Molecular relationships between type Asia 1 new strain from China and type O Panasia strains of foot-and-mouth-disease virus

Abstract

The complete genome of Asia 1/HNK/CHA/05 strain of foot-and-mouth disease virus (FMDV) was sequenced, which was isolated from Chinese Hongkong in 2005. It is 8187 nt long in size and contains 5'-UTR, polyprotein region, and 3'-UTR. Polyprotein region can be divided into four parts of L, P1, P2 and P3. In this report, these six parts of the whole genome of the strain were compared with 12 reference strains using DNAStar and Simplot softwares. The comparison of P1 confirmed that Asia 1/HNK/CHA/05 has a high identity with nine type Asia 1 reference sequences from 85.9 to 92.6% (Ind/491/97 strain is the highest) but from 69.6 to 69.7% with three type O Panasia sequences. The identities of 5'-UTR, L, P2, P3 and 3'-UTR with three Panasia strains are from 89.0 to 90.6%, 92.5 to 93.4%, 94.8 to 95.5%, 96.0 to 96.7% and 90.7 to 92.5% separately, but with nine type Asia 1 strains are from 83.5 to 85.9%, 87.7 to 90.7%, 87.0 to 91.6%, 91.6 to 92.8% and 86.0 to 100% separately, which illuminates the closer relationship between Asia 1/HNK/CHA/05 and Panasia strains in 5'-UTR, L, nonstructural region and 3'-UTR although they do not belong to the same serotype. The SimPlot software was used to examine the authentic relationships of Asia 1/HNK/CHA/05 with 12 reference sequences. It was found that Asia 1/HNK/CHA/05 strain has a highest similarity with three Panasia strains especially Tibet/CHA/99 in 5'-UTR, L, nonstructural region and 3'-UTR but has a highest similarity with Asia 1/Ind/491/97 strain in P1 region, which suggested that the gene recombination had occurred around nucleotide position 1811 and 3971in the polyprotein region between Tibet/CHA/99 and Ind/491/97 to recombine the Asia 1/HNK/CHA/05 strain.