title: Molecular epidemiological study of feline coronavirus strains in Japan using RT-PCR targeting nsp14 gene.
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.
authors.affiliation: Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary & Life Science University, 1-7-1 Kyounan, Musashino, Tokyo, 180-8602, Japan. ytanaka@nvlu.ac.jp.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Tanaka
authors.affiliation: Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary & Life Science University, 1-7-1 Kyounan, Musashino, Tokyo, 180-8602, Japan. hiteiha@juntendo.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Sasaki
authors.affiliation: Department of Veterinary Hygiene, Veterinary School, Nippon Veterinary & Life Science University, 1-7-1 Kyounan, Musashino, Tokyo, 180-8602, Japan. oyradustam@gmail.com.
authors.forename: Ryo
authors.initials: R
authors.lastname: Matsuda
authors.affiliation: Canine Lab., Inc., Nokodai-Tamakoganei Venture Port 302, 2-24-16, Koganei, Tokyo, 184-0012, Japan. uematsu@canine-lab.jp.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Uematsu
authors.affiliation: Canine Lab., Inc., Nokodai-Tamakoganei Venture Port 302, 2-24-16, Koganei, Tokyo, 184-0012, Japan. yamaguchi@canine-lab.jp.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Yamaguchi
mesh_terms: D000818:Animals; D002415:Cats / Q000821:virology; D016765:Coronavirus, Feline / Q000235:genetics*; D004587:Electrophoresis, Agar Gel / Q000662:veterinary; D016766:Feline Infectious Peritonitis / Q000453:epidemiology* / Q000821:virology; D060005:Genotyping Techniques / Q000662:veterinary; D007564:Japan / Q000453:epidemiology; D017720:Molecular Epidemiology; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods / Q000662:veterinary*; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D017361:Viral Nonstructural Proteins