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Molecular Pathogens
MP2011, Vol.2, No.1
http://mp.sophiapublisher.com
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Table 1 The genomic structure of O/YM/YN/2000 (nucleotides and amino acids) and sequence similarities compared with other
FMDV reference strains
Nucleotide similarity (%)
Amino acid similarity (%)
Regions
Nucleotides
Amino acids
Minimum
Maximum
Minimum
Maximum
5´
-
UTR
1053
-
66.7
88.9
-
-
L
603
201
63.4
93.7
61.2
95.3
VP4
255
85
80.2
95.4
91.6
99.2
VP2
654
218
67.8
92.6
70.1
97.4
VP3
660
220
64.0
92.2
59.4
98.9
VP1
633
211
52.1
93.9
45.6
95.7
2A
54
18
80.6
98.1
93.7
100.0
2B
462
154
86.5
95.8
90.2
100.0
2C
954
318
85.2
94.3
89.8
98.1
3A
429
143
68.7
97.6
68.2
96.6
3B
213
71
87.8
99.5
92.3
99.2
3C
639
213
78.7
93.9
85.6
99.6
3D
1410
470
87.0
94.8
94.2
99.4
3´
-
UTR
113
-
74.7
90.4
-
-
1.4 Phylogenetic analysis
Sequence analysis of O/YM/YN/2000 with the
references of 19 other reported FMDV genomes
suggested that the O/YM/YN/2000 strain should be of
serotype O. Figure 2 showed a neighboring-joining
(NJ) tree constructed based on the sequence alignment
of employed 20 genomes, which were distinctly
divided into 7 serotypes. O/YM/YN/2000 was tightly
clustered in the O serotype and closely linked to
O/HKN/2002
、
O/Taiwan/97
、
O/Chu-pei
、
O/LZ and
O/ES/2001, with close genetic distances.
Moreover, based on the study of molecular
epidemiology using the nucleotide sequence of the
known
VP1
gene, the
VP1
gene of O/YM/YN/2000
represented the eight topotypes of serotype O
compared with other 40 reference strains. The
phylogenetic analysis indicated that O/YM/YN/2000
should belong to the same branch as Cathay topotype
(Figure 3), and its typical biological characteristic of
this lineage virus strain was highly pathogenic in swine.
1.5 Comparison of 5
´
-
UTR between O/YM/YN/
2000 and reference strains
The 5´
-
UTR of O/YM/YN/2000 has 1036 nt in length
(excluding the poly C), containing a short segment,
S-fragment, between 5´
-
end of genome and ploy C
tract which is 364 nt in length. A 4
nt deletion in
S-fragment of O/YM/YN/2000 is evident (Figure 4A).
The predicated RNA secondary structure of the S
fragment would be a single long stem-loop structure
(not shown figure). Although the deletion has no any
evidence to influence on the predicted secondary
structures, this deletion might change some biological
characteristics of the virus, because the S-fragment
presumably involved in replication. The S-fragment
and poly(C) tract are followed by a segment of RNA
of 672
nt in length that can form a number of highly
conserved secondary structures. These structures
include tandem repeat pseudoknots (PKs), the cis-
acting replication element (
cre
), and the Internal
Ribosome Entry Site(IRES). Most FMDV strains have
four PK structures, PK
Ⅰ
,
Ⅱ
,
Ⅲ
and
Ⅳ
sequentially,
located in the function unknown region (FUR) at the
3´
-
end of poly (C) tract. Compared with the reference
strains, a 43
nt consecutive deletion occurring in the
5´
-
UTR of O/YM/YN/2000 results in lost of one of
PK structure, and this deletion exists in 5 strains
including strains of the Cathay and Middle-East South
Asia ( ME-SA) topotype (Figure 4B). It is unknown
whether or not the function of missing PK
Ⅱ
structure
does change the tropism of virus.
1.6 Comparison of VP1 and 3A protein between
O/YM/YN/2000 and reference strains
Comparison of structural protein VP1 amino acid
sequences between O/YM/YN/2000 and reference
strains were conducted in this research. The results of
three major antigenic sites, 40~60, 133~160, and