About: Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene

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About: Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene
Creator	Sasaki, Takashi Tanaka, Yoshikazu Matsuda, Ryo Uematsu, Yosuke Yamaguchi, Tomohiro
Source	Medline; PMC
abstract	BACKGROUND: Feline infectious peritonitis is a fatal disease of cats caused by infection with feline coronavirus (FCoV). For detecting or genotyping of FCoV, some RT-PCR plus nested PCR techniques have been reported previously. However, referring to the whole genome sequences (WGSs) registered at NCBI, there are no detection methods that can tolerate the genetic diversity among FCoV population. In addition, the quasispecies nature of FCoV, which consists of heterogeneous variants, has been also demonstrated; thus, a universal method for heteropopulations of FCoV variants in clinical specimens is desirable. RESULTS: To develop an RT-PCR method for detection and genotyping of FCoV, we performed comparative genome analysis using WGSs of 32 FCoV, 7 CCoV and 5 TGEV strains obtained from NCBI. As the PCR target, we focused on the nsp14 coding region, which is highly conserved and phylogenetically informative, and developed a PCR method targeting nsp14 partial sequences. Among 103 ascites, 45 pleural effusion and 214 blood specimens from clinically ill cats, we could detect FCoV in 55 (53.4%), 14 (31.1%) and 19 (8.9%) specimens using the present method. Direct sequencing of PCR products and phylogenetic analysis allowed discrimination between type I- and II-FCoV serotypes. Our nsp14 amino acid sequence typing (nsp14 aa ST) showed that the FCoV clone with sequence type (ST) 42, which was the most predominant genotype of WGS strains, was prevalent in domestic cats in Japan. CONCLUSIONS: Our nsp14 PCR scheme will contribute to virus detection, epidemiology and ecology of FCoV strains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0372-2) contains supplementary material, which is available to authorized users.
has issue date	2015-03-11(xsd:dateTime)
bibo:doi	10.1186/s12917-015-0372-2
bibo:pmid	25889235
has license	cc-by
sha1sum (hex)	78fb5545880b83bbbef7058bf5c99ff618b35f7b
schema:url	https://doi.org/10.1186/s12917-015-0372-2
resource representing a document's title	Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene
has PubMed Central identifier	PMC4359392
has PubMed identifier	25889235
schema:publication	BMC Vet Res
resource representing a document's body	covid:78fb5545880b83bbbef7058bf5c99ff618b35f7b#body_text
is schema:about of	named entity 'STRAINS' named entity 'disease' named entity 'Japan' named entity 'prevalent' named entity 'fatal' named entity 'coding region' named entity 'genotype' named entity 'peritonitis' named entity 'MOLECULAR' named entity 'PREDOMINANT' named entity 'DETECTION METHODS' named entity 'DETECTION' named entity 'CLONE' named entity 'WHOLE GENOME' named entity 'GENOTYPING' named entity 'USING' named entity 'TARGETING' named entity 'DOMESTIC' named entity 'DIRECT SEQUENCING' named entity 'TGEV' named entity 'TECHNIQUES' named entity 'CONTRIBUTE ' named entity 'TYPING' named entity 'SEQUENCE TYPE' named entity 'BACKGROUND' named entity 'WGS' named entity 'NESTED PCR ' named entity 'DISCRIMINATION' named entity 'JAPAN' named entity 'CATS' named entity 'PRODUCTS' named entity 'STRAINS' named entity 'PLEURAL EFFUSION' named entity 'INFECTION' named entity 'METHOD' named entity 'PRESENT' named entity 'RT-PCR' named entity 'VARIANTS' named entity 'HAVE' named entity 'WGSS' named entity 'UNIVERSAL' named entity 'SPECIMENS' named entity 'CAUSED BY' named entity 'EPIDEMIOLOGICAL STUDY' named entity 'JAPAN' named entity 'RT-PCR' named entity 'ECOLOGY' named entity 'REGISTERED' named entity 'NCBI' named entity 'FOCUSED' named entity 'REFERRING' named entity 'OUR' named entity 'GENOTYPE' named entity '288' named entity 'CONCLUSIONS' named entity 'CODING REGION' named entity 'QUASISPECIES' named entity 'PCR' named entity 'HIGHLY' named entity 'ADDITION' named entity 'TARGETING' named entity 'TYPE I' named entity 'EPIDEMIOLOGY' named entity '214' named entity 'INFORMATIVE' named entity 'ASCITES' named entity 'COMPARATIVE GENOME' named entity 'FELINE INFECTIOUS PERITONITIS' named entity 'USING' named entity 'PREVIOUSLY' named entity 'OBTAINED' named entity 'ALLOWED' named entity 'ILL' named entity 'CONSERVED' named entity 'PHYLOGENETIC ANALYSIS' named entity 'GENOME ANALYSIS' named entity 'FATAL DISEASE'

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