Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples

• Published in: Journal of medical microbiology Vol. 63; no. 5; pp. 715 - 720
• Main Authors: Yamashita, Teruo, Adachi, Hirokazu, Hirose, Emi, Nakamura, Noriko, Ito, Miyabi, Yasui, Yoshihiro, Kobayashi, Shinichi, Minagawa, Hiroko
• Format: Journal Article
• Language: English
• Published: Reading Society for General Microbiology 01.05.2014
• Subjects: Biological and medical sciences; Cluster Analysis; Fundamental and applied biological sciences. Psychology; Humans; Infectious diseases; Japan; Kobuvirus - classification; Kobuvirus - genetics; Kobuvirus - isolation & purification; Medical sciences; Microbiology; Molecular Sequence Data; Phylogeny; Reverse Transcriptase Polymerase Chain Reaction; RNA, Viral - genetics; Sequence Analysis, DNA; Sequence Homology; Sewage - virology; Viral Proteins - genetics; Japan; Fissipedia; Carnivora; Vertebrata; Mammalia; Nucleotide sequence; Detection; Veterinary; Dog
• ISSN: 0022-2615; 1473-5644; 1473-5644
• DOI: 10.1099/jmm.0.070987-0

Between 2001 and 2005, 207 raw sewage samples were collected at the inflow of a sewage treatment plant in Aichi Prefecture, Japan. Of the 207 sewage samples, 137 (66.2 %) were found to be positive for amplification of Aichi virus (AiV) nucleotide using reverse transcription (RT)-PCR with 10 forward and 10 reverse primers in the 3D region corresponding to the nucleotide sequence of all kobuviruses. AiV genotype A sequences were detected in all 137 samples. New sequences of AiV were detected in nine samples, exhibiting 83 % similarity with AiV A846/88, but 95 % similarity with canine kobuvirus (CKV) US-PC0082 in this region. The nucleotide sequences from the VP3 region to the 3′ untranslated region (UTR) of sewage sample Y12/2004 were determined. The number of nucleotides in each region was the same as that of CKV. The similarity of the nucleotide (amino acid) identity of a complete VP1 region was 90.5 % (94.8 %) between Y12/2004 and CKV US-PC0082. The phylogenic analyses based on the nucleotide and the deduced amino acid sequences of VP1 and 3D showed that Y12/2004 was independent from AiV, but closely related to CKV. These results suggested that CKV is present in Aichi Prefecture, Japan.