title: Genome variability of foot-and-mouth disease virus during the short period of the 2010 epidemic in Japan.
abstract: Foot-and-mouth disease virus (FMDV) is highly contagious and has a high mutation rate, leading to extensive genetic variation. To investigate how FMDV genetically evolves over a short period of an epidemic after initial introduction into an FMD-free area, whole L-fragment sequences of 104 FMDVs isolated from the 2010 epidemic in Japan, which continued for less than three months were determined and phylogenetically and comparatively analyzed. Phylogenetic analysis of whole L-fragment sequences showed that these isolates were classified into a single group, indicating that FMDV was introduced into Japan in the epidemic via a single introduction. Nucleotide sequences of 104 virus isolates showed more than 99.56% pairwise identity rates without any genetic deletion or insertion, although no sequences were completely identical with each other. These results indicate that genetic substitutions of FMDV occurred gradually and constantly during the epidemic and generation of an extensive mutant virus could have been prevented by rapid eradication strategy. From comparative analysis of variability of each FMDV protein coding region, VP4 and 2C regions showed the highest average identity rates and invariant rates, and were confirmed as highly conserved. In contrast, the protein coding regions VP2 and VP1 were confirmed to be highly variable regions with the lowest average identity rates and invariant rates, respectively. Our data demonstrate the importance of rapid eradication strategy in an FMD epidemic and provide valuable information on the genome variability of FMDV during the short period of an epidemic.
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Nishi
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Yamada
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Fukai
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Shimada
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Morioka
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Yoshida
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Sakamoto
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Kanno
authors.affiliation: Exotic Disease Research Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1, Josui-honcho, Kodaira, Tokyo, 187-0022, Japan. Electronic address: yamato@affrc.go.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Yamakawa
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology / Q000821:virology*; D058872:Epidemics / Q000662:veterinary*; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D007564:Japan / Q000453:epidemiology; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: Comparative analysis; Foot-and-mouth disease virus; Genome variability