Family: Picornaviridae
Genus: Aphthovirus
Distinguishing features
The genus is distinguished on the basis of genetic characters.
Virion
Morphology
The crystal structures of several foot-and-mouth disease viruses (FMDV) and equine rhinitis A viruses (ERAV) have been resolved (Fry et al., 2005, Tuthill et al., 2009). The capsid of FMDV is thin-walled (mean thickness ca. 33 Å), and has an unusually smooth surface. A long (17–23 aa), mobile loop, the G-H loop, projects from the surface of 1D. There is a pore at the 5-fold axis, where part of the underlying 1C is exposed. Some serotypes of FMDV accumulate empty capsids.
Physicochemical and physical properties
Virions are acid labile; FMDV particles are unstable below pH 6.8; ERAV particles are unstable below pH 5.5. The buoyant density in CsCl is 1.43–1.45 g cm-3. Virions of FMDV sediment at 146S, empty capsids at 75S.
Nucleic acid
Genome (Forss et al., 1984, Carroll et al., 1984, Li et al., 1996, Wutz et al., 1996, Hollister et al., 2008, Hause et al., 2015): 7,250–8,203 nt (5′-UTR: up to 1,112 nt; ORF: 6,657–7,020 nt; 3′-UTR: 32–110 nt). There is a poly(C) tract close to the 5′-terminus of the genome. In FMDV genomic RNA, it is located about 360 nt from the end, and varies from 100 to more than 400 nt. Current data suggest that the poly(C) tract in ERAV genomic RNA is shorter (ca. 40 nt) and closer to the 5′-end. In the RNA of FMDV there is a series of 3–4 pseudoknots on the 3′-side of the poly(C); in ERAV RNA, these pseudoknots are upstream of the poly(C) and are formed by perfectly repeated sequences each consisting of 21 bases; the total 5′-UTR is thus extremely long. No pseudoknots have so far been identified in the RNA of bovine rhinitis viruses. The IRES is of type II. The FMDV cre is located in the 5′-UTR between the repeated pseudoknots and the IRES, but has not been identified for the other aphthovirus species. ERAV and FMDV differ by approximately 50% in nt sequence across the entire genome.
Genome organization and replication
Genome layout:
VPg-5′-UTRIRES-II-[Lpro/1A-1B-1C-1D-2Anpgp/2B-2C/3A-3B1-(3B2-3B3)-3C-3D]-3′-UTR-poly(A)
The deduced polyproteins range from 2,218–2,339 aa. Translation starts at two alternative in-frame initiation sites, resulting in two forms of the L protein (Lab and Lb). L is a papain-like cysteine proteinase which cleaves itself from the virus polyprotein. The 2A polypeptide is very short (chain length = 18 aa in FMDV), and is involved in NPGP-dependent polypeptide chain interruption at its C-terminus. The genome of FMDV encodes 3 copies of VPg while those of ERAV, bovine rhinitis A virus (BRAV) and bovine rhinitis B virus (BRBV) encode only one.
Biology
This genus is comprised of viruses which primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Clinical manifestations of FMDV infections include foot-and-mouth disease (vesicular lesions), sometimes with associated acute fatal myocarditis in young animals. ERAV causes upper respiratory tract infections of horses, but may infect a number of other species including man. Bovine rhinitis A virus (BRAV) and bovine rhinitis B virus (BRBV) infect the respiratory tract of cattle. FMDV and ERAV may produce persistent upper respiratory tract infections. FMDV infects cells by binding to integral membrane proteins of the integrin family through its 1D G-H loop; the principle integrin used is αvβ6. Heparan sulphate proteoglycans may also serve as receptors in cell cultures and at least one other unidentified receptor has been proposed. ERAV can use sialic acid to bind to cells. Cap-dependent translation of host mRNA is inhibited by Lpro, which cleaves the host eIF-4G.
Antigenicity
Seven types of FMDV (A, O, C, SAT 1, SAT 2, SAT 3, Asia 1), two types of BRAV and five types of BRBV have been described by serologic and genetic means. Up to five independent antigenic sites have been reported in FMDV type O virions, two of which have determinants in the G-H loop of 1D.
Derivation of names
Aphthovirus-: from Greek aphthae, "vesicles in the mouth"; English: aphtha, a thrush infection of the mouth; French: fièvre aphteuse, “foot-and-mouth disease”
Species demarcation criteria
Members of a species of the genus Aphthovirus:
- are less than 30% divergent in polyprotein aa sequence
- are less than 40% divergent in P1 aa sequence
- are less than 20% divergent in 2C + 3CD aa sequence
- share a natural host range
- share a common genome organization
The divergence (number of differences per site between sequences) of members of different Aphthovirus species ranges from 0.54–0.65 for P1 and 0.4–0.56 for 3CD.