Analysis of SAT Type Foot-And-Mouth Disease Virus Capsid Proteins and the Identification of Putative Amino Acid Residues Affecting Virus Stability
Rieder E (2013) Analysis of SAT Type Foot-And-Mouth Disease Virus Capsid Proteins and the Identification of Putative
Amino Acid Residues Affecting Virus Stability. PLoS ONE 8(5): e61612. doi:10.1371/journal.pone.0061612
Analysis of SAT Type Foot-And-Mouth Disease Virus Capsid Proteins and the Identification of Putative Amino Acid Residues Affecting Virus Stability
Francois F. Maree 0
Belinda Blignaut 0
Tjaart A. P. de Beer 0
Elizabeth Rieder 0
Jianming Qiu, University of Kansas Medical Center, United States of America
0 1 Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council , Onderstepoort, Pretoria , South Africa , 2 Department of Veterinary Tropical Diseases, Faculty of Veterinary Sciences, University of Pretoria , Onderstepoort , South Africa , 3 Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria , Pretoria , South Africa , 4 Bioinformatics and Computational Biology Unit, University of Pretoria , Pretoria , South Africa , 5 European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, Cambridge, United Kingdom, 6 Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center , Greenport, New York , United States of America
Foot-and-mouth disease virus (FMDV) initiates infection by adhering to integrin receptors on target cells, followed by cell entry and disassembly of the virion through acidification within endosomes. Mild heating of the virions also leads to irreversible dissociation into pentamers, a characteristic linked to reduced vaccine efficacy. In this study, the structural stability of intra- and inter-serotype chimeric SAT2 and SAT3 virus particles to various conditions including low pH, mild temperatures or high ionic strength, was compared. Our results demonstrated that while both the SAT2 and SAT3 infectious capsids displayed different sensitivities in a series of low pH buffers, their stability profiles were comparable at high temperatures or high ionic strength conditions. Recombinant vSAT2 and intra-serotype chimeric viruses were used to map the amino acid differences in the capsid proteins of viruses with disparate low pH stabilities. Four His residues at the interpentamer interface were identified that change protonation states at pH 6.0. Of these, the H145 of VP3 appears to be involved in interactions with A141 in VP3 and K63 in VP2, and may be involved in orientating H142 of VP3 for interaction at the inter-pentamer interfaces.
Funding: Research findings documented in this manuscript are in part the result of a cooperative research and development agreement between the
Agricultural Research Council, Onderstepoort Veterinary Institute of South Africa and the United States Department of Agriculture, Agricultural Research Service,
entitled, Genetic engineering of antigenically stable strains of foot-and-mouth disease virus for vaccine production, agreement number 58-3K95-M-894.
Additional financial support was received from the Red meat Research and Development trust of SA and MSD Animal Health (previously Intervet/Schering
Plough), The Netherlands. The funders had no role in study design, data collection and analysis, or preparation of the manuscript. The funders were consulted in
regards to the publication of the results and approved the manuscript for publication.
Competing Interests: The authors state that the research findings documented in this manuscript are in part the result of a cooperative research and
development agreement between the Agricultural Research Council, Onderstepoort Veterinary Institute of South Africa and the United States Department of
Agriculture, Agricultural Research Service, (agreement number 58-3K95-M-894). Additional financial support was received from the Red meat Research and
Development trust of SA and MSD Animal Health (previously Intervet/Schering Plough), The Netherlands. This does not alter the authors adherence to all the
PLOS ONE policies on sharing data and materials.
Control of highly contagious diseases such as foot-and-mouth
disease (FMD) by means of vaccination relies strongly on the
chemical inactivation of complete viral particles. One of the
principle factors which influences the potency of vaccine
preparations and permits the induction of a protective antibody
response, is the structural integrity of the intact virion typified by a
sedimentation rate of 146S . Other characteristics that play a
role in vaccine efficacy include the productivity and replication
efficiency of the vaccine strain in the production cell line, a close
antigenic relationship to field viruses circulating in current
outbreaks, and the ability to provide protection against a wide
range of antigenic variants in the field [2,3]. However, adaptation
of new vaccine strains in the production cell line (BHK-21) is
difficult and hampered by low amounts of stable antigen, often
rendering this method inefficient for commercial vaccine
manufacturing purposes . In addition, the hot climate in
subSaharan Africa, where the South African Territories (SAT) types
are prevalent, also calls for vaccines with improved stability which
are less reliant on a cold chain during storage and handling.
The aetiological agent, FMD virus (FMDV), is a single-stranded
(ss) positive-sense RNA virus belonging to the genus Aphthovirus in
the family Picornaviridae and exists as seven serotypes, i.e. A, C, O,
SAT1, 2, 3, and Asia-1, with absence of cross protection .
Elucidation of the crystal structure of FMDV over 20 years ago
 enabled assessment of the effects of acid and heat on the virus
capsid structure and identification of protein-protein interactions
that may correlate with enhanced acid or heat stability .
Reverse genetics combined with targeted mutagenesis of residues
involved in the stability of the capsid is a powerful tool for the
improvement of vaccines [15,16], given that thermostability was
linked to vaccine potency since the 1980s . The self-assembly
and stability of a multimeric protein capsid, such as FMDV,
depends on the occurrence of numerous non-covalent interactions
between multiple polypeptide subunits [11,12,14,1720]. The
non-enveloped, icosahedral virion of FMDV is composed of 60
repetitions of four viral structural proteins, VP1-4. The three
surface-exposed proteins, VP1, VP2 and VP3, assemble into a
protomeric subunit, with the smaller VP4 located internally
[9,11,12]. Subsequently, five protomers assemble into a
pentameric intermediate and finally, 12 pentamers self-assemble
through complex protein-protein interactions into a complete
Even though FMDV, especially the SAT types, exhibit large
intra- and inter-serotype genetic variability , the multiple
and repetitive intersubunit interactions appear to have evolved
under stringent and selective constraints [11,13,26,27]. As a result
the viral properties of each serotype are constrained within
fundamental structural requirements of the virus capsid .
Viral capsid inter-subunit interactions are required to be
sufficiently robust in order to provide stability to the capsid under
environmental denaturing conditions [12,13], whilst still
permitting intracellular uncoating and release of viral RNA. Acidification
of FMDV within cellular endosomes disrupts the interactions
between VP2 and VP3 at the pentemeric interfaces leading to
dissociation of the structure into pentamers, thereby releasing the
viral RNA . Mild heating of FMDV virions also leads to
irreversible dissociation into pentamers, a characteristic associated
with poor vaccine performance. This phenomenon, therefore,
highlights the importance of a cold chain in the preservation of
FMD vaccines [1,13,14].
The amino acid residues involved in protein-protein
interactions at the pentameric interfaces and their intolerance to variation
within serotype A and C viruses have previously been
demonstrated [13,14]. However, very little is known about residues
located at the SAT pentameric interfaces involved in structural
stability. Furthermore, by comparison to isolates from serotypes A,
O and C, the SAT viral capsids are generally considered to be less
stable . Consequently, the principle aim of this study was to
investigate the stability of SAT2 and SAT3 isolates in mildly
acidic, heat or high ionic strength conditions. Interestingly, we
showed that the SAT2 virions display similar acid lability
compared to virions from serotypes A, O and C. In addition,
our results demonstrate that amino acid residues at the pentameric
interfaces may also contribute to acid stability of the SAT2 and
SAT3 viruses. This is the first report that describes the
identification of residues in the SAT virus capsids that may be
replaced to allow the engineering of more stable capsids and
consequently improved recombinant FMD vaccines.
Materials and Methods
Cells and viruses
Baby hamster kidney (BHK) clone 13 cells (strain 21; ATCC
CCL-10) were maintained as described previously . Virus
stocks were prepared and titrated in BHK-21 cells using the
plaque assay method . Cultured BHK-21 cells were also used
for RNA transfection and virus recovery. In addition, plaque
assays were performed in either IB-RS-2 (Instituto Biologico renal
suino) cells or Chinese hamster ovary (CHO) cells (strain K1;
ATCC CCL-61), respectively propagated in RPMI medium
(Sigma) and Hams F-12 medium (Invitrogen) supplemented with
10% foetal calf serum (FCS, Delta Bioproducts). The
GAGdeficient CHO derivative, pgsA-677 (CRL-2242), was also
maintained in Hams F-12 medium containing 10% FCS.
COS1 cells, transiently expressing the bovine integrin aV subunit and
either the b1, b3 or b6 subunits were used for cell binding studies
The wild-type SAT2 viruses used in this study were kindly
provided by either the Transboundary Animal Diseases
Programme (TADP, ARC-Onderstepoort Veterinary Institute, SA) or
the FMD World Reference Laboratory at the Institute for Animal
Health (IAH, Pirbright, UK). These viruses were subsequently
either isolated on primary pig kidney (PK) or bovine thyroid (BTY)
cells as part of the strategic stock maintenance and the passage
history of the isolates have been described previously . The
viruses selected for this study included (1) three SAT2 viruses
isolated from buffalo which originated from western Zimbabwe
(SAT2/ZIM/7/83, SAT2/ZIM/17/91 and SAT2/ZIM/14/90);
(2) a SAT2 virus from cattle outbreak in Zambia, (SAT2/ZAM/
7/96); (3) a SAT3 virus isolated from buffalo originating in
Zambia, (SAT3/ZAM/4/96). The passage history, host, country
of origin and topotype are summarised in Table 1. For serial
passages, infected or transfected 35-mm BHK-21 cell monolayers
were frozen and thawed, and 1/10th of the volume was used to
inoculate a fresh BHK-21 monolayer. Following virus adsorption
(with periodical rocking for 60 min at 37uC), virus growth medium
(VGM; Eagles basal medium (BME) with 1% FCS, 1% HEPES
and antibiotics) was added, and the culture was incubated for no
longer than 48 h at 37uC, after which the infected cells were
frozen for subsequent passaging of the viruses.
vSAT2; Y1169H, E1181A, L1182V
vSAT2ZIM17SAT2; V2015L, A2077T,
C2164G, C1134G, E1179K
vSAT2ZAM7SAT2; G2020R, E2214K, E1083K,
The amino acid differences between the 1B/C/D-2A chimeric viruses and the parental isolates are indicated.
aTopotypes refers to genotypes distributed to specific geographic regions. The topotypes for the SAT serotypes were previously described [24,25].
bViruses recovered by transfection of BHK-21 cells with chimeric plasmids are designated v followed by the parental isolate number and the SAT2 plasmid used for
cloning purposes. The amino acid residues have been numbered independently for each protein. For each residue, the first digit indicates the protein (VP1, VP2 or VP3)
and the last three digits the amino acid position.
cThe amino acid differences within the 1B/C/D-2A region of chimeric viruses and the parental viruses are indicated next to each respective viral protein.
Figure 1. Schematic representation of (A) the genomes of the parental field viruses and (B) the chimeric FMDV constructs described
in this study. Plaque morphologies of the parental and genetically engineered viruses obtained on monolayers of BHK-21, IB-RS-2 and CHO-K1 cells
are shown. Cells infected with the respective viral strains were incubated for either 40 h (BHK-21 and CHO-K1) or 28 h (IB-RS-2).
Figure 2. One-step growth kinetic studies were performed in BHK-21 cells. The average log virus titers are shown at different times p.i. with
the vSAT2, vSAT2ZIM17-SAT2, vSAT2ZIM14-SAT2, vSAT2ZAM7-SAT2 and vSAT3ZAM4-SAT2 viruses (A) and the parental SAT2 and SAT3 viruses (B). For
comparison of the relative release of virus particles from cells infected with the parental and chimeric viruses, the average virus titers were
determined at different times p.i (2, 4, 6, 8, 10, 12, 16 and 20 h). The standard deviations of the titers determined from quadruple wells are indicated
on the graph.
Titration and kinetics of virus production
Titrations were performed at least in duplicate in standard
plaque assays by infecting monolayer cells in 35 mm cell culture
plates (NuncTM) with the respective viruses for 1 h, followed by the
addition of a 2 ml tragacanth overlay . Following incubation at
37uC for 28 or 40 h the overlayed infected monolayers were
stained with 1% (w/v) methylene blue in 10% ethanol and 10%
formaldehyde in phosphate buffered saline, pH 7.4.
One-step growth kinetic analyses were carried out in BHK-21
cells. Briefly, BHK-21 cells were infected with the virus strain for
1 h at a m.o.i. of 24 pfu/cell, washed with MBS-buffer (25 mM
morpholine-ethanesulfonic acid, 145 mM NaCl, pH 5.5).
Following incubation at 37uC for the indicated time intervals, the infected
cells were harvested at 2, 4, 6, 8, 10, 12, 16 and 20 h post-infection
(p.i.) and subsequently frozen at 270uC. Virus titers were
determined and expressed as plaque forming units per millilitre
Monolayers of CHO-K1 or CHO-677 cells in 35 mm cell
culture plates (NuncTM) were infected with an m.o.i. of 5
10 PFU/ml of the parental and recombinant viruses. After 1 h of
adsorption, cells were washed with MBS-buffer and then
incubated with virus growth medium (VGM; Hams F-12 with
1% FCS) at 37uC for 1 h and 24 h for each CHO cell type and
frozen at 270uC. Virus titers were determined in BHK-21 cells
and viral growth was calculated by subtracting the 1 h titer results
from the 24 h titer results. Positive titers were interpreted as an
indication that the viruses were able to infect and replicate in the
RNA extraction, cDNA synthesis and construction of
infectious, chimera cDNA clones
RNA was extracted from infected cell lysates with TRIzolH
reagent (InVitrogen) according to the manufacturers
specifications and used as template for cDNA synthesis. Viral cDNA was
synthesised with SuperScript IIITM (InVitrogen). The ca. 2.2 kb
outer capsid-coding region of the SAT2 or SAT3 field isolates was
obtained by PCR amplification. Unique SspI and XmaI sites were
introduced at the 59 and 39 termini of the amplicons, respectively,
to facilitate cloning into pSAT2 plasmid . Briefly, the
corresponding 2.2 kb fragment was excised from pSAT2 by
digestion with SspI and XmaI restriction enzymes and the
remaining fragment was ligated to the SAT2 and SAT3-specific
amplicons. The resultant chimeric constructs, i.e.
pSAT2ZIM17SAT2, pSAT2ZIM14-SAT2, pSAT2ZAM7-SAT2 and
pSAT3ZAM4SAT2, were verified by sequencing using genome-specific
oligonucleotides and the ABI PRISMTM BigDye Terminator Cycle
Sequencing Ready Reaction Kit v3.0 (Applied Biosystems).
In vitro RNA synthesis, transfection and virus recovery
RNA was synthesized from SwaI-linearised plasmid DNA
templates with the MEGAscriptTM T7 kit (Ambion). The
transcript RNAs were examined by agarose gel electrophoresis
to evaluate their integrity and the RNA concentrations were
determined spectrometrically. BHK-21 cell monolayers, in 35-mm
cell culture wells (NuncTM), were transfected with the in
vitrogenerated RNA using Lipofectamine2000TM (InVitrogen). The
transfection medium was removed after 35 h and replaced with
VGM, followed by incubation at 37uC for up to 48 h with a 5%
CO2 influx. After one freeze-thaw cycle, the transfection
supernatants were used for serial passaging on BHK-21 cells.
BHK-21 monolayers in 35-mm cell culture wells were infected
using 1/10th of clarified infected supernatants and incubated for
48 h at 37uC. Viruses were subsequently harvested from infected
cells by a freeze-thaw cycle and passaged four times on BHK-21
cells, using 10% of the supernatant from the previous passage. The
recombinant viruses derived from the infectious chimeric cDNA
clones were designated vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2,
vSAT2ZAM7-SAT2 and vSAT3ZAM4-SAT2. Following the
recovery of viable viruses, the presence of the inserts was verified once
again with automated sequencing. Unless otherwise stated, viruses
that were passaged four times were used for analysis.
Cell-binding studies were essentially performed as described
previously [36,37]. This entails the infection of COS-1 cells,
transiently expressing the bovine integrin aV subunit and either
the b1, b3 or b6 subunits, with the vSAT2, pSAT2ZIM17-SAT2
and pSAT2ZIM14-SAT2 viruses, respectively. Sixteen hours after
infection, cells were labelled with [35S]methionine and viral
protein synthesis analyzed by radio-immunoprecipitation (RIP) of
equal amounts of trichloroacetic acid-precipitable counts per
minute using a SAT2 polyclonal serum followed by sodium
dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE).
Radio-labelled proteins from non-transfected COS-1 cells and
BHK-21 cells infected with vSAT2 were included as controls.
Virus Neutralization test
The antigenic cross-reactivity of the SAT2/ZIM/7/83, SAT2/
ZIM/17/91, SAT2/ZIM/14/90, SAT2/ZAM/7/96, vSAT2,
pSAT2ZIM17-SAT2, pSAT2ZIM14-SAT2 and
pSAT2ZAM7-SAT2viruses was determined using the micro-neutralization test
essentially as described in the OIE Manual of Standards .
ar-values are expressed as the ratio between the heterologous/homologous
end point serum titers of the last dilution of serum to neutralize 100 TCID50 in
50% of the wells in VN assay. The average of two repeats is shown. The
homologous r-values are in bold (n.d. = not done).
bThe sera used in the VN assays were prepared by two consecutive vaccinations
on day 0 and 28 and subsequently bled on day 38 with reference SAT2 viruses,
i.e. SAT2/KNP/19/89, SAT2/ZIM/7/83 and SAT2/ERI/12/89.
cThe SAT2/KNP/19/89 virus, belonging to SAT2 topotype 1  and its
homologous serum was included as a SAT2 control in the VN assay.
dSAT2/ERI/12/89 belong to the SAT2 topotype 12  viruses from East Africa.
eVNTs were not performed against the SAT3 viruses using SAT2 antisera.
Figure 3. COS-1 cells were co-transfected with cDNA plasmids encoding the bovine integrin aV subunit and either the b1, b3 or b6
subunits. Transfected cells were infected with the recombinant SAT2 viruses and proteins were radiolabelled with [35S]methionine. Viral protein
synthesis were analyzed by radiolabelled immune-precipitation and SDS-PAGE. Immune-precipitated proteins from non-transfected but infected
celllysates are indicated by NT, and the location of the viral structural proteins from lysates prepared from FMDV-infected BHK-21 cells is indicated by
Reference cattle sera were prepared by two consecutive
vaccinations (vaccinated on day 0, boosted on day 28 and bled on day 38)
with the SAT2/ZIM/7/83, SAT2/KNP/19/89 and SAT2/ERI/
12/98 vaccines. Cattle were housed in the isolation facility at
TADP and all procedures were approved by the Onderstepoort
Veterinary Institute Animal Ethics Committee and were
performed according to national and international guidelines.
IB-RS2 cells were used as the indicator system in the neutralization test.
The end point titer of the serum against homologous (SAT2/
ZIM/7/83) and heterologous (SAT2/KNP/19/89 and SAT2/
ERI/12/98) viruses was calculated as the reciprocal of the last
dilution of serum to neutralise 100 TCID50 virus in 50% of the
wells . One-way antigenic relationships (r1-values) of the field
isolates and engineered viruses relative to the reference sera were
calculated and expressed as the ratio between the heterologous/
homologous serum titer. All neutralization titer determinations
were repeated at least twice and presented as an average.
Sucrose density gradient purification
Culture fluids were harvested, clarified by centrifugation,
concentrated with 8% PEG (w/v) and resolved on 1050% (w/
v) sucrose density gradients (SDG) by rate zonal centrifugation at
36,000 g for 16 h at 4uC. The gradients were fractionated and
analysed spectrophotometrically by measuring the absorbancy at
260 nm. Fractions containing 146S virions were calculated using
the extinction coefficient E259nm = 79.9  and pooled for
analysis. The presence of the outer capsid proteins were verified
using SDS-PAGE analysis, while the integrity of the RNA was
verified by RT-PCR and sequencing of the 1D-coding region.
Capsid dissociation assays and measurements of rate
The wild-type and recombinant SAT virus particles present in
the cell culture supernatants or SDG purified samples were
prepared in TNE buffer (100 mM Tris pH 7.4, 10 mM EDTA,
150 mM NaCl) essentially as described . Briefly, 106 to 107
pfu/ml of infectious particles were mixed with TNE buffer ranging
from pH 5.6 to 9.0 (60.02) at a ratio of 1:50 respectively. The
mixtures were subsequently incubated for 30 min at room
temperature. As a control, virus particles were also mixed with
VGM at the same ratio as above. The samples were subsequently
neutralised with 1 M Tris (pH 7.4), 150 mM NaCl and titrated on
BHK-21 cells. Similarly, virus particles were treated for 30 min
with TNE buffers with a constant pH of 7.4, containing NaCl
Figure 4. pH and ionic strength stability profiles of vSAT2 (black), vSAT2ZIM14-SAT2 (dark grey), vSAT2ZIM17-SAT2 (light grey),
vSAT2ZAM7-SAT2 (white) and vSAT3ZAM4-SAT2 (medium grey). (A) Inactivation of SDG-purified virus particles following treatment with TNE
(100 mM Tris, 150 mM NaCl, 10 mM EDTA) buffers ranging from pH 9.0 to 6.0 for 30 min. The average virus titers of two inactivation experiments at
each pH are plotted. (B) The viruses were incubated in buffers with varying NaCl concentrations and the average log titers of two experiments are
Figure 5. pH and thermal inactivation kinetics of vSAT2, vSAT2ZIM17-SAT2, vSAT2ZIM14-SAT2, vSAT2ZAM7-SAT2 and
vSAT3ZAM4SAT2 viruses. (A & C) Inactivation of SDG-purified vSAT2, vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2, vSAT2ZAM7-SAT2, and vSAT3ZAM4-SAT2 particles
following treatment with TNE buffer at pH 6.0 (A) and heat treated at 42uC (C) for up to 3 h. The average log10 virus titers, as determined in two
different inactivation experiments are shown. The respective logarithmic values of the virus titers at the different time points (0, 15, 30, 45, 60, 90, 120
and 180 min p.i.) were linearly fitted and the slopes were determined. (B & D) The average virus titers following pH treatment (B) or heat inactivation
(D) were used to determine the percentage of residual infectivity over time.
concentrations ranging from 0.051.5 M (1:50 virus particles to
buffer), followed by titrations on BHK-21 cells. Alternatively the
virus particles in TNE buffer (pH 7.4) were treated at
temperatures of 25uC, 37uC, 45uC or 55uC for 30 minutes, after which the
samples were cooled on ice and titrated. The 1:50 dilution of the
SDG purified particles ensured that the stabilising effect of sucrose
was negligible as it was calculated the viscosity was less than 1%.
All assays were performed in duplicate and the average virus titers
In addition, SDG-purified particles with an approximate titer of
486106 pfu/ml were either treated at pH 6.0, or heated at 42uC
for different time intervals following a 1:50 dilution in the
appropriate TNE buffer. The number of infectious particles
remaining after treatment was determined by plaque titrations on
BHK-21 cells. The respective logarithmic values of the virus titers
at the different time points (0, 15, 30, 45, 60, 90, 120 and 180 min
p.i) were linearly fitted and the slopes were determined [42,43]
using the R statistical software . The percentage of remaining
infectious particles was also calculated and plotted along with the
exponential decline used to calculate the inactivation rate constant
as described .
Structural analysis of variable amino acids in capsid
Three-dimensional models of protomers comprising the four
capsid proteins (1A, 1B, 1C and 1D) of the SAT2 viruses were
constructed based on the crystallographic coordinates of O1BFS
(1FOD) , while pentameric models were built using the capsid
coordinates, A1061 (1ZBE). The models were based on an optimal
amino acid alignment of the capsid proteins. Sequence alignments
were performed with ClustalX software  using the default
parameter setting. The modelling scripts were generated using the
structural module in the FunGIMS software pakage and models
were built using the Modeller 9v1 programme . The homology
structure was calculated by the satisfaction of spatial restraints as
described by empirical databases. Structures were visualised with
PyMol v0.98 (DeLano Scientific LLC). A PROPKA  analysis
of each protomer was carried out to identify major protonation
states affected by a pH of 6.0. Yasara  was used to analyse any
hydrogen bond networks that were present.
pH-dependent differences between pentamers were investigated
using a molecular dynamics simulation for ,2.5 ns . The
simulation was performed at a pH of 6.0, water density of
0.997 g/ml and a NaCl concentration of 0.9% using the Amber99
force-field with periodic boundary conditions at a temperature of
298 K. A molecule consisting of two protomers (henceforth called
the dimer) was also generated to analyse the interface between two
Construction and in vitro characterization of genetically
To study the stability of SAT2 and SAT3 virions and the amino
acid differences responsible for altered stabilities in a defined
genetic background, we constructed infectious chimeric cDNA
clones, containing the 1B/C/D/2A-coding region of SAT2 and
SAT3 field isolates in the defined genetic background of an
infectious pSAT2 genome-length clone (ZIM/7/83) . Clones
containing the capsid-coding region of southern Africa SAT2
isolates, i.e. SAT2/ZIM14/90, SAT2/ZIM/17/91 and SAT2/
Figure 6. Variation observed in VP1-3 mapped to the structural models of the SAT2 (A) pentamers and (B) protomers. The amino
alignment and effect of the variable residues is shown in Table S1. Residues predicted to play a role in the capsid stability are shown here. Variable
positions are coloured in red, VP1 in cyan, VP2 in green, VP3 in magenta and VP4 in yellow. (C) The Ca RMSD variation of SAT2/ZIM/7/83 (in red),
vSAT2 (in black) and vSAT2ZAM7-SAT2 (in green) over the ,2.5 ns simulation time at pH 6.0 using the pentamers.
Figure 7. The interaction interface between two adjacent pentamers. (A) One protomer of each pentamer is shown. The dashed line
indicates the interaction surface. VP3 residues H145, H142 and K63 using Van der Waals surfaces are coloured red. (B) The hydrogen bond network
found in the pentamer interface. When VP3 H145 is neutral, it forms a hydrogen bond with VP2 K63 and VP3 A141. The neutral state seems to prevent
pentamer association through H142 and H145. Yellow dashed lines indicate hydrogen bonds and the white dashed line indicates pentamer interface.
The + indicates the charged dipole of the a-helix.
ZAM/7/96, as well as a SAT3 virus, SAT3/ZAM/4/96, were
selected to synthesize RNA. The transcript RNAs were transfected
into BHK-21 cells and viable chimeric viruses recovered. The
recombinant viruses derived from the infectious chimeric cDNA
clones were designated vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2,
vSAT2ZAM7-SAT2 and vSAT3ZAM4-SAT2, respectively (Fig. 1).
The vSAT3ZAM4-SAT2 is the only inter-serotype chimera
containing the SAT3 outer capsid-coding region in a SAT2
Plaque morphologies, growth and antigenic properties of the
recombinant viruses were examined to determine whether they
resembled those of the parental viruses. As illustrated in Fig. 1,
SAT2 and SAT3 field viruses, and the derived chimeric viruses
produced large plaques (78 mm) on BHK-21 cells. The SAT2/
ZIM/7/83 parental virus (passage history: B1BHK5B1) produced
large plaques while its genetically-cloned derivative, vSAT2
(passage history: BHK3), produced a mixture of large and small
(35 mm) plaques on BHK-21 cells. A porcine kidney cell line
(IBRS-2), known to express aVb8 , was also included in the
analysis. The distribution of large plaques (78 mm) formed by the
parental SAT2 and SAT3 viruses and vSAT2ZAM7-SAT2 on
IBRS-2 cells were similar to those observed on BHK-21 cells (Fig. 1).
The vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2 and
vSAT3ZAM4SAT2 viruses formed medium plaques (35 mm) on IB-RS-2 cells
(Fig. 1). In CHO-K1 (wild-type, glycosaminoglycan or GAG
positive) cells, only the SAT2 vaccine strain, ZIM/7/83 and its
derivative, vSAT2, were able to propagate, yielding small plaques
(,2 mm) 48 h post-infection (p.i.) (Fig. 1). SAT2 and SAT3 field
viruses, as well as their genetically-cloned derivatives,
vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2, vSAT2ZAM7-SAT2 and
vSAT3ZAM4-SAT2, were unable to produce plaques on CHO-K1 cells
(Fig. 1). Subsequently, CHO-677 (GAG-deficient cell line) were
also infected with the respective recombinant SAT viruses, but
none of these viruses were able to replicate (not shown).
The growth kinetics of both field SAT2 and SAT3 and
genetically-engineered intra- and inter-serotype viruses illustrates
that the growth of the chimeric viruses, vSAT2ZIM14-SAT2,
vSAT2ZIM17-SAT2, vSAT2ZAM7-SAT2 and vSAT3ZAM4-SAT2,
were similar to that of the vSAT2 (Fig. 2A) and parental field
viruses (Fig. 2B). Following infection of BHK-21 cells at a m.o.i. of
25 pfu/cell all viruses yielded high and comparable titers at 20 h
p.i., after which their growth became indistinguishable.
Next we compared the antigenic profiles of the parental and the
three intra-serotype chimeric viruses using SAT2 antisera from
prototype strains in a virus neutralization (VN) assay (Table 2).
The antigenic variation of the parental SAT2 isolates with the
antisera was pronounced, returning r1-values of lower than 0.2,
even though SAT2/ZIM/7/83, SAT2/ZIM/14/90 and SAT2/
ZIM/17/91 belonged to the same topotype . Based on the VN
assay results, the r1-values of the chimeric viruses (Table 2)
indicated that the sera reacted similarly to the recombinant SAT2
viruses, suggesting the absence of significant alterations in the
structure of antigenic determinants on the chimeric virions. The
r1-values of SAT2/ZAM/7/96 and vSAT2ZAM7-SAT2 against the
reference sera were below 0.2. Hence, the results from the plaque
morphology, growth kinetics and VN assays demonstrate that the
immunological characteristics and receptor preferences of the
parental field isolates were transferred to the chimeric viruses.
Analysis of receptor usage by the engineered SAT type
The receptor specificity of the chimeric SAT2 viruses was
investigated using COS-1 cells, co-transfected with bovine aV
integrin subunit and either of the b1, b3 or b6 subunit cDNAs.
Replication of vSAT2 and the SAT2 chimeric viruses,
vSAT2ZIM14-SAT2 and vSAT2ZIM17-SAT2, was demonstrated in
cultured cells expressing aVb6 (Fig. 3). The bovine avb1 integrins
were not able to sustain infection for any of these viruses. Only low
level virus protein synthesis was detected in bovine
avb3expressing cells infected with vSAT2, vSAT2ZIM14-SAT2 and
Stability of SAT viruses to biophysical conditions
The stability of SAT2 and SAT3 chimeric viruses to different
pH, ionic strength and temperature conditions was evaluated.
Treatment of the SDG-purified SAT2 and SAT3 chimeric viruses
to buffered solutions of varying pH revealed intra-serotype
differences with respect to viral capsid stability in mild acidic pH
(Fig. 4A). Both vSAT2ZIM17-SAT2 and vSAT2ZIM14-SAT2
chimeric infectious particles (western lineage) displayed a
comparable decrease in titer when the pH of the buffers were reduced
from 9.0 to 6.2, with 2125% infectivity remaining after
30 minutes at pH 6.2 (Fig. 4A). This stability profile was
comparable to vSAT2 where 23% infectivity remained at pH
6.2, with a sudden drop in titer at a pH ,6.2 (Fig. 4A). For the
chimeric SAT2 viruses, the pH50 values, defined as the pH where
50% of infectivity is measurable, were calculated as 6.46 and 6.48
for vSAT2ZIM14-SAT2 and vSAT2ZIM17-SAT2, respectively. The
pH50 value vSAT2 was calculated to be 6.51.
Conversely, vSAT2ZAM7-SAT2 revealed a significantly higher
sensitivity in buffers at and below pH 6.5 as evidenced by a
260fold decrease in infectious particles (1.5% infectivity remaining)
within 30 min of incubation at pH 6.2, compared to the virus titer
measured at pH 7.4 (Fig. 4A). At pH 6.0, no vSAT2ZAM7-SAT2
infectious particles were detected, while vSAT2,
vSAT2ZIM14SAT2 and vSAT2ZIM17-SAT2 maintained a titer of 102 pfu/ml
(Fig. 4A). The SAT3 inter-serotype chimera, vSAT3ZAM4-SAT2,
showed a .2000-fold drop in titer when the pH was lowered from
7.4 to 6.2 and it diminished rapidly with no infectious particles
detected at pH 6.0 (Fig. 4A). The pH50 values for the infectious
virus particles were calculated as 6.8 and 6.81 for
vSAT2ZAM7SAT2 and vSAT3ZAM4-SAT2, respectively.
The recombinant virions showed remarkable resilience in a
series of buffers with increasing ionic strengths (0.051.5 M NaCl;
Fig. 4B). Similar virus titers were observed for purified vSAT2,
vSAT2ZIM14-SAT2, vSAT2ZIM17-SAT2 and vSAT2ZAM7-SAT2
infectious 146 S particles in buffered solutions containing varying
NaCl concentrations of between 0.051.5 M (Fig. 4B). Although
differences in titers were observed, it is not believed to carry any
biological relevance, with the exception of vSAT2 incubated in
1.5 M NaCl. A significant drop in titer was observed for vSAT2
after 30 min incubation in 1.5 M NaCl. It has been reported for
A24 Cruzeiro empty capsids that increasing ionic strength (50 to
250 mM) destabilizes the capsids . Although we did not
investigate the effect of ionic strength on the SAT2 empty capsids,
the destabilizing effect on infectious particles was observed at ten
times the physiological salt concentration (1.5 M NaCl).
When incubated at temperatures ranging from 20uC to 55uC,
the vSAT2, and the chimeric viruses, displayed similar
thermostability with 614% residual infectivity remaining after incubation
at 45uC for 30 min (data not shown). No infectious particles were
detected after incubation at 55uC for 30 min.
Heat and pH inactivation of SAT2 and SAT3 viruses
The differences in the stability of the chimeric virions were
further elucidated using pH and heat inactivation assays. These
inactivation assays were done in a similar way, essentially
SDGpurified chimeric particles at an approximate titer of 4
96106 pfu/ml, were either treated in a pH 6.0 buffer or at
42uC in a pH 7.4 buffer for different time intervals as indicated in
Fig. 5. The observed inactivation profiles of the particles in a
pH 6.0-buffered solution did not conform to a linear, but rather a
logarithmic decrease in the number of infectious viral particles
(Fig. 5A). When plotting the logarithmic titers over time, the acid
lability of the chimeric viruses was reflected by the inactivation
rate constant values at pH 6.0, which were 0.002, 0.008, 0.013,
0.013 and 0.012 per minute (min21) for vSAT2,
vSAT2ZIM14SAT2, vSAT2ZIM17-SAT2, vSAT2ZAM7-SAT2 and
vSAT3ZAM4SAT2, respectively. The inactivation rates of vSAT2ZIM17-SAT2,
vSAT2ZAM7-SAT2 and vSAT3ZAM4-SAT2 were higher than that
of vSAT2 and vSAT2ZIM14-SAT2 viruses and were a reflection of
the faster deterioration of the infectious particles following
treatment in a pH 6.0 buffer (Fig. 5A). The vSAT2 virus showed
the slowest rate of inactivation which resulted in ca. 24% of
infectious particles remaining after 3 h treatment at pH 6.0
Contrary to the pH inactivation rates, no substantial differences
with respect to thermostability were demonstrated between the
vSAT2 and chimeric viruses (Fig. 5C). Temperature inactivation
profiles can be drawn by plotting the decrease in virus logarithmic
titers over time. The inactivation rate constants were then
determined from the slope of the linear plots. The inactivation
rate constant values at 42uC for vSAT2ZAM7-SAT2 and vSAT2
were 0.013 and 0.015 min21, respectively, while the value for the
remaining three chimeras was determined to be to be 0.018 min21
(Fig. 5C). The decrease in the percentage of infectivity was similar
to vSAT2 with 612% residual infectivity after 3 h at 42uC
(Fig. 5D). Taken together, the results reveal that contrary to what
we suspected, despite the variation in the outer capsid proteins the
thermal stability of the FMDV particles was remarkably
Molecular dynamics and the role of variable amino acids
in the FMDV interpentameric interactions
Structural mapping of variable amino acid residues within the
outer capsid proteins of the chimeric SAT2 viruses that may play a
role in the altered acid sensitivities was performed. The amino acid
differences in the outer capsid proteins were mapped on the
structure of a pentameric unit (Fig. 6) and their involvement in
VP2VP3 and VP2VP2 pairwise contacts at the pentameric
interface were analysed (Fig. S1, Table S1). The 50 amino acid
differences that were observed between vSAT2 and the less
acidstable vSAT2ZAM7-SAT2 may suggest that some of these residues
play a critical role in virion stability (Table S1).
Alignment of the capsid proteins showed that 10.5% of the
residues were variable. The internally located 1A protein of the
chimeric viruses and the vSAT2 virus shared 100% identity, due
to the cloning strategy followed (Fig. 1). Although 1A may be
involved in protein-RNA interaction or exert a small effect on
inter-protomer interactions, the overall effect of 1A in the stability
of the SAT2 virions was not taken into consideration in this
analysis. The variation within the outer capsid proteins could be
categorised into three groups, i.e. those having no effects
(surfaceexposed variable residues with no change in the local structure or
interactions); those affecting the intra-protomer association; and
those affecting the inter-protomer interactions (Fig. 6A).
The majority of the variable residues were surface-exposed,
suggesting that these changes may exert a minimal effect on the
stability of the capsid. At least 17 of the observed differences
appeared to have putative effects on protomer-protomer
interactions based on the predicted models (Fig. 6A and B). Although six
of the variable residues could be considered as neutral and did not
appear to influence the structure significantly, at least 11 of the 17
variable residues appeared to result in the addition or loss of
interactions. Five of these residues mapped to the protomer
particularly at the pentameric interface and adjacent to the pores
located at the 3-fold axis (Fig. 6A and B). These differences may
indeed influence the capsid assembly and disassembly dynamics,
but still needs to be confirmed experimentally.
Molecular dynamics simulations were performed for ,2.5 ns
with the vSAT2, SAT2/ZIM/7/83 and vSAT2ZAM7-SAT2
pentamers. The root mean-square deviation (RMSD) variation
over time for each of the pentamers at pH 6.0 is shown in Fig. 6C.
Contrary to the lower acid stability observed for the purified
vSAT2ZAM7-SAT2 infectious particles, there was no noteworthy
difference in the RMSD of the pentamers of the viruses included
in the study. Any significant difference between the infectious
particles, such as pentamer dissociation, was expected to result in
high RMSD values.
PROPKA analysis of the modelled FMDV protomer structures,
however, indicated four His residues that play putative roles in
capsid stability, i.e. H81 and H115 in VP2 and H145 and H172 in
VP3. Of these, the His residue at position 145 of VP3 correlated
with the residues at the pentameric interfaces that were previously
identified and shown to contribute to virion stability . These
His residues are most likely involved in inter-pentamer interactions
and are buried in the dimer interface, thereby concealing them
from the aqueous phase. Changes in pKa values of the His
residues in either a single protomer or two adjacent protomers
(dimer) were determined with PROPKA analysis. The predicted
pKa values of the protomers indicated that the four His residues
changed protonation states in the region of pH 6.0. When the
pattern of binding by these His residues was taken into
consideration, it appeared as if none of the protomers of the
SAT2 viruses, ZIM/7/83, vSAT2 or vSAT2ZAM7-SAT2, gained
or lost a nett amount of bonds. However, when the residues were
mapped to the predicted protein models, bond changes occurring
between adjacent VP3 chains in the pentamer interfaces were
There is a large body of evidence suggesting that thermal
stability of complete 146S FMDV particles and the
immunogenicity of the particles could be linked to vaccine efficacy . There
is a common believe that SAT viruses are particularly unstable
and very little is known about residues located at the SAT
pentameric interfaces involved in structural stability.
Consequently, we have investigated the biophysical stability of infectious
virions generated from southern African isolates of the SAT2 and
SAT3 serotypes under various controlled environmental
conditions which are relevant during the vaccine production process.
We have demonstrated that chimeric viruses, containing the
outer capsid of dissimilar viruses in a SAT2 genetic background,
retained the plaque phenotypes, infectivity kinetics and
immunological profiles of the parental strains (isolated during an outbreak)
from which they were derived. With respect to cellular receptor
preferences [50,51], the SAT2 and SAT3 viruses originating from
buffalo grew in BHK-21 or IB-RS2 cells following amplification in
cell culture, but were unable to infect and replicate in CHO-K1
cells, suggesting that these field viruses do not utilize GAG
receptors for cell entry. The interaction of SAT2 viruses with three
aVb-integrin molecules was demonstrated in this study by
expressing these integrin molecules transiently in COS cells. The
results indicated that not all the integrins are used with the same
affinity for cell entry by the SAT2 viruses. Whereas the SAT2
viruses were able to infect and replicate in COS cells expressing
the aVb6 integrins, we found that these viruses displayed a poor
ability to infect cells expressing aVb3 integrins, the result of which
is in agreement with previous findings. with regards to the low
affinity of type O1 viruses for aVb3 receptors [50,52,53]. This
observation may be attributed to the G-H loop in VP1 that is
structurally not optimal for binding to the aVb3 integrin .
Contrary to the ability of type O1 viruses to utilize aVb1 and aVb6
with a high efficiency [50,52,53], the aVb1 integrins were not able
to mediate infection of any of the SAT2 viruses under the
We found that virus particles of the SAT2 serotype, which differ
by less than 11% in the capsid protein amino acid sequences, are
stable in mild acidic conditions from pH 6.5 to 7.0. However, their
infectivity was rapidly lost in buffers with a pH below 6.5, although
infectious particles could still be detected at pH 6.0. The range of
pH50 variation for the SAT2 serotype was 0.4 pH units between
pH 6.8 and 6.4, with vSAT2ZAM7-SAT2 (SAT2/ZAM/7/96
derivative) being the least stable. The infectious
vSAT3ZAM4SAT2 particles also displayed a pronounced sensitivity under
acidic conditions, losing 50% of its infectivity at pH 6.81. This
variation in pH sensitivity did not appear to hamper the growth
properties of the SAT2 or SAT3 viruses in cultured cells, an
attribute to be expected of a virus that depends on acidification
within endosomes for RNA release and replication .
SAT2 and SAT3 chimeric infectious particles were sensitive to
mild heating. Thermal dynamics indicated that the SAT infectious
particles decreased at a rate fitted best to single first order kinetics
that is consistent with simple dissociation and similar to the
behavior of a type C virus under mild temperature conditions .
It is known that mild heating of FMDV virions leads to irreversible
dissociation into stable pentamers or 12S particles [1,14].
Consequently, the first order kinetics observed for the SAT
inactivation suggests similar dissociation of the infectious virions.
The dissociation of virions in an acidic environment is considered
to similarly lead to dissociation into pentamers and the observed
inactivation rate was typified by a linear decrease of the
logarithmic titer. Contrary to the thermal dynamics and acid
lability of the SAT2 and SAT3 infectious particles, these particles
were consistently stable in solutions with a high ionic strength and
a pH as high as 9.0.
The stability of the FMD virion can be described as an
equilibrium of multimeric electrostatic and hydrophobic
interactions between the protein subunits and disruption of these
interaction causes dissociation of the virion [11,55,56,14]. Two
likely residues, i.e. H142 and H143 in VP3, responsible for the
destabilization of serotype A viruses as a function of pH, have been
described previously [57,58]. In an attempt to identify the relevant
residues and side chain interaction that may cause the SAT2/
ZAM/7/96 to be less stable in mild acidic conditions compared to
the other SAT2 viruses, we mapped the amino acid variation to a
modeled structure of the SAT2 capsid. While some of the amino
acid variation was mapped to the surface of the virion, most of the
variation was adjacent to the pore at the five fold axis of the virion
(Table S1). These residues have the potential of interacting with
VP4 or viral RNA at the inside of the pore . When the
variable surface-exposed residues were ignored on the basis that
they may be involved in virus neutralisation or cell entry and,
therefore, their effect on virion stability regarded to be minimal, at
least 11 amino acid residues revealed potential protein-protein
interaction. Five residues mapped to the pentamer interface, three
(T2099A, K2215M and I3128V) of which shows interactions with
residues at the C-terminus of the VP2 a-helix, responsible for
interactions across the interface. A2191T and F3064V form
hydrogen bonds across the interface at the 3-fold axis.
The pentamer models for vSAT2, SAT2/ZIM/7/83 and
SAT2/ZAM/7/96 were built on the same template, therefore
RMSD deviation after dynamic simulation could be directly
compared. The molecular dynamics simulations of the related
vSAT2 and SAT2/ZIM/7/83, and the distant SAT2/ZAM/7/96
showed that the pentamers were stable during the simulation as
seen from the RMSD curves in Fig. 6. This indicates that the effect
on the stability of the virus particles should be seen at the level of
pentamer assembly into virions and not at a level of protomers
assembling into pentamers. We also could not detect any change
in the protonation state in any of the residue changes among the
The pKa predictions results for the protomers indicated four
His residues which change protonation states around pH 6.0.
H145 in VP3 is involved in inter-protomer interaction on the
pentameric interfaces and hydrogen bond analysis of the dimer
molecule showed that this residue interacts with A141 in VP3 and
with K63 in VP2 of the adjacent protomer (Fig. 7). The PROPKA
results for the dimer molecule show the pKa for VP3 H145 to be
1.12. Thus, from these results it appears that a pH below 6.0
would disrupt interactions at the pentamer interface. A significant
proportion of VP3 H145 needs to be neutral for pentamers to
assemble into a capsid. This confirms previous observations that
VP3 H145 plays a role in capsid disassembly and vaccine stability
[12,13,57]. The VP3 H142 residue was also shown to be
important in the association between the pentamers. The
hydrogen bond analysis showed that VP3 H145 made a hydrogen
bond with the backbone of VP3 A141 (Fig. 7B). This backbone
hydrogen bond seems to be important is helping to orientate the
VP3 H142 containing loop correctly to form the association with
the charged dipole of the alpha-helix. The VP3 H145 also makes a
hydrogen bond with VP2 K63 in the adjacent pentamer, thus
providing extra interaction and stabilization between the
pentamers (Fig. 7B). The loss of the hydrogen bonds with either VP2
K63 or VP3 A141 would have a significant effect on the
Our study provides evidence that SAT2 viruses isolated from
buffalo enters the cell host with a preference for aVb6 integrin
receptors. Moreover, the SAT virus particles were shown to
dissociate within a range of mild acidic conditions which does not
significantly impact on viral functions or infectivity. Furthermore,
chimeric SAT viruses containing the immunological outer
capsidcoding region of an emerging virus in the genetic background of a
stable vaccine strain are infectious. Together, the data
demonstrate the utility of recombinant DNA technology to produce
chimeric viruses as vaccine seed stock with desirable properties
and thermal-stability for the improvement of virus
immunogenicity and vaccine efficacy.
Table S1 A summary of the variable amino acids in an
alignment of the capsid proteins of the SAT2 viruses ZIM/7/83,
ZIM/14/90, ZIM/17/91 and ZAM/7/96 and the possible
interactions of the residues in the complete capsids.
The authors would like to express their gratitude to the personnel at the
ARC-OVI (TADP) for their contributions to virus isolation and animal
work. Many thanks to Jan Esterhuysen for his contribution with
performing VNTs and Geoff Fosgate for the statistic performed in this
study. We would also like to thank Drs Sonja Maree, Katherine Scott, Ben
Mans and Jacques Theron for commenting and critical reading of the
Conceived and designed the experiments: FM TdB ER. Performed the
experiments: FM BB TdB ER. Analyzed the data: FM TdB ER.
Contributed reagents/materials/analysis tools: FM ER. Wrote the paper:
FM TdB ER.
1. Doel TR , Baccarini PJ ( 1981 ) Thermal stability of foot-and-mouth disease virus . Arch Virol 70 : 21 - 32 .
2. Barnett PV , Carabin H ( 2002 ) A review of emergency foot-and-mouth disease (FMD) vaccines . Vaccine 20 : 1505 - 14 .
3. Doel TR ( 2003 ) FMD vaccines . Virus Res 91 : 81 - 99 .
4. Pay TWF , Rweyemamu MM , O'Reilly KJ ( 1978 ) Experiences with Type SAT 2 foot-and-mouth disease vaccines in Southern Africa. XVth Conference of the Office International Des Epizzoties Permanent Commision on foot-and-mouth disease . p1- 25 .
5. Preston KJ , Owens H , Mowat GN ( 1982 ) Sources of variations encountered during the selection and production of three strains of FMD virus for the development of vaccine for use in Nigeria . J Biol Stand 10 : 35 - 45 .
6. Amadori M , Berneri C , Archetti IL ( 1994 ) Immunogenicity of foot-and-mouth disease virus grown in BHK-21 suspension cells. Correlation with cell ploidy alterations and abnormal expression of the alpha 5 beta 1 integrin . Vaccine 12 : 159 - 166 .
7. Bachrach HL ( 1968 ) Foot-and-mouth disease . Annu Rev Microbiol 22 : 201 - 244 .
8. Pereira HG ( 1978 ) Antigenic variation in relation to epidemiology and control of foot and mouth disease . Br Vet J 35 : 167 - 74 .
9. Sobrino F , Saiz M , Jimenez-Clavero MA , Nu nez JI , Rosas MF , et al. ( 2001 ) Foot-and-mouth disease virus: a long known virus, but a current threat . Vet Res 32 : 1 - 30 .
10. Domingo E , Baranowski E , Escarms C, Sobrino F ( 2002 ) Foot-and-mouth disease virus . Comp Immunol Microbiol Infect Dis 25 : 297 - 308 .
11. Acharya R , Fry E , Stuart D , Fox G , Rowlands D , Brown F ( 1989 ) The threedimensional structure of foot-and-mouth disease virus at 2.9 A resolution . Nature 337 : 709 - 716 .
12. Curry S , Fry E , Blakemore W , Abu-Ghazaleh R , Jackson T , et al. ( 1996 ) Perturbations in the surface structure of A22 Iraq foot-and-mouth disease virus accompanying coupled changes in host cell specificity and antigenicity . Structure 4 : 135 - 145 .
13. Ellard FM , Drew J , Blakemore WE , Stuart DI , King AM ( 1999 ) Evidence for the role of His-142 of protein 1C in the acid-induced disassembly of foot-and-mouth disease virus capsids . J Gen Virol 80 : 1911 - 1918 .
14. Mateo R , Daz A , Baranowski E , Mateu MG ( 2003 ) Complete alanine scanning of intersubunit interfaces in a foot-and-mouth disease virus capsid reveals critical contributions of many side chains to particle stability and viral function . J Biol Chem 278 : 41019 - 41027 .
15. Van Rensburg HG , Henry T , Mason PW ( 2004 ) Studies of genetically defined chimeras of a European type A virus and a South African Territories type 2 virus reveal growth determinants for foot-and-mouth disease virus . J Gen Virol 85 : 61 - 68 .
16. Maree FF , Blignaut B , de Beer TAP , Visser N , Rieder E ( 2010 ) Mapping of amino acid residues responsible for adhesion of cell culture-adapted foot-andmouth disease SAT type viruses . Virus Res 153 : 82 - 91 .
17. Liljas L ( 1986 ) The structure of spherical viruses . Prog Biophys Mol Biol 48 : 1 - 36 .
18. Rossmann MG , Johnson JE ( 1989 ) Icosahedral RNA virus structure . Annu Rev Biochem 58 : 533 - 573 .
19. Reguera J , Carreira A , Riolobos L , Almendral JM , Mateu MG ( 2004 ) Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid . Proc Natl Acad Sci USA 101 : 2724 - 2729 .
20. Reguera J , Grueso E , Carreira A , Sanchez-Martnez C, Almendral JM , et al. ( 2005 ) Functional relevance of amino acid residues involved in interactions with ordered nucleic acid in a spherical virus . J Biol Chem 280 : 17969 - 77 .
21. Mateo R , Luna E , Rincon V , Mateu MG ( 2008 ) Engineering viable foot-andmouth disease viruses with increased thermostability as a step in the development of improved vaccines . J Virol 82 : 12232 - 40 .
22. Vosloo W , Kirkbride E , Bengis RG , Keet DF , Thomson GR ( 1995 ) Genome variation in the SAT types of foot-and-mouth disease viruses prevalent in buffalo (Syncerus caffer) in the Kruger National Park and other regions of southern Africa , 1986 - 93 . Epidemiol Infect 114 : 203 - 218 .
23. Van Rensburg HG , Nel LH ( 1999 ) Characterization of the structural-proteincoding region SAT 2 type foot-and-mouth disease virus . Virus Genes 19 : 229 - 233 .
24. Bastos ADS , Haydon DT , Forsberg R , Knowles NJ , Anderson EC , et al. ( 2001 ) Genetic heterogeneity of SAT-1 type foot-an-d-mouth disease viruses in southern Africa . Arch Virol 146 : 1537 - 1551 .
25. Bastos ADS , Haydon DT , Sangare O , Boshoff CI , Edrich JL , et al. ( 2003 ) The implications of virus diversity within the SAT 2 serotype for control of foot-andmouth disease in sub-Saharan Africa . J Gen Virol 84 : 1595 - 1606 .
26. Mateu MG ( 1995 ) Antibody recognition of picornaviruses and escape from neutralization: a structural view . Virus Res 38 : 1 - 24 .
27. Mateu MG , Valero ML , Andreu D , Domingo E ( 1996 ) Systematic replacement of amino acid residues within an Arg-Gly-Asp-containing loop of foot-andmouth disease virus and effect on cell recognition . J Biol Chem 271 : 12814 - 12819 .
28. Samuel AR , Knowles NJ ( 2001 ) Foot-and-mouth disease virus: cause of the recent crisis for the UK livestock industry . Trends Genet 17 : 421 - 424 .
29. Rossmann MG , Greve JM , Kolatkar PR , Olson NH , Smith TJ , et al. ( 1997 ) in Structural Biology of Viruses (Chiu W, Garcea R , Burnette R , eds). 105 - 133 , Oxford University, Press, Oxford.
30. Brown F , Cartwright ( 1963 ) Purification of radioactive foot-and-mouth disease virus . Nature 199 : 1168 - 70 .
31. Burroughs JN , Rowlands DJ , Sangar DV , Talbot P , Brown F ( 1971 ) Further evidence for multiple proteins in the foot-and-mouth disease virus particle . J Gen Virol 13 : 73 - 84 .
32. Carrillo EC , Giachetti C , Campos RH ( 1984 ) Effect of lysosomotropic agents on the foot-and-mouth disease virus replication . Virology 135 : 542 - 545 .
33. Curry S , Fry E , Blakemore W , Abu-Ghazaleh R , Jackson T , et al. ( 1997 ) Dissecting the roles of VP0 cleavage and RNA packaging in picornavirus capsid stabilization: the structure of empty capsids of foot-and-mouth disease virus . J Virol 71 : 9743 - 9752 .
34. Van Vlijmen HWT , Curry S , Schaefer M , Karplus M ( 1998 ) Titration calculations of foot-and-mouth disease virus capsid and their stabilities as a function of pH . J Mol Biol 275 : 295 - 308 .
35. Rieder E , Bunch T , Brown F , Mason PW ( 1993 ) Genetically engineered footand-mouth disease viruses with poly(C) tracts of two nucleotides are virulent in mice . J Virol 67 : 5139 - 5145 .
36. Duque H , Baxt B ( 2003 ) FMDV receptors: comparison of bovine av integrin utilization by type A and O Viruses . J Virol 77 : 2500 - 2511 .
37. Duque H , LaRocco M , Golde WT , Baxt B ( 2004 ) Interactions of foot-andmouth disease virus with soluble bovine aVb3 and aVb6 integrins . J Virol 78 : 9773 - 81 .
38. Office International des Epizooties ( 2009 ). In Manual of Diagnostic Tests and Vaccines for Terrestrial Animals 2009 , Chapter 2 .1.5. 1 - 25 . Office International des Epizooties, Paris, France.
39. Rweyemamu MM , Ouldridge EJ , Head M , Ferrari R ( 1984 ) The effect of antiserum quality on strain specificity assessment of foot and mouth disease virus by the neutralization reaction . J Biol Stand 12 : 295 - 303 .
40. Doel TR , Mowat GN ( 1985 ) An international collaborative study on foot and mouth disease virus assay methods . 2. Quantification of 146S particles . J Biol Stand 13 : 335 - 44 .
41. Knipe T , Rieder E , Baxt B , Ward G , Mason P ( 1997 ) Characterization of synthetic foot-and-mouth disease virus provirions separates acid-mediated disassembly from infectivity . J Virol 71 : 2851 - 2856 .
42. Mateo R , Mateu MG ( 2007 ) Deterministic, compensatory mutational events in the capsid of foot-and-mouth disease virus in response to the introduction of mutations found in viruses from persistent infections . J Virol 81 : 1879 - 87 .
43. Mateo R , Luna E , Mateu MG ( 2007 ) Thermostable variants are not generally represented in foot-and-mouth disease virus quasispecies . J Gen Virol 88 : 859 - 864 .
44. R Development Core Team ( 2009 ) R: A Language and Environment for Statistical Computing .
45. Logan D , Abu-Ghazaleh R , Blakemore W , Curry S , Jackson T , et al. ( 1993 ) Structure of a major immunogenic site on foot-and-mouth disease virus . Nature 362 : 566 - 568 .
46. Thompson JD , Gibson TJ , Plewniak F , Jeanmougin F , Higgins DG ( 1997 ) The CLUSTAL _ X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools . Nucleic Acids Res 25 : 4876 - 82 .
47. Fiser A , Sali A ( 2003 ) Modeller: generation and refinement of homology-based protein structure models . Methods Enzymol 374 : 461 - 491 .
48. Li H , Robertson AD , Jensen JH ( 2005 ) Very fast empirical prediction and rationalization of protein pKa values . Proteins 61 : 704 - 721 .
49. Krieger E , Nielsen JE , Spronk CA , Vriend G ( 2006 ) Fast empirical pKa prediction by Ewald summation . J Mol Graph Model 25 : 481 - 486 .
50. Burman A , Clark S , Abrescia NG , Fry EE , Stuart DI , et al. ( 2006 ) Specificity of the VP1 GH Loop of foot-and-mouth disease virus for av integrins . J Virol 80 : 9798 - 9810 .
51. Jackson T , Clarck SJ , Berryman S , Burman A , Cambier S , et al. ( 2004 ) Integrin avb8 functions as a receptor for foot-and-mouth disease virus: Role of the bchain cytodomain in integrin-mediated infection . J Virol 78 : 4533 - 4540 .
52. Jackson T , Mould AP , Sheppard D , King AMQ ( 2002 ) Integrin avb1 is a receptor for foot-and-mouth disease virus . J Virol 76 : 935 - 941 .
53. Neff S , Mason PW , Baxt B ( 2000 ) High-efficiency utilization of the bovine integrin avb3 as a receptor for foot-and-mouth disease virus is dependent on the bovine b3 subunit . J Virol 74 : 7298 - 7306 .
54. Boettiger D , Lynch L , Blystone S , Huber F ( 2001 ) Distinct ligand-binding modes for integrin avb3-mediated adhesion to fibronectin versus vitronectin . J Biol Chem 276 : 31684 - 90 .
55. Lea S , Hernandez J , Blakemore W , Brocchi E , Curry S , et al. ( 1994 ) The structure and antigenicity of a type C foot-and-mouth disease virus . Structure 2 : 123 - 139 .
56. Lea S , Abu-Ghazaleh R , Blakemore W , Curry S , Fry E , et al. ( 1995 ) Structural comparison of two strains of foot-and-mouth disease virus subtype O1 and a laboratory antigenic variant G67 . Structure 3: 571 - 580 .
57. Twomey T , France LL , Hassard S , Burrage TG , Newman JFE , et al. ( 1995 ) Characterization of an acid-resistant mutant of foot-and-mouth disease virus . Virology 206 : 69 - 75 .
58. Curry S , Abrams CC , FryE, Crowther JC , Belsham GJ , et al. ( 1995 ) Viral RNA modulates the acid sensitivity of Foot-and-mouth disease virus capsids . J Virol 69 : 430 - 438 .