs, non-randomly distributed throughout prokaryotic and eukaryotic genomes. Limited knowledge is available about distribution of microsatellites in single stranded DNA (ssDNA) viruses, particularly vertebrate infecting viruses. We studied microsatellite distribution in 118 ssDNA virus genomes belonging to three families of vertebrate infecting viruses namely Circoviridae, Parvoviridae, and Anelloviridae, and found that microsatellites constitute an important component of these virus genomes. Mononucleotide repeats were predominant followed by dinucleotide and trinucleotide repeats. A strong positive relationship existed between number of mononucleotide repeats and genome size among all the three virus families. A similar relationship existed for the occurrence of DTTPH (di-, tri-, tetra-, penta- and hexa-nucleotide) repeats in the families Anelloviridae and Parvoviridae only. Relative abundance and relative density of mononucleotide repeats showed a strong positive relationship with genome size in Circoviridae and Parvoviridae. However, in the case of DTTPH repeats, these features showed a strong relationship with genome size in Circoviridae only. On the other hand, relative microsatellite abundance and relative density of mononucleotide repeats were negatively correlated with GC content (%) in Parvoviridae genomes. On the basis of available annotations, our analysis revealed maximum occurrence of mononucleotide as well as DTTPH repeats in the coding regions of these virus genomes. Interestingly, after normalizing the length of the coding and non-coding regions of each virus genome, we found relative density of microsatellites much higher in the non-coding regions. We understand that the present study will help in the better characterization of the stability, genome organization and evolution of these virus classes and may provide useful leads to decipher the etiopathogenesis of these viruses.


Assuntos
Anelloviridae/genética , Circoviridae/genética , Genoma Viral , Repetições de Microssatélites , Parvoviridae/genética , DNA de Cadeia Simples/genética , Tamanho do Genoma
19.
Proc Biol Sci ; 281(1791): 20141122, 2014 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-25080342

RESUMO

We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii, the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna- and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.


Assuntos
Bornaviridae/genética , Circoviridae/genética , Crotalus/genética , Crotalus/virologia , Evolução Molecular , Genoma , Hepadnaviridae/genética , Sequência de Aminoácidos , Animais , Evolução Biológica , Bornaviridae/fisiologia , Circoviridae/fisiologia , Feminino , Genes Virais , Hepadnaviridae/fisiologia , Dados de Sequência Molecular , Filogenia
20.
J Gen Virol ; 95(Pt 11): 2553-64, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25078300

RESUMO

We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.


Assuntos
Gatos/virologia , Genoma Viral , Anelloviridae/genética , Anelloviridae/isolamento & purificação , Animais , Astroviridae/genética , Astroviridae/isolamento & purificação , Bocavirus/genética , Bocavirus/isolamento & purificação , Caliciviridae/genética , Caliciviridae/isolamento & purificação , California , Circoviridae/genética , Circoviridae/isolamento & purificação , Fezes/virologia , Peixes/virologia , Variação Genética , Herpesviridae/genética , Herpesviridae/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Vírus de Insetos/genética , Metagenômica , Dados de Sequência Molecular , Parvoviridae/genética , Parvoviridae/isolamento & purificação , Filogenia , Picobirnavirus/genética , Picobirnavirus/isolamento & purificação , Vírus de Plantas/genética , RNA Replicase/genética , Proteínas Virais/genética
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