Whole Genome Sequencing of a Candidate Strain for FMDV Vaccine: Genomic Structure and Genetic Variation  

Aiguo Xin1 , Le Li2 , Mingwang Zhu2 , Haisheng Miao1 , Chenhong Shi2 , Dufang Liao1 , Yongqin Yang1 , Huachun Li1
1. Key Laboratory for Tropical and Subtropical Animal Virus Disease, Ministry of Agricultrue, Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, P.R. China
2. Baoshan Vaccine Plant of Yunnan Province, Baoshan, 678000, P.R. China
Author    Correspondence author
Molecular Pathogens, 2011, Vol. 2, No. 1   doi: 10.5376/mp.2011.02.0001
Received: 12 Apr., 2011    Accepted: 17 Jun., 2011    Published: 27 Jun., 2011
© 2011 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Xin et al., 2011, Whole Genome Sequencing of a Candidate Strain for FMDV Vaccine: Genomic Structure and Genetic Variation, Molecular Pathogens, doi:10.5376/mp.2011.02.0001

Abstract

The complete genome of foot-and-mouth disease virus (FMDV) vaccine candidate strain O/YM/YN/2000 was sequenced and analyzed. Seven overlapping cDNA fragment which covered the O/YM/YN/2000 genome were amplified by RT-PCR and sequenced. The results showed that the complete genome of the strain O/YM/YN/2000 has 8 133 nucleotides (nt) in length including a 1 053 nt 5′- untranslated region (UTR) (including 18 nt poly C), a 6 969 nt open reading frame (ORF), a 93 nt 3′-UTR and at least 18 nt poly A tail. The homologous comparison and phylogenetic analysis of the nucleotide and deduced amino acid (aa) sequences among O/YM/YN/2000 and other FMDV strains available deposited in GenBank were performed. Phylogenetic analysis based on the complete genome and VP1 revealed that that the strain O/YM/YN/2000 is clustered in the FMDV serotype O cathay topotype. Fragment deletions mutation in O/YM/YN/2000 were revealed, deletions involving 4 nt in the S fragment of 5′-UTR, 43 nt which possibly contributed to the loss of pseudo-knot domain II of 5′-UTR and 10 aa residues in 3A protein. The results in this research might provide some information for screening FMDV vaccine strain

Keywords
FMDV (foot-and-mouth disease virus); Vaccine; Genome sequence; Genomic structure and Genetic variation
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