Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detection of mink astrovirus in Poland and further phylogenetic comparison with other European and Canadian astroviruses.

ABSTRACT: Mink astrovirus infection remains a poorly understood disease entity, and the aetiological agent itself causes disease with a heterogeneous course, including gastrointestinal and neurological symptoms. This paper presents cases of astrovirus infection in mink from continental Europe. RNA was isolated from the brains and intestines of animals showing symptoms typical of shaking mink syndrome (n = 6). RT-PCR was used to amplify astrovirus genetic material, and the reaction products were separated on a 1% agarose gel. The specificity of the reaction was confirmed by sequencing fragment coding RdRP protein (length of sequencing product 170 bp) from all samples. The presence of astrovirus RNA was detected in each of the samples tested. Sequencing and bioinformatic analysis indicated the presence of the same variant of the virus in all samples. Comparison of the variant with the sequences available in bioinformatics databases confirmed that the Polish isolates form a separate clade, closely related to Danish isolates. The dissimilarity of the Polish variant to those isolated in other countries ranged from 2.4% (in relation to Danish isolates) to 7.1% (in relation to Canadian isolates). Phylogenetic relationships between variants appear to be associated with the geographic distances between them. To our knowledge, this work describes the first results on the molecular epidemiology of MAstV in continental Europe. The detection of MAstV in Central Europe indicates the need for further research to broaden our understanding of the molecular epidemiology of MAstV in Europe.

SUBMITTER: Jakubczak A

PROVIDER: S-EPMC8164600 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

RT-qPCR assay for detection of mink astrovirus in outbreaks of diarrhea on Danish mink farms.

Project description:Diarrhea in mink kits is a major cause of disease and mortality in the mink production. The etiology remains unknown in most outbreaks due to a lack of diagnostic assays. In the current study we present an RT-qPCR method to detect mink astrovirus in fecal samples from mink kits with diarrhea. All sampled animals were classified based on age and patoanatomical evaluation as having pre-weaning diarrhea, diarrhea in the growth period or as having no macroscopic signs of diarrhea. Fecal samples were analyzed for MiAstV with RT-qPCR, next generation sequencing and electron microscopy in parallel. Mink astrovirus was detected with RT-qPCR in 92 out of 203 samples. This detection was confirmed by next generation sequencing in a high proportion of samples (22/27), and by visualization of astrovirus particles with EM in some of the samples. Mink astrovirus was highly prevalent (68%) among kits in the outbreaks of pre-weaning diarrhea, in particular outbreaks from May, while less prevalent in outbreaks in June. Mink astrovirus was detected in outbreaks of diarrhea in the growth period, though in a much lesser extent than in the pre-weaning period. The role of mink astrovirus in the diarrhea disease complex of mink remain to be investigated, and for that purpose this sensitive and robust RT-qPCR can be a valuable tool in the future.

| S-EPMC8153481 | biostudies-literature

Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses.

Project description:Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins.

| S-EPMC7086720 | biostudies-literature

Detection and sequence analysis of Danish and Swedish strains of mink astrovirus.

Project description:The sequences of mink astroviruses collected from 11 farms in Denmark and Sweden were analyzed and found to be homologous with one another but different from those of other astroviruses. A species-specific reverse transcriptase-PCR for mink astrovirus was established and shown to be suitable for the analysis of clinical samples.

| S-EPMC262547 | biostudies-literature

Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics.

Project description:In 2000, farmed mink kits in Denmark were affected by a neurological disorder. The characteristic clinical signs included shaking, staggering gait, and ataxia. The disease, given the name shaking mink syndrome, was reproduced by the inoculation of brain homogenate from affected mink kits into healthy ones. However, the etiology remained unknown despite intensive efforts. In this study, random amplification and large-scale sequencing were used, and an astrovirus was detected in the brain tissue of three experimentally infected mink kits. This virus also was found in the brain of three mink kits naturally displaying the disease but not in the six healthy animals investigated. The complete coding region of the detected astrovirus was sequenced and compared to those of both a mink astrovirus associated with preweaning diarrhea and to a recently discovered human astrovirus associated with a case of encephalitis in a boy with x-linked agammaglobulinemia. The identities were 80.4 and 52.3%, respectively, showing that the virus described in this study was more similar to the preweaning diarrhea mink astrovirus. For the nonstructural coding regions the sequence identity was around 90% compared to that of the astrovirus, which is associated with preweaning diarrhea in mink. The region coding for the structural protein was more diverse, showing only 67% sequence identity. This finding is of interest not only because the detected virus may be the etiological agent of the shaking mink syndrome but also because this is one of the first descriptions of an astrovirus found in the central nervous system of animals.

| S-EPMC3008476 | biostudies-literature

Detection and phylogenetic characterization of astroviruses in insectivorous bats from Central-Southern Italy.

Project description:In recent years, bats have been found to harbour many viruses, raising several questions about their role as reservoirs and potential disseminators of zoonotic viruses. We investigated the presence of six virus families in bats in three regions of Central-Southern Italy. Astroviruses were identified in seven of 13 bat species. Sequence analysis revealed marked genetic heterogeneity among the astroviruses identified, with nucleotide identity ranging between 60.26% and 87.62%. Astrovirus diversity was not associated with the bat species, the geographic areas or the bat colony, suggesting the circulation of several astrovirus strains in Italian ecosystems. Genetic diversification and interspecies transmission appear common in bat astroviruses and could provide, potentially, the bases for transmission to humans and other mammals. Yet overemphasizing this risk might have detrimental consequences for bat conservation and preservation of the important ecosystem services bats provide.

| S-EPMC7165808 | biostudies-literature

Phylogenetic Analysis of European Brown Hare Syndrome Virus Strains from Poland (1992-2004).

Project description:European brown hare syndrome (EBHS) is lethal to several species of free-living hares worldwide. The genetic characterization of its virus (EBHSV) strains in European circulation and epidemiological knowledge of EBHSV infections is not yet complete. The study determined the nucleotide sequences of the genomes of EBHSV strains from Poland and analyzed their genetic and phylogenetic relationships to a group of hare lagoviruses. The genome of five virus strains detected in Poland between 1992 and 2004 was obtained by RT-PCR and sequencing of the obtained amplicons. The genetic relationships of the EBHSV strains were analyzed using the full genome and VP60 gene sequences. Additionally, the amino acid sequence of the VP60 gene was analyzed to identify mutations specific to recognized EBHSV subgroups. Partial amplification of the virus open reading frame (ORF)1 and ORF2 regions obtained nearly complete nucleotide genome sequences of the EBHSV strains. Phylogenetic analysis placed them in a GII.1 cluster with other European strains related to nonpathogenic hare caliciviruses. VP60 gene analysis allocated these EBHSV strains to the G1.2, G2.2-2.3 or G3 virus genetic groups. The amino acid sequence differences in the entire genome ranged from 1.1 to 2.6%. Compared to a reference French EBHSV-GD strain, 22 variable amino acid sites were identified in the VP60 region of the Polish strains, but only six were in VP10. Single amino acid changes appeared in different sequence positions among Polish and other European virus strains from different genetic groups, as well as in VP10 sequences of nonpathogenic hare caliciviruses. The results of the study showed a high genetic homogeneity of EBHSV strains from Poland despite their different location occurrence and initial detection times. These strains are also phylogenetically closely related to other EBHSV strains circulating in Europe, likely confirming the slow evolutionary dynamics of this lagovirus species.

| S-EPMC8539919 | biostudies-literature

Comparison of novel MLB-clade, VA-clade and classic human astroviruses highlights constrained evolution of the classic human astrovirus nonstructural genes.

Project description:Eight serotypes of human astroviruses (the classic human astroviruses) are causative agents of diarrhea. Recently, five additional astroviruses belonging to two distinct clades have been described in human stool, including astroviruses MLB1, MLB2, VA1, VA2 and VA3. We report the discovery in human stool of two novel astroviruses, astroviruses MLB3 and VA4. The complete genomes of these two viruses and the previously described astroviruses VA2 and VA3 were sequenced, affording seven complete genomes from the MLB and VA clades for comparative analysis to the classic human astroviruses. Comparison of the genetic distance, number of synonymous mutations per synonymous site (dS), number of non-synonymous mutations per non-synonymous site (dN) and the dN/dS ratio in the protease, polymerase and capsid of the classic human, MLB and VA clades suggests that the protease and polymerase of the classic human astroviruses are under distinct selective pressure.

| S-EPMC3545029 | biostudies-literature

Mink SARS-CoV-2 Infection in Poland - Short Communication.

Project description:IntroductionSince April 2020, when the first SARS-CoV-2 infection was reported in mink and subsequently in mink farm workers in the Netherlands, it has been confirmed that human-to-mink and mink-to-human transmission can occur. Later, SARS-CoV-2 infections in mink were reported in many European and North American countries.Material and methodsSamples from 590 mink from a total of 28 farms were tested by real-time RT-PCR. Whole genome sequences from one positive farm were generated and genetic relatedness was established.ResultsSARS-CoV-2 RNA was detected on a breeder farm with stock of 5,850 mink. Active viraemia was confirmed in individually tested samples with Ct values respectively between 19.4 and 29.6 for E and N gene fragments. Further testing of samples from culled animals revealed 70% positivity in throat swabs and 30% seropositivity in blood samples. Phylogenetic analysis of full-length nucleotide sequences of two SARS-CoV-2 isolates revealed that they belong to the 20B Nextstrain clade. Several nucleotide mutations were found in analysed samples compared to the reference Wuhan HU-1 strain and some of them were nonsynonymous.ConclusionWe report the infection of mink with SARS-CoV-2 on one farm in Poland and the results of subsequent analysis of virus sequences from two isolates. These data can be useful for assessment of the epidemiological situation of SARS-CoV-2 in Poland and how it endangers public health.

| S-EPMC8009592 | biostudies-literature

Detection of Astrovirus, Rotavirus C, and Hepatitis E Viral RNA in Adult and Juvenile Farmed Mink (<i>Neovison vison</i>).

Project description:Mink astrovirus (MiAstV) is known to play a major role in mink pre-weaning diarrhea, and rotavirus and hepatitis E virus (HEV) are both considered potentially zoonotic agents. These viruses are not monitored in commercial mink, and the role of these viral infections in mink health is not well understood. This study assessed the prevalence of mink astrovirus, rotavirus C, mink HEV and swine HEV in 527 pooled healthy adult female mink and mink kit fecal samples from 50 Canadian mink farms in two seasons over 4 years. Viral RNA was extracted and amplified in RT-PCR to detect mink astrovirus and HEV RdRp genes, swine HEV ORF2, and rotavirus C VP6 gene. At least 26% of all positive samples for each virus was sequenced for phylogenetic analysis. Fourteen percent of samples were astrovirus positive, while 3 and 9% of samples were rotavirus C and mink HEV positive, respectively. One adult female sample was found to be positive by PCR for swine HEV. A significantly higher number of kit samples were astrovirus- and HEV-positive compared to adult female samples (p = 0.01 and p < 0.0001, respectively). Astrovirus was detected in significantly more summer samples from adult females compared to winter samples from adult females (p = 0.001). The detected sequences were closely related to previously reported MiAstV, swine rotavirus C, and mink and swine HEV strains. Two astrovirus sequences were distantly related to all other detected sequences as well as previously reported MiAstVs. These results demonstrate low to moderate prevalence of the three viruses in feces from clinically healthy Canadian commercial mink, and suggest that further monitoring of these viruses may provide a better understanding of how these potentially zoonotic agents may play a role in mink enteritis and overall productivity.

| S-EPMC6020771 | biostudies-literature

Detection of Astrovirus in Historical Cases of European Sporadic Bovine Encephalitis, Switzerland 1958-1976.

Project description:European sporadic bovine encephalitis is a frequent diagnosis in neurologically diseased cattle, but its etiology remained unresolved. Using in situ hybridization, we have detected a recently discovered neurotropic bovine astrovirus in historical tissues in a high proportion of brain samples of affected cattle. Our results suggest that astroviruses were already involved in the pathogenesis of the disease several decades ago, but have gone undetected.

| S-EPMC5058262 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data