Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains

• Published in: Biochemical and biophysical research communications Vol. 323; no. 1; pp. 254 - 263
• Main Authors: Feng, Qian, Yu, Huan, Liu, Yingying, He, Chengqiang, Hu, Jingsong, Sang, Huachun, Ding, Neizheng, Ding, Mingxiao, Fung, Yin-Wan Wendy, Lau, Lok-Ting, Yu, Albert Cheung-Hoi, Chen, Jianguo
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 08.10.2004
• Subjects: 3' Untranslated Regions; 5' Untranslated Regions; Alignment; Amino Acid Sequence; Base Sequence; Capsid Proteins; Cloning, Molecular; Foot-and-mouth disease virus; Foot-and-Mouth Disease Virus - genetics; Gene Deletion; Genome, Viral; Molecular Sequence Data; Mutation; Nucleotides - chemistry; Oligopeptides - genetics; Open Reading Frames; Phylogenesis; Phylogeny; Picornavirus; Protein Structure, Tertiary; Sequence; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Serotype; Species Specificity; Viral Proteins - genetics; Picornavirus; Phylogenesis; Alignment; Serotype; Sequence
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2004.08.086

The genome of a novel foot-and-mouth disease virus, HKN/2002, was 8104 nucleotides (nt) in length (excluding the poly(C) tract and poly(A) tail) and was composed of a 1042-nt 5′-untranslated region (UTR), a 6966-nt open reading frame, and a 93-nt 3′-UTR. Genome sequences of HKN/2002 and other known FMDV strains were compared. The VP1, VP2, and VP3-based neighbor-joining (NJ) trees were divided into distinct clusters according to different serotypes, while other region-based NJ trees exhibited some degree of intercross among serotypes. Mutations in HKN/2002 were revealed, including frequent deletions and insertions in the G–H loop of VP1, and deletion involving 10 amino acid residues in the 3A protein. An evolutionary relationship of HKN/2002 with an Asian FMDV lineage isolated from a Hong Kong swine host in 1970 was postulated. A 43-nt deletion identified in the 5′-UTR of HKN/2002 possibly contributed to the loss of one pseudo-knot domain.