Comparative Immunology, Microbiology

& Infectious Diseases 25 (2002) 297308

www.elsevier.com/locate/cimid

Foot-and-mouth disease virus

Esteban Domingoa,*, Eric Baranowskib, Cristina Escarmsa,
Francisco Sobrinoa,b
a

Centro de Biologa Molecular Severo Ochoa, Universidad Autonoma de Madrid, Cantoblanco, Madrid, Spain
b
Centro de Investigacion en Sanidad Animal (INIA), 28130 Valdeolmos, Madrid, Spain

Abstract
Foot-and-mouth disease virus (FMDV) is an aphthovirus of the family Picornaviridae and the
etiological agent of the economically most important animal disease. As a typical picornavirus, FMD
virions are nonenveloped particles of icosahedral symmetry and its genome is a single stranded RNA
of about 8500 nucleotides and of positive polarity. FMDV RNA is infectious and it replicates via a
complementary, minus strand RNA. FMDV RNA replication is error-prone so that viral populations
consist of mutant spectra (quasispecies) rather than a defined genomic sequence. Therefore FMDV in
nature is genetically and antigenically diverse. This poses important challenges for the diagnosis,
prevention and control of FMD. A deeper understanding of FMDV population complexity and
evolution has suggested requirements for a new generation of anti-FMD vaccines. This is relevant to
the current debate on the adequacy of non-vaccination versus vaccination policies for the control of
FMD. q 2002 Elsevier Science Ltd. All rights reserved.
Keywords: Quasispecies; Picornavirus; Vaccine

Resume
Le virus de la fie`vre aphteuse est un aphtovirus de la famille des Picornaviridae et lagent de la
maladie animale la plus importante sur le plan economique. En tant que picornavirus typique, le
virus de la fie`vre aphteuse est nu, sous forme dicosae`dre et son genome comprend un acide
ribonucleique monobrin avec environ 8500 nucleotides et une polarite positive. Lacide
ribonucleique de ce virus est infectieux et il se replique par lintermediaire dun brin dARN
moins, complementaire. La replication de lacide nucleique de ce virus conduit a` des erreurs, de telle
sorte que les populations virales comprennent un ensemble de mutants (quasi espe`ce) plutot quune
sequence genomique bien definie. Par suite, le virus de la fie`vre aphteuse est genetiquement et
antigeniquement varie. Ceci entrane des difficultes importantes pour le diagnostic, la prevention et
la matrise de la fie`vre aphteuse. Une connaissance plus approfondie de la complexite et de
levolution de la population de ce virus a conduit a` des besoins pour une nouvelle generation de

* Corresponding author. Tel.: 34-91-3978485; fax: 34-91-3974799.

E-mail address: edomingo@cbm.uam.es (E. Domingo).
0147-9571/02/$ - see front matter q 2002 Elsevier Science Ltd. All rights reserved.
PII: S 0 1 4 7 - 9 5 7 1 ( 0 2 ) 0 0 0 2 7 - 9

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E. Domingo et al. / Comp. Immun. Microbiol. Infect. Dis. 25 (2002) 297308

vaccines aphteux. Ceci est lie au debat actuel sur le choix dune politique de vaccination ou de nonvaccination dans la lutte contre la fie`vre aphteuse. q 2002 Elsevier Science Ltd. All rights reserved.
Mots-cle: Fie`vre aphteuse; Virus; Picornavirus; Evolution virale; Quasi espe`ce; Vaccin; Matrise de maladie

1. Introduction
Foot-and-mouth disease virus (FMDV) is the causative agent of the economically most
important animal viral disease world-wide. Although mortality associated with FMD is
usually low, the disease decreases livestock productivity, and affected countries cannot
participate in international trade of animals and animal products. Unfortunately, in many
underdeveloped regions of Asia, Africa and South America FMD is enzootic, preventing a
possible source of economic development. For reviews of FMD and its world-wide
impact, see Refs. [1 3]. The 2001/2002 European outbreak of FMD which has affected
mainly the UK will have an estimated cost of 6000 million Euros [4,5]. Because of the
difficulties for its effective control and its economic impact, FMD ranks first in the A list of
infectious diseases of animals, published by the Office International des Epizooties. A
number of review articles [3 5] and web sites (http://www.oie.int;http://iah.bbsrc.ac.uk/
virus/Picornaviridae/Aphthovirus/fmd.htm) provide updated information on FMD. This
article reviews the structure and genome organization of FMDV and the application of
new technologies to the diagnosis and prevention of FMD.

2. FMDV particles
FMDV is a non-enveloped virus with icosahedral symmetry that belongs to the
aphthovirus genus of the Picornaviridae family [6]. Its genome is a single stranded RNA
molecule of about 8500 nucleotides of positive polarity. Crystallographic studies have
allowed the elucidation at atomic resolution of the three-dimensional structure of several
FMDV isolates and antigenic variants [7 11]. Particles are about 30 nm in diameter and
are composed of 60 copies of each of four capsid proteins termed VP1, VP2, VP3 and VP4.
VP1, VP2, VP3 are external and VP4 is internal, in contact with the RNA and modified by
a myristate group at its amino terminus. One copy of each capsid protein assembles to
produce a protomer; in turn, five protomers form a pentamer, and 12 pentamers conform
the complete capsid (Fig. 1). The individual surface capsid proteins share a structure
consisting of an eight-stranded b-barrel. Surface loops connecting the b-strands include
antigenic determinants (B-cell epitopes) involved in neutralization of infectivity by
antibodies. Four major antigenic sites have been identified by combining immunologic,
genetic and biochemical procedures [11]. Particularly interesting is a major, immunodominant site located within the G H loop of VP1. This loop appears as highly disordered
according to the X-ray diffraction patterns of crystal of native virions. A structure for the
loop was obtained by crystallographic analysis of chemically modified FMDV [12], and it
consists of a short b-strand which precedes an Arg-Gly-Asp (RGD) which adopts an openturn conformation, followed by a short helical region at the carboxy side of the RGD. This

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Fig. 1. The FMDV capsid and location of antigenic sites. In the upper part the relative position of the three surface
proteins VP1, VP2 and VP3 in the particle of icosahedral symmetry is indicated [based on Ref. [7]]. In the lower
part the location of the major antigenic sites in FMDV of serotypes O, A and C is given. The three boxes (not
drawn to scale) correspond to capsid proteins VP2, VP3 and VP1. The letters on top of each box indicate the
antigenic loops (Ct is the carboxy-terminal region of VP1). Antigenic sites are indicated in gray boxes. The letters
and numbers inside these boxes refer to site designation for FMDV serotypes O, A and C; ( ) indicates sites not
specifically named in the original references. The numbers at the bottom indicate the amino acid positions
(counted individually for each protein) at which the different loops and domains are located (based on Ref. [11]).

loop structure is very similar to that found in crystals of complexes between the Fab fragment
of MAbs which recognize this antigenic site and synthetic peptides representing several
variant versions of the loop residues [1115]. The loop appears to display a hinge movement
about the capsid surface and it occupies different positions when bound to different antibodies
[1618]; its being exposed and mobile may contribute to its immunodominance.
A remarkable feature of the GH loop of VP1 is that the RGD has a dual function in
recognition of integrins that serve as cellular receptors for FMDV and in antibody binding [11,
13,19,20]. The RGD is a critical part of several epitopes involved in FMDV neutralization that
have been mapped within the loop [11,14]. An overlap between antigenic sites and receptor
recognition sites is not unique to FMDV since it was first observed with human influenza virus
and more recently with a variety of animal viruses [19]. Such an overlap permits coevolution
of antigenicity and host cell tropism, and this is particularly relevant for highly variable RNA
viruses since it favors virus adaptability and complicates viral disease prevention and control.

3. The FMDV genome

FMDV RNA is polyadenylated at its 30 -end, and has a small protein, VPg, covalently

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Fig. 2. Scheme of the FMDV genome. Regulatory regions (50 UTR or 50 non-coding region, and 30 UTR or 30 noncoding region) are indicated by horizontal lines. Different subregions within the 50 UTR have been expanded. The
coding region (single open-reading frame, with two functional AUG initiation codons) is depicted as a horizontal
box with indication of the encoded proteins: L to 3D. VPg is the protein covalently linked to the 50 -end of the
RNA and (A)n is the 30 terminal polyadenylate tract (based on Ref. [3] and references therein).

linked to its 50 -end. The FMDV genome can be divided into three main functional regions:
(i) the 50 non-coding, regulatory region; (ii) the protein-coding region (subdivided in L/P1,
P2 and P3); and (iii) the 30 non-coding, regulatory region (Fig. 2). For reviews of the
picornavirus and aphthovirus genome organization and expression see Refs. [3,21,22].
The 50 non-coding region includes from the 50 -end a highly structured S fragment of about
370 residues followed by an internal polyribocytidylate (polyC) tract of variable length
(usually 100 400 residues). Downstream of the polyC tract there is a pseudoknot region
which precedes the internal ribosome entry site (IRES), a stretch of about 440 residues
which serves for the internal initiation of protein synthesis in a CAP-independent fashion
[23]. The roles of the RNA domains preceding the IRES are poorly understood. Protein
synthesis starts at two functional, in-frame AUG codons separated by about 80 nucleotides
that delimit a long open-reading frame to encode a polyprotein of about 2330 amino acids.
Differences in length of coding and non-coding regions are observed among natural
isolates of FMDV and some times among viruses with a different passage history in cell
culture. Because of the double initiation of protein synthesis, two forms of protease L are
made. They both catalyze their own cleavage from the rest of the polyprotein, and also the
cleavage of eIF-4G of the CAP complex contributing to the shut-off of host cell protein
synthesis. P1 encodes the four capsid proteins, and P2 P3 encode non-structural proteins
involved in RNA genome replication and viral maturation. The function of several nonstructural proteins is still poorly understood although some of their homologous proteins in
poliovirus have been studied in some detail. Protein 3C is a serin protease that catalyzes
most of the cleavages necessary for polyprotein processing; 2C is involved in RNA
synthesis and is the site of mutations that confer FMDV resistance to guanidine
hydrochloride; 3B encodes three copies of VPg, the protein covalently linked to the 50 -end
of the RNA (Fig. 2). Protein 3D is the viral RNA-dependent RNA polymerase (or viral
replicase), which shows 34% amino acid sequence identity with poliovirus 3D, an enzyme
whose three-dimensional structure has been resolved by X-ray crystallography [24].
Finally, the 30 non-coding region of about 90 residues is likely to be a site of interaction
with viral and host proteins for RNA replication; the 30 -end contains a polyA tract which is
genetically coded and heterogeneous in length [3,21,22]. Despite the classically
established distinction between regulatory and coding regions, there is increasing
evidence that coding regions of the picornaviral genomes may also be involved in

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301

regulatory functions [for example, Ref. [25]]. This dual role may be of relevance for the
interpretation of evolutionary parameters of FMDV.
Purified genomic FMDV RNA can act as messenger RNA in vitro and in vivo [5,21,
22]. The RNA extracted from virions or transcribed from full-length cDNA copies of the
viral genome is infectious. This permits manipulation of DNA copies of specific FMDV
genomic segments to study the phenotypic effects of mutations and other genomic
alterations. The application of reverse genetics has allowed the constructions of chimeric
FMDVs to define determinants of viral replication, cell recognition and virulence [5,21].

4. FMDV genome replication and generation of heterogeneity and diversity

Replication of FMDV RNA follows the same general pattern as replication of other
picornaviruses and although some features have been established with FMDV, others are
assumed to be those established for poliovirus and other members of the same family [5,
21,22,26]. The site of RNA genome replication is a membrane-bound replication complex
at the cell cytoplasm. Genome copying occurs via a complementary negative (or minus)
strand RNA and the formation of double stranded replicative form, and perhaps partially
double-stranded replicative intermediates. Minus strands are found in hundredfold lower
concentrations than plus strands in infected cells, suggesting that each minus strand may
serve as template for the synthesis of many plus strands [26]. The kinetics of RNA
synthesis are not well understood and the number of rounds of template copying in
infected cells is unknown. This is true of most RNA viruses and it is of relevance to
interpret viral evolution [27]. In particular it is difficult to relate a rate of occurrence of
mutations (either advantageous or detrimental) and their frequency in viral populations.
Many such calculations require a number of assumptions and are based on inferences that
are distant from the actual experimental results; they are of limited value.
As for other RNA viruses (or viruses which include in their replication cycle an RNA
intermediate), FMDV RNA genome replication is error-prone. This has been documented
experimentally by determining nucleotide sequences of progeny from a single genome,
and also from the frequencies of MAb-resistant mutants in clonal preparations and natural
isolates of FMDV, among other lines of evidence (Refs. [27 29] and references therein).
Low fidelity copying is expected from the absence of proofreading repair activity in the
viral replicase [24,27,30]. Because of high mutation rates (between 0.2 and 1 mutations are
introduced every time a plus or minus strand is copied into an RNA product) FMDV
populations consist of distributions of related but non-identical genomes. The consensus
nucleotide sequence (the one determined by current sequencing methodology) is but an
average of many different sequences, and a genome with a nucleotide sequence identical to
the consensus may not exist in the population. Thus, the FMDV genome is statistically
defined but individually undetermined. This population structure is shared with other RNA
viruses and it is termed the quasispecies nature of RNA viruses, in recognition of the first
theory that regarded ensembles of replicons as the target of selection and considered the
wild type as an average of many different sequences [31]. Quasispecies can be applied to
RNA virus populations [32 34] and it has provided an adequate theoretical framework to
understand RNA viruses at the population level, including FMDV [3,22,27,30 34]. Since

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a viral population consists of a swarm of genetic and phenotypic variants in perpetual

renewal as genome replication proceeds in infected hosts, the quasispecies structure and
dynamics of FMDV has implications not only for its adaptability and evolution but also for
viral pathogenesis [5,19,26 30].
Current concepts on RNA virus evolution provide the following picture for generation
of FMDV diversity: (i) Replication unavoidably results in the generation of FMDV
quasispecies. Therefore infection of an animal, even in those cases in which infection is
initiated by a single FMDV genome, will result in mutant swarms which will be subjected
to positive selection, negative selection (ranking of variant frequencies according to
relative fitness) and random drift within the animal (for example in the invasion of a new
tissue or organ by one infectious mutant taken by chance from a pool of mutants). (ii)
Transmission of FMDV from an infected animal to a susceptible host will initiate a new
round of evolutionary events summarized in (i). This short-term (intra-host) FMDV
evolution is essentially the result of differential growth of subpopulations of mutant
FMDVs [3,28]. (iii) Successive rounds of intra-host evolution and transmission events
lead to the progressive divergence of FMDV in nature. Because of the complexity of
selective constraints encountered by the virus in different host species, the mechanisms of
FMDV diversification in nature are largely unknown. (iv) Functional and structural
constraints at the RNA and protein levels modulate variation despite high mutation rates
[27,35]. Rates of evolution of FMDV in nature are not constant with time and they range
between 1021 and 1024 substitutions per nucleotide per year [[5,27] and references
therein]. (v) In FMDV there is an overlap between some antigenic sites and some cell
receptor recognition sites, which may result in coevolution of antigenicity and host range
[19].

5. FMDV types, subtypes and isolates

The FMDVs isolated over the 20th century were grouped in seven serological types,
termed A, O, C, Asia 1, SAT1, SAT2 and SAT3 [1 3]. FMDVs were assigned to a
different serotype on the basis of lack of cross-protection following infection
(convalescent animals) or vaccination. Viruses showing partial cross-protection were
assigned to the same serotype but to a different subtype. About 65 subtypes of FMDV were
defined, but about two decades ago it was realized that with the use of increasing numbers
of MAbs virtually each isolate could be regarded as an antigenic variant [3,36,37].
Antigenic diversity is a direct consequence of genetic variation. A significant observation
was the generation of an epitope previously assigned to a FMDV subtype as a consequence
of an amino acid replacement in a FMDV of another subtype [38].
Classifications of FMDV isolates based on phylogenetic methods (Fig. 3) are gradually
replacing the traditional groupings based on serological criteria. Phylogenies are based on
RT-PCR amplification of genomic FMDV RNA isolates and nucleotide sequencing of
specific genomic regions, usually those encoding capsid proteins, particularly VP1 [3,36].
Such procedures have established, for example, the relatedness among the O type FMDV
isolates that originate from some initial strain in the center of Asia, expanded westward
and eastward, causing the European outbreak of 2001/2002. This outbreak has represented

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Fig. 3. Phylogenetic relationships among FMDV isolates of seven serotypes, based on amino acid sequences of
capsid protein VP1. The segment indicates a 10 amino acid distance. The spheres at the tip of each branch
emphasize that each virus isolate is in reality a cloud of mutants, as discussed in the text (adapted from Ref. [3]
and references therein).

the unprecedented penetration of FMDV of Asiatic origin into Europe, contributing to

concerns on further FMDV spread in the face of an increasingly global economy [3 5].
The potential for rapid evolution and the antigenic diversity of FMDV are complicating
factors for the diagnosis, prevention and control of FMD.

6. Diagnosis and control of FMD: a growing challenge

Intensive farm animal breeding and livestock production in the context of global trade
connections necessitate rapid and reliable diagnosis of FMD to distinguish it from other
vesicular diseases, notably swine vesicular disease or vesicular stomatitis [1 3]. The
classical complement fixation and serum neutralization tests have been largely replaced by
ELISA and genetic typing techniques [3]. ELISA employs serotype-specific sera or MAbs

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[39]. However, use of MAbs meets with the epitopic diversity among FMDV isolates [3,
36 38]. Perhaps multinational collaborations to investigate cocktails of neutralizing and
non-neutralizing MAbs [which often define conserved epitopes [37]] could produce
reliable reagents for ELISA typing. For trade purposes, diagnostic procedures should
distinguish animals that have been vaccinated from those that have been infected with
FMDV. This distinction is now feasible by detecting antibodies against some of the nonstructural proteins by ELISA, in particular antibodies against 3AB and 3ABC. Such
antibodies are found in animals which at some time have been infected with FMDV but not
in vaccinated animals (Ref. [3] and references therein).
RT-PCR amplification techniques are increasingly providing a versatile tool for an
efficient and rapid diagnosis of FMD [3,40,41]. Coupled to automated nucleotide
sequencing and phylogenetic analysis, these techniques can achieve a detailed virus
identification to trace the origin of FMDVs associated with new outbreaks [3,4].
Reliability and rapidity in FMD diagnosis are a priority since a delay in the
implementation of control or preventive measures may result in the uncontrollable spread
of disease with devastating economic consequences [1 4].
Control of FMD is based on two major strategies: the slaughtering of affected and
contact animals (the so called stamping out procedure) or the regular vaccination of the
major host species for FMDV (always cattle and when indicated also swine). Both
strategies can be combined so that a ring vaccination can be established around a focus
area where affected and contact animals have been slaughtered [1 5]. As a consequence of
the massive killing of animals during the 2001/2002 European outbreak, and the
increasing awareness of the community on animal welfare, there is presently a vivid
debate towards whether a vaccination strategy may not be preferable to the stamping-out
and non-vaccination procedure in operation in the EU since 1991. Such regulation was
adopted for economic considerations, but left susceptible animals in a vast territory
defenseless in the face of an accidental introduction of the virus in the region, a situation
that historically has been known to favor the occurrence of large epizootics [1 5]. In the
event of a return to a vaccination policy, basic investigations over the last decade should
provide the basis for manufacturing more effective and safer vaccines than those presently
available. Such new vaccines could replace current vaccines in those territories where a
vaccination policy is presently in operation. The basic rules that should be considered for
the development of new anti-FMD vaccines are [3,42]: (i) Vaccines should include
multiple B-cell and T-cell epitopes to produce an ample humoral (antibody) and cellular
immune response, in particular, T helper responses for antibody production [3,43]. Such
an ample response is required to delay, and ideally abolish, a possible selection in the field
of FMDV variants showing partial resistance to the immune response evoked by the
vaccine [3,5,19,42]. The B cell epitope map has been investigated with considerable detail
[11], and a number of T-cell epitopes have been identified in structural and non-structural
proteins of FMDV [[3,43 45] and references therein]. Therefore, it should be possible to
present an ample epitopic repertoire either with synthetic constructs or with complete,
non-infectious particles. Research along these lines is currently in progress. (ii) Although
FMDV infection is usually acute, and viremia and lesions occur within days after
infection, ruminants can establish an asymptomatic carrier state in which the virus
replicates in the oesopharyngeal region of the animals [46,47]. The presence of carriers

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305

jeopardizes animal trade since it cannot be excluded that carrier animals could on
occasions originate acute disease when in contact with susceptible animals. Classical
vaccines cannot prevent the establishment of persistent FMDV infection in cattle, and a
new vaccine should target systemic and mucosal immunity, hoping that the latter may
minimize chances of establishing the carrier state. (iii) Vaccine manufacturing should not
require the handling of virus because of the danger of virus escaping from vaccine
factories. Also, classical, inactivated whole-virus vaccines may be at the origin of
outbreaks if inactivation prior to vaccine formulation was not complete. There is good
evidence that some FMD outbreaks probably had a vaccine origin [3]. These constitute
powerful arguments to design vaccines that do not require infectious virus at any stage of
their preparation [48,49]. (iv) Finally, vaccines must be marked to distinguish vaccination
from infection, as discussed above for diagnostic purposes. A vaccine could be marked
positively by the presence of some genetic tag or negatively by the absence of a gene
product systematically found during a natural infection [3,40].
The recent European epizootic of FMD at the onset of the 21 century has made us aware
of the great economic losses to be endured because no effective preventive and control
measures are available for FMD. We should not forget, however, that underdeveloped
countries in need for active livestock trade have suffered FMD-related losses for decades.
Interest on new vaccines and basic epidemiology to define the strategies for a more
effective control of FMD has been boosted as a consequence of the recent European
epizootic. Yet, active research on FMD and FMDV should have never been interrupted
[5]. It is hoped that application of new molecular techniques and increasing computation
capacities for epidemiological modeling, will contribute to a more effective control of
FMD in Europe and also in underdeveloped countries. Experience tells us that what we
learn with FMDV is likely to be of value also to understand and control some other viruses.

Acknowledgments
We thank many colleagues for important contributions to FMDV research.
Unavoidably, space limitations did not allow quoting all relevant work. Research
supported by grants DGES PM97-0060-C02-01, BIO 99-0833-01, BMC 2001-1823-C0201, and Fundacion Ramon Areces from Spain, and FAIR 5 PL97-3665, CT97-3665 and
341 from the EU.

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