Complete nucleotide sequence of a Chinese serotype Asia1 vaccine strain of foot-and-mouth disease virus

The full-length nucleotide sequence of the Chinese vaccine strain Asia1/YNBS/58 of foot-and-mouth disease virus (FMDV) was determined. The results showed that the complete genome of YNBS/58 is 8,164 nucleotides (nt) in length including a 1,061-nt 5′ untranslated region (UTR), a 6,990-nt open reading frame (ORF), and a 113-nt 3′ UTR. Genome sequences of Asia1/YNBS/58 and other known FMDV strains were compared. The homology analysis indicated that non-structural proteins are more conserved than structural proteins in FMDV and that the 5′ UTR is more conserved than the 3′ UTR. Phylogenetic analysis revealed that Asia1/YNBS/58 is clustered in the Asia1 serotype and is linked to three other isolates, Asia1/IND/63/72, Asia1/3kimron/63, and Asia1/2ISRL/63, suggesting that they have a close genetic relationship. The VP1-, VP2-, and VP3-based phylogenetic trees divided into distinct clusters according to the different serotypes, while other gene-based phylogenetic trees exhibited some degree of intercrossing among serotypes. According to the nucleotide similarities between Asia1/YNBS/58 and two recent Chinese Asia1 isolates, Asia1/HKN/05, and Asia1/JS/05, each forms a distinct genotype. This study is the first description of the full-length genomic sequence of FMDV Chinese serotype Asia1.