title: Genetic characterization of a new pandemic Southeast Asia topotype strain of serotype O foot-and-mouth disease virus isolated in China during 2010.
abstract: The full-length nucleotide sequence of the foot-and-mouth disease virus O/BY/CHA/2010 strain, Mya-98 lineage of Southeast Asia (SEA) topotype, was determined and compared with O/HKN/20/2010 and other known FMDV strains. Homology analysis indicated >98.0% nucleotide identity between O/BY/CHA/2010 and the epidemic strains, O/HKN/20/2010, and O/VN/2009. However, with the exception of the VP4, 2A, and 3BCD regions, O/BY/CHA/2010 showed a lower similarity with SEA topotype strains, O/VN/2006, and HLJOC12/03. A comparison of O/BY/CHA/2010 with non-SEA topotype strains showed the highest level of homology (97.4-100%) with UKG/7B/2007, Akesu/58, and the PanAsia strains in the 2A, P2, and 3CD regions, which suggested the presence of similar characteristics among these strains. Phylogenetic analysis revealed that O/BY/CHA/2010 is clustered in the Mya-98 lineage of the SEA topotype and is linked to four other isolates: HKN/20/2010, O/VN/2009, O/VN/2006, and HLJOC12/03. The VP1-based phylogenetic tree was divided into distinct clusters according to the different topotypes, while other gene-based phylogenetic trees exhibited some degree of intercrossing among topotypes. Furthermore, sequence analysis of the Lpro gene revealed a single amino acid insertion in O/HKN/20/2010 and a single amino acid deletion in O/BY/CHA/2010, in addition to a 70-nucleotide deletion within the 5'-untranslated region of O/HKN/20/2010. The majority of strains were shown to be homologous in the pseudoknots region although some exceptions were noted. This study provides a comprehensive genetic characterization of a novel FMDV isolate of the Mya-98 lineage.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
authors.forename: Haixue
authors.initials: H
authors.lastname: Zheng
authors.forename: Jijun
authors.initials: J
authors.lastname: He
authors.forename: Jianhong
authors.initials: J
authors.lastname: Guo
authors.forename: Ye
authors.initials: Y
authors.lastname: Jin
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.forename: Lv
authors.initials: L
authors.lastname: Lv
authors.forename: Xiangtao
authors.initials: X
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001210:Asia, Southeastern / Q000453:epidemiology; D001483:Base Sequence; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology / Q000821:virology*; D002681:China / Q000453:epidemiology; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D016415:Sequence Alignment; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*