Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular analysis of parapoxvirus detected in eight calves in Japan.

ABSTRACT: Molecular analysis of parapoxvirus envelope genes was performed. Parapoxvirus DNA was detected in eight calves from eight farms in Iwate Prefecture, Japan, between April and September 2010. Seven of the detected viruses were identified as bovine papular stomatitis virus (BPSV) by sequencing, because their nucleotide identity was more than 96.8% similar compared with BPSV strain V660. Among them, two formed a subgroup, because their amplicons were digested with Xmn I (a marker for BPSV) and Hinc II and exhibited a T61C nucleotide substitution in the sequenced region. The remaining virus was pseudocowpox virus that had not been reported previously in Japan. Our results demonstrate the presence of a new BPSV variant in Japan with genetic variability in the envelope gene.

SUBMITTER: Yaegashi G

PROVIDER: S-EPMC3942923 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular analysis of parapoxvirus detected in eight calves in Japan.

Yaegashi Gakuji G Sasaki Ieharu I Chiba Shin S Murakami Kenji K

The Journal of veterinary medical science 20130707 10

Molecular analysis of parapoxvirus envelope genes was performed. Parapoxvirus DNA was detected in eight calves from eight farms in Iwate Prefecture, Japan, between April and September 2010. Seven of the detected viruses were identified as bovine papular stomatitis virus (BPSV) by sequencing, because their nucleotide identity was more than 96.8% similar compared with BPSV strain V660. Among them, two formed a subgroup, because their amplicons were digested with Xmn I (a marker for BPSV) and Hinc ...[more]

PMID: 23748974

Similar Datasets

Molecular characterization of Cryptosporidium parvum detected in Japanese black and Holstein calves in Iwate Prefecture and Tanegashima Island, Kagoshima Prefecture, Japan.

Project description:Cryptosporidium oocysts were found in 43 out of 77 calves from two farms in Iwate Prefecture and nine farms on Tanegashima Island, Kagoshima Prefecture, Japan. The DNA fragments of 18S ribosomal RNA (18S rRNA) gene were amplified by a nested PCR from 43 oocyst-positive as well as one oocyst-negative samples. All of them were precisely identified as C. parvum by analyzing the nucleotide sequences of the 18S rRNA gene. C. parvum oocyst-positive calves ranged in age from 6 to 13 days old and significantly have watery diarrhea (P<0.05). Sequences of the gene encoding the 60-kDa glycoprotein (GP60) in 43 Cryptosporidium oocyst-positive samples were identical to that of the zoonotic IIaA15G2R1 subtype. We therefore suggest that calves could be potential sources of C. parvum infections in humans.

| S-EPMC4565827 | biostudies-literature

Molecular phylogenetic analysis of bovine papular stomatitis viruses detected in Saga, Japan.

Project description:In this study, we performed a molecular phylogenetic analysis of six bovine papular stomatitis virus (BPSV) field strains detected from Japanese beef calves kept on a farm in Saga prefecture, a southwest part of Japan, from 2017 to 2020. The phylogenetic analysis based on a partial B2L gene (554-nt) showed that these field strains were divided into two lineages, a lineage (A-lineage) constructed by a Saga strain and strains obtained from various regions of Japan and the world, and other lineage (B-lineage) constructed by five Saga strains and strains obtained from France, USA and Iwate prefecture (a north part of Japan). Furthermore, a Saga field strain named BPSV_SAGAbv2 and strains obtained from USA and Iwate prefecture belonged to a sub-lineage blanched from B-lineage. This is the first report elucidating molecular epidemiological characters of field BPSVs obtained from Saga prefecture. The existence of the multiple lineages was thought to be related to a history of calf introduction from various regions of Japan into Saga prefecture.

| S-EPMC8498829 | biostudies-literature

Molecular characterization of noroviruses detected in diarrheic stools of Michigan and Wisconsin dairy calves: circulation of two distinct subgroups.

Project description:Noroviruses have emerged as the leading worldwide cause of acute non-bacterial gastroenteritis in humans. The presence of noroviruses in diarrheic stool samples from calves on Michigan and Wisconsin dairy farms was investigated by RT-PCR. Norovirus-positive samples were found on all eight farms studied in Michigan and on 2 out of 14 farms in Wisconsin. Phylogenetic analyses of partial polymerase and capsid sequences, derived for a subset of these bovine noroviruses, showed that these strains formed a group which is genetically distinct from the human noroviruses, but more closely related to genogroup I than to genogroup II human noroviruses. Examination of 2 full and 10 additional partial capsid (ORF2) sequences of these bovine strains revealed the presence of two genetic subgroups or clusters of bovine noroviruses circulating on Michigan and Wisconsin farms. One subgroup is "Jena-like", the other "Newbury agent-2-like".

| S-EPMC7127749 | biostudies-literature

Congenital Malformations of Calves Infected with Shamonda Virus, Southern Japan.

Project description:In 2015 and 2016, we observed 15 malformed calves that were exposed to intrauterine infection with Shamonda virus, a Simbu serogroup orthobunyavirus, in Japan. Characteristic manifestations were arthrogryposis and gross lesions in the central nervous system. Our results indicate that this arbovirus should be considered a teratogenic virus in ruminants.

| S-EPMC5443447 | biostudies-literature

Congenital abnormalities in calves associated with Peaton virus infection in Japan.

Project description:Peaton virus (PEAV; family Peribunyaviridae, genus Orthobunyavirus) appears to be capable of producing congenital malformations in ruminants; however, its pathogenicity remains unknown given its relatively low incidence. We evaluated the relationship between congenital abnormalities of calves and PEAV infection by serologic, epidemiologic, pathologic, and virologic investigations using specimens from 31 malformed calves in the years 1996-2016 in Japan. Antibody testing was carried out for known teratogenic viruses, including Akabane, Aino, Chuzan, and bovine viral diarrhea viruses, in the precolostral sera of these abnormal calves, but all results were negative. However, all 31 malformed calves were positive for antibodies against PEAV. A PEAV-specific gene was amplified from central nervous system tissues from a stillborn calf delivered in April 2007, and its nucleotide sequence was identical with that of PEAV isolated from healthy sentinel cattle in September 2006. These findings indicate that PEAV can cause bovine congenital anomalies.

| S-EPMC6505853 | biostudies-literature

Molecular Epidemiology of Rubella Virus Strains Detected Around the Time of the 2012-2013 Epidemic in Japan.

Project description:A nationwide rubella epidemic occurred from 2012 to 2013 in Japan, resulting in around 17,000 rubella cases and the birth of 45 infants with congenital rubella syndrome. The aim of this study was to genetically characterize the rubella viruses (RVs) circulating around the time of the epidemic in Japan. In total, 221 RV strains detected from 14 prefectures in Japan between 2010 and 2014 were sequenced in the 739 nucleotide-window region within the E1 gene. The virus strains were chronologically and geographically characterized into groups based on phylogenetic analysis. Among the 221 strains analyzed, 192 (87%), 26 (12%), and 3 (1%) strains were classified into genotypes 2B, 1E, and 1J, respectively. The majority (n = 184) of the genotype 2B strains belonged to lineage 2B-L1 and shared nucleotide homology with the strains detected in Southeast and East Asian countries. Phylogenetic analyses demonstrated that at least six distinct clusters of RV strains (clusters 1-6) induced outbreaks in Japan between 2010 and 2014. Among them, strains from clusters 3, 4, and 6 circulated almost simultaneously during 2012-2013. The cluster 3 strains circulated locally, whereas strains from cluster 4 spread nationwide. The findings suggest that RVs were introduced into Japan many times from neighboring countries. The 2012-2013 epidemic was a complex of outbreaks induced by at least three clusters of RV strains.

| S-EPMC5553008 | biostudies-literature

Molecular karyotype analysis of Cryptosporidium parvum: evidence for eight chromosomes and a low-molecular-size molecule.

Project description:We report improved separation of chromosome-sized DNA molecules of the coccidian parasite Cryptosporidium parvum with contour-clamped homogeneous electric fields (CHEF). We used scanning densitometry to determine that the most likely number of chromosomes is eight. Molecular probes consisting of cloned genes were used to distinguish each of five bands visible on CHEF gels. We have also identified a low-molecular-size DNA molecule possibly related to the 35-kb circular DNAs found in other Apicomplexa.

| S-EPMC170468 | biostudies-other

Prevalence and molecular analyses of hemotrophic Mycoplasma spp. (hemoplasmas) detected in sika deer (Cervus nippon yesoensis) in Japan.

Project description:Hemotropic mycoplasmas (hemoplasmas) are cell-wall deficient, epierythrocytic bacteria that cause infectious anemia in several mammalian species. The prevalence of hemoplasma species was examined by screening and species-specific PCR using blood samples collected from 51 sika deer in Hokkaido, Japan. Molecular analyses were performed for the 16S rRNA, 23S rRNA and RNase P RNA (rnpB) gene sequences. A total of 23/51 (45%) deer DNA samples were positive for hemoplasmas in the screening PCR. Using species-specific PCR, 12 and 17 samples were positive for 'Candidatus Mycoplasma haemocervae' and 'Candidatus M. erythrocervae', respectively. Sequencing and phylogenetic trees of those three genes indicate that the 'Candidatus M. haemocervae' and 'Candidatus M. erythrocervae' detected in Japanese deer are potentially different species from the cervine hemoplasma found in deer from America and Brazil.

| S-EPMC4013367 | biostudies-literature

Molecular characterisation and risk factor analysis of Cryptosporidium spp. in calves from Italy.

Project description:To provide up-to-date information on the occurrence of Cryptosporidium in pre-weaned calves from Sardinia (Italy), the species implicated and their zoonotic potential, 147 faecal samples from 22 cattle herds were microscopically examined for Cryptosporidium oocysts; positive isolates were molecularly characterised. A questionnaire was developed to identify risk factors for Cryptosporidium infection. Overall, the percentage of positive calves and farms was 38.8 and 68.2%, respectively. The SSU rRNA-based PCR identified two Cryptosporidium species, Cryptosporidium parvum (95.8%) and C. bovis (4.2%). Sequence analyses of the glycoprotein (gp60) gene revealed that all C. parvum isolates belonged to the subtype family IIa (IIaA15G2R1 and IIaA16G3R1), with the exception of three isolates that belonged to the subtype family IId (IIdA20G1b and IIdA20). Mixed logistic regression results indicated that calves aged 15-21 days were more likely to be Cryptosporidium-positive. The risk of being positive was also significantly higher in herds from Central Sardinia and in farms using non-slatted flooring. In addition, the application of disinfectants and milk replacers was significantly associated with higher Cryptosporidium prevalence. In contrast, the risk of being positive was significantly reduced in halofuginone-treated calves. Our results reveal that a significant percentage of suckling calves are carriers of zoonotic subtypes of C. parvum. Thus, both healthy and diarrhoeic calves younger than 1 month may represent a risk for the transmission of cryptosporidiosis in humans and animals.

| S-EPMC7088234 | biostudies-literature

Comparative analysis of eight DNA extraction methods for molecular research in mealybugs.

Project description:For molecular research, the quality and integrity of DNA obtained will affect the reliability of subsequent results. Extracting quality DNA from scale insects, including mealybugs, can be difficult due to their small body size and waxy coating. In this study, we evaluate eight commonly used DNA extraction methods to determine their efficacy in PCR analysis across life stages and preservation times. We find that fresh samples, immediately upon collection or after 2 wks, resulted in the most effective DNA extraction. Methods using the DNeasy Blood & Tissue kit, NaCl, SDS-RNase A, and SDS isolated DNA of sufficient quality DNA. The SDS method gave high DNA yield, while the NaCl and SDS-RNase A methods gave lower yield. NaCl, SDS-RNase A, SDS, chloroform-isopentyl alcohol, and the salting-out methods all resulted in sufficient DNA for PCR, and performed equal to or better than that of the DNeasy Blood & Tissue kit. When time and cost per extraction were considered, the SDS method was most efficient, especially for later life stages of mealybug, regardless of preservation duration. DNA extracted from a single fresh sample of a female adult mealybug was adequate for more than 10,000 PCR reactions. For earlier stages, including the egg and 1st instar nymph samples, DNA was most effectively extracted by the Rapid method. Our results provide guidelines for the choice of effective DNA extraction method for mealybug or other small insects across different life stages and preservation status.

| S-EPMC6938366 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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