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Molecular Pathogens
MP 2011, Vol.2, No.1
http://mp.sophiapublisher.com
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Research Article Open Access
Whole Genome Sequencing of A Candidate Strain for FMDV Vaccine: Genomic
Structure and Genetic Variation
Aiguo Xin
1
, Le Li
1
, Mingwang Zhu
2
, Haisheng Miao
1
, Chenhong Shi
2
, Dufang Liao
1
, Yongqin
Yang
1
, Huachun Li
1
1. Key Laboratory for Tropical and Subtropical Animal Virus Disease, Ministry of Agriculture, 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
Corresponding author; kmvir@yahoo.com.cn; li_huachun@hotmail.com;
Authors
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
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 as:
Xin et al., 2011, Whole Genome Sequencing of A Candidate Strain for FMDV Vaccine: Genomic Structure and Genetic Variation, Molecular Pathogens, Vol.2
No.1 (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 candidate strain.
Keywords
FMDV (foot-and-mouth disease virus); Vaccine; Genome sequence; Genomic structure and Genetic variation
Background
Foot-and-mouth disease (
Aphtae epizooticae
), belongs
to Picornaviridae family of
Aphthovirus
genus, is an
infectious and fatal viral disease that affects
cloven-hoofed animals, including domestic and wild
animals, which is a severe plague for animal farming
due to its highly infectious and easy spread.
Foot-and-mouth disease virus (FMDV) causes a high
fever for two or three days, followed by blisters inside
the mouth and on the feet that may rupture and cause
lameness. FMDV has a positive-sense single-stranded
RNA genome and exists in seven immunologically
distinct serotypes, i.e. Euroasiatic serotypes A, O, C,
Asia 1, South African territories SAT 1
-
3) and
multiple subtypes (Brown, 2003). Infection with one
of serotype virus does not confer immunologically
protection against other serotypes and antigenic
variation within serotypes might come out outbreak
strains that vaccines must be carefully matched to
ensure efficacy (Parida, 2009). The FMDV genome,
which has about 8.0 kb in size, contains a
5´
-
untranslated region (5´
-
UTR), a single open
reading frame (ORF) and a 3´
-
untranslated region
(3´
-
UTR) (Mason et al., 2003). The 5´
-
UTR consists
of a short fragment (S fragment), a poly (C) tract, a
long fragment with three or four tandem repeat
pseudoknots (PKs) and an internal ribosome entry site
(IRES) (Belsham, 2005; Mason et al., 2003). The
FMDV ORF encodes a polypeptide that is cleaved to
form mature polypeptide products, which includes
four structural proteins (VP1, VP2, VP3 and VP4) and
eight non-structural proteins (2B, 2C, 3A, 3B, 3D, L
pro
,
2A and 3C
pro
) (Belsham, 2005; Carrillo et al., 2005;
Mason et al., 2003). The 3´
-
UTR is about 90 nt in
length with a 35~100 nt poly (A) tail (Belsham, 2005;
Carrillo et al., 2005).
Molecular epidemiological studies on FMDV were